├── .gitignore
├── .pypirc
├── .travis.yml
├── LICENSE.txt
├── MANIFEST.in
├── README.md
├── __init__.py
├── docker
    ├── entrypoint.sh
    └── radiomics_docker
    │   └── Dockerfile
├── documentation
    ├── Example_Scripts
    │   ├── Artifical_Motion.py
    │   ├── Calculate_DICOM_RT_Statistics.py
    │   ├── DCE_Database.py
    │   ├── Process_DRO_Phantoms.py
    │   ├── Process_JPG_ROI.py
    │   └── Process_Multiple_JPG_ROI.py
    ├── Tutorial_Modules
    │   └── Machine_Learning_and_Feature_Extraction_Tutorial
    │   │   ├── Feature_Extraction_Answers
    │   │       ├── GLCM_square_phantom.csv
    │   │       ├── intensity_square_phantom.csv
    │   │       ├── shape_mri_phantom.csv
    │   │       ├── size_square_phantom.csv
    │   │       └── square_intensity_phantom.csv
    │   │   ├── Feature_Extraction_Tutorial
    │   │       ├── Feature_Extraction_Tutorial.ipynb
    │   │       ├── GLCM_Angle.PNG
    │   │       ├── GLCM_Distance.PNG
    │   │       ├── Intensity_Phantom.PNG
    │   │       ├── Shape_MRI.PNG
    │   │       └── Size_Phantom.PNG
    │   │   ├── Lung_Challenge_Features
    │   │       ├── Lung_Feature_Results_Final.csv
    │   │       ├── TBT_TRN_001-label.nii.gz
    │   │       ├── TBT_TRN_001.nii.gz
    │   │       ├── TBT_TRN_002-label.nii.gz
    │   │       └── TBT_TRN_002.nii.gz
    │   │   ├── Phantom_Data
    │   │       ├── MR_Tumor_Shape
    │   │       │   ├── MR_BrainTumor_ShapeTest-label.nii.gz
    │   │       │   └── MR_BrainTumor_ShapeTest.nii.gz
    │   │       ├── MR_Tumor_Size
    │   │       │   ├── MR_BrainTumor_SizeTest-label.nii.gz
    │   │       │   └── MR_BrainTumor_SizeTest.nii.gz
    │   │       ├── Phantom_GLCM
    │   │       │   ├── GLCM_Grid_0_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_0_Phantom.nii.gz
    │   │       │   ├── GLCM_Grid_1_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_1_Phantom.nii.gz
    │   │       │   ├── GLCM_Grid_2_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_2_Phantom.nii.gz
    │   │       │   ├── GLCM_Grid_3_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_3_Phantom.nii.gz
    │   │       │   ├── GLCM_Grid_4_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_4_Phantom.nii.gz
    │   │       │   ├── GLCM_Grid_5_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Grid_5_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_0_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_0_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_1_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_1_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_2_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_2_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_3_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_3_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_4_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_4_Phantom.nii.gz
    │   │       │   ├── GLCM_Horizontal_5_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Horizontal_5_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_0_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Vertical_0_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_1_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Vertical_1_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_2_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Vertical_2_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_3_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Vertical_3_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_4_Phantom-label.nii.gz
    │   │       │   ├── GLCM_Vertical_4_Phantom.nii.gz
    │   │       │   ├── GLCM_Vertical_5_Phantom-label.nii.gz
    │   │       │   └── GLCM_Vertical_5_Phantom.nii.gz
    │   │       ├── Phantom_Intensity
    │   │       │   ├── Intensity_checker_Phantom-label.nii.gz
    │   │       │   ├── Intensity_checker_Phantom.nii.gz
    │   │       │   ├── Intensity_grey_Phantom-label.nii.gz
    │   │       │   ├── Intensity_grey_Phantom.nii.gz
    │   │       │   ├── Intensity_noisy_grey_Phantom-label.nii.gz
    │   │       │   ├── Intensity_noisy_grey_Phantom.nii.gz
    │   │       │   ├── Intensity_one_spot_Phantom-label.nii.gz
    │   │       │   ├── Intensity_one_spot_Phantom.nii.gz
    │   │       │   ├── Intensity_split_Phantom-label.nii.gz
    │   │       │   └── Intensity_split_Phantom.nii.gz
    │   │       └── Phantom_Size
    │   │       │   ├── Size_0_Phantom-label.nii.gz
    │   │       │   ├── Size_0_Phantom.nii.gz
    │   │       │   ├── Size_1_Phantom-label.nii.gz
    │   │       │   ├── Size_1_Phantom.nii.gz
    │   │       │   ├── Size_2_Phantom-label.nii.gz
    │   │       │   ├── Size_2_Phantom.nii.gz
    │   │       │   ├── Size_4_Phantom-label.nii.gz
    │   │       │   ├── Size_4_Phantom.nii.gz
    │   │       │   ├── Size_5_Phantom-label.nii.gz
    │   │       │   ├── Size_5_Phantom.nii.gz
    │   │       │   ├── Size_6_Phantom-label.nii.gz
    │   │       │   ├── Size_6_Phantom.nii.gz
    │   │       │   ├── Size_7_Phantom-label.nii.gz
    │   │       │   ├── Size_7_Phantom.nii.gz
    │   │       │   ├── Size_8_Phantom-label.nii.gz
    │   │       │   ├── Size_8_Phantom.nii.gz
    │   │       │   ├── Size_9_Phantom-label.nii.gz
    │   │       │   └── Size_9_Phantom.nii.gz
    │   │   ├── PredictionsLungData.csv
    │   │   ├── Preprocessing_Tutorial
    │   │       ├── Kaggle_Preprocessing.ipynb
    │   │       └── Kaggle_Preprocessing.py
    │   │   ├── ResultsLungData.csv
    │   │   └── Simple_Machine_Learning_Example
    │   │       └── Simple_Machine_Learning_Example.py
    └── iPython_Walkthroughs
    │   └── qtim_dce
    │       ├── DCE_Processing_Notebook.ipynb
    │       ├── DCE_Processing_Notebook.py
    │       ├── QIBA_Phantom_Expected_Results.png
    │       └── QIBA_Phantom_Input.PNG
├── package_resources
    └── logos
    │   └── qtim_tools.png
├── qtim_tools
    ├── __init__.py
    ├── __main__.py
    ├── external
    │   ├── 1d_tool.py
    │   ├── afni_base.py
    │   ├── afni_util.py
    │   ├── fdt_rotate_bvecs.sh
    │   ├── lib_afni1D.py
    │   ├── lib_textdata.py
    │   ├── module_test_lib.py
    │   └── option_list.py
    ├── qtim_dce
    │   ├── README.md
    │   ├── __init__.py
    │   ├── dce_util.py
    │   ├── process_dce_file.py
    │   ├── tofts_parametric_mapper.py
    │   └── tofts_worker.py
    ├── qtim_dti
    │   ├── __init__.py
    │   └── fit_dti.py
    ├── qtim_features
    │   ├── GLCM.py
    │   ├── README.md
    │   ├── __init__.py
    │   ├── extract_features.py
    │   ├── morphology.py
    │   ├── phantoms.py
    │   ├── statistics.py
    │   └── test.py
    ├── qtim_learning
    │   ├── README.md
    │   ├── __init__.py
    │   └── nn_preprocessing.py
    ├── qtim_pipelines
    │   ├── README.md
    │   ├── __init__.py
    │   ├── coregistration.py
    │   ├── create_config.py
    │   ├── deep_learning.py
    │   ├── default_configs
    │   │   └── deep_learning_experiment.yaml
    │   ├── dti_conversion.py
    │   ├── label_statistics.py
    │   └── process_dce.py
    ├── qtim_preprocessing
    │   ├── README.md
    │   ├── __init__.py
    │   ├── bias_correction.py
    │   ├── image.py
    │   ├── motion_correction.py
    │   ├── normalization.py
    │   ├── orientation.py
    │   ├── registration.py
    │   ├── resample.py
    │   ├── signal.py
    │   ├── skull_strip.py
    │   └── threshold.py
    ├── qtim_slicer
    │   └── convert_dicom.py
    ├── qtim_stats
    │   ├── __init__.py
    │   └── image_stats.py
    ├── qtim_utilities
    │   ├── README.md
    │   ├── __init__.py
    │   ├── array_util.py
    │   ├── convert_util.py
    │   ├── dicom_util.py
    │   ├── file_util.py
    │   ├── format_util.py
    │   ├── image_util.py
    │   ├── nifti_util.py
    │   ├── nrrd_util.py
    │   ├── scratch_util.py
    │   ├── text_util.py
    │   └── transform_util.py
    ├── qtim_visualization
    │   ├── README.md
    │   ├── __init__.py
    │   ├── d3.py
    │   ├── d3_templates
    │   │   └── labeled_scatter.html
    │   ├── database.py
    │   └── image.py
    └── test_data
    │   ├── __init__.py
    │   ├── load.py
    │   ├── test_data_dce
    │       ├── gradient_tofts_v6-AIF-label.nii.gz
    │       ├── gradient_tofts_v6.nii.gz
    │       ├── tofts_v6-AIF-label.nii.gz
    │       ├── tofts_v6-label.nii.gz
    │       ├── tofts_v6.nii.gz
    │       ├── tofts_v9-AIF-label.nii.gz
    │       ├── tofts_v9-label.nii.gz
    │       └── tofts_v9.nii.gz
    │   └── test_data_features
    │       ├── MRBrainTumor2-label.nii.gz
    │       ├── MRBrainTumor2.nii.gz
    │       ├── MRHead-label.nii.gz
    │       ├── MRHead.nii.gz
    │       ├── MR_Tumor_Shape
    │           ├── MR_BrainTumor_ShapeTest-label.nii.gz
    │           └── MR_BrainTumor_ShapeTest.nii.gz
    │       ├── MR_Tumor_Size
    │           ├── MR_BrainTumor_SizeTest-label.nii.gz
    │           └── MR_BrainTumor_SizeTest.nii.gz
    │       ├── Phantom_GLCM
    │           ├── GLCM_Grid_0_Phantom-label.nii.gz
    │           ├── GLCM_Grid_0_Phantom.nii.gz
    │           ├── GLCM_Grid_1_Phantom-label.nii.gz
    │           ├── GLCM_Grid_1_Phantom.nii.gz
    │           ├── GLCM_Grid_2_Phantom-label.nii.gz
    │           ├── GLCM_Grid_2_Phantom.nii.gz
    │           ├── GLCM_Grid_3_Phantom-label.nii.gz
    │           ├── GLCM_Grid_3_Phantom.nii.gz
    │           ├── GLCM_Grid_4_Phantom-label.nii.gz
    │           ├── GLCM_Grid_4_Phantom.nii.gz
    │           ├── GLCM_Grid_5_Phantom-label.nii.gz
    │           ├── GLCM_Grid_5_Phantom.nii.gz
    │           ├── GLCM_Horizontal_0_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_0_Phantom.nii.gz
    │           ├── GLCM_Horizontal_1_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_1_Phantom.nii.gz
    │           ├── GLCM_Horizontal_2_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_2_Phantom.nii.gz
    │           ├── GLCM_Horizontal_3_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_3_Phantom.nii.gz
    │           ├── GLCM_Horizontal_4_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_4_Phantom.nii.gz
    │           ├── GLCM_Horizontal_5_Phantom-label.nii.gz
    │           ├── GLCM_Horizontal_5_Phantom.nii.gz
    │           ├── GLCM_Vertical_0_Phantom-label.nii.gz
    │           ├── GLCM_Vertical_0_Phantom.nii.gz
    │           ├── GLCM_Vertical_1_Phantom-label.nii.gz
    │           ├── GLCM_Vertical_1_Phantom.nii.gz
    │           ├── GLCM_Vertical_2_Phantom-label.nii.gz
    │           ├── GLCM_Vertical_2_Phantom.nii.gz
    │           ├── GLCM_Vertical_3_Phantom-label.nii.gz
    │           ├── GLCM_Vertical_3_Phantom.nii.gz
    │           ├── GLCM_Vertical_4_Phantom-label.nii.gz
    │           ├── GLCM_Vertical_4_Phantom.nii.gz
    │           ├── GLCM_Vertical_5_Phantom-label.nii.gz
    │           └── GLCM_Vertical_5_Phantom.nii.gz
    │       ├── Phantom_Intensity
    │           ├── Intensity_checker_Phantom-label.nii.gz
    │           ├── Intensity_checker_Phantom.nii.gz
    │           ├── Intensity_grey_Phantom-label.nii.gz
    │           ├── Intensity_grey_Phantom.nii.gz
    │           ├── Intensity_noisy_grey_Phantom-label.nii.gz
    │           ├── Intensity_noisy_grey_Phantom.nii.gz
    │           ├── Intensity_one_spot_Phantom-label.nii.gz
    │           ├── Intensity_one_spot_Phantom.nii.gz
    │           ├── Intensity_split_Phantom-label.nii.gz
    │           └── Intensity_split_Phantom.nii.gz
    │       ├── Phantom_Size
    │           ├── Size_0_Phantom-label.nii.gz
    │           ├── Size_0_Phantom.nii.gz
    │           ├── Size_1_Phantom-label.nii.gz
    │           ├── Size_1_Phantom.nii.gz
    │           ├── Size_2_Phantom-label.nii.gz
    │           ├── Size_2_Phantom.nii.gz
    │           ├── Size_4_Phantom-label.nii.gz
    │           ├── Size_4_Phantom.nii.gz
    │           ├── Size_5_Phantom-label.nii.gz
    │           ├── Size_5_Phantom.nii.gz
    │           ├── Size_6_Phantom-label.nii.gz
    │           ├── Size_6_Phantom.nii.gz
    │           ├── Size_7_Phantom-label.nii.gz
    │           ├── Size_7_Phantom.nii.gz
    │           ├── Size_8_Phantom-label.nii.gz
    │           ├── Size_8_Phantom.nii.gz
    │           ├── Size_9_Phantom-label.nii.gz
    │           └── Size_9_Phantom.nii.gz
    │       └── README.MD
├── requirements.txt
├── setup.cfg
├── setup.py
├── sphinx
    ├── Makefile
    ├── _build
    │   ├── doctrees
    │   │   ├── environment.pickle
    │   │   ├── index.doctree
    │   │   ├── modules.doctree
    │   │   ├── qtim_tools.doctree
    │   │   ├── qtim_tools.qtim_dce.doctree
    │   │   ├── qtim_tools.qtim_features.doctree
    │   │   ├── qtim_tools.qtim_learning.doctree
    │   │   ├── qtim_tools.qtim_pipelines.doctree
    │   │   ├── qtim_tools.qtim_preprocessing.doctree
    │   │   ├── qtim_tools.qtim_tools.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_dce.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_features.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_learning.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_pipelines.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_preprocessing.doctree
    │   │   ├── qtim_tools.qtim_tools.qtim_utilities.doctree
    │   │   ├── qtim_tools.qtim_tools.test_data.doctree
    │   │   ├── qtim_tools.qtim_utilities.doctree
    │   │   ├── qtim_tools.qtim_visualization.doctree
    │   │   └── qtim_tools.test_data.doctree
    │   └── html
    │   │   ├── .buildinfo
    │   │   ├── _modules
    │   │       ├── index.html
    │   │       └── qtim_tools
    │   │       │   ├── qtim_dce
    │   │       │       ├── dce_util.html
    │   │       │       ├── process_dce_file.html
    │   │       │       ├── tofts_parameter_calculator.html
    │   │       │       ├── tofts_parametric_mapper.html
    │   │       │       └── tofts_worker.html
    │   │       │   ├── qtim_features.html
    │   │       │   ├── qtim_features
    │   │       │       ├── GLCM.html
    │   │       │       ├── document_test.html
    │   │       │       ├── extract_features.html
    │   │       │       ├── morphology.html
    │   │       │       ├── phantoms.html
    │   │       │       ├── statistics.html
    │   │       │       └── test.html
    │   │       │   ├── qtim_learning
    │   │       │       └── nn_preprocessing.html
    │   │       │   ├── qtim_preprocessing
    │   │       │       ├── image.html
    │   │       │       ├── normalization.html
    │   │       │       ├── registration.html
    │   │       │       ├── signal.html
    │   │       │       └── threshold.html
    │   │       │   ├── qtim_utilities
    │   │       │       ├── array_util.html
    │   │       │       ├── dicom_util.html
    │   │       │       ├── file_util.html
    │   │       │       ├── format_util.html
    │   │       │       ├── image_util.html
    │   │       │       ├── nifti_util.html
    │   │       │       ├── nrrd_util.html
    │   │       │       └── transform_util.html
    │   │       │   ├── qtim_visualization
    │   │       │       └── image_database.html
    │   │       │   └── test_data
    │   │       │       └── load.html
    │   │   ├── _sources
    │   │       ├── index.txt
    │   │       ├── modules.txt
    │   │       ├── qtim_tools.qtim_dce.txt
    │   │       ├── qtim_tools.qtim_features.txt
    │   │       ├── qtim_tools.qtim_learning.txt
    │   │       ├── qtim_tools.qtim_pipelines.txt
    │   │       ├── qtim_tools.qtim_preprocessing.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_dce.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_features.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_learning.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_pipelines.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_preprocessing.txt
    │   │       ├── qtim_tools.qtim_tools.qtim_utilities.txt
    │   │       ├── qtim_tools.qtim_tools.test_data.txt
    │   │       ├── qtim_tools.qtim_tools.txt
    │   │       ├── qtim_tools.qtim_utilities.txt
    │   │       ├── qtim_tools.qtim_visualization.txt
    │   │       ├── qtim_tools.test_data.txt
    │   │       └── qtim_tools.txt
    │   │   ├── _static
    │   │       ├── ajax-loader.gif
    │   │       ├── alabaster.css
    │   │       ├── basic.css
    │   │       ├── comment-bright.png
    │   │       ├── comment-close.png
    │   │       ├── comment.png
    │   │       ├── css
    │   │       │   ├── badge_only.css
    │   │       │   └── theme.css
    │   │       ├── doctools.js
    │   │       ├── down-pressed.png
    │   │       ├── down.png
    │   │       ├── file.png
    │   │       ├── fonts
    │   │       │   ├── Inconsolata-Bold.ttf
    │   │       │   ├── Inconsolata-Regular.ttf
    │   │       │   ├── Lato-Bold.ttf
    │   │       │   ├── Lato-Regular.ttf
    │   │       │   ├── RobotoSlab-Bold.ttf
    │   │       │   ├── RobotoSlab-Regular.ttf
    │   │       │   ├── fontawesome-webfont.eot
    │   │       │   ├── fontawesome-webfont.svg
    │   │       │   ├── fontawesome-webfont.ttf
    │   │       │   └── fontawesome-webfont.woff
    │   │       ├── jquery.js
    │   │       ├── js
    │   │       │   ├── modernizr.min.js
    │   │       │   └── theme.js
    │   │       ├── minus.png
    │   │       ├── plus.png
    │   │       ├── pygments.css
    │   │       ├── searchtools.js
    │   │       ├── underscore.js
    │   │       ├── up-pressed.png
    │   │       ├── up.png
    │   │       └── websupport.js
    │   │   ├── genindex.html
    │   │   ├── index.html
    │   │   ├── modules.html
    │   │   ├── objects.inv
    │   │   ├── py-modindex.html
    │   │   ├── qtim_tools.html
    │   │   ├── qtim_tools.qtim_dce.html
    │   │   ├── qtim_tools.qtim_features.html
    │   │   ├── qtim_tools.qtim_learning.html
    │   │   ├── qtim_tools.qtim_pipelines.html
    │   │   ├── qtim_tools.qtim_preprocessing.html
    │   │   ├── qtim_tools.qtim_tools.html
    │   │   ├── qtim_tools.qtim_tools.qtim_dce.html
    │   │   ├── qtim_tools.qtim_tools.qtim_features.html
    │   │   ├── qtim_tools.qtim_tools.qtim_learning.html
    │   │   ├── qtim_tools.qtim_tools.qtim_pipelines.html
    │   │   ├── qtim_tools.qtim_tools.qtim_preprocessing.html
    │   │   ├── qtim_tools.qtim_tools.qtim_utilities.html
    │   │   ├── qtim_tools.qtim_tools.test_data.html
    │   │   ├── qtim_tools.qtim_utilities.html
    │   │   ├── qtim_tools.qtim_visualization.html
    │   │   ├── qtim_tools.test_data.html
    │   │   ├── search.html
    │   │   └── searchindex.js
    ├── conf.py
    ├── make.bat
    ├── modules.rst
    ├── qtim_tools.qtim_dce.rst
    ├── qtim_tools.qtim_features.rst
    ├── qtim_tools.qtim_learning.rst
    ├── qtim_tools.qtim_pipelines.rst
    ├── qtim_tools.qtim_preprocessing.rst
    ├── qtim_tools.qtim_utilities.rst
    ├── qtim_tools.qtim_visualization.rst
    ├── qtim_tools.rst
    ├── qtim_tools.test_data.rst
    └── requirements.txt
├── test_script.py
└── tests
    └── initial_test.py


