diff --git a/.gitignore b/.gitignore index e43b0f9..b0e5f1d 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,153 @@ .DS_Store +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintainted in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +.idea/ \ No newline at end of file diff --git a/README.md b/README.md index 64ad1e7..11f94d2 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,8 @@ Light-weighted data for testing/tutorial * `_labels-disc-manual`: dummy label (single voxel), which is supposed to represent disc label. WARNING: this is *not* an actual label that represent the anatomy, but is only here for the purpose of testing the workflow of `ivadomed` codebase. * bounding\_box.json: dictionary to test a specific function from `ivadomed/scripts/bounding_box.py`. * dataset\_description.json: this file is needed to described the dataset. -* df\_ref.csv: Used to test a specific function from `ivadomed/loader/utils.py`. +* df\_ref.csv: Used to test loader DataFrame specific function from `ivadomed/loader/utils.py`. +* df\_ref_multi.csv: Used to test loader DataFrame specific function from `ivadomed/loader/utils.py`. * participants.csv: table with subject name and potential metadata. * temporary\_results.csv: Used to test `ivadomed/scripts/compare_models.py`. diff --git a/df_ref.csv b/df_ref.csv index caa99a7..7c38cc5 100644 --- a/df_ref.csv +++ b/df_ref.csv @@ -2,6 +2,8 @@ filename,AcquisitionMatrixPE,AcquisitionNumber,AcquisitionTime,BaseResolution,Bo sub-unf01_T1w.nii.gz,260,1,12:33:7.032500,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,,0.00372,,9,"[0, 1, 0, -0.00523601, 0, -0.999986]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",ROW,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,,1,3D,3,Siemens,Prisma_fit,MR,2,1,HFS,81.25,259,,1,150,spine_generic,T1w,%SiemensSeq%_tfl,"HC1-7;NC1,2",HeadNeck_64,320,2,0.0601922,IR,GR_IR,_tfl3d1_16,SK_SP_MP,T1w,2,"[620, -7194, -9127, 77, 28, -20, -10, -23]",1,syngo_MR_E11,MRC35049,266.247,anat,.nii.gz,unf01,T1w,sub-unf01,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown sub-unf01_T1w_lesion-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-unf01_T1w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +sub-unf01_T2star_lesion-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +sub-unf01_T2star_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-unf01_T2w.nii.gz,320,1,12:39:2.805000,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,2.5e-06,0.12,76,120,"[0, 1, 4.897e-12, 0, 4.897e-12, -1]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",COL,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,Department,,3D,3,Siemens,Prisma_fit,MR,3,1,HFS,100,422,0.8,1,625,spine_generic,T2w,%SiemensSeq%_tse_vfl,"HC5-7;NC1,2;SP1",Spine_32,320,1.5,0.533389,PFP,SE,_spcR_100,SK_SP_OSP,T2w,3,"[620, -7194, -9127, 77, 28, -20, -10, -23]",0.8,syngo_MR_E11,MRC35049,283.131,anat,.nii.gz,unf01,T2w,sub-unf01,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown sub-unf01_T2w_lesion-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/df_ref_multi.csv b/df_ref_multi.csv index 3580c0a..68d4395 100644 --- a/df_ref_multi.csv +++ b/df_ref_multi.csv @@ -11,5 +11,6 @@ sub-rat3_ses-02_sample-data11_run-2_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-unf01_T1w.nii.gz,260,1,12:33:7.032500,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,,0.00372,,9,"[0, 1, 0, -0.00523601, 0, -0.999986]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",ROW,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,,1,3D,3,Siemens,Prisma_fit,MR,2,1,HFS,81.25,259,,1,150,spine_generic,T1w,%SiemensSeq%_tfl,"HC1-7;NC1,2",HeadNeck_64,320,2,0.0601922,IR,GR_IR,_tfl3d1_16,SK_SP_MP,T1w,2,"[620, -7194, -9127, 77, 28, -20, -10, -23]",1,syngo_MR_E11,MRC35049,266.247,anat,.nii.gz,unf01,T1w,sub-unf01,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown,,,,,,,,,,,,,,,,, sub-unf01_T1w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +sub-unf01_T2star_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, sub-unf01_T2w.nii.gz,320,1,12:39:2.805000,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,2.5e-06,0.12,76,120,"[0, 1, 4.897e-12, 0, 4.897e-12, -1]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",COL,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,Department,,3D,3,Siemens,Prisma_fit,MR,3,1,HFS,100,422,0.8,1,625,spine_generic,T2w,%SiemensSeq%_tse_vfl,"HC5-7;NC1,2;SP1",Spine_32,320,1.5,0.533389,PFP,SE,_spcR_100,SK_SP_OSP,T2w,3,"[620, -7194, -9127, 77, 28, -20, -10, -23]",0.8,syngo_MR_E11,MRC35049,283.131,anat,.nii.gz,unf01,T2w,sub-unf01,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown,,,,,,,,,,,,,,,,, sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,