MSI HDIpreprocessing
This notebook reads the MSI data and runs an optimized form of UMAP on the data
[1]:
# import custom modules
from miaaim.proc.hdiproc import HDIpreprocessing
from miaaim.io.imread import _import
# import other modules
import pandas as pd
import numpy as np
from pathlib import Path
from tqdm import tqdm
# check versions and environment executable
import sys
sys.version
sys.executable
2023-04-23 22:02:22.066589: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[1]:
'/opt/conda/envs/miaaim-dev/bin/python'
Set paths to data and get marker information
[2]:
# set path to data folder
data_folder = Path("/opt/miaaim-20220912-TMA4/data")
# read csv file with MSI data
msiRMS = pd.read_csv(data_folder.joinpath("msi_rms_tma_peptides.csv"))
# get list of cores
coreFolders = [ x for x in list(data_folder.iterdir()) if x.is_dir() ]
# get unique TMA core names
coreNames = [ list(msiRMS.Region.unique())[i].replace(" ","") for i in range(len(msiRMS.Region.unique())) ]
Iterate Through Cores and Extract Data
[3]:
# iterate through cores and extract data
for c in tqdm(coreNames):
# get the corresponding core folder
coreFolder = [ x for x in coreFolders if x.name.endswith(c) ][0]
# get the name of this folder
name = coreFolder.name
# get the input folder
inputMSIFolder = coreFolder.joinpath("input/msi")
# set input imc folder
processedIMCfolder = coreFolder.joinpath("preprocessing/imc")
# create preprocessing object (read hdf5 and associated mask)
msi = HDIpreprocessing(
paths=inputMSIFolder,
path_to_markers=None,
flatten=True,
subsample=None,
mask=True,
save_mem=False
)
# read imc data
imcIm = _import.HDIreader(path_to_data=processedIMCfolder,
path_to_markers=None,
flatten=False,
subsample=False,
method=None,
mask=True,
save_mem=False,
data=None,
image=None,
channels=None,
filename=None
)
# get shape of imc image
imcX, imcY, imcC = imcIm.hdi.data.image.shape
# run dimension reduction for registration preprocessing
msi.RunOptimalUMAP(n_jobs=-1,channels=None,random_state=0,landmarks=None)
# map pixels to spatial coordinates
msi.SpatiallyMapUMAP(method='coordinate')
# export core image
msi.Export(
suffix="_core_msi_UMAP.nii",
padding=(5,5),
target_size=(imcX, imcY)
)
# export mask
msi.ExportMask(
suffix="_core_msi_mask.tif",
padding=(5,5),
target_size=(imcX, imcY)
)
# export documentation and QC images
msi.QC()
0%| | 0/48 [00:00<?, ?it/s]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/input/msi/ROI010_PROSTATE_TMA001_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/input/msi/ROI010_PROSTATE_TMA001.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/imc/ROI010_PROSTATE_TMA001_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/imc/ROI010_PROSTATE_TMA001_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/input/msi/ROI010_PROSTATE_TMA001.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi/ROI010_PROSTATE_TMA001_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi/ROI010_PROSTATE_TMA001_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi/ROI010_PROSTATE_TMA001_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi/ROI010_PROSTATE_TMA001_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/msi/ROI010_PROSTATE_TMA001_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/qc/preprocessing/msi/ROI010_PROSTATE_TMA001_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/qc/preprocessing/msi/ROI010_PROSTATE_TMA001_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/qc/preprocessing/msi/ROI010_PROSTATE_TMA001_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/provenance/miaaim-preprocessing-msi.sh
2%|██▍ | 1/48 [01:29<1:09:53, 89.22s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/input/msi/ROI011_PROSTATE_TMA002_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/input/msi/ROI011_PROSTATE_TMA002.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/imc/ROI011_PROSTATE_TMA002_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/imc/ROI011_PROSTATE_TMA002_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/input/msi/ROI011_PROSTATE_TMA002.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi/ROI011_PROSTATE_TMA002_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi/ROI011_PROSTATE_TMA002_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi/ROI011_PROSTATE_TMA002_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi/ROI011_PROSTATE_TMA002_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/msi/ROI011_PROSTATE_TMA002_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/qc/preprocessing/msi/ROI011_PROSTATE_TMA002_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/qc/preprocessing/msi/ROI011_PROSTATE_TMA002_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/qc/preprocessing/msi/ROI011_PROSTATE_TMA002_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/provenance/miaaim-preprocessing-msi.sh
4%|████▉ | 2/48 [02:44<1:02:02, 80.92s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/input/msi/ROI012_PROSTATE_TMA003_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/input/msi/ROI012_PROSTATE_TMA003.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/imc/ROI012_PROSTATE_TMA003_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/imc/ROI012_PROSTATE_TMA003_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/input/msi/ROI012_PROSTATE_TMA003.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi/ROI012_PROSTATE_TMA003_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi/ROI012_PROSTATE_TMA003_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi/ROI012_PROSTATE_TMA003_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi/ROI012_PROSTATE_TMA003_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/msi/ROI012_PROSTATE_TMA003_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/qc/preprocessing/msi/ROI012_PROSTATE_TMA003_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/qc/preprocessing/msi/ROI012_PROSTATE_TMA003_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/qc/preprocessing/msi/ROI012_PROSTATE_TMA003_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/provenance/miaaim-preprocessing-msi.sh
6%|███████▌ | 3/48 [03:57<57:58, 77.30s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/input/msi/ROI013_PROSTATE_TMA004_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/input/msi/ROI013_PROSTATE_TMA004.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/imc/ROI013_PROSTATE_TMA004_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/imc/ROI013_PROSTATE_TMA004_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/input/msi/ROI013_PROSTATE_TMA004.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi/ROI013_PROSTATE_TMA004_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi/ROI013_PROSTATE_TMA004_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi/ROI013_PROSTATE_TMA004_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi/ROI013_PROSTATE_TMA004_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/msi/ROI013_PROSTATE_TMA004_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/qc/preprocessing/msi/ROI013_PROSTATE_TMA004_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/qc/preprocessing/msi/ROI013_PROSTATE_TMA004_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/qc/preprocessing/msi/ROI013_PROSTATE_TMA004_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/provenance/miaaim-preprocessing-msi.sh
8%|██████████ | 4/48 [05:08<54:52, 74.83s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/input/msi/ROI014_PROSTATE_TMA005_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/input/msi/ROI014_PROSTATE_TMA005.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/imc/ROI014_PROSTATE_TMA005_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/imc/ROI014_PROSTATE_TMA005_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/input/msi/ROI014_PROSTATE_TMA005.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi/ROI014_PROSTATE_TMA005_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi/ROI014_PROSTATE_TMA005_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi/ROI014_PROSTATE_TMA005_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi/ROI014_PROSTATE_TMA005_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/msi/ROI014_PROSTATE_TMA005_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/qc/preprocessing/msi/ROI014_PROSTATE_TMA005_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/qc/preprocessing/msi/ROI014_PROSTATE_TMA005_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/qc/preprocessing/msi/ROI014_PROSTATE_TMA005_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/provenance/miaaim-preprocessing-msi.sh