/.gitignore:
--------------------------------------------------------------------------------
 1 | # Custom
 2 | *.jpg
 3 | *.csv
 4 | 
 5 | # Byte-compiled / optimized / DLL files
 6 | __pycache__/
 7 | *.py[cod]
 8 | *$py.class
 9 | 
10 | # C extensions
11 | *.so
12 | 
13 | # Distribution / packaging
14 | .Python
15 | env/
16 | build/
17 | develop-eggs/
18 | dist/
19 | downloads/
20 | eggs/
21 | .eggs/
22 | lib/
23 | lib64/
24 | parts/
25 | sdist/
26 | var/
27 | wheels/
28 | *.egg-info/
29 | .installed.cfg
30 | *.egg
31 | 
32 | # PyInstaller
33 | #  Usually these files are written by a python script from a template
34 | #  before PyInstaller builds the exe, so as to inject date/other infos into it.
35 | *.manifest
36 | *.spec
37 | 
38 | # Installer logs
39 | pip-log.txt
40 | pip-delete-this-directory.txt
41 | 
42 | # Unit test / coverage reports
43 | htmlcov/
44 | .tox/
45 | .coverage
46 | .coverage.*
47 | .cache
48 | nosetests.xml
49 | coverage.xml
50 | *,cover
51 | .hypothesis/
52 | 
53 | # Translations
54 | *.mo
55 | *.pot
56 | 
57 | # Django stuff:
58 | *.log
59 | local_settings.py
60 | 
61 | # Flask stuff:
62 | instance/
63 | .webassets-cache
64 | 
65 | # Scrapy stuff:
66 | .scrapy
67 | 
68 | # Sphinx documentation
69 | docs/_build/
70 | 
71 | # PyBuilder
72 | target/
73 | 
74 | # Jupyter Notebook
75 | .ipynb_checkpoints
76 | 
77 | # pyenv
78 | .python-version
79 | 
80 | # celery beat schedule file
81 | celerybeat-schedule
82 | 
83 | # dotenv
84 | .env
85 | 
86 | # virtualenv
87 | .venv/
88 | venv/
89 | ENV/
90 | 
91 | # Spyder project settings
92 | .spyderproject
93 | 
94 | # Rope project settings
95 | .ropeproject
96 | 
97 | # Testing
98 | hidden/
99 | 


--------------------------------------------------------------------------------
/.pypirc:
--------------------------------------------------------------------------------
 1 | [distutils]
 2 | index-servers =
 3 |   pypi
 4 |   pypitest
 5 | 
 6 | [pypi]
 7 | username=abeers
 8 | password=
 9 | 
10 | [pypitest]
11 | username=abeers
12 | password=


--------------------------------------------------------------------------------
/.travis.yml:
--------------------------------------------------------------------------------
 1 | language: python
 2 | python:
 3 |   - "2.7"
 4 | before_install:
 5 |   - pip install --upgrade pip setuptools wheel
 6 |   - pip install --only-binary=numpy,scipy numpy scipy
 7 | # command to install dependencies
 8 | install:
 9 |   - pip install travis-sphinx
10 |   - pip install numpydoc
11 |   - pip install sphinx_rtd_theme
12 |   - pip install .
13 | 
14 | notifications:
15 |   slack: qtim:jp1UTPVP5wscM2R6eyFHJIb4
16 | 
17 | # command to run tests
18 | script: 
19 |   - "python ./tests/initial_test.py"
20 |   - travis-sphinx build --nowarn
21 |     
22 | after_success:
23 |   - travis-sphinx deploy


--------------------------------------------------------------------------------
/MANIFEST.in:
--------------------------------------------------------------------------------
1 | # Include the license file
2 | include LICENSE.txt
3 | 
4 | # Include the data files
5 | recursive-include qtim_tools\test_data\test_data_features *
6 | 
7 | # If using Python 2.6 or less, then have to include package data, even though
8 | # it's already declared in setup.py
9 | # include sample/*.dat


--------------------------------------------------------------------------------
/__init__.py:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/QTIM-Lab/qtim_tools/b92e73127da5031f166174c047b3b56253be2486/__init__.py


--------------------------------------------------------------------------------
/docker/entrypoint.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | exec "$@"


--------------------------------------------------------------------------------
/docker/radiomics_docker/Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM python:2.7
 2 | 
 3 | RUN pip install --no-cache-dir numpy scipy matplotlib
 4 | 
 5 | RUN git clone https://github.com/QTIM-Lab/qtim_tools /home/qtim_tools
 6 | WORKDIR /home/qtim_tools
 7 | 
 8 | RUN echo 6
 9 | 
10 | RUN git pull
11 | RUN python /home/qtim_tools/setup.py develop
12 | 
13 | # Commands at startup.
14 | WORKDIR "/"
15 | RUN chmod 777 /home/qtim_tools/docker/entrypoint.sh
16 | ENTRYPOINT ["/home/qtim_tools/docker/entrypoint.sh"]


--------------------------------------------------------------------------------
/documentation/Example_Scripts/Process_JPG_ROI.py:
--------------------------------------------------------------------------------
 1 | from qtim_tools.qtim_preprocessing.image import fill_in_convex_outline
 2 | from qtim_tools.qtim_utilities.nifti_util import replace_slice
 3 | from qtim_tools.qtim_preprocessing.registration import register_all_to_one
 4 | from qtim_tools.qtim_features import extract_features
 5 | 
 6 | import numpy as np
 7 | 
 8 | def Convert_JPG_ROI_2_Nifti(input_image, output_nifti, reference_nifti, ROI_color_range, slice_number):
 9 | 
10 |     # This function takes the image defined by input_image, fills in closed lines in the color range defined by ROI_color_range,
11 |     # and saves it to a new one-slice nifti file with a header defined by reference_nifti.
12 |     fill_in_convex_outline(input_image, output_nifti, reference_nifti = reference_nifti, color_threshold_limits = ROI_color_range)
13 | 
14 |     # This function expands your one-slice nifti into a full 3D volume according to a provided reference Nifti volume. Slice number
15 |     # is required to orient the original 2D volume in space.
16 |     replace_slice(input_nifti_slice_filepath = output_nifti, reference_nifti_filepath = reference_nifti, output_file = output_nifti, slice_number = slice_number, orientation_commands=[np.rot90, np.flipud])
17 | 
18 |     return
19 | 
20 | def Register_Folder_to_One_Volume(fixed_volume, moving_volume_folder, output_folder, output_suffix, Slicer_Path):
21 | 
22 |     # Registers all volumes in a folder to one chosen fixed volume using Slicer's BRAINSFit registration.
23 |     register_all_to_one(fixed_volume = fixed_volume, moving_volume_folder = moving_volume_folder, output_folder=output_folder, output_suffix=output_suffix, Slicer_Path=Slicer_Path)
24 | 
25 |     return
26 | 
27 | def Extract_Features_From_Folder(input_folder, output_csv, label_identifier):
28 | 
29 |     # Extract texture and shape features using QTIM's feature extraction package. Erode labels by 3 voxels in the XY plane.
30 |     extract_features(input_folder, output_csv, set_label=label_identifier, erode=[3,3,0])
31 | 
32 |     return
33 | 
34 | def Full_Pipeline():
35 | 
36 |     # Parameters for JPG -> NIFTI conversion.
37 |     # #-----------------------------------------------------#
38 |     input_image = '/home/abeers/Junk/Tata_Test/image_with_roi.jpg'
39 |     reference_nifti = '/home/abeers/Junk/Tata_Test/7_Ax_T2_PROPELLER.nii.gz'
40 |     output_nifti = '/home/abeers/Junk/Tata_Test/image_with_roi-label.nii.gz'
41 |     ROI_color_range = [[100,300],[0,100],[0,100]] # RGB -> Bright Red
42 |     slice_number = 10
43 |     Convert_JPG_ROI_2_Nifti(input_image, output_nifti, reference_nifti, ROI_color_range, slice_number)
44 | 
45 |     # Parameters for group registration.
46 |     # #-----------------------------------------------------#
47 |     # Slicer_Path = '"/opt/Slicer/Slicer"'
48 |     # fixed_volume = '/home/abeers/Junk/Tata_Test7_Ax_T2_PROPELLER.nii.gz'
49 |     # moving_volume_folder = '/home/abeers/Junk/Tata_Test/Drawn_ROI_TestFiles/'
50 |     # output_folder = '/home/abeers/Junk/Tata_Test/Registered_Volumes/'
51 |     # output_suffix = '_registered_T2'
52 |     # Register_Folder_to_One_Volume(fixed_volume, moving_volume_folder, output_folder, output_suffix, Slicer_Path)
53 | 
54 |     # Parameters for feature extraction.
55 |     # #-----------------------------------------------------#
56 |     input_folder = '/home/abeers/Junk/Tata_Test/'
57 |     output_csv = '/home/abeers/Junk/Tata_Test/out.csv'
58 |     # Our feature extractor looks for a label in the same folder as input_folder with the filename below.
59 |     label_identifier = 'image_with_roi-label.nii.gz'
60 |     Extract_Features_From_Folder(input_folder, output_csv, label_identifier)
61 | 
62 | if __name__ == "__main__":
63 |     Full_Pipeline()


