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MEDomics-UdeS · Dec 4, 2023 · b53d216 · b53d216
2 parents 41d2b6b + 24ed92b
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diff --git a/.gitignore b/.gitignore
@@ -156,5 +156,6 @@ renderer/public/pythonCode/local_dir/*
 path2condaenv_toDeleteInProd.txt
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+pythonCode/local_dir/*
 
 !*.gitkeep
diff --git a/pythonCode/local_dir/.gitkeep b/pythonCode/local_dir/.gitkeep
diff --git a/pythonCode/submodules/MEDimage b/pythonCode/submodules/MEDimage
diff --git a/pythonCode/submodules/MEDprofiles b/pythonCode/submodules/MEDprofiles
+149 −77		MEDimage/MEDscan.py
+1 −1		MEDimage/__init__.py
+129 −96		MEDimage/biomarkers/BatchExtractor.py
+2 −1		MEDimage/biomarkers/diagnostics.py
+10 −10		MEDimage/biomarkers/glcm.py
+45 −45		MEDimage/biomarkers/int_vol_hist.py
+2 −2		MEDimage/biomarkers/intensity_histogram.py
+9 −2		MEDimage/biomarkers/local_intensity.py
+138 −128		MEDimage/biomarkers/morph.py
+2 −2		MEDimage/biomarkers/ngldm.py
+31 −22		MEDimage/biomarkers/stats.py
+50 −40		MEDimage/filters/apply_filter.py
+26 −19		MEDimage/filters/gabor.py
+12 −12		MEDimage/filters/laws.py
+11 −11		MEDimage/filters/log.py
+9 −9		MEDimage/filters/mean.py
+12 −11		MEDimage/filters/wavelet.py
+53 −29		MEDimage/processing/interpolation.py
+34 −34		MEDimage/processing/segmentation.py
+2 −1		MEDimage/utils/__init__.py
+13 −7		MEDimage/utils/create_radiomics_table.py
+21 −0		MEDimage/utils/get_full_rad_names.py
+8 −7		MEDimage/utils/get_institutions_from_ids.py
+0 −59		MEDimage/utils/initMEDimage.py
+5 −5		MEDimage/utils/inpolygon.py
+8 −6		MEDimage/utils/json_utils.py
+0 −28		MEDimage/utils/save_MEDimage.py
+30 −0		MEDimage/utils/save_MEDscan.py
+1 −0		MEDimage/utils/write_radiomics_csv.py
+308 −264		MEDimage/wrangling/DataManager.py
+69 −51		MEDimage/wrangling/ProcessDICOM.py
+65 −25		README.md
+8 −8		docs/Installation.rst
+3 −3		docs/MEDscan.rst
+444 −75		docs/configuration_file.rst
+81 −13		docs/csv_file.rst
+ −		docs/figures/BatchExtractor-overview.png
+ −		docs/figures/DataManager-overview.png
+ −		docs/figures/InputDataSummary.png
+ −		docs/figures/ROILabelExample.png
+ −		docs/figures/RoiNamesExample.png
+ −		docs/figures/pakcage-overview.png
+0 −19		docs/filter.rst
+59 −0		docs/filters.rst
+1 −0		docs/index.rst
+104 −0		docs/input_data.rst
+2 −2		docs/modules.rst
+8 −8		docs/tutorials.rst
+2 −10		docs/utils.rst
+1 −0		environment.yml
+143 −130		notebooks/demo/Glioma-Demo.ipynb
+ −		notebooks/demo/data/Glioma-TCGA-02-0003__T1.MRscan.npy
+8 −9		notebooks/ibsi/ibsi1p1.ipynb
+23 −29		notebooks/ibsi/ibsi1p2.ipynb
+11 −11		notebooks/ibsi/ibsi2p1.ipynb
+20 −47		notebooks/ibsi/ibsi2p2.ipynb
+33 −5		notebooks/tutorial/BatchExtractor-Tutorial.ipynb
+67 −64		notebooks/tutorial/DataManager-Tutorial.ipynb
+40 −47		notebooks/tutorial/MEDscan-Tutorial.ipynb
+ −		notebooks/tutorial/images/BatchExtractionFolderStructure.png
+ −		notebooks/tutorial/images/DataManager-workflow.png
+ −		notebooks/tutorial/images/DataManagerFolderStructure.png
+ −		notebooks/tutorial/images/MEDimageClassDiagram.png
+ −		notebooks/tutorial/images/MEDimageFlowchart.png
+ −		notebooks/tutorial/images/MEDimageFolderStructure.png
+16 −4		notebooks/tutorial/settings/MEDimage-Tutorial.json
+1 −1		python.md
+2 −1		requirements.txt
+43 −0		scripts/process_dataset.py
+2 −0		.gitignore
+95 −0		.idea/workspace.xml
+ −		MEDclasses/__pycache__/MEDbaseObject.cpython-38.pyc
+ −		MEDclasses/__pycache__/MEDcohort.cpython-38.pyc
+ −		MEDclasses/__pycache__/MEDprofile.cpython-38.pyc
+ −		MEDclasses/__pycache__/MEDtab.cpython-38.pyc
+21 −5		MEDprofiles/MEDclasses/MEDcohort.py
+1 −1		MEDprofiles/MEDclasses/MEDprofile.py
+1 −2		MEDprofiles/MEDclasses/MEDtab.py
+2 −0		MEDprofiles/__init__.py
+2 −1		MEDprofiles/src/__init__.py
+25 −12		MEDprofiles/src/back/create_classes_from_master_table.py
+21 −8		MEDprofiles/src/back/instantiate_data_from_master_table.py
+5 −5		MEDprofiles/src/semi_front/MEDcohortFigure.py
+2 −2		MEDprofiles/src/semi_front/MEDprofileFigure.py
+2 −3		MEDprofiles/src/semi_front/utils/MEDcohort_utils.py
+2 −3		MEDprofiles/src/semi_front/utils/MEDprofiles_utils.py
+ −		data/meningioma/__pycache__/create_master_table.cpython-38.pyc
+ −		data/mimic/__pycache__/create_master_table.cpython-38.pyc
+4 −2		requirements.txt
+1 −1		setup.py
+ −		src/back/__pycache__/constant.cpython-38.pyc
+ −		src/back/__pycache__/create_classes_from_master_table.cpython-38.pyc
+ −		src/back/__pycache__/instantiate_data_from_master_table.cpython-38.pyc
+ −		src/semi_front/__pycache__/MEDcohort_utils.cpython-38.pyc
+ −		src/semi_front/__pycache__/MEDprofiles_utils.cpython-38.pyc