10%|████████████▌ | 5/48 [06:22<53:21, 74.46s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/input/msi/ROI015_PROSTATE_TMA006_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/input/msi/ROI015_PROSTATE_TMA006.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/imc/ROI015_PROSTATE_TMA006_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/imc/ROI015_PROSTATE_TMA006_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/input/msi/ROI015_PROSTATE_TMA006.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi/ROI015_PROSTATE_TMA006_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi/ROI015_PROSTATE_TMA006_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi/ROI015_PROSTATE_TMA006_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi/ROI015_PROSTATE_TMA006_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/msi/ROI015_PROSTATE_TMA006_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/qc/preprocessing/msi/ROI015_PROSTATE_TMA006_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/qc/preprocessing/msi/ROI015_PROSTATE_TMA006_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/qc/preprocessing/msi/ROI015_PROSTATE_TMA006_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/provenance/miaaim-preprocessing-msi.sh
12%|███████████████▏ | 6/48 [07:02<44:00, 62.87s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/input/msi/ROI016_PROSTATE_TMA007_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/input/msi/ROI016_PROSTATE_TMA007.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/imc/ROI016_PROSTATE_TMA007_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/imc/ROI016_PROSTATE_TMA007_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/input/msi/ROI016_PROSTATE_TMA007.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi/ROI016_PROSTATE_TMA007_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi/ROI016_PROSTATE_TMA007_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi/ROI016_PROSTATE_TMA007_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi/ROI016_PROSTATE_TMA007_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/msi/ROI016_PROSTATE_TMA007_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/qc/preprocessing/msi/ROI016_PROSTATE_TMA007_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/qc/preprocessing/msi/ROI016_PROSTATE_TMA007_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/qc/preprocessing/msi/ROI016_PROSTATE_TMA007_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/provenance/miaaim-preprocessing-msi.sh
15%|█████████████████▋ | 7/48 [08:26<47:35, 69.64s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/input/msi/ROI017_PROSTATE_TMA008_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/input/msi/ROI017_PROSTATE_TMA008.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/imc/ROI017_PROSTATE_TMA008_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/imc/ROI017_PROSTATE_TMA008_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/input/msi/ROI017_PROSTATE_TMA008.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi/ROI017_PROSTATE_TMA008_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi/ROI017_PROSTATE_TMA008_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi/ROI017_PROSTATE_TMA008_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi/ROI017_PROSTATE_TMA008_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/msi/ROI017_PROSTATE_TMA008_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/qc/preprocessing/msi/ROI017_PROSTATE_TMA008_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/qc/preprocessing/msi/ROI017_PROSTATE_TMA008_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/qc/preprocessing/msi/ROI017_PROSTATE_TMA008_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/provenance/miaaim-preprocessing-msi.sh
17%|████████████████████▏ | 8/48 [09:48<49:03, 73.58s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/input/msi/ROI018_PROSTATE_TMA009_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/input/msi/ROI018_PROSTATE_TMA009.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/imc/ROI018_PROSTATE_TMA009_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/imc/ROI018_PROSTATE_TMA009_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/input/msi/ROI018_PROSTATE_TMA009.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi/ROI018_PROSTATE_TMA009_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi/ROI018_PROSTATE_TMA009_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi/ROI018_PROSTATE_TMA009_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi/ROI018_PROSTATE_TMA009_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/msi/ROI018_PROSTATE_TMA009_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/qc/preprocessing/msi/ROI018_PROSTATE_TMA009_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/qc/preprocessing/msi/ROI018_PROSTATE_TMA009_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/qc/preprocessing/msi/ROI018_PROSTATE_TMA009_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/provenance/miaaim-preprocessing-msi.sh
19%|██████████████████████▋ | 9/48 [11:11<49:47, 76.61s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/input/msi/ROI021_PROSTATE_TMA012_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/input/msi/ROI021_PROSTATE_TMA012.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/imc/ROI021_PROSTATE_TMA012_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/imc/ROI021_PROSTATE_TMA012_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/input/msi/ROI021_PROSTATE_TMA012.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi/ROI021_PROSTATE_TMA012_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi/ROI021_PROSTATE_TMA012_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi/ROI021_PROSTATE_TMA012_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi/ROI021_PROSTATE_TMA012_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/msi/ROI021_PROSTATE_TMA012_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/qc/preprocessing/msi/ROI021_PROSTATE_TMA012_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/qc/preprocessing/msi/ROI021_PROSTATE_TMA012_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/qc/preprocessing/msi/ROI021_PROSTATE_TMA012_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/provenance/miaaim-preprocessing-msi.sh
21%|█████████████████████████ | 10/48 [12:18<46:44, 73.81s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/input/msi/ROI022_PROSTATE_TMA013_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/input/msi/ROI022_PROSTATE_TMA013.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/imc/ROI022_PROSTATE_TMA013_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/imc/ROI022_PROSTATE_TMA013_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/input/msi/ROI022_PROSTATE_TMA013.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi/ROI022_PROSTATE_TMA013_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi/ROI022_PROSTATE_TMA013_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi/ROI022_PROSTATE_TMA013_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi/ROI022_PROSTATE_TMA013_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/msi/ROI022_PROSTATE_TMA013_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/qc/preprocessing/msi/ROI022_PROSTATE_TMA013_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/qc/preprocessing/msi/ROI022_PROSTATE_TMA013_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/qc/preprocessing/msi/ROI022_PROSTATE_TMA013_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/provenance/miaaim-preprocessing-msi.sh
23%|███████████████████████████▌ | 11/48 [13:39<46:46, 75.86s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/input/msi/ROI023_PROSTATE_TMA015_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/input/msi/ROI023_PROSTATE_TMA015.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/imc/ROI023_PROSTATE_TMA015_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/imc/ROI023_PROSTATE_TMA015_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/input/msi/ROI023_PROSTATE_TMA015.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi/ROI023_PROSTATE_TMA015_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi/ROI023_PROSTATE_TMA015_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi/ROI023_PROSTATE_TMA015_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi/ROI023_PROSTATE_TMA015_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/msi/ROI023_PROSTATE_TMA015_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/qc/preprocessing/msi/ROI023_PROSTATE_TMA015_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/qc/preprocessing/msi/ROI023_PROSTATE_TMA015_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/qc/preprocessing/msi/ROI023_PROSTATE_TMA015_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/provenance/miaaim-preprocessing-msi.sh