--------------------------------------------------------------------------------
/documentation/Example_Scripts/Process_Multiple_JPG_ROI.py:
--------------------------------------------------------------------------------
 1 | from qtim_tools.qtim_preprocessing.image import fill_in_convex_outline
 2 | from qtim_tools.qtim_utilities.nifti_util import replace_slice, generate_identity_affine, save_numpy_2_nifti_no_reference
 3 | from qtim_tools.qtim_utilities.dicom_util import get_dicom_dictionary, dcm_2_numpy
 4 | from qtim_tools.qtim_utilities.array_util import generate_identity_affine
 5 | from qtim_tools.qtim_features import extract_features
 6 | 
 7 | from optparse import OptionParser
 8 | 
 9 | import numpy as np
10 | import nibabel as nib
11 | import glob
12 | import os
13 | import re
14 | 
15 | def Convert_JPG_ROI_2_Nifti(roi_folder, original_folder, output_nifti, output_nifti_label, ROI_color_range=[[200,300],[0,100],[0,100]]):
16 | 
17 |     original_dicom_dict = get_dicom_dictionary(original_folder)
18 | 
19 |     spacing = [original_dicom_dict['PixelSpacing'][0], original_dicom_dict['PixelSpacing'][1], original_dicom_dict['SpacingBetweenSlices']]
20 |     spacing = [float(i) for i in spacing]
21 | 
22 |     original_numpy_data = dcm_2_numpy(original_folder)
23 | 
24 |     roi_numpy_data = np.zeros_like(original_numpy_data)
25 | 
26 |     ROI_list = sort_human(glob.glob(os.path.join(roi_folder, '*')))
27 | 
28 |     for ROI_idx, ROI in enumerate(ROI_list):
29 |         roi_numpy_data[..., ROI_idx] = fill_in_convex_outline(ROI, color_threshold_limits = ROI_color_range)
30 | 
31 |     nifti_volume = save_numpy_2_nifti_no_reference(original_numpy_data)
32 |     nifti_label = save_numpy_2_nifti_no_reference(roi_numpy_data)
33 | 
34 |     nifti_volume.header['pixdim'][1:4] = spacing  
35 |     nifti_label.header['pixdim'][1:4] = spacing
36 | 
37 |     nib.save(nifti_volume, output_nifti)
38 |     nib.save(nifti_label, output_nifti_label)
39 | 
40 |     return
41 | 
42 | def Extract_Features_From_Folder(input_folder, input_label, output_csv):
43 | 
44 |     # Extract texture and shape features using QTIM's feature extraction package. Erode labels by 3 voxels in the XY plane.
45 |     extract_features(input_folder, output_csv, set_label=input_label, erode=[3,3,0])
46 | 
47 |     return
48 | 
49 | def Full_Pipeline(roi_folder, original_folder, output_nifti, output_nifti_label, feature_input_folder, output_features):
50 | 
51 |     Convert_JPG_ROI_2_Nifti(roi_folder, original_folder, output_nifti, output_nifti_label)
52 |     Extract_Features_From_Folder(feature_input_folder, output_nifti_label, output_features)
53 | 
54 | def sort_human(l):
55 |     convert = lambda text: float(text) if text.isdigit() else text
56 |     alphanum = lambda key: [ convert(c) for c in re.split('([-+]?[0-9]*\.?[0-9]*)', key) ]
57 |     l.sort( key=alphanum )
58 |     return l
59 | 
60 | if __name__ == "__main__":
61 |     parser = OptionParser()
62 |     parser.add_option("--in_roi", "--roi_folder", dest="roi_folder", help="Folder containing JPG Segmentations to be translated into Nifti files")
63 |     parser.add_option("--in_original", "--original_folder", dest="original_folder", help="Folder containing original DICOM files.")
64 |     parser.add_option("--out_nifti", "--output_nifti", dest="output_nifti", help="Output Nifti file converted from the original DICOM files")
65 |     parser.add_option("--out_label", "--output_nifti_label", dest="output_nifti_label", help="Output segmentation file converted from the JPG files")
66 |     parser.add_option("--in_features", "--feature_folder", dest="feature_input_folder", help="Input folder for feature extraction")
67 |     parser.add_option("--out_features", "--output_features_csv", dest="output_features", help="Output csv file for feature extraction")
68 |     (options, args) = parser.parse_args()
69 |     Full_Pipeline(options.roi_folder, options.original_folder, options.output_nifti, options.output_nifti_label, options.feature_input_folder, options.output_features)
70 | 
71 | # python Process_Multiple_JPG_ROI.py --roi_folder ".\subject data\Subject ROI marked" --original_folder ".\subject data\Subject original sequence\SE5" --output_nifti ".\subject data\test_subject.nii.gz" --output_nifti_label ".\subject data\test_subject-label.nii.gz" --feature_folder ".\subject data" --output_features_csv ".\subject data\output_features.csv" 


--------------------------------------------------------------------------------
/documentation/Tutorial_Modules/Machine_Learning_and_Feature_Extraction_Tutorial/Feature_Extraction_Answers/intensity_square_phantom.csv:
--------------------------------------------------------------------------------
1 | index,mean,min,max,median,range,standard_deviation,variance,energy,entropy,kurtosis,skewness,COV,histogram_percent_-inf_-1000,histogram_percent_-1000_-950,histogram_percent_-950_-650,histogram_percent_-650_-300,histogram_percent_-300_0,histogram_percent_0_100,histogram_percent_100_600,histogram_percent_600_inf
2 | Intensity_checker_Phantom-label.nii.gz,75.0,50.0,150.0,50.0,100.0,43.30127018922193,1875.0,7348.469228349534,-2409117.7408715887,-0.6666666666666665,1.1547005383792515,0.5773502691896257,0.0,0.0,0.0,0.0,0.0,0.75,0.25,0.0
3 | Intensity_grey_Phantom-label.nii.gz,100.0,100.0,100.0,100.0,0.0,0.0,0.0,8485.28137423857,-3315722.5339114256,-3.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
4 | Intensity_noisy_grey_Phantom-label.nii.gz,100.16064400325992,63.00874163716922,136.70731027859344,100.06269411194424,73.69856864142422,10.171805666970855,103.46563052662037,8542.62639422184,-3325945.320313802,-0.011454209208579869,-0.0033168780876134518,0.10155491478908416,0.0,0.0,0.0,0.0,0.0,0.4970833333333333,0.5029166666666667,0.0
5 | Intensity_one_spot_Phantom-label.nii.gz,105.55555555555556,100.0,150.0,100.0,50.0,15.713484026367722,246.91358024691357,9055.385138137417,-3548585.154323929,4.125000000000002,2.4748737341529163,0.14886458551295736,0.0,0.0,0.0,0.0,0.0,0.0,0.1111111111111111,0.0
6 | Intensity_split_Phantom-label.nii.gz,100.0,50.0,150.0,100.0,100.0,50.0,2500.0,9486.832980505138,-3409907.1997890444,-2.0,0.0,0.5,0.0,0.0,0.0,0.0,0.0,0.5,0.5,0.0
7 | 


--------------------------------------------------------------------------------
/documentation/Tutorial_Modules/Machine_Learning_and_Feature_Extraction_Tutorial/Feature_Extraction_Answers/shape_mri_phantom.csv:
--------------------------------------------------------------------------------
 1 | index,voxel_count,volume,surface_area,volume_surface_area_ratio,compactness,compactness_alternate,spherical_disproportion,sphericity
 2 | MR_BrainTumor_ShapeTest-label_1.nii,1552.0,1909.6875,1125.1406121253967,0.5891752509902257,9.959774411662496,0.2895720105866663,1.5115220005242382,0.6615848129588399
 3 | MR_BrainTumor_ShapeTest-label_2.nii,12576.0,15474.375,5671.687446758151,0.3665212615539013,27.451325594334033,0.1484368529299517,1.8886555271866194,0.5294771786624427
 4 | MR_BrainTumor_ShapeTest-label_3.nii,27355.0,33659.47265625,12958.1483117491,0.3849777577945206,34.42207715329948,0.05888953833151542,2.5703205202654633,0.3890565367686982
 5 | MR_BrainTumor_ShapeTest-label_4.nii,1648.0,2027.8125,2153.7656065821648,1.062112797204951,6.859943959411558,0.04654924622372035,2.779899630017075,0.3597252178467529
 6 | MR_BrainTumor_ShapeTest-label_5.nii,2377.0,2924.82421875,2757.3749674111605,0.94274895213689,8.391912523174673,0.04614922670112022,2.7879085510890596,0.35869182280364365
 7 | MR_BrainTumor_ShapeTest-label_6.nii,7368.0,9066.09375,5927.671815901995,0.6538286476358128,15.616696445146694,0.044631381674628906,2.8191610691027216,0.35471545452288694
 8 | MR_BrainTumor_ShapeTest-label_7.nii,11794.0,14512.1484375,21390.515613779426,1.4739730444394736,10.625334392464408,0.002433615918526403,7.4344581460435,0.13450879409848907
 9 | MR_BrainTumor_ShapeTest-label_8.nii,9740.0,11984.765625,18212.765420749784,1.5196597072168263,9.76796316122103,0.0026889565357029518,7.191266870644386,0.1390575566152495
10 | MR_BrainTumor_ShapeTest-label_9.nii,13284.0,16345.546875,5825.554617717862,0.3564001047054513,28.48391406302193,0.15284085172830847,1.870338370420516,0.5346626128271995
11 | MR_BrainTumor_ShapeTest-label_10.nii,33633.0,41384.35546875,19790.366962999105,0.47820889654650134,31.912343251261905,0.024989825494255075,3.42041597020831,0.29236210119177336
12 | 


--------------------------------------------------------------------------------
/documentation/Tutorial_Modules/Machine_Learning_and_Feature_Extraction_Tutorial/Feature_Extraction_Answers/size_square_phantom.csv:
--------------------------------------------------------------------------------
 1 | index,voxel_count,volume,surface_area,volume_surface_area_ratio,compactness,compactness_alternate,spherical_disproportion,sphericity
 2 | Size_0_Phantom-label.nii.gz,625.0,769.04296875,1229.8828102648258,1.5992380923316591,3.779779933973287,0.035955256433352206,3.0297900604171604,0.3300558718785663
 3 | Size_1_Phantom-label.nii.gz,2601.0,3200.44921875,4839.820307940245,1.5122315578656593,6.310782016940102,0.010218485716816501,4.608268966998722,0.21700122261988553
 4 | Size_2_Phantom-label.nii.gz,5929.0,7295.44921875,10826.320305615664,1.483982683039036,8.410526583945803,0.004743663078098273,5.951531294196814,0.16802398417615214
 5 | Size_4_Phantom-label.nii.gz,10609.0,13054.04296875,19189.382803291082,1.4699953760860476,10.275337540500868,0.0027274665282141274,7.157261034932097,0.13971825187307663
 6 | Size_5_Phantom-label.nii.gz,16384.0,20160.0,29471.99998855591,1.4619047613370986,11.920903870400306,0.001795579357420605,8.227447733101872,0.1215443759036783
 7 | Size_6_Phantom-label.nii.gz,23409.0,28804.04296875,41951.882798820734,1.456458138336172,13.45997363746751,0.0012708810485520092,9.232054625052427,0.10831824990358753
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  2 | 1.0,4.0
  3 | 3.0,3.0
  4 | 2.0,2.0
  5 | 4.0,1.0
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  7 | 2.0,2.0
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  9 | 1.0,2.0
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 74 | 2.0,3.0
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 80 | 1.0,1.0
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100 | 3.0,1.0
101 | 1.0,2.0
102 | 1.0,4.0
103 | 4.0,5.0
104 | 4.0,5.0
105 | 5.0,5.0
106 | 4.0,4.0
107 | 3.0,3.0
108 | 2.0,2.0
109 | 1.0,2.0
110 | 3.0,3.0
111 | 1.0,3.0
112 | 3.0,1.0
113 | 3.0,3.0
114 | 2.0,1.0
115 | 2.0,2.0
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117 | 1.0,1.0
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127 | 3.0,1.0
128 | 2.0,2.0
129 | 1.0,4.0
130 | 1.0,1.0
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177 | 4.0,3.0
178 | 5.0,1.0
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181 | 3.0,3.0
182 | 1.0,2.0
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244 | 


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1 | 1.0,0.493333333333
2 | 2.0,0.424242424242
3 | 3.0,0.392156862745
4 | 4.0,0.363636363636
5 | 5.0,0.222222222222
6 | 


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/documentation/iPython_Walkthroughs/qtim_dce/DCE_Processing_Notebook.py:
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 1 | 
 2 | from qtim_tools.test_data import load_test_file
 3 | 
 4 | # test_file = "your_file_here.nii.gz"
 5 | test_file = load_test_file(data="dce_tofts_v6")
 6 | print('Test File Loaded: ' + test_file)
 7 | 
 8 | from qtim_tools.qtim_dce import tofts_parametric_mapper
 9 | 
10 | # Input Parameters
11 | T1_tissue=1000
12 | T1_blood=1440
13 | relaxivity=.0045
14 | TR=5
15 | TE=2.1 
16 | scan_time_seconds=(11*60) 
17 | hematocrit=0.45
18 | injection_start_time_seconds=60 
19 | flip_angle_degrees=30
20 | 
21 | test_file_label = load_test_file(data="dce_tofts_v6_label")
22 | print('Loaded test label: ' + test_file_label)
23 | 
24 | # Label File Parameters
25 | label_file=test_file_label
26 | 
27 | # AIF Parameters
28 | AIF_label_file=[]
29 | AIF_text_file=[]
30 | AIF_mode="population" # options: population, label, textfile
31 | 
32 | # T1 Map Parameters
33 | T1_map_file=[]
34 | 
35 | # Output and Processing Parameters.
36 | processes = 2;
37 | output_filepath_prefix = "./Example_Breast_Data_"
38 | 
39 | tofts_parametric_mapper.execute(input_filepath=test_file,
40 | T1_tissue=T1_tissue,
41 | T1_blood=T1_blood,
42 | relaxivity=relaxivity,
43 | TR=TR, 
44 | TE=TE, 
45 | scan_time_seconds=scan_time_seconds, 
46 | hematocrit=hematocrit, 
47 | injection_start_time_seconds=injection_start_time_seconds, 
48 | flip_angle_degrees=flip_angle_degrees, 
49 | label_file=test_file_label,
50 | T1_map_file=[],
51 | AIF_label_file=[],
52 | AIF_text_file=[],
53 | AIF_mode=AIF_mode,
54 | outfile_prefix=output_filepath_prefix, 
55 | processes=processes)
56 | 
57 | 
58 | 
59 | 
60 | 
61 | 
62 | 