25%|██████████████████████████████ | 12/48 [15:11<48:24, 80.69s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/input/msi/ROI024_PROSTATE_TMA016_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/input/msi/ROI024_PROSTATE_TMA016.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/imc/ROI024_PROSTATE_TMA016_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/imc/ROI024_PROSTATE_TMA016_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/input/msi/ROI024_PROSTATE_TMA016.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi/ROI024_PROSTATE_TMA016_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi/ROI024_PROSTATE_TMA016_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi/ROI024_PROSTATE_TMA016_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi/ROI024_PROSTATE_TMA016_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/msi/ROI024_PROSTATE_TMA016_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/qc/preprocessing/msi/ROI024_PROSTATE_TMA016_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/qc/preprocessing/msi/ROI024_PROSTATE_TMA016_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/qc/preprocessing/msi/ROI024_PROSTATE_TMA016_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/provenance/miaaim-preprocessing-msi.sh
27%|████████████████████████████████▌ | 13/48 [16:27<46:15, 79.29s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/input/msi/ROI025_PROSTATE_TMA017_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/input/msi/ROI025_PROSTATE_TMA017.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/imc/ROI025_PROSTATE_TMA017_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/imc/ROI025_PROSTATE_TMA017_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/input/msi/ROI025_PROSTATE_TMA017.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi/ROI025_PROSTATE_TMA017_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi/ROI025_PROSTATE_TMA017_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi/ROI025_PROSTATE_TMA017_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi/ROI025_PROSTATE_TMA017_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/msi/ROI025_PROSTATE_TMA017_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/qc/preprocessing/msi/ROI025_PROSTATE_TMA017_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/qc/preprocessing/msi/ROI025_PROSTATE_TMA017_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/qc/preprocessing/msi/ROI025_PROSTATE_TMA017_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/provenance/miaaim-preprocessing-msi.sh
29%|███████████████████████████████████ | 14/48 [17:45<44:46, 79.03s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/input/msi/ROI026_PROSTATE_TMA018_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/input/msi/ROI026_PROSTATE_TMA018.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/imc/ROI026_PROSTATE_TMA018_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/imc/ROI026_PROSTATE_TMA018_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/input/msi/ROI026_PROSTATE_TMA018.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi/ROI026_PROSTATE_TMA018_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi/ROI026_PROSTATE_TMA018_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi/ROI026_PROSTATE_TMA018_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi/ROI026_PROSTATE_TMA018_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/msi/ROI026_PROSTATE_TMA018_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/qc/preprocessing/msi/ROI026_PROSTATE_TMA018_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/qc/preprocessing/msi/ROI026_PROSTATE_TMA018_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/qc/preprocessing/msi/ROI026_PROSTATE_TMA018_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/provenance/miaaim-preprocessing-msi.sh
31%|█████████████████████████████████████▌ | 15/48 [18:49<40:59, 74.52s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/input/msi/ROI027_PROSTATE_TMA019_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/input/msi/ROI027_PROSTATE_TMA019.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/imc/ROI027_PROSTATE_TMA019_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/imc/ROI027_PROSTATE_TMA019_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/input/msi/ROI027_PROSTATE_TMA019.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi/ROI027_PROSTATE_TMA019_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi/ROI027_PROSTATE_TMA019_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi/ROI027_PROSTATE_TMA019_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi/ROI027_PROSTATE_TMA019_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/msi/ROI027_PROSTATE_TMA019_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/qc/preprocessing/msi/ROI027_PROSTATE_TMA019_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/qc/preprocessing/msi/ROI027_PROSTATE_TMA019_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/qc/preprocessing/msi/ROI027_PROSTATE_TMA019_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/provenance/miaaim-preprocessing-msi.sh
33%|████████████████████████████████████████ | 16/48 [20:11<40:51, 76.60s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/input/msi/ROI028_PROSTATE_TMA020_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/input/msi/ROI028_PROSTATE_TMA020.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/imc/ROI028_PROSTATE_TMA020_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/imc/ROI028_PROSTATE_TMA020_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/input/msi/ROI028_PROSTATE_TMA020.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi/ROI028_PROSTATE_TMA020_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi/ROI028_PROSTATE_TMA020_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi/ROI028_PROSTATE_TMA020_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi/ROI028_PROSTATE_TMA020_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/msi/ROI028_PROSTATE_TMA020_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/qc/preprocessing/msi/ROI028_PROSTATE_TMA020_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/qc/preprocessing/msi/ROI028_PROSTATE_TMA020_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/qc/preprocessing/msi/ROI028_PROSTATE_TMA020_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/provenance/miaaim-preprocessing-msi.sh
35%|██████████████████████████████████████████▌ | 17/48 [21:26<39:19, 76.13s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/input/msi/ROI029_PROSTATE_TMA022_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/input/msi/ROI029_PROSTATE_TMA022.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/imc/ROI029_PROSTATE_TMA022_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/imc/ROI029_PROSTATE_TMA022_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/input/msi/ROI029_PROSTATE_TMA022.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi/ROI029_PROSTATE_TMA022_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi/ROI029_PROSTATE_TMA022_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi/ROI029_PROSTATE_TMA022_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi/ROI029_PROSTATE_TMA022_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/msi/ROI029_PROSTATE_TMA022_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/qc/preprocessing/msi/ROI029_PROSTATE_TMA022_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/qc/preprocessing/msi/ROI029_PROSTATE_TMA022_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/qc/preprocessing/msi/ROI029_PROSTATE_TMA022_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/provenance/miaaim-preprocessing-msi.sh