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/package_resources/logos/qtim_tools.png:
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/qtim_tools/__init__.py:
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1 | import qtim_tools.qtim_features
2 | import qtim_tools.qtim_dce
3 | import qtim_tools.qtim_learning
4 | import qtim_tools.qtim_utilities
5 | import qtim_tools.qtim_preprocessing
6 | import qtim_tools.qtim_visualization
7 | import qtim_tools.qtim_pipelines
8 | import qtim_tools.test_data
9 | 


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/qtim_tools/external/fdt_rotate_bvecs.sh:
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 1 | #!/bin/bash
 2 | 
 3 | if [ "$3" == "" ] ; then 
 4 |  echo "Usage: <original bvecs> <rotated bvecs> <ecclog>"
 5 |  echo ""
 6 |  echo "<ecclog> is the output log file from ecc"
 7 |  echo ""
 8 |  exit 1;
 9 | fi
10 | 
11 | i=$1
12 | o=$2
13 | ecclog=$3
14 | 
15 | if [ ! -e $1 ] ; then
16 |     echo "Source bvecs $1 does not exist!"
17 |     exit 1
18 | fi
19 | if [ ! -e $ecclog ]; then
20 |     echo "Ecc log file $3 does not exist!"
21 |     exit 1
22 | fi
23 | 
24 | ii=1
25 | rm -f $o
26 | tmpo=${o}$$
27 | 
28 | cat ${ecclog} | while read line; do
29 |     if [ "$line" == "" ];then break;fi
30 |     read line;
31 |     read line;
32 |     read line;
33 | 
34 |     echo $line  > $tmpo
35 |     read line    
36 |     echo $line >> $tmpo
37 |     read line    
38 |     echo $line >> $tmpo
39 |     read line    
40 |     echo $line >> $tmpo
41 |     read line   
42 | 
43 |     ####print lines of $tmpo | grab nth line | print nth value of line
44 |     m11=`cat $tmpo | sed '1q;d' | awk '{print $1}'`
45 |     m12=`cat $tmpo | sed '1q;d' | awk '{print $2}'`
46 |     m13=`cat $tmpo | sed '1q;d' | awk '{print $3}'`
47 |     m21=`cat $tmpo | sed '2q;d' | awk '{print $1}'`
48 |     m22=`cat $tmpo | sed '2q;d' | awk '{print $2}'`
49 |     m23=`cat $tmpo | sed '2q;d' | awk '{print $3}'`
50 |     m31=`cat $tmpo | sed '3q;d' | awk '{print $1}'`
51 |     m32=`cat $tmpo | sed '3q;d' | awk '{print $2}'`
52 |     m33=`cat $tmpo | sed '3q;d' | awk '{print $3}'`
53 | 
54 |     X=`cat $i | head -n $ii| tail -n 1 | awk -v N=1 '{print $N}' | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}'`
55 |     Y=`cat $i | head -n $ii| tail -n 1 |awk -v N=2 '{print $N}' | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}'`
56 |     Z=`cat $i | head -n $ii| tail -n 1 | awk -v N=3 '{print $N}' | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}'`
57 | 
58 |     rX=`echo "scale=7;  ($m11 * $X) + ($m12 * $Y) + ($m13 * $Z)" | bc -l`
59 |     rY=`echo "scale=7;  ($m21 * $X) + ($m22 * $Y) + ($m23 * $Z)" | bc -l`
60 |     rZ=`echo "scale=7;  ($m31 * $X) + ($m32 * $Y) + ($m33 * $Z)" | bc -l`
61 |     if [ "$ii" -eq 1 ];then
62 |     echo $rX > $o;echo $rY >> $o;echo $rZ >> $o
63 |     else
64 |     cp $o $tmpo
65 |     (echo $rX;echo $rY;echo $rZ) | paste $tmpo - > $o
66 |     fi
67 |     
68 |     let "ii+=1"
69 | 
70 | done
71 | rm -f $tmpo
72 | 


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/qtim_tools/qtim_dce/README.md:
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1 | # QtimDCE - qtim_dce
2 | This is a repository for scripts meant to analyze and quantify dynamic-contrast MRI images (DCE).
3 | 


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/qtim_tools/qtim_dce/__init__.py:
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1 | import qtim_tools.qtim_dce.tofts_parametric_mapper
2 | import qtim_tools.qtim_dce.dce_util
3 | #import tofts_worker
4 | 


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/qtim_tools/qtim_dce/process_dce_file.py:
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 1 | import argparse
 2 | import ConfigParser as configparser
 3 | 
 4 | import tofts_parameter_calculator
 5 | 
 6 | __author__ = 'Andrew Beers'
 7 | 
 8 | def parse_args():
 9 | 	
10 | 	parser = argparse.ArgumentParser(description='qtim_tools.qtim_dce.process_dce_file calculates DCE parameters maps (e.g. ktrans, ve, auc) for a given 4D Nifti file.')
11 | 	
12 | 	parser.add_argument('-input', required=True, help = 'File to be processed.')
13 | 	parser.add_argument('-config', required=False, help = 'Filepath of configuration file.')
14 | 
15 | 	parser.add_argument('-output_prefix', required=True, help = 'Output path to write parameters maps to. Files will be written in the format of [prefix][parameter]. For the prefix \"output_\", and example would be \"output_ktrans.nii.gz\"')
16 | 	parser.add_argument('-outputs', required=False, nargs='+', help = 'Parameter maps to generate. kTrans, Ve, and AUC maps are generated by default.')
17 | 
18 | 	parser.add_argument('-label', required=False, help = 'Filepath of ROI or other labels (.nii or .nii.gz)')
19 | 
20 | 	parser.add_argument('-AIF_label', required=False, help = 'Filepath of an ROI from which to generate an AIF (.nii or .nii.gz)')
21 | 	parser.add_argument('-AIF_values', required=False, help = 'Filepath of a list of AIF values (.txt, separated by \";\"). If the AIF file has fewer timepoints than the volume, the starting values will be filled in with zeros. If the AIF does not need to be converted into concentration, set -convert_AIF_values to \"False\"')
22 | 	parser.add_argument('-convert_AIF_values', required=False, help = 'If an AIF is provided, set this option to \"True\" or \"False\" to convert that AIF from intensity values to concentration values.')
23 | 
24 | 	parser.add_argument('-T1_tissue', required=False, help = 'Static T1 value in tissue to be used for calculations if there is no T1 map. Default is 1000.')
25 | 	parser.add_argument('-T1_blood', required=False, help = 'Static T1 value in blood to be used for AIF calculations. Default is 1440.')
26 | 	parser.add_argument('-T1_map', required=False, help = 'Filepath to a T1 map to be used in parameter calculations')
27 | 
28 | 	parser.add_argument('-relaxivity', required=False, help = 'Relaxivity of the chosen contrast agent to be used for parameter map calculations.')
29 | 
30 | def main():
31 | 	return
32 | 
33 | if __name__ == "__main__":
34 | 	main()
35 | 
36 | # def main(argv=None):
37 | 
38 | # 	if argv==None:
39 | # 		argv = sys.argv
40 | 
41 | 
42 | 
43 | # 	try:
44 | # 		opts, args = getpot.getpot(argv)
45 | 
46 | # 	except Usage, err:
47 | # 		print(>>sys.stderr, err.msg)
48 | # 		print(>>sys.stderr, "Invalid options/parameters. For parameter help, type -help or -h.")
49 | # 		return 2
50 | 
51 | 	tofts_parameter_calculator.calc_DCE_properties_single(filepath, label_file=[], param_file=[], AIF_label_file=[], AIF_value_data=AIF_value_data, convert_AIF_values=False, outputs=['ktrans','ve','auc'], T1_tissue=1500, T1_blood=1440, relaxivity=.0039, TR=6.8, TE=2.1, scan_time_seconds=(6*60), hematocrit=0.45, injection_start_time_seconds=160, flip_angle_degrees=10, label_suffix=[], AIF_mode='population', AIF_label_suffix='-AIF-label', AIF_label_value=1, label_mode='separate', default_population_AIF=False, initial_fitting_function_parameters=[.01,.1], outfile_prefix='mead_cobyal_high_ktrans_max_individual_ktrans_no_mask', processes=22, mask_threshold=20, mask_value=-1, gaussian_blur=.65, gaussian_blur_axis=2)
52 | 
53 | # if __name__ == '__main__':
54 | # 	sys.exit(main())
55 | 


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/qtim_tools/qtim_dce/tofts_worker.py:
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 1 | import tofts_parameter_calculator
 2 | # from ..qtim_utilities import nifti_util
 3 | 
 4 | def test(filepath=[]):
 5 | 	tofts_parameter_calculator.test_method_3d(filepath)
 6 | 
 7 | def run_test():
 8 | 
 9 | 	# You must install the packages nibabel and pydicom before running this program.
10 | 
11 | 	filepath='C:/Users/abeers/Documents/GitHub/Public_QTIM/qtim_tools/qtim_tools/test_data/test_data_dce/tofts_v6.nii.gz'
12 | 	
13 | 	label_file=[]
14 | 	label_suffix=[]
15 | 	label_value=1
16 | 	label_mode='separate'
17 | 
18 | 	T1_map_file=[]
19 | 	T1_map_suffix=[]
20 | 
21 | 	AIF_value_data=[]
22 | 	AIF_value_suffix=[]
23 | 	convert_AIF_values=False
24 | 	default_population_AIF=False
25 | 	
26 | 	AIF_label_file=[]
27 | 	AIF_mode='label_average'
28 | 	AIF_label_suffix='-AIF-label'
29 | 	AIF_label_value=1
30 | 
31 | 	T1_tissue=1000
32 | 	T1_blood=1440
33 | 	relaxivity=.0045
34 | 	TR=5
35 | 	TE=2.1
36 | 	scan_time_seconds=(11*60)
37 | 	hematocrit=0.45
38 | 	injection_start_time_seconds=60
39 | 	flip_angle_degrees=30
40 | 	initial_fitting_function_parameters=[.3,.1]
41 | 	
42 | 	outputs=['ktrans','ve','auc']
43 | 	outfile_prefix='tofts_v6_test_'
44 | 	processes=2
45 | 	
46 | 	mask_threshold=20
47 | 	mask_value=-1
48 | 	
49 | 	gaussian_blur=0
50 | 	gaussian_blur_axis=-1
51 | 
52 | 	param_file=[]
53 | 
54 | 	tofts_parameter_calculator.calc_DCE_properties_single(filepath, T1_tissue, T1_blood, relaxivity, TR, TE, scan_time_seconds, hematocrit, injection_start_time_seconds, flip_angle_degrees, label_file, label_suffix, label_value, mask_value, mask_threshold, T1_map_file, T1_map_suffix, AIF_label_file,  AIF_value_data, AIF_value_suffix, convert_AIF_values, AIF_mode, AIF_label_suffix, AIF_label_value, label_mode, param_file, default_population_AIF, initial_fitting_function_parameters, outputs, outfile_prefix, processes, gaussian_blur, gaussian_blur_axis)
55 | 
56 | if __name__ == '__main__':
57 | 
58 | 	print('Entered program..')
59 | 	run_test()
60 | 
61 | 	# test('C:/Users/azb22/Documents/Junk/dce_mc_st_corrected.nii')
62 | 	# test()
63 | 	# tofts_parameter_calculator.test_method_3d()
64 | 	# tofts_parameter_calculator.test_method_2d()
65 | 


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/qtim_tools/qtim_dti/__init__.py:
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https://raw.githubusercontent.com/QTIM-Lab/qtim_tools/b92e73127da5031f166174c047b3b56253be2486/qtim_tools/qtim_dti/__init__.py


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/qtim_tools/qtim_dti/fit_dti.py:
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 1 | import subprocess
 2 | import os
 3 | 
 4 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
 5 | from ..qtim_utilities.format_util import convert_input_2_numpy
 6 | 
 7 | 
 8 | def run_dtifit(
 9 |     input_data,
10 |     input_bvec,
11 |     input_bval,
12 |     input_mask="",
13 |     output_fileprefix="",
14 |     method="fsl",
15 |     command="dtifit",
16 |     temp_dir="./",
17 | ):
18 |     """This will fail if used in numpy mode, currently."""
19 | 
20 |     motion_correction_methods = ["fsl"]
21 |     if method not in motion_correction_methods:
22 |         print(
23 |             'Input "method" parameter is not available. Available methods: ',
24 |             motion_correction_methods,
25 |         )
26 |         return
27 | 
28 |     if method == "fsl":
29 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
30 | 
31 |         temp_input, temp_output = False, False
32 | 
33 |         if not isinstance(input_data, str):
34 |             input_filename = os.path.join(temp_dir, "temp.nii.gz")
35 |             save_numpy_2_nifti(input_data, input_filename)
36 |             temp_input = True
37 |         else:
38 |             input_filename = input_data
39 | 
40 |         if output_fileprefix == "":
41 |             temp_output = True
42 |             output_fileprefix = os.path.join(temp_dir, "temp_out.nii.gz")
43 | 
44 |         # TODO: Figure out what last parameter, reference number, means.
45 |         print(
46 |             " ".join(
47 |                 [
48 |                     command,
49 |                     "-V",
50 |                     "--sse",
51 |                     "-k",
52 |                     input_filename,
53 |                     "-o",
54 |                     output_fileprefix,
55 |                     "-m",
56 |                     input_mask,
57 |                     "-r",
58 |                     input_bvec,
59 |                     "-b",
60 |                     input_bval,
61 |                 ]
62 |             )
63 |         )
64 |         subprocess.call(
65 |             [
66 |                 command,
67 |                 "-V",
68 |                 "--sse",
69 |                 "-k",
70 |                 input_filename,
71 |                 "-o",
72 |                 output_fileprefix,
73 |                 "-m",
74 |                 input_mask,
75 |                 "-r",
76 |                 input_bvec,
77 |                 "-b",
78 |                 input_bval,
79 |             ]
80 |         )
81 | 
82 |         if temp_input:
83 |             os.remove(input_filename)
84 |             pass
85 | 
86 |         if temp_output:
87 |             output = convert_input_2_numpy(output_fileprefix)
88 |             os.remove(output_fileprefix)
89 |             return output
90 | 
91 | 
92 | def run_test():
93 |     return
94 | 
95 | 
96 | if __name__ == "__main__":
97 |     run_test()
98 | 


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/qtim_tools/qtim_features/README.md:
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1 | # qtim_features
2 | This is a repository for scripts that extract features (texture, morphology, etc.) from imaging datasets.
3 | 


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/qtim_tools/qtim_features/__init__.py:
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1 | from qtim_tools.qtim_features.extract_features import *
2 | # from test import *
3 | import qtim_tools.qtim_features.GLCM
4 | import qtim_tools.qtim_features.morphology
5 | import qtim_tools.qtim_features.statistics
6 | import qtim_tools.qtim_features.phantoms
7 | 


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/qtim_tools/qtim_learning/README.md:
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1 | # qtim_learning
2 | 
3 | This package contains utilities for applying deep learning and other machine learning techniques to medical imaging data.
4 | 


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/qtim_tools/qtim_learning/__init__.py:
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1 | from qtim_tools.qtim_learning.nn_preprocessing import *
2 | 


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/qtim_tools/qtim_learning/nn_preprocessing.py:
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1 | 
2 | def run_test():
3 | 	return
4 | 
5 | if __name__ == '__main__':
6 | 	run_test()


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/qtim_tools/qtim_pipelines/README.md:
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1 | # qtim_wrappers
2 | This will be a repository for wrapper scripts that either concatenate or simply other qtim-tools scripts.