38%|█████████████████████████████████████████████ | 18/48 [22:48<38:58, 77.96s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/input/msi/ROI030_PROSTATE_TMA023_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/input/msi/ROI030_PROSTATE_TMA023.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/imc/ROI030_PROSTATE_TMA023_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/imc/ROI030_PROSTATE_TMA023_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/input/msi/ROI030_PROSTATE_TMA023.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi/ROI030_PROSTATE_TMA023_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi/ROI030_PROSTATE_TMA023_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi/ROI030_PROSTATE_TMA023_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi/ROI030_PROSTATE_TMA023_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/msi/ROI030_PROSTATE_TMA023_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/qc/preprocessing/msi/ROI030_PROSTATE_TMA023_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/qc/preprocessing/msi/ROI030_PROSTATE_TMA023_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/qc/preprocessing/msi/ROI030_PROSTATE_TMA023_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/provenance/miaaim-preprocessing-msi.sh
40%|███████████████████████████████████████████████▌ | 19/48 [24:10<38:19, 79.28s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/input/msi/ROI031_PROSTATE_TMA024_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/input/msi/ROI031_PROSTATE_TMA024.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/imc/ROI031_PROSTATE_TMA024_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/imc/ROI031_PROSTATE_TMA024_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/sklearn/manifold/_spectral_embedding.py:274: UserWarning: Graph is not fully connected, spectral embedding may not work as expected.
warnings.warn(
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/input/msi/ROI031_PROSTATE_TMA024.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi/ROI031_PROSTATE_TMA024_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi/ROI031_PROSTATE_TMA024_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi/ROI031_PROSTATE_TMA024_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi/ROI031_PROSTATE_TMA024_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/msi/ROI031_PROSTATE_TMA024_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/qc/preprocessing/msi/ROI031_PROSTATE_TMA024_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/qc/preprocessing/msi/ROI031_PROSTATE_TMA024_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/qc/preprocessing/msi/ROI031_PROSTATE_TMA024_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/provenance/miaaim-preprocessing-msi.sh
42%|██████████████████████████████████████████████████ | 20/48 [25:20<35:42, 76.53s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/input/msi/ROI032_PROSTATE_TMA025_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/input/msi/ROI032_PROSTATE_TMA025.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/imc/ROI032_PROSTATE_TMA025_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/imc/ROI032_PROSTATE_TMA025_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/hdiproc.py:651: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
fig, axs = plt.subplots()
working on /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/input/msi/ROI032_PROSTATE_TMA025.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi/ROI032_PROSTATE_TMA025_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi/ROI032_PROSTATE_TMA025_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi/ROI032_PROSTATE_TMA025_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi/ROI032_PROSTATE_TMA025_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/msi/ROI032_PROSTATE_TMA025_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/qc/preprocessing/msi/ROI032_PROSTATE_TMA025_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/qc/preprocessing/msi/ROI032_PROSTATE_TMA025_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/qc/preprocessing/msi/ROI032_PROSTATE_TMA025_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/provenance/miaaim-preprocessing-msi.sh
44%|████████████████████████████████████████████████████▌ | 21/48 [26:46<35:39, 79.24s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/input/msi/ROI033_PROSTATE_TMA026_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/input/msi/ROI033_PROSTATE_TMA026.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/imc/ROI033_PROSTATE_TMA026_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/imc/ROI033_PROSTATE_TMA026_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/input/msi/ROI033_PROSTATE_TMA026.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi/ROI033_PROSTATE_TMA026_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi/ROI033_PROSTATE_TMA026_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi/ROI033_PROSTATE_TMA026_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi/ROI033_PROSTATE_TMA026_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/msi/ROI033_PROSTATE_TMA026_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/qc/preprocessing/msi/ROI033_PROSTATE_TMA026_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/qc/preprocessing/msi/ROI033_PROSTATE_TMA026_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/qc/preprocessing/msi/ROI033_PROSTATE_TMA026_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/provenance/miaaim-preprocessing-msi.sh
46%|███████████████████████████████████████████████████████ | 22/48 [27:50<32:20, 74.64s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/input/msi/ROI037_PROSTATE_TMA028_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/input/msi/ROI037_PROSTATE_TMA028.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/imc/ROI037_PROSTATE_TMA028_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/imc/ROI037_PROSTATE_TMA028_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/input/msi/ROI037_PROSTATE_TMA028.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi/ROI037_PROSTATE_TMA028_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi/ROI037_PROSTATE_TMA028_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi/ROI037_PROSTATE_TMA028_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi/ROI037_PROSTATE_TMA028_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/msi/ROI037_PROSTATE_TMA028_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/qc/preprocessing/msi/ROI037_PROSTATE_TMA028_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/qc/preprocessing/msi/ROI037_PROSTATE_TMA028_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/qc/preprocessing/msi/ROI037_PROSTATE_TMA028_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/provenance/miaaim-preprocessing-msi.sh
48%|█████████████████████████████████████████████████████████▌ | 23/48 [29:02<30:46, 73.85s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/input/msi/ROI038_PROSTATE_TMA030_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/input/msi/ROI038_PROSTATE_TMA030.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/imc/ROI038_PROSTATE_TMA030_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/imc/ROI038_PROSTATE_TMA030_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/input/msi/ROI038_PROSTATE_TMA030.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi/ROI038_PROSTATE_TMA030_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi/ROI038_PROSTATE_TMA030_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi/ROI038_PROSTATE_TMA030_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi/ROI038_PROSTATE_TMA030_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/msi/ROI038_PROSTATE_TMA030_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/qc/preprocessing/msi/ROI038_PROSTATE_TMA030_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/qc/preprocessing/msi/ROI038_PROSTATE_TMA030_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/qc/preprocessing/msi/ROI038_PROSTATE_TMA030_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/provenance/miaaim-preprocessing-msi.sh