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/qtim_tools/qtim_pipelines/__init__.py:
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1 | import qtim_tools.qtim_pipelines.label_statistics
2 | import qtim_tools.qtim_pipelines.dti_conversion
3 | import qtim_tools.qtim_pipelines.deep_learning
4 | import qtim_tools.qtim_pipelines.coregistration
5 | 


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/qtim_tools/qtim_pipelines/create_config.py:
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https://raw.githubusercontent.com/QTIM-Lab/qtim_tools/b92e73127da5031f166174c047b3b56253be2486/qtim_tools/qtim_pipelines/create_config.py


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/qtim_tools/qtim_pipelines/default_configs/deep_learning_experiment.yaml:
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 1 | Train:
 2 |   Study: 
 3 |     - FMS:
 4 |       - Patients:
 5 |         - '1,2':
 6 |           - Visits:
 7 |             - all
 8 |   Modalities:
 9 |     - 'MPRAGE_POST'
10 |   GroundTruth:
11 |     - 'SUV'
12 | 
13 | Test:
14 |   Study: 
15 |     - FMS:
16 |       - Patients:
17 |         - '5':
18 |           - Visits:
19 |             - all
20 |   Modalities:
21 |     - 'MPRAGE_POST'
22 |   GroundTruth:
23 |     - 'SUV'


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/qtim_tools/qtim_pipelines/process_dce.py:
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 1 | """ TODO: Delete this file once our DCE pipeline is set up.
 2 | """
 3 | 
 4 | import DCE_Property_Calculator
 5 | 
 6 | """
 7 | Put the paths to whatever files you are analyzing in this section. If you don't need a certain file, you can leave it as ''. 
 8 | 
 9 | If you only want to calculate properties in a certain ROI, put the filepath to that ROI in label_filepath.
10 | 
11 | If you want to take your AIF from a ROI of, say, and artery, then put the filepath to that ROI in AIF_filepath.
12 | 
13 | If you want to use a T1Map to calculate ktrans, ve, and AUC, put that filepath under T1_map_filepath.
14 | 
15 | """
16 | 
17 | filepath = 'dce1_mc_ss.nii.gz'
18 | label_filepath = ''
19 | AIF_filepath = ''
20 | T1_map_filepath = ''
21 | 
22 | 
23 | """
24 | If your files don't have a specific name, you can instead provide suffixes. For example, say your filepath is dce1_ss.nii.gz. If you know your ROI is named dce1_ss-label.nii.gz, then you can grab it by changing the label_suffix parameter to "-label". The same goes for the other parameters.
25 | 
26 | """
27 | 
28 | label_suffix = ''
29 | AIF_suffix = ''
30 | T1_map_suffix = ''
31 | 
32 | """
33 | Set your parameters for the DCE processing here. 
34 | 
35 | T1_tissue and T1_blood are for if you are using static T1 values instead of a T1Map. T1_blood should be higher than T1_tissue.
36 | 
37 | Relaxivity is specific to the contrast agent used. I think ours is usually .0039.
38 | 
39 | If you don't know the proper hematocrit, keep it at .45. I don't think it matters as much as the other parameters.
40 | 
41 | TR, TE, scan_time_seconds, injection_start_time_seconds, and flip_angle_degrees are essential. You can find them from a DICOM header.
42 | """
43 | 
44 | T1_tissue=1000
45 | T1_blood=1440
46 | relaxivity=.0045
47 | hematocrit=0.45
48 | TR=5
49 | TE=2.1
50 | scan_time_seconds=360
51 | injection_start_time_seconds=60
52 | flip_angle_degrees=30
53 | 
54 | """
55 | The program will skip over pixels that are equal to the mask_value in the first time point. This can be useful for skull-stripped images - otherwise, it would try and calculate over empty space.
56 | 
57 | Alternatively, you can speciy a mask_threshold. This means that all voxels with an intensity below mask_threshold at time point zero would be skipped. It is set to 0 here, so only negative voxels will be skipped.
58 | """
59 | 
60 | mask_value=0
61 | mask_threshold=0
62 | 
63 | """
64 | Specify your output prefix here. The results will be three files titled "[prefix]ktrans.nii.gz", "[prefix]ve.nii.gz", and ''[prefix]auc.nii.gz".
65 | AUC is currently not being calculated, so that will be an empty volume.
66 | """
67 | 
68 | outfile_prefix='dce_'
69 | 
70 | """
71 | For now, don't worry about these parameters.
72 | """
73 | 
74 | AIF_mode = 'label_average'
75 | intial_fitting_function_parameters = [1,1]
76 | default_population_AIF = False
77 | label_mode = 'separate'
78 | AIF_values_file = ''
79 | label_value=1
80 | AIF_label_value=1
81 | param_file=[]
82 | outputs=['ktrans','ve','auc']
83 | 
84 | if __name__ == '__main__':
85 | 	DCE_Property_Calculator.calc_DCE_properties_single(filepath, T1_tissue=T1_tissue, T1_blood=T1_blood, relaxivity=relaxivity, TR=TR, TE=TE, scan_time_seconds=scan_time_seconds, hematocrit=hematocrit, injection_start_time_seconds=injection_start_time_seconds, flip_angle_degrees=flip_angle_degrees, label_file=label_file, label_suffix=label_suffix, label_value=label_value, mask_value=mask_value, mask_threshold=mask_threshold, T1_map_file=T1_map_file, T1_map_suffix=T1_map_suffix, AIF_label_file=AIF_filepath,  AIF_values_file=AIF_values_file, AIF_mode=AIF_mode, AIF_label_suffix=AIF_suffix, AIF_label_value=AIF_label_value, label_mode=label_mode, param_file=param_file, default_population_AIF=default_population_AIF, intial_fitting_function_parameters=intial_fitting_function_parameters, outputs=outputs, outfile_prefix=outfile_prefix)


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/qtim_tools/qtim_preprocessing/README.md:
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1 | # qtim_preprocessing
2 | This project, yet to be started, will be a repository for scripts involved in preprocessing medical imaging data (e.g. image registration).
3 | 


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/qtim_tools/qtim_preprocessing/__init__.py:
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https://raw.githubusercontent.com/QTIM-Lab/qtim_tools/b92e73127da5031f166174c047b3b56253be2486/qtim_tools/qtim_preprocessing/__init__.py


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/qtim_tools/qtim_preprocessing/bias_correction.py:
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 1 | import subprocess
 2 | import os
 3 | 
 4 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
 5 | from ..qtim_utilities.format_util import convert_input_2_numpy
 6 | 
 7 | def bias_correction(input_data, output_filename='', mask_filename='', method="ants", command="/home/abeers/Software/ANTS/ANTs.2.1.0.Debian-Ubuntu_X64/N4BiasFieldCorrection", temp_dir='./'):
 8 | 
 9 |     """ A catch-all function for motion correction. Will perform motion correction on an input volume
10 |         depending on the 'method' and 'command' inputted.
11 | 
12 |         Parameters
13 |         ----------
14 |         input_data: str or array
15 |             Can be a 4D volume or a filename.
16 |         output_filename: str
17 |             Location to save output data to. If left as '', will return numpy array.
18 |         method: str
19 |             Will perform motion correction according to the provided method.
20 |             Currently available: ['fsl']
21 |         command: str
22 |             The literal command-line string to be inputted via Python's subprocess module.
23 |         temp_dir: str
24 |             If temporary files are created, they will be saved here.
25 | 
26 |         Returns
27 |         -------
28 |         output: array
29 |             Output data, only if output_filename is left as ''.
30 |     """
31 | 
32 |     bias_correction_methods = ['ants', 'slicer']
33 |     if method not in bias_correction_methods:
34 |         print('Input \"method\" parameter is not available. Available methods: ', bias_correction_methods)
35 |         return
36 | 
37 |     if method == 'ants':
38 | 
39 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
40 | 
41 |         temp_input, temp_output = False, False
42 | 
43 |         if not isinstance(input_data, str):
44 |             input_filename = os.path.join(temp_dir, 'temp.nii.gz')
45 |             save_numpy_2_nifti(input_data, input_filename)
46 |             temp_input = True
47 |         else:
48 |             input_filename = input_data
49 | 
50 |         if output_filename == '':
51 |             temp_output = True
52 |             output_filename = os.path.join(temp_dir, 'temp_out.nii.gz')
53 | 
54 |         print(' '.join([command, '-i', input_filename, '-o', output_filename, '-x', mask_filename]))
55 |         if mask_filename != '':
56 |             subprocess.call([command, '-i', input_filename, '-o', output_filename, '-x', mask_filename])
57 |         else:
58 |             subprocess.call([command, '-i', input_filename, '-o', output_filename])
59 | 
60 |         if temp_input:
61 |             os.remove(input_filename)
62 |             pass
63 | 
64 |         if temp_output:
65 |             output = convert_input_2_numpy(output_filename)
66 |             os.remove(output_filename)
67 |             return output
68 | 
69 |     if method == 'slicer':
70 | 
71 |         print('Slicer method not yet implemented! Sorry...')
72 | 
73 | 
74 | def run_test():
75 |     return
76 | 
77 | if __name__ == '__main__':
78 |     run_test()
79 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/image.py:
--------------------------------------------------------------------------------
 1 | """ This preprocessing module is a little vague. As currently construed, it is meant to
 2 |     work on images received in .PNG, .JPG format, etc.
 3 | """
 4 | 
 5 | import numpy as np
 6 | import nibabel as nib
 7 | import glob
 8 | 
 9 | from subprocess import call
10 | from shutil import copy
11 | from scipy import misc, ndimage
12 | from skimage import measure
13 | 
14 | from qtim_tools.qtim_utilities.nifti_util import nifti_2_numpy, save_numpy_2_nifti
15 | from qtim_tools.qtim_utilities.format_util import convert_input_2_numpy
16 | 
17 | def fill_in_convex_outline(input_data, output_file=None, reference_nifti=None, threshold_limit=[0,100], color_threshold_limits= [[100,300],[0,100],[0,100]], output_label_num=1):
18 | 
19 |     """ Thresholds a jpg according to certain color parameters. Uses a hole-filling algorithm to color in
20 |         regions of interest.
21 | 
22 |         TODO: Reorganize into two separate tracks, instead of two winding tracks.
23 |     """
24 | 
25 |     image_nifti, image_type = convert_input_2_numpy(input_data, return_type=True)
26 | 
27 |     label_nifti = np.zeros_like(image_nifti)
28 | 
29 |     if image_type == 'image':
30 | 
31 |         red_range = np.logical_and(color_threshold_limits[0][0] < image_nifti[:,:,0], image_nifti[:,:,0] < color_threshold_limits[0][1])
32 |         green_range = np.logical_and(color_threshold_limits[1][0] < image_nifti[:,:,1], image_nifti[:,:,1] < color_threshold_limits[1][1])
33 |         blue_range = np.logical_and(color_threshold_limits[2][0] < image_nifti[:,:,2], image_nifti[:,:,2] < color_threshold_limits[2][1])
34 |         valid_range = np.logical_and(red_range, green_range, blue_range)
35 | 
36 |         label_nifti[valid_range] = 1
37 | 
38 |         label_nifti = ndimage.morphology.binary_fill_holes(label_nifti[:,:,0]).astype(label_nifti.dtype)
39 |     
40 |         if output_file is not None:
41 |             misc.imsave(output_file, label_nifti*255)
42 | 
43 |     else:
44 |         image_nifti[image_nifti != 0] = output_label_num
45 |         if image_nifti.ndim == 3:
46 |             for z in range(image_nifti.shape[2]):
47 |                 label_nifti[..., z] = ndimage.morphology.binary_fill_holes(image_nifti[...,z]).astype(image_nifti.dtype)
48 |         else:
49 |             label_nifti = ndimage.morphology.binary_fill_holes(image_nifti).astype(image_nifti.dtype)
50 | 
51 |         print(np.sum(label_nifti), 'HOLE FILLED SUM')
52 | 
53 |         if output_file is not None:
54 |             save_numpy_2_nifti(label_nifti, reference_nifti, output_file)
55 | 
56 |     return label_nifti
57 | 
58 | def split_islands():
59 |     pass
60 | 
61 | if __name__ == "__main__":
62 | 
63 |     pass
64 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/motion_correction.py:
--------------------------------------------------------------------------------
 1 | import subprocess
 2 | import os
 3 | 
 4 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
 5 | from ..qtim_utilities.format_util import convert_input_2_numpy
 6 | 
 7 | 
 8 | def motion_correction(
 9 |     input_data, output_filename="", method="fsl", command="eddy_correct", temp_dir="./"
10 | ):
11 |     """A catch-all function for motion correction. Will perform motion correction on an input volume
12 |     depending on the 'method' and 'command' inputted.
13 | 
14 |     Parameters
15 |     ----------
16 |     input_data: str or array
17 |         Can be a 4D volume or a filename.
18 |     output_filename: str
19 |         Location to save output data to. If left as '', will return numpy array.
20 |     method: str
21 |         Will perform motion correction according to the provided method.
22 |         Currently available: ['fsl']
23 |     command: str
24 |         The literal command-line string to be inputted via Python's subprocess module.
25 |     temp_dir: str
26 |         If temporary files are created, they will be saved here.
27 | 
28 |     Returns
29 |     -------
30 |     output: array
31 |         Output data, only if output_filename is left as ''.
32 |     """
33 | 
34 |     motion_correction_methods = ["fsl"]
35 |     if method not in motion_correction_methods:
36 |         print(
37 |             'Input "method" parameter is not available. Available methods: ',
38 |             motion_correction_methods,
39 |         )
40 |         return
41 | 
42 |     if method == "fsl":
43 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
44 | 
45 |         temp_input, temp_output = False, False
46 | 
47 |         if not isinstance(input_data, str):
48 |             input_filename = os.path.join(temp_dir, "temp.nii.gz")
49 |             save_numpy_2_nifti(input_data, input_filename)
50 |             temp_input = True
51 |         else:
52 |             input_filename = input_data
53 | 
54 |         if output_filename == "":
55 |             temp_output = True
56 |             output_filename = os.path.join(temp_dir, "temp_out.nii.gz")
57 | 
58 |         print(" ".join([command, input_filename, output_filename, "0"]))
59 |         subprocess.call([command, input_filename, output_filename, "0"])
60 | 
61 |         if temp_input:
62 |             os.remove(input_filename)
63 |             pass
64 | 
65 |         if temp_output:
66 |             output = convert_input_2_numpy(output_filename)
67 |             os.remove(output_filename)
68 |             return output
69 | 
70 | 
71 | def run_test():
72 |     return
73 | 
74 | 
75 | if __name__ == "__main__":
76 |     run_test()
77 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/normalization.py:
--------------------------------------------------------------------------------
 1 | """ A general module for normalization methods. Likely to
 2 | 	be borrowing heavily from other packages. TODO: Fill in
 3 | 	these methods.
 4 | """
 5 | 
 6 | from ..qtim_utilities.format_util import convert_input_2_numpy
 7 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
 8 | 
 9 | import numpy as np
10 | 
11 | def zero_mean_unit_variance(input_volume, input_mask=None, output_filename=None):
12 | 
13 |     """ Normalizes an image by subtracting its mean and dividing by its standard
14 |         deviation. If provided a mask, the normalization will only occur within the
15 |         mask.
16 | 
17 |         TODO: Add support for not-equal-to masking.
18 |         TODO: Add support for other replacement_values, a-la scikit-learn.
19 | 
20 |         Parameters
21 |         ----------
22 | 
23 |         input_data: N-dimensional array or str
24 |             The volume to be normalized. Can be filename or numpy array.
25 |         input_mask: N-dimensional array or str
26 |             A label mask. Must be the same size as input_data
27 |         output_filename: str
28 |             Optional, save output to filename.
29 | 
30 |         Returns
31 |         -------
32 |         input_numpy: array
33 |             Transformed input array.
34 |     """
35 | 
36 |     input_numpy = convert_input_2_numpy(input_volume)
37 | 
38 |     if input_mask is not None:
39 |         mask_numpy = convert_input_2_numpy(input_mask)
40 |     else:
41 |         mask_numpy = []
42 | 
43 |     if mask_numpy is None:
44 |         vol_mean = np.mean(input_numpy)
45 |         vol_std = np.std(input_numpy)
46 |         output_numpy = (input_numpy - vol_mean) / vol_std        
47 |     else:
48 |         masked_numpy = np.ma.masked_where(mask_numpy == 0, input_numpy)
49 |         vol_mean = np.ma.mean(masked_numpy)
50 |         vol_std = np.ma.std(masked_numpy)
51 |         output_numpy = (masked_numpy - vol_mean) / vol_std
52 |         output_numpy[mask_numpy == 0] = 0
53 | 
54 |     if output_filename is not None:
55 |         if isinstance(input_volume, str):
56 |             save_numpy_2_nifti(output_numpy, input_volume, output_filename)
57 |         else:
58 |             save_numpy_2_nifti(output_numpy, '', output_filename)
59 |     else:
60 |         return output_numpy
61 | 
62 | 
63 | def histogram_normalization(image_numpy, mode='uniform'):
64 | 
65 |     """ TODO
66 |     """
67 | 
68 |     return
69 | 
70 | if __name__ == '__main__':
71 | 	pass
72 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/orientation.py:
--------------------------------------------------------------------------------
 1 | """ This module should be used for functions that null out values in an array
 2 |     based on a condition. Primarily used for masking.
 3 | """
 4 | 
 5 | import subprocess
 6 | import os
 7 | import numpy as np
 8 | 
 9 | from ..qtim_utilities.format_util import convert_input_2_numpy
10 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
11 | 
12 | def orient(input_data, output_filename='', method="slicer", command="Slicer", temp_dir='./', orientation='RAI'):
13 | 
14 |     """ A catch-all function for resampling. Will resample a 3D volume to given dimensions according
15 |         to the method provided.
16 | 
17 |         TODO: Add resampling for 4D volumes.
18 |         TODO: Add dimension, interpolation, reference parameter. Currently set to linear/isotropic.
19 | 
20 |         Parameters
21 |         ----------
22 |         input_data: str or array
23 |             Can be a 3D volume or a filename.
24 |         output_filename: str
25 |             Location to save output data to. If left as '', will return numpy array.
26 |         input_transform: str
27 |             detatails TBD, unimplemented
28 |         method: str
29 |             Will perform motion correction according to the provided method.
30 |             Currently available: ['fsl']
31 |         command: str
32 |             The literal command-line string to be inputted via Python's subprocess module.
33 |         temp_dir: str
34 |             If temporary files are created, they will be saved here.
35 | 
36 |         Returns
37 |         -------
38 |         output: array
39 |             Output data, only if output_filename is left as ''.
40 |     """
41 | 
42 |     orientation_methods = ['slicer']
43 |     if method not in orientation_methods:
44 |         print('Input \"method\" parameter is not available. Available methods: ', orientation_methods)
45 |         return
46 | 
47 |     if method == 'slicer':
48 | 
49 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
50 | 
51 |         temp_input, temp_output = False, False
52 | 
53 |         if not isinstance(input_data, str):
54 |             input_filename = os.path.join(temp_dir, 'temp.nii.gz')
55 |             save_numpy_2_nifti(input_data, input_filename)
56 |             temp_input = True
57 |         else:
58 |             input_filename = input_data
59 | 
60 |         if output_filename == '':
61 |             temp_output = True
62 |             output_filename = os.path.join(temp_dir, 'temp_out.nii.gz')
63 | 
64 |         orientation_command = [command, '--launch', 'OrientScalarVolume', '-o', orientation, input_filename, output_filename]
65 |         print(' '.join(orientation_command))
66 |         subprocess.call(orientation_command)
67 |         
68 |         if temp_input:
69 |             os.remove(input_filename)
70 |             pass
71 | 
72 |         if temp_output:
73 |             output = convert_input_2_numpy(output_filename)
74 |             os.remove(output_filename)
75 |             return output
76 | 
77 | def run_test():
78 |     return
79 | 
80 | if __name__ == '__main__':
81 |     run_test()
82 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/registration.py:
--------------------------------------------------------------------------------
 1 | """ This is a wrapper script for BRAINSFit registration by 3D Slicer. In the future, there could be an all-Python
 2 |     implementation of registration in this function. In the meantime, one will need 3D Slicer (or a Docker container
 3 |     with 3DSlicer inside).
 4 | """
 5 | 
 6 | import numpy as np
 7 | import glob
 8 | import os
 9 | from subprocess import call
10 | from shutil import copy
11 | 
12 | def register_all_to_one(fixed_volume, moving_volume_folder, output_folder='', output_suffix = '_r', file_regex='*.nii*', exclusion_phrase='label', software='slicer_brainsfit',Slicer_Path='Slicer', transform_type='Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine', transform_mode = 'useMomentsAlign', interpolation_mode = 'Linear', sampling_percentage = .02):
13 | 
14 |     """ Registers a folder of volumes to one pre-specified volumes using the BRAINSFit module in 3DSlicer. Must already have 3DSlicer installed.
15 |     """
16 | 
17 |     if output_folder == '':
18 |         output_folder = moving_volume_folder
19 | 
20 |     BRAINSFit_base_command = [Slicer_Path,'--launch', 'BRAINSFit', '--fixedVolume', '"' + fixed_volume + '"', '--transformType', transform_type, '--initializeTransformMode', transform_mode, '--interpolationMode', interpolation_mode, '--samplingPercentage', str(sampling_percentage)]
21 | 
22 |     moving_volumes = glob.glob(os.path.join(moving_volume_folder + file_regex))
23 | 
24 |     if len(moving_volumes) == 0:
25 |         print('No nifti volumes found in provided moving volume folder. Skipping this folder: ' + moving_volume_folder)
26 | 
27 |     if exclusion_phrase != '':
28 |         moving_volumes = [x for x in moving_volumes if exclusion_phrase not in x]
29 | 
30 |     for moving_volume in moving_volumes:
31 | 
32 |         no_path = str.split(moving_volume ,'\\')
33 |         file_prefix = str.split(no_path[-1], '.nii')[0]
34 | 
35 |         if '.nii.gz' in moving_volume:
36 |             output_filename = output_folder + file_prefix + output_suffix + '.nii.gz'
37 |         else:
38 |             output_filename = output_folder + file_prefix + output_suffix + '.nii'
39 | 
40 |         BRAINSFit_specific_command = BRAINSFit_base_command + ['--movingVolume','"' + no_path[0] +  '/' + no_path[1] + '"','--outputVolume','"' + output_filename + '"']
41 | 
42 |         try:
43 |             print(' '.join(BRAINSFit_specific_command))
44 |             call(' '.join(BRAINSFit_specific_command), shell=True)
45 |         except:
46 |             print('Registration command failed. Did you provide the correct path to your Slicer insallation? Provided Slicer Path: ' + Slicer_Path)
47 |             continue
48 | 
49 |     return
50 | 
51 | def register_volume(moving_volume, fixed_volume, output_volume_filename=None, output_transform_filename=None, method='slicer_brainsfit', Slicer_Path='Slicer', transform_type='Rigid,ScaleVersor3D,ScaleSkewVersor3D,Affine', transform_mode = 'useMomentsAlign', interpolation_mode = 'Linear', sampling_percentage = .02):
52 | 
53 |     """ Registers a folder of volumes to one pre-specified volumes using the BRAINSFit module in 3DSlicer. Must already have 3DSlicer installed.
54 |     """
55 | 
56 |     # A good reason to have a Class for qtim methods is to cut through all of this extra code.
57 | 
58 | 
59 |     if method == 'slicer_brainsfit':
60 | 
61 |         BRAINSFit_command = [Slicer_Path,'--launch', 'BRAINSFit', '--fixedVolume', '"' + fixed_volume + '"', '--movingVolume', '"' + moving_volume + '"', '--transformType', transform_type, '--initializeTransformMode', transform_mode, '--interpolationMode', interpolation_mode, '--samplingPercentage', str(sampling_percentage)]
62 | 
63 |         if output_volume_filename is not None:
64 |             BRAINSFit_command += ['--outputVolume', output_volume_filename]
65 | 
66 |         if output_transform_filename is not None:
67 |             BRAINSFit_command += ['--outputTransform', output_transform_filename]
68 | 
69 |         print(' '.join(BRAINSFit_command))
70 |         call(' '.join(BRAINSFit_command), shell=True)
71 | 
72 |         return
73 | 
74 | if __name__ == "__main__":
75 |     pass
76 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/resample.py:
--------------------------------------------------------------------------------