50%|████████████████████████████████████████████████████████████ | 24/48 [30:14<29:17, 73.25s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/input/msi/ROI039_PROSTATE_TMA031_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/input/msi/ROI039_PROSTATE_TMA031.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/imc/ROI039_PROSTATE_TMA031_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/imc/ROI039_PROSTATE_TMA031_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/input/msi/ROI039_PROSTATE_TMA031.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi/ROI039_PROSTATE_TMA031_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi/ROI039_PROSTATE_TMA031_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi/ROI039_PROSTATE_TMA031_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi/ROI039_PROSTATE_TMA031_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/msi/ROI039_PROSTATE_TMA031_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/qc/preprocessing/msi/ROI039_PROSTATE_TMA031_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/qc/preprocessing/msi/ROI039_PROSTATE_TMA031_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/qc/preprocessing/msi/ROI039_PROSTATE_TMA031_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/provenance/miaaim-preprocessing-msi.sh
52%|██████████████████████████████████████████████████████████████▌ | 25/48 [31:31<28:30, 74.36s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/input/msi/ROI040_PROSTATE_TMA032_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/input/msi/ROI040_PROSTATE_TMA032.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/imc/ROI040_PROSTATE_TMA032_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/imc/ROI040_PROSTATE_TMA032_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/input/msi/ROI040_PROSTATE_TMA032.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi/ROI040_PROSTATE_TMA032_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi/ROI040_PROSTATE_TMA032_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi/ROI040_PROSTATE_TMA032_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi/ROI040_PROSTATE_TMA032_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/msi/ROI040_PROSTATE_TMA032_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/qc/preprocessing/msi/ROI040_PROSTATE_TMA032_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/qc/preprocessing/msi/ROI040_PROSTATE_TMA032_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/qc/preprocessing/msi/ROI040_PROSTATE_TMA032_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/provenance/miaaim-preprocessing-msi.sh
54%|█████████████████████████████████████████████████████████████████ | 26/48 [32:57<28:32, 77.85s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/input/msi/ROI041_PROSTATE_TMA033_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/input/msi/ROI041_PROSTATE_TMA033.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/imc/ROI041_PROSTATE_TMA033_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/imc/ROI041_PROSTATE_TMA033_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/input/msi/ROI041_PROSTATE_TMA033.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi/ROI041_PROSTATE_TMA033_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi/ROI041_PROSTATE_TMA033_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi/ROI041_PROSTATE_TMA033_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi/ROI041_PROSTATE_TMA033_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/msi/ROI041_PROSTATE_TMA033_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/qc/preprocessing/msi/ROI041_PROSTATE_TMA033_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/qc/preprocessing/msi/ROI041_PROSTATE_TMA033_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/qc/preprocessing/msi/ROI041_PROSTATE_TMA033_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/provenance/miaaim-preprocessing-msi.sh
56%|███████████████████████████████████████████████████████████████████▌ | 27/48 [34:15<27:14, 77.86s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/input/msi/ROI042_PROSTATE_TMA034_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/input/msi/ROI042_PROSTATE_TMA034.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/imc/ROI042_PROSTATE_TMA034_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/imc/ROI042_PROSTATE_TMA034_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/input/msi/ROI042_PROSTATE_TMA034.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi/ROI042_PROSTATE_TMA034_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi/ROI042_PROSTATE_TMA034_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi/ROI042_PROSTATE_TMA034_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi/ROI042_PROSTATE_TMA034_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/msi/ROI042_PROSTATE_TMA034_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/qc/preprocessing/msi/ROI042_PROSTATE_TMA034_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/qc/preprocessing/msi/ROI042_PROSTATE_TMA034_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/qc/preprocessing/msi/ROI042_PROSTATE_TMA034_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/provenance/miaaim-preprocessing-msi.sh
58%|██████████████████████████████████████████████████████████████████████ | 28/48 [35:30<25:41, 77.06s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/input/msi/ROI043_PROSTATE_TMA035_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/input/msi/ROI043_PROSTATE_TMA035.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/imc/ROI043_PROSTATE_TMA035_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/imc/ROI043_PROSTATE_TMA035_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/input/msi/ROI043_PROSTATE_TMA035.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi/ROI043_PROSTATE_TMA035_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi/ROI043_PROSTATE_TMA035_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi/ROI043_PROSTATE_TMA035_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi/ROI043_PROSTATE_TMA035_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/msi/ROI043_PROSTATE_TMA035_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/qc/preprocessing/msi/ROI043_PROSTATE_TMA035_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/qc/preprocessing/msi/ROI043_PROSTATE_TMA035_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/qc/preprocessing/msi/ROI043_PROSTATE_TMA035_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/provenance/miaaim-preprocessing-msi.sh
60%|████████████████████████████████████████████████████████████████████████▌ | 29/48 [36:46<24:20, 76.89s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/input/msi/ROI044_PROSTATE_TMA036_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/input/msi/ROI044_PROSTATE_TMA036.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/imc/ROI044_PROSTATE_TMA036_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/imc/ROI044_PROSTATE_TMA036_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/input/msi/ROI044_PROSTATE_TMA036.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi/ROI044_PROSTATE_TMA036_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi/ROI044_PROSTATE_TMA036_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi/ROI044_PROSTATE_TMA036_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi/ROI044_PROSTATE_TMA036_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/msi/ROI044_PROSTATE_TMA036_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/qc/preprocessing/msi/ROI044_PROSTATE_TMA036_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/qc/preprocessing/msi/ROI044_PROSTATE_TMA036_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/qc/preprocessing/msi/ROI044_PROSTATE_TMA036_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/provenance/miaaim-preprocessing-msi.sh
62%|███████████████████████████████████████████████████████████████████████████ | 30/48 [37:48<21:42, 72.38s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/input/msi/ROI045_PROSTATE_TMA038_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/input/msi/ROI045_PROSTATE_TMA038.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/imc/ROI045_PROSTATE_TMA038_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/imc/ROI045_PROSTATE_TMA038_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/input/msi/ROI045_PROSTATE_TMA038.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi/ROI045_PROSTATE_TMA038_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi/ROI045_PROSTATE_TMA038_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi/ROI045_PROSTATE_TMA038_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi/ROI045_PROSTATE_TMA038_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/msi/ROI045_PROSTATE_TMA038_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/qc/preprocessing/msi/ROI045_PROSTATE_TMA038_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/qc/preprocessing/msi/ROI045_PROSTATE_TMA038_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/qc/preprocessing/msi/ROI045_PROSTATE_TMA038_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/provenance/miaaim-preprocessing-msi.sh