 1 | """ This module should be used for functions that null out values in an array
 2 |     based on a condition. Primarily used for masking.
 3 | """
 4 | 
 5 | import subprocess
 6 | import os
 7 | import numpy as np
 8 | 
 9 | from ..qtim_utilities.format_util import convert_input_2_numpy
10 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
11 | 
12 | def resample(input_data, output_filename='', input_transform=None, method="slicer", command="Slicer", temp_dir='./', interpolation='linear', dimensions= [1,1,1], reference_volume=None):
13 | 
14 |     """ A catch-all function for resampling. Will resample a 3D volume to given dimensions according
15 |         to the method provided.
16 | 
17 |         TODO: Add resampling for 4D volumes.
18 |         TODO: Add dimension, interpolation, reference parameter. Currently set to linear/isotropic.
19 | 
20 |         Parameters
21 |         ----------
22 |         input_data: str or array
23 |             Can be a 3D volume or a filename.
24 |         output_filename: str
25 |             Location to save output data to. If left as '', will return numpy array.
26 |         input_transform: str
27 |             detatails TBD, unimplemented
28 |         method: str
29 |             Will perform motion correction according to the provided method.
30 |             Currently available: ['fsl']
31 |         command: str
32 |             The literal command-line string to be inputted via Python's subprocess module.
33 |         temp_dir: str
34 |             If temporary files are created, they will be saved here.
35 | 
36 |         Returns
37 |         -------
38 |         output: array
39 |             Output data, only if output_filename is left as ''.
40 |     """
41 | 
42 |     skull_strip_methods = ['slicer']
43 |     if method not in skull_strip_methods:
44 |         print('Input \"method\" parameter is not available. Available methods: ', skull_strip_methods)
45 |         return
46 | 
47 |     if method == 'slicer':
48 | 
49 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
50 | 
51 |         temp_input, temp_output = False, False
52 | 
53 |         if not isinstance(input_data, str):
54 |             input_filename = os.path.join(temp_dir, 'temp.nii.gz')
55 |             save_numpy_2_nifti(input_data, input_filename)
56 |             temp_input = True
57 |         else:
58 |             input_filename = input_data
59 | 
60 |         if output_filename == '':
61 |             temp_output = True
62 |             output_filename = os.path.join(temp_dir, 'temp_out.nii.gz')
63 | 
64 |         dimensions = str(dimensions).strip('[]').replace(' ', '')
65 | 
66 |         if reference_volume or input_transform is not None:
67 |             resample_command = [command, '--launch', 'ResampleScalarVectorDWIVolume', input_filename, output_filename, '-R', reference_volume, '--interpolation', interpolation]
68 |             if input_transform is not None:
69 |                 resample_command += ['-f', input_transform]
70 |             print(' '.join(resample_command))
71 |             subprocess.call(resample_command)
72 |         else:
73 |             resample_command = [command, '--launch', 'ResampleScalarVolume', '-i', interpolation, '-s', dimensions, input_filename, output_filename]
74 |             print(' '.join(resample_command))
75 |             subprocess.call(resample_command)
76 |         
77 |         if temp_input:
78 |             os.remove(input_filename)
79 |             pass
80 | 
81 |         if temp_output:
82 |             output = convert_input_2_numpy(output_filename)
83 |             os.remove(output_filename)
84 |             return output
85 | 
86 | def run_test():
87 |     return
88 | 
89 | if __name__ == '__main__':
90 |     run_test()
91 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/signal.py:
--------------------------------------------------------------------------------
  1 | """ This module is a series of scripts relating to extracting signal from noise
  2 |     in medical imaging files. Blurring, PCA, other scripts (most likely using
  3 |     scikit) will be put here.
  4 | """
  5 | 
  6 | from scipy.ndimage.filters import gaussian_filter
  7 | import numpy as np
  8 | import random
  9 | 
 10 | def gaussian_blur(image_numpy=[], gaussian_blur=0, gaussian_blur_axes=[]):
 11 | 
 12 |     """ Gaussian blurring greatly improves fitting performance on DCE
 13 |         phantom data. Consider removing, adds almost nothing to scipy's
 14 |         function.
 15 |     """
 16 | 
 17 |     return
 18 | 
 19 |     # if gaussian_blur > 0:
 20 | 
 21 |     #     dims = image_numpy.ndim
 22 | 
 23 |     #     # This may throw an error..
 24 |     #     if gaussian_blur_axes == []:
 25 |     #         blur_axes = [gaussian_blur]*dims
 26 |     #     else:
 27 |     #         blur_axes = [0]*dims
 28 |     #         blur_axes[] = gaussian_blur
 29 | 
 30 |     #     output_numpy = gaussian_filter(image_numpy, blur_axes)     
 31 | 
 32 |     #     return output_numpy
 33 | 
 34 |     # else:
 35 |     #     return image_numpy
 36 | 
 37 | def create_PCA_maps(image_numpy, PCA_levels = 10, PCA_axis = -1, return_eigenvalues=False):
 38 | 
 39 |     """ Takes in an image with pixels/voxels that change over time, or some other final axis,
 40 |         and return an image with the specified amount of PCA levels, ordered from most important
 41 |         to least important.
 42 |     """
 43 | 
 44 |     # Support for other PCA axes other than the last one? Seems extravagant. Maybe one day..
 45 | 
 46 |     pca_curve_data = np.reshape(image_numpy, (np.product(image_numpy.shape[0:-1]), image_numpy.shape[-1]))  
 47 |     pca_curve_data_dot_matrix = np.dot(pca_curve_data.T, pca_curve_data)
 48 | 
 49 |     # TODO: Understand PCA better, give these more descriptive names.
 50 |     eigenvector, eigenmatrix = np.linalg.eig(pca_curve_data_dot_matrix)
 51 |     sorting_indices = np.argsort(eigenvector)
 52 | 
 53 |     eigenvector_sorted = np.sort(eigenvector)
 54 |     eigenmatrix_sorted = eigenmatrix[sorting_indices.astype(int),:]
 55 | 
 56 |     pca_curve_data = np.dot(pca_curve_data, eigenmatrix_sorted)
 57 |     pca_curve_data = np.reshape(pca_curve_data[..., 0:PCA_levels], image_numpy.shape[0:-1] + (PCA_levels,))
 58 | 
 59 |     if return_eigenvalues:
 60 |         return pca_curve_data, eigenvector_sorted, eigenmatrix_sorted
 61 |     else:
 62 |         return pca_curve_data
 63 | 
 64 | 
 65 | def PCA_reduce(image_numpy, PCA_levels = 10, PCA_axis = -1):
 66 | 
 67 |     """ Recomposes spatial-curve data based on however many PCA_levels are specified.
 68 |     """
 69 | 
 70 |     pca_maps, eigenvector_sorted, eigenmatrix_sorted = create_PCA_maps(image_numpy, PCA_levels, PCA_axis, return_eigenvalues=True)
 71 | 
 72 |     pca_reduced_data = np.reshape(pca_maps, (np.product(pca_maps.shape[0:-1]), pca_maps.shape[-1]))
 73 |     pca_reduced_data = np.dot(pca_reduced_data, eigenmatrix_sorted[0:PCA_levels,:])
 74 |     pca_reduced_data = np.reshape(pca_reduced_data, image_numpy.shape)
 75 | 
 76 |     return pca_reduced_data
 77 | 
 78 | # def PCA_threshold(image_numpy, PCA_levels = 10, PCA_axis = -1, pca_thresholds=[[1,0,'greater']], replacement_value=-.01):
 79 | 
 80 | #     """ This program is written very poorly. It is meant to threshold based on pre-specified primary
 81 | #         components. Has only been useful with DCE.
 82 | #     """
 83 | 
 84 | #     pca_maps = create_PCA_maps(image_numpy, PCA_levels, PCA_axis)
 85 | 
 86 | #     for pca_threshold in pca_thresholds:
 87 | 
 88 | #         map_num = pca_threshold[0]
 89 | #         threshold_num = pca_threshold[1]
 90 | 
 91 | #         if len(pca_threshold) == 3:
 92 | #             threshold_sign = 'greater'
 93 | 
 94 | #         if threshold_sign == 'greater':
 95 | 
 96 | #         image_numpy = image_numpy[pca_maps[..., map_num] > threshold_num] = replacement_value
 97 | 
 98 | #     return image_numpy
 99 | 
100 | 
101 | if __name__ == '__main__':
102 |     np.random.seed(1)
103 |     print(PCA_reduce(np.random.rand(10,10,10,20), PCA_levels = 10).shape)
104 |     pass
105 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/skull_strip.py:
--------------------------------------------------------------------------------
  1 | import subprocess
  2 | import os
  3 | 
  4 | from shutil import move
  5 | 
  6 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
  7 | from ..qtim_utilities.format_util import convert_input_2_numpy
  8 | 
  9 | 
 10 | def skull_strip(
 11 |     input_data,
 12 |     output_filename="",
 13 |     output_mask_filename="",
 14 |     method="bet",
 15 |     command="bet2",
 16 |     temp_dir="./",
 17 |     extra_parameters={},
 18 | ):
 19 |     """A catch-all function for skull-stripping. Will perform skull-stripping on an input volume
 20 |     depending on the 'method' and 'command' inputted. Will output a binary skull-mask to
 21 |     output_mask_filename if provided.
 22 | 
 23 |     Parameters
 24 |     ----------
 25 |     input_data: str or array
 26 |         Can be a 3D volume or a filename.
 27 |     output_filename: str
 28 |         Location to save output data to.
 29 |     output_mask_filename: str
 30 |         Location to save binary skull mask to.
 31 |     method: str
 32 |         Will perform motion correction according to the provided method.
 33 |         Currently available: ['fsl']
 34 |     command: str
 35 |         The literal command-line string to be inputted via Python's subprocess module.
 36 |     temp_dir: str
 37 |         If temporary files are created, they will be saved here.
 38 |     extra_parameters: dict
 39 |         A dictionary of method-specific parameters that one may submit.
 40 | 
 41 |     Returns
 42 |     -------
 43 |     output: array, array
 44 |         Output data, only if output_filename is left as ''.
 45 |     """
 46 | 
 47 |     skull_strip_methods = ["bet"]
 48 |     if method not in skull_strip_methods:
 49 |         print(
 50 |             'Input "method" parameter is not available. Available methods: ',
 51 |             skull_strip_methods,
 52 |         )
 53 |         return
 54 | 
 55 |     if method == "bet":
 56 |         # A good reason to have a Class for qtim methods is to cut through all of this extra code.
 57 | 
 58 |         temp_input, temp_output, temp_mask_output = False, False, False
 59 | 
 60 |         if not isinstance(input_data, str):
 61 |             input_filename = os.path.join(temp_dir, "temp.nii.gz")
 62 |             save_numpy_2_nifti(input_data, input_filename)
 63 |             temp_input = True
 64 |         else:
 65 |             input_filename = input_data
 66 | 
 67 |         if output_filename == "":
 68 |             temp_output = True
 69 |             output_filename = os.path.join(temp_dir, "temp_out.nii.gz")
 70 | 
 71 |         if output_mask_filename == "":
 72 |             temp_mask_output = True
 73 |             output_mask_filename = os.path.join(temp_dir, "temp_mask_out.nii.gz")
 74 | 
 75 |         # if extra_parameters['fsl_threshold'] is None:
 76 |         extra_parameters["fsl_threshold"] = 0.5
 77 | 
 78 |         print(
 79 |             " ".join(
 80 |                 [
 81 |                     command,
 82 |                     input_filename,
 83 |                     output_filename,
 84 |                     "-f",
 85 |                     str(extra_parameters["fsl_threshold"]),
 86 |                     "-g",
 87 |                     "0",
 88 |                     "-m",
 89 |                 ]
 90 |             )
 91 |         )
 92 |         subprocess.call(
 93 |             [
 94 |                 command,
 95 |                 input_filename,
 96 |                 output_filename,
 97 |                 "-f",
 98 |                 str(extra_parameters["fsl_threshold"]),
 99 |                 "-g",
100 |                 "0",
101 |                 "-m",
102 |             ]
103 |         )
104 | 
105 |         if output_mask_filename != "":
106 |             move(output_filename + "_mask.nii.gz", output_mask_filename)
107 | 
108 |         if temp_input:
109 |             os.remove(input_filename)
110 |             pass
111 | 
112 |         if temp_output or temp_mask_output:
113 |             output, output_mask = convert_input_2_numpy(
114 |                 output_filename
115 |             ), convert_input_2_numpy(output_mask_filename)
116 |             os.remove(output_filename)
117 |             os.remove(output_mask_filename)
118 |             return output, output_mask
119 | 
120 | 
121 | def run_test():
122 |     return
123 | 
124 | 
125 | if __name__ == "__main__":
126 |     run_test()
127 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_preprocessing/threshold.py:
--------------------------------------------------------------------------------
 1 | """ This module should be used for functions that null out values in an array
 2 |     based on a condition. Primarily used for masking.
 3 | """
 4 | 
 5 | import numpy as np
 6 | 
 7 | from ..qtim_utilities.format_util import convert_input_2_numpy
 8 | from ..qtim_utilities.nifti_util import save_numpy_2_nifti
 9 | 
10 | def crop_with_mask(input_data, label_data, output_filename='', mask_value=0, return_labels=None, replacement_value=0):
11 | 
12 |     """ Crops and image with a predefined mask image. Values equal to mask value
13 |         are replaced with replacement_value.
14 | 
15 |         TODO: Add support for not-equal-to masking.
16 |         TODO: Add support for other replacement_values, a-la scikit-learn.
17 |         TODO: Add support for multiple return_labels.
18 | 
19 |         Parameters
20 |         ----------
21 | 
22 |         input_data: N-dimensional array or str
23 |             The volume to be cropped. Can be filename or numpy array.
24 |         label_data: N-dimensional array or str
25 |             A label mask. Must be the same size as input_data
26 |         mask_value: int or float
27 |             Values equal to mask_value will be replaced with replacement_value.
28 |         return_labels: float or list
29 |             Label values to be preserved at the exclusion of other values.
30 |         replacement_value: int or float
31 |             Values equal to mask_value or not in return_labels will be replaced with replacement_value.
32 | 
33 |         Returns
34 |         -------
35 |         input_numpy: array
36 |             Transformed input array.
37 |     """
38 | 
39 |     input_numpy, label_numpy = convert_input_2_numpy(input_data), convert_input_2_numpy(label_data)
40 | 
41 |     input_numpy[label_numpy == mask_value] = replacement_value
42 | 
43 |     # if not isinstance(return_labels, list): 
44 |     #     return_labels = [return_labels]
45 | 
46 |     # if len(return_labels) > 0:
47 |     #     # [TODO FIX]
48 |     #     input_numpy[label_numpy != return_labels[0]] = replacement_value
49 | 
50 |     if output_filename != '':
51 |         if isinstance(input_data, str):
52 |             save_numpy_2_nifti(input_numpy, input_data, output_filename)
53 |         else:
54 |             save_numpy_2_nifti(input_numpy, output_path=output_filename)
55 |     else:
56 |         return input_numpy
57 | 
58 | def run_test():
59 |     return
60 | 
61 | if __name__ == '__main__':
62 |     run_test()
63 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_slicer/convert_dicom.py:
--------------------------------------------------------------------------------
 1 | import os
 2 | import glob
 3 | import fnmatch
 4 | 
 5 | from optparse import OptionParser
 6 | 
 7 | def grab_files_recursive(input_directory, regex='*'):
 8 | 
 9 |     """ A convenience wrapper around os.walk. Returns a list of all files in
10 |         a directory and all of its subdirectories.
11 |     """
12 | 
13 |     output_list = []
14 | 
15 |     for root, subFolders, files in os.walk(input_directory):
16 |         try:
17 |             for file in files:
18 |                 if fnmatch.fnmatch(file, regex):
19 |                     output_list += [os.path.join(root, file)]
20 |         except:
21 |             continue
22 | 
23 |     return output_list
24 | 
25 | def convert_dicom(input_folder, output_folder, plugins='DICOMScalarVolumePlugin'):
26 |     
27 |     dicom_files = grab_files_recursive(input_folder)
28 | 
29 |     if slicer.dicomDatabase == None:
30 |         slicer.dicomDatabase = ctk.ctkDICOMDatabase()
31 |         slicer.dicomDatabase.openDatabase(os.path.dirname(os.path.realpath(__file__)) + "/Slicer_Dicom_Database/ctkDICOM.sql", "SLICER")
32 |     db = slicer.dicomDatabase
33 | 
34 |     if not plugins is list:
35 |         plugins = [plugins]
36 | 
37 |     plugins = [slicer.modules.dicomPlugins[p]() for p in plugins]
38 | 
39 |     slicer.util.quit()
40 | 
41 |     for plugin in plugins:
42 |         # try:
43 |         if plugin:
44 |             loadables = plugin.examine([dicom_files])
45 | 
46 |             if len(loadables) == 0:
47 |                 print('plugin failed to interpret this series')
48 |             else:
49 | 
50 |                 patientID = db.fileValue(loadables[0].files[0],'0010,0020')
51 |                 seriesDescription = db.fileValue(loadables[0].files[0],'0008,103e')
52 |                 seriesDescription = "".join(x for x in seriesDescription if x.isalnum())
53 |                 seriesDate = db.fileValue(loadables[0].files[0],'0008,0020')
54 |                 seriesTime = db.fileValue(loadables[0].files[0],'0008,0031')
55 |                 flipAngle = db.fileValue(loadables[0].files[0],'0018,1314')
56 |                 echoTime = db.fileValue(loadables[0].files[0],'0018,0081')
57 |                 repTime = db.fileValue(loadables[0].files[0],'0018,0080')
58 | 
59 |                 output_filename =  os.path.join(output_folder, patientID + '_' + seriesDescription + '_' + seriesDate + '.nrrd')
60 | 
61 |                 volume = plugin.load(loadables[0])
62 |                 if volume:
63 |                     slicer.util.saveNode(volume,output_filename)
64 |                     slicer.util.quit()
65 |                     return
66 | 
67 |         else:
68 |             continue
69 | 
70 |         # except:
71 |             # continue
72 | 
73 |     slicer.util.quit()
74 |     return
75 | 
76 | if __name__ == '__main__':
77 | 
78 |     # try:
79 | 
80 |         parser = OptionParser()
81 |         parser.add_option("-i", "--inputfolder", dest="InputFolder", help="Input DICOM Folder")
82 |         parser.add_option("-o", "--outputfolder", dest="OutputFolder", help="Output Nifti Folder")
83 |         parser.add_option("-p", "--plugins", dest="Plugins", help="DICOM Loading Plugins")
84 |         (options, args) = parser.parse_args()
85 |         convert_dicom(options.InputFolder, options.OutputFolder, options.Plugins)
86 | 
87 |     # except:
88 | 
89 |         # slicer.util.quit()
90 | 
91 | # /opt/Slicer-4.5.0-1-linux-amd64/Slicer --no-main-window --disable-cli-modules --python-script /home/abeers/Github/qtim_tools/qtim_tools/qtim_slicer/convert_dicom.py -i "/home/abeers/Projects/DCE_Motion_Phantom/RIDER_DATA/RIDER NEURO MRI/RIDER Neuro MRI-1023805636" -o "/home/abeers/Projects/DCE_Motion_Phantom/RIDER_DATA/" -p 'MultiVolumeImporterPlugin'