65%|█████████████████████████████████████████████████████████████████████████████▌ | 31/48 [39:23<22:23, 79.02s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/input/msi/ROI046_PROSTATE_TMA039_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/input/msi/ROI046_PROSTATE_TMA039.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/imc/ROI046_PROSTATE_TMA039_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/imc/ROI046_PROSTATE_TMA039_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/input/msi/ROI046_PROSTATE_TMA039.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi/ROI046_PROSTATE_TMA039_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi/ROI046_PROSTATE_TMA039_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi/ROI046_PROSTATE_TMA039_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi/ROI046_PROSTATE_TMA039_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/msi/ROI046_PROSTATE_TMA039_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/qc/preprocessing/msi/ROI046_PROSTATE_TMA039_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/qc/preprocessing/msi/ROI046_PROSTATE_TMA039_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/qc/preprocessing/msi/ROI046_PROSTATE_TMA039_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/provenance/miaaim-preprocessing-msi.sh
67%|████████████████████████████████████████████████████████████████████████████████ | 32/48 [40:32<20:19, 76.21s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/input/msi/ROI048_PROSTATE_TMA042_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/input/msi/ROI048_PROSTATE_TMA042.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/imc/ROI048_PROSTATE_TMA042_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/imc/ROI048_PROSTATE_TMA042_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/input/msi/ROI048_PROSTATE_TMA042.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi/ROI048_PROSTATE_TMA042_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi/ROI048_PROSTATE_TMA042_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi/ROI048_PROSTATE_TMA042_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi/ROI048_PROSTATE_TMA042_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/msi/ROI048_PROSTATE_TMA042_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/qc/preprocessing/msi/ROI048_PROSTATE_TMA042_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/qc/preprocessing/msi/ROI048_PROSTATE_TMA042_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/qc/preprocessing/msi/ROI048_PROSTATE_TMA042_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/provenance/miaaim-preprocessing-msi.sh
69%|██████████████████████████████████████████████████████████████████████████████████▌ | 33/48 [41:41<18:27, 73.85s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/input/msi/ROI049_PROSTATE_TMA044_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/input/msi/ROI049_PROSTATE_TMA044.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/imc/ROI049_PROSTATE_TMA044_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/imc/ROI049_PROSTATE_TMA044_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/input/msi/ROI049_PROSTATE_TMA044.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi/ROI049_PROSTATE_TMA044_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi/ROI049_PROSTATE_TMA044_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi/ROI049_PROSTATE_TMA044_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi/ROI049_PROSTATE_TMA044_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/msi/ROI049_PROSTATE_TMA044_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/qc/preprocessing/msi/ROI049_PROSTATE_TMA044_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/qc/preprocessing/msi/ROI049_PROSTATE_TMA044_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/qc/preprocessing/msi/ROI049_PROSTATE_TMA044_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/provenance/miaaim-preprocessing-msi.sh
71%|█████████████████████████████████████████████████████████████████████████████████████ | 34/48 [42:53<17:07, 73.42s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/input/msi/ROI050_PROSTATE_TMA045_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/input/msi/ROI050_PROSTATE_TMA045.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/imc/ROI050_PROSTATE_TMA045_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/imc/ROI050_PROSTATE_TMA045_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/input/msi/ROI050_PROSTATE_TMA045.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi/ROI050_PROSTATE_TMA045_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi/ROI050_PROSTATE_TMA045_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi/ROI050_PROSTATE_TMA045_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi/ROI050_PROSTATE_TMA045_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/msi/ROI050_PROSTATE_TMA045_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/qc/preprocessing/msi/ROI050_PROSTATE_TMA045_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/qc/preprocessing/msi/ROI050_PROSTATE_TMA045_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/qc/preprocessing/msi/ROI050_PROSTATE_TMA045_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/provenance/miaaim-preprocessing-msi.sh
73%|███████████████████████████████████████████████████████████████████████████████████████▌ | 35/48 [44:30<17:28, 80.63s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/input/msi/ROI054_PROSTATE_TMA048_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/input/msi/ROI054_PROSTATE_TMA048.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/imc/ROI054_PROSTATE_TMA048_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/imc/ROI054_PROSTATE_TMA048_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/input/msi/ROI054_PROSTATE_TMA048.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi/ROI054_PROSTATE_TMA048_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi/ROI054_PROSTATE_TMA048_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi/ROI054_PROSTATE_TMA048_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi/ROI054_PROSTATE_TMA048_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/msi/ROI054_PROSTATE_TMA048_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/qc/preprocessing/msi/ROI054_PROSTATE_TMA048_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/qc/preprocessing/msi/ROI054_PROSTATE_TMA048_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/qc/preprocessing/msi/ROI054_PROSTATE_TMA048_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/provenance/miaaim-preprocessing-msi.sh
75%|██████████████████████████████████████████████████████████████████████████████████████████ | 36/48 [45:43<15:38, 78.17s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/input/msi/ROI055_PROSTATE_TMA049_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/input/msi/ROI055_PROSTATE_TMA049.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/imc/ROI055_PROSTATE_TMA049_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/imc/ROI055_PROSTATE_TMA049_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/input/msi/ROI055_PROSTATE_TMA049.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi/ROI055_PROSTATE_TMA049_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi/ROI055_PROSTATE_TMA049_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi/ROI055_PROSTATE_TMA049_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi/ROI055_PROSTATE_TMA049_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/msi/ROI055_PROSTATE_TMA049_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/qc/preprocessing/msi/ROI055_PROSTATE_TMA049_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/qc/preprocessing/msi/ROI055_PROSTATE_TMA049_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/qc/preprocessing/msi/ROI055_PROSTATE_TMA049_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/provenance/miaaim-preprocessing-msi.sh
77%|████████████████████████████████████████████████████████████████████████████████████████████▌ | 37/48 [46:46<13:29, 73.57s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/input/msi/ROI056_PROSTATE_TMA054_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/input/msi/ROI056_PROSTATE_TMA054.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/imc/ROI056_PROSTATE_TMA054_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/imc/ROI056_PROSTATE_TMA054_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 5
working on /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/input/msi/ROI056_PROSTATE_TMA054.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi/ROI056_PROSTATE_TMA054_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi/ROI056_PROSTATE_TMA054_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi/ROI056_PROSTATE_TMA054_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi/ROI056_PROSTATE_TMA054_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/msi/ROI056_PROSTATE_TMA054_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/qc/preprocessing/msi/ROI056_PROSTATE_TMA054_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/qc/preprocessing/msi/ROI056_PROSTATE_TMA054_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/qc/preprocessing/msi/ROI056_PROSTATE_TMA054_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/provenance/miaaim-preprocessing-msi.sh
79%|███████████████████████████████████████████████████████████████████████████████████████████████ | 38/48 [47:53<11:56, 71.68s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/input/msi/ROI057_PROSTATE_TMA055_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/input/msi/ROI057_PROSTATE_TMA055.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/imc/ROI057_PROSTATE_TMA055_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/imc/ROI057_PROSTATE_TMA055_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/input/msi/ROI057_PROSTATE_TMA055.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi/ROI057_PROSTATE_TMA055_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi/ROI057_PROSTATE_TMA055_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi/ROI057_PROSTATE_TMA055_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi/ROI057_PROSTATE_TMA055_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/msi/ROI057_PROSTATE_TMA055_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/qc/preprocessing/msi/ROI057_PROSTATE_TMA055_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/qc/preprocessing/msi/ROI057_PROSTATE_TMA055_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/qc/preprocessing/msi/ROI057_PROSTATE_TMA055_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/provenance/miaaim-preprocessing-msi.sh
81%|█████████████████████████████████████████████████████████████████████████████████████████████████▌ | 39/48 [48:58<10:28, 69.81s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/input/msi/ROI058_PROSTATE_TMA056_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/input/msi/ROI058_PROSTATE_TMA056.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/imc/ROI058_PROSTATE_TMA056_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/imc/ROI058_PROSTATE_TMA056_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/input/msi/ROI058_PROSTATE_TMA056.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi/ROI058_PROSTATE_TMA056_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi/ROI058_PROSTATE_TMA056_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi/ROI058_PROSTATE_TMA056_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi/ROI058_PROSTATE_TMA056_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/msi/ROI058_PROSTATE_TMA056_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/qc/preprocessing/msi/ROI058_PROSTATE_TMA056_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/qc/preprocessing/msi/ROI058_PROSTATE_TMA056_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/qc/preprocessing/msi/ROI058_PROSTATE_TMA056_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/provenance/miaaim-preprocessing-msi.sh
83%|████████████████████████████████████████████████████████████████████████████████████████████████████ | 40/48 [50:14<09:32, 71.62s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/input/msi/ROI059_PROSTATE_TMA057_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/input/msi/ROI059_PROSTATE_TMA057.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/imc/ROI059_PROSTATE_TMA057_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/imc/ROI059_PROSTATE_TMA057_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/input/msi/ROI059_PROSTATE_TMA057.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi/ROI059_PROSTATE_TMA057_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi/ROI059_PROSTATE_TMA057_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi/ROI059_PROSTATE_TMA057_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi/ROI059_PROSTATE_TMA057_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/msi/ROI059_PROSTATE_TMA057_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/qc/preprocessing/msi/ROI059_PROSTATE_TMA057_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/qc/preprocessing/msi/ROI059_PROSTATE_TMA057_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/qc/preprocessing/msi/ROI059_PROSTATE_TMA057_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/provenance/miaaim-preprocessing-msi.sh
85%|██████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 41/48 [51:24<08:16, 70.89s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/input/msi/ROI061_PROSTATE_TMA060_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/input/msi/ROI061_PROSTATE_TMA060.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/imc/ROI061_PROSTATE_TMA060_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/imc/ROI061_PROSTATE_TMA060_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/input/msi/ROI061_PROSTATE_TMA060.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi/ROI061_PROSTATE_TMA060_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi/ROI061_PROSTATE_TMA060_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi/ROI061_PROSTATE_TMA060_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi/ROI061_PROSTATE_TMA060_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/msi/ROI061_PROSTATE_TMA060_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/qc/preprocessing/msi/ROI061_PROSTATE_TMA060_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/qc/preprocessing/msi/ROI061_PROSTATE_TMA060_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/qc/preprocessing/msi/ROI061_PROSTATE_TMA060_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/provenance/miaaim-preprocessing-msi.sh
88%|█████████████████████████████████████████████████████████████████████████████████████████████████████████ | 42/48 [52:25<06:48, 68.10s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/input/msi/ROI062_PROSTATE_TMA061_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/input/msi/ROI062_PROSTATE_TMA061.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/imc/ROI062_PROSTATE_TMA061_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/imc/ROI062_PROSTATE_TMA061_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/input/msi/ROI062_PROSTATE_TMA061.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi/ROI062_PROSTATE_TMA061_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi/ROI062_PROSTATE_TMA061_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi/ROI062_PROSTATE_TMA061_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi/ROI062_PROSTATE_TMA061_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/msi/ROI062_PROSTATE_TMA061_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/qc/preprocessing/msi/ROI062_PROSTATE_TMA061_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/qc/preprocessing/msi/ROI062_PROSTATE_TMA061_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/qc/preprocessing/msi/ROI062_PROSTATE_TMA061_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/provenance/miaaim-preprocessing-msi.sh
90%|███████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 43/48 [53:43<05:55, 71.13s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/input/msi/ROI063_PROSTATE_TMA062_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/input/msi/ROI063_PROSTATE_TMA062.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/imc/ROI063_PROSTATE_TMA062_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/imc/ROI063_PROSTATE_TMA062_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/input/msi/ROI063_PROSTATE_TMA062.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi/ROI063_PROSTATE_TMA062_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi/ROI063_PROSTATE_TMA062_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi/ROI063_PROSTATE_TMA062_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi/ROI063_PROSTATE_TMA062_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/msi/ROI063_PROSTATE_TMA062_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/qc/preprocessing/msi/ROI063_PROSTATE_TMA062_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/qc/preprocessing/msi/ROI063_PROSTATE_TMA062_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/qc/preprocessing/msi/ROI063_PROSTATE_TMA062_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/provenance/miaaim-preprocessing-msi.sh
92%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 44/48 [54:59<04:50, 72.53s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/input/msi/ROI067_PROSTATE_TMA065_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/input/msi/ROI067_PROSTATE_TMA065.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/imc/ROI067_PROSTATE_TMA065_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/imc/ROI067_PROSTATE_TMA065_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/input/msi/ROI067_PROSTATE_TMA065.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi/ROI067_PROSTATE_TMA065_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi/ROI067_PROSTATE_TMA065_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi/ROI067_PROSTATE_TMA065_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi/ROI067_PROSTATE_TMA065_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/msi/ROI067_PROSTATE_TMA065_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/qc/preprocessing/msi/ROI067_PROSTATE_TMA065_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/qc/preprocessing/msi/ROI067_PROSTATE_TMA065_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/qc/preprocessing/msi/ROI067_PROSTATE_TMA065_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/provenance/miaaim-preprocessing-msi.sh
94%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 45/48 [56:13<03:38, 72.98s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/input/msi/ROI068_PROSTATE_TMA066_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/input/msi/ROI068_PROSTATE_TMA066.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/imc/ROI068_PROSTATE_TMA066_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/imc/ROI068_PROSTATE_TMA066_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/input/msi/ROI068_PROSTATE_TMA066.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi/ROI068_PROSTATE_TMA066_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi/ROI068_PROSTATE_TMA066_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi/ROI068_PROSTATE_TMA066_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi/ROI068_PROSTATE_TMA066_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/msi/ROI068_PROSTATE_TMA066_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/qc/preprocessing/msi/ROI068_PROSTATE_TMA066_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/qc/preprocessing/msi/ROI068_PROSTATE_TMA066_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/qc/preprocessing/msi/ROI068_PROSTATE_TMA066_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/provenance/miaaim-preprocessing-msi.sh
96%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 46/48 [57:25<02:25, 72.70s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/input/msi/ROI069_PROSTATE_TMA067_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/input/msi/ROI069_PROSTATE_TMA067.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/imc/ROI069_PROSTATE_TMA067_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/imc/ROI069_PROSTATE_TMA067_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/input/msi/ROI069_PROSTATE_TMA067.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi/ROI069_PROSTATE_TMA067_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi/ROI069_PROSTATE_TMA067_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi/ROI069_PROSTATE_TMA067_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi/ROI069_PROSTATE_TMA067_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/msi/ROI069_PROSTATE_TMA067_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/qc/preprocessing/msi/ROI069_PROSTATE_TMA067_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/qc/preprocessing/msi/ROI069_PROSTATE_TMA067_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/qc/preprocessing/msi/ROI069_PROSTATE_TMA067_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/provenance/miaaim-preprocessing-msi.sh
98%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 47/48 [58:33<01:11, 71.31s/it]
MIAAIM PREPROCESSING
MIAAIM VERSION 0.0.2
METHOD: HDIpreprocessing
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070
RESULTS FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/qc/preprocessing/msi
IMPORTING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/input/msi/ROI070_PROSTATE_TMA070_mask.tiff
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/input/msi/ROI070_PROSTATE_TMA070.hdf5
Finished parsing data
PROCESSING DATA
mask: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/imc/ROI070_PROSTATE_TMA070_core_mask.tif
Valid path...
Valid file extension...
file name: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/imc/ROI070_PROSTATE_TMA070_core_UMAP.nii
Finished parsing nifti
Finished
RunOptimalUMAP: computing optimal UMAP embedding
Reloading using processed mask for dimension reduction
Computing UMAP simplicial set on 702 image channels...
Embedding in dimension 1
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 2
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 3
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 4
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 5
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 6
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 7
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 8
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 9
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Embedding in dimension 10
Finished embedding
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:104: RuntimeWarning: divide by zero encountered in log
Psi_summands[w0] = np.log(1 - Psi[w0])
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/proc/_fuzzy_ops.py:106: RuntimeWarning: divide by zero encountered in log
(1 - weights[other]), np.log(1 - Psi[other])
Finding optimal embedding dimension through exponential fit...
Optimal UMAP embedding dimension is 4
working on /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/input/msi/ROI070_PROSTATE_TMA070.hdf5...
Reconstructing image...
Finished spatial mapping
Export: exporting processed image
Exporting f/opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi/ROI070_PROSTATE_TMA070_core_msi_UMAP.nii...
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi/ROI070_PROSTATE_TMA070_core_msi_UMAP.nii
ExportMask: exporting processed mask
Exporting f/opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi/ROI070_PROSTATE_TMA070_core_msi_mask.tif...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi/ROI070_PROSTATE_TMA070_core_msi_mask.tif is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/msi/ROI070_PROSTATE_TMA070_core_msi_mask.tif
QC: extracting quality control information
Extracting countour from processed masks
Exporting f/opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/qc/preprocessing/msi/ROI070_PROSTATE_TMA070_qcMask.tiff...
/opt/conda/envs/miaaim-dev/lib/python3.10/site-packages/miaaim/io/imwrite/_export.py:66: UserWarning: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/qc/preprocessing/msi/ROI070_PROSTATE_TMA070_qcMask.tiff is a boolean image: setting True to 255 and False to 0. To silence this warning, please convert the image using img_as_ubyte.
skimage.io.imsave(self.path, arr, plugin="tifffile")
Finished exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/qc/preprocessing/msi/ROI070_PROSTATE_TMA070_qcMask.tiff
Extracting subsampled masks if used for dimension reduction
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/parameters/miaaim-preprocessing-msi.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/provenance/miaaim-preprocessing-msi.sh
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 48/48 [59:46<00:00, 74.72s/it]