--------------------------------------------------------------------------------
/qtim_tools/qtim_stats/__init__.py:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/QTIM-Lab/qtim_tools/b92e73127da5031f166174c047b3b56253be2486/qtim_tools/qtim_stats/__init__.py


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/README.md:
--------------------------------------------------------------------------------
1 | # qtim_utilities
2 | This is a repository for utilities that can be shared across all other repositories, and that may not necessarily be tied around any one theme.


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/__init__.py:
--------------------------------------------------------------------------------
1 | import qtim_tools.qtim_utilities.nifti_util
2 | import qtim_tools.qtim_utilities.nrrd_util
3 | import qtim_tools.qtim_utilities.dicom_util
4 | import qtim_tools.qtim_utilities.format_util
5 | import qtim_tools.qtim_utilities.file_util
6 | import qtim_tools.qtim_utilities.array_util
7 | import qtim_tools.qtim_utilities.text_util
8 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/convert_util.py:
--------------------------------------------------------------------------------
 1 | 
 2 | from nrrd_util import nrrd_2_numpy
 3 | from nifti_util import nifti_2_numpy
 4 | 
 5 | def nifti_4d_2_nrrd_4d(input_nifti, output_nrrd, TR, TE):
 6 | 
 7 |     nrrd_2_numpy()
 8 | 
 9 |     return
10 | 
11 | def run_test():
12 |     return
13 | 
14 | if __name__ == '__main__':
15 |     run_test()


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/image_util.py:
--------------------------------------------------------------------------------
 1 | """ Utilities for dealing with 2D image files, like JPG, PNG,
 2 |     etc. Most functions will likely be wrappers around other
 3 |     libraries, e.g. PIL, skimage, etc. Consider merging the
 4 |     image library from qtim_preprocessing.
 5 | """
 6 | 
 7 | import nibabel as nib
 8 | import numpy as np
 9 | import scipy.misc
10 | 
11 | def img_2_numpy(input_image):
12 |     
13 |     """ Loads image data and returns a numpy array. There
14 |         will likely be many parameters to specify because
15 |         of the strange quantization issues seemingly inherent
16 |         in loading images.
17 |     """
18 | 
19 |     image_nifti = misc.imread(filepath)
20 | 
21 |     return image_nifti
22 | 
23 | def save_numpy_2_img(input_numpy, output_filename, output_dimensions=[], rescale=0):
24 | 
25 |     if output_dimensions:
26 |         input_numpy = scipy.misc.imresize(input_numpy, output_dimensions)
27 | 
28 |     elif rescale > 0:
29 |         input_numpy = scipy.mis.imresize(input_numpy, rescale)
30 | 
31 |     scipy.misc.imsave(output_filename, input_numpy)


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/nrrd_util.py:
--------------------------------------------------------------------------------
 1 | """ Utilities for dealing with NRRD files. So far, this is mostly
 2 | 	a nifti library, so these will probably just be conversion
 3 | 	utilities. The existence of this library should imply the creation
 4 | 	of an array_util, as many of the functions in nifti_util are not
 5 | 	specific to niftis.
 6 | """
 7 | 
 8 | import nibabel as nib
 9 | import numpy as np
10 | import nrrd
11 | 
12 | def nrrd_2_numpy(input_nrrd, return_header=False):
13 | 	
14 | 	""" Loads nrrd data and optionally return a nrrd header
15 | 		in pynrrd's format. If array is 4D, swaps axes so
16 | 		that time dimension is last to match nifti standard.
17 | 	"""
18 | 
19 | 	nrrd_data, nrrd_options = nrrd.read(input_nrrd)
20 | 
21 | 	if nrrd_data.ndim == 4:
22 | 		nrrd_data = np.rollaxis(nrrd_data, 0, 4)
23 | 
24 | 	if return_header:
25 | 		return nrrd_data, nrrd_options
26 | 	else:
27 | 		return nrrd_data
28 | 
29 | def save_numpy_2_nrrd(input_numpy, reference_nrrd=[], output_filepath=''):
30 |     return


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/scratch_util.py:
--------------------------------------------------------------------------------
 1 | """ This is a scratch utilty folder, for idiosyncratic functions
 2 |     that don't fit anywhere else but might want to be kept later.
 3 | """
 4 | from nifti_utils import *
 5 | import nibabel
 6 | 
 7 | def save_alternate_nifti(filepath, levels, reference_image=[], method="z_score", mask_value=0):
 8 | 
 9 |     """ Consider for deletion, or scrap pile
10 |     """
11 | 
12 |     image = nib.load(filepath)
13 |     image_numpy = image.get_fdata()
14 |     image_affine = image.affine
15 | 
16 |     if reference_image == []:
17 |         reference_image = np.copy(image_numpy)
18 | 
19 |     image_numpy = coerce_levels(image_numpy, levels=levels, reference_image=reference_image, method=method, mask_value=mask_value)
20 | 
21 |     print('image_transformed!')
22 | 
23 |     new_img = nib.Nifti1Image(image_numpy, image_affine)
24 | 
25 |     print('new_image_created!')
26 | 
27 |     print('zmapped_' + str.split(filepath, '//')[-1])
28 | 
29 |     nib.save(new_img, 'zmapped_' + str.split(filepath, '//')[-1])
30 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_utilities/text_util.py:
--------------------------------------------------------------------------------
 1 | """ This will be a utility for reading human-readable data passed in through
 2 |     text-based formats. These data may be transformation matrices, AIFs, bvectors,
 3 |     or other relevant information.
 4 | """
 5 | 
 6 | import numpy as np
 7 | import csv
 8 | 
 9 | def save_numpy_2_csv(input_numpy, output_csv, ignore_value=False):
10 | 
11 |     """ A convenience function to write a numpy array to a csv
12 |         file. Numpy has a method to do this, but I often find it
13 |         counterintuitive. This also allows you to not write certain
14 |         rows depending on a value in the first column.
15 | 
16 |         Parameters
17 |         ----------
18 | 
19 |         input_numpy: array
20 |             An array, preferably of object datatype, to write.
21 |         output_csv: str
22 |             A csv file to write to.
23 |         ignore_value: str or bool
24 |             If ignore_value is in the first column, this row will
25 |             be skipped. Default is set to False, which does not
26 |             ignore any value.
27 |     """
28 | 
29 |     with open(output_csv, 'wb') as writefile:
30 |         csvfile = csv.writer(writefile, delimiter=',')
31 |         for row in input_numpy:
32 |             if (ignore_value or ignore_value == '') and row[0] == ignore_value:
33 |                 continue
34 |             csvfile.writerow(row)
35 | 
36 | def run_test():
37 |     return
38 | 
39 | if __name__ == '__main__':
40 |     run_test()


--------------------------------------------------------------------------------
/qtim_tools/qtim_visualization/README.md:
--------------------------------------------------------------------------------
1 | # qtim_visualization
2 | This project, yet to be started, will be a repository for scripts involving visualizing medical imaging data, or the analyses derived from medical imaging data.


--------------------------------------------------------------------------------
/qtim_tools/qtim_visualization/__init__.py:
--------------------------------------------------------------------------------
1 | import qtim_tools.qtim_visualization.database
2 | import qtim_tools.qtim_visualization.d3
3 | import qtim_tools.qtim_visualization.image
4 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_visualization/d3.py:
--------------------------------------------------------------------------------
 1 | import os
 2 | import numpy as np
 3 | 
 4 | from shutil import copy
 5 | from bs4 import BeautifulSoup
 6 | 
 7 | from ..qtim_utilities.format_util import FORMAT_LIST, convert_input_2_numpy
 8 | from ..qtim_utilities.array_util import extract_maximal_slice, truncate_image
 9 | from ..qtim_utilities.image_util import save_numpy_2_img
10 | from ..qtim_utilities.text_util import save_numpy_2_csv
11 | 
12 | 
13 | def labeled_scatter(input_data, html_directory, image_col=0, labels=False, label_col=1, x_col=2, y_col=3, color_col=-1, data_columns=-1, dimensions=[], rescale=0, extract_maximal_slice_mode='', mask_value=0, save_labels=True, ignore_errors=True, overwrite=True):
14 | 
15 |     """ DOCUMENTATION TODO
16 | 
17 |         Also, this function should likely take a YAML config file.
18 |     """
19 | 
20 |     # Check for csv input
21 |     if isinstance(input_data, str):
22 |         input_data = np.genfromtxt(input_data, delimiter=',', dtype=object)
23 | 
24 |     # Check for existence of destination folder.
25 |     if not os.path.exists(html_directory):
26 |         os.mkdir(html_directory)
27 |     if not os.path.exists(os.path.join(html_directory, 'imgs')):
28 |         os.mkdir(os.path.join(html_directory, 'imgs'))
29 | 
30 |     # Check for labels when picking the largest slice.
31 |     if extract_maximal_slice_mode == '':
32 |         if labels:
33 |             extract_maximal_slice_mode = 'max_label'
34 |         else:
35 |             extract_maximal_slice_mode = 'max_intensity'
36 | 
37 |     # Create a new csv, required for modified image_paths.
38 |     output_csv = np.copy(input_data).astype(object)
39 | 
40 |     for row_idx, row in enumerate(input_data):
41 | 
42 |         if row_idx == 0:
43 |             continue
44 | 
45 |         filename = row[image_col]
46 | 
47 |         _, file_extension = os.path.splitext(filename)
48 | 
49 |         file_basename = os.path.basename(os.path.abspath(filename))
50 | 
51 |         if file_extension not in FORMAT_LIST['image']:
52 | 
53 |             output_filename = os.path.join(html_directory, 'imgs', str.split(file_basename, '.')[0] + '.png')
54 | 
55 |             if os.path.exists(output_filename) and not overwrite:
56 |                 continue
57 | 
58 |             array_3d = convert_input_2_numpy(filename)
59 |             label_3d = []
60 | 
61 |             if labels:
62 |                 label_3d = convert_input_2_numpy(os.path.abspath(row[label_col]))
63 | 
64 |             maximal_slice, slice_index = extract_maximal_slice(array_3d, label_3d, mode=extract_maximal_slice_mode, return_index=True)
65 | 
66 |             maximal_slice[label_3d[:,:,slice_index] == mask_value] = 0
67 | 
68 |             maximal_slice = truncate_image(np.squeeze(maximal_slice))
69 | 
70 |             save_numpy_2_img(np.squeeze(maximal_slice), output_filename, dimensions, rescale)
71 | 
72 |         else:
73 | 
74 |             output_filename = os.path.join(html_directory, 'imgs', file_basename)
75 | 
76 |             copy(filename, output_filename)
77 | 
78 |         output_csv[row_idx, 0] = os.path.join('.','imgs', os.path.basename(output_filename))
79 | 
80 |     save_numpy_2_csv(output_csv, os.path.join(html_directory, 'viz_data.csv'))
81 | 
82 |     template_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'd3_templates', 'labeled_scatter.html')
83 |     copy(template_file, os.path.join(html_directory, 'labeled_scatter.html'))
84 | 
85 | def run_test():
86 |     return
87 | 
88 | if __name__ == '__main__':
89 |     run_test()
90 | 


--------------------------------------------------------------------------------
/qtim_tools/qtim_visualization/database.py:
--------------------------------------------------------------------------------
 1 | """ This module will create python dictionaries linking together image/volume URLs, label URLs, attributes, and data. These databases can then be exported into formats acceptable by d3.js, Shiny, or other visualization apps.
 2 | """
 3 | 
 4 | import glob
 5 | 
 6 | # from ..core.internals import qtim_Exception
 7 | 
 8 | # def create_image_database(input_dictionary={}, input_array=[], image_file_col=0, label_file_col=1):
 9 | 
10 | #     """ Take in either a string array or a directory full of images, and return a python dictionary that is pre-formatted to work
11 | #         well with all other qtim_visualization generators. Can
12 | #         optionally associate images with a list of labels.
13 | 
14 | #         Parameters
15 | #         ----------
16 | #         image_list : list, optional
17 | #             A list of filenames to enter into the image database. Each
18 | #             filename will serve as a key in the dictionary. Can also
19 | #             take image filename / label filename pairs.
20 | #         image_regex: str, optional
21 | #             A linux-type search expression for image filenames. For 
22 | #             example, to grab all jpg files in a folder, enter 
23 | #             '~/folder/*.jpg'. Can be combined with image_list.
24 | #         label_identifier: str, optional
25 | #             A identification phrase to search for labels from provided
26 | #             image filenames. Filenames containing both an image filename
27 | #             and the label_identifier will be added as labels.
28 | #         ignore_missings: bool, optional
29 | #             If data cannot be verified to exist (e.g. filenames), or
30 | #             label data cannot be found, supply a missing data identifier
31 | #             instead of returning an error.
32 | #     """
33 | 
34 | #     if len(input_dictionary) > 0:
35 | #         return input_dictionary
36 | 
37 | #     return
38 | 
39 | def run_test():
40 |     pass
41 | 
42 | if __name__ == '__main__':
43 |     run_test()


--------------------------------------------------------------------------------
/qtim_tools/test_data/__init__.py:
--------------------------------------------------------------------------------
1 | from qtim_tools.test_data.load import *
2 | 


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/qtim_tools/test_data/load.py:
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 1 | """ A convenient function for loading test data store in the qtim_tools
 2 |     package. In the future, we may not want to store this data, some of
 3 |     which can be huge, in the package, and instead out to download it
 4 |     from a separate online hosting point.
 5 | """
 6 | 
 7 | import os
 8 | 
 9 | def load_test_file(data, return_type="filepath", retrieval_type="local"):
10 | 
11 |     """ Loads test files. In the future, should download them from an online
12 |         repository. In this case, returning a filepath might be interesting...
13 |     """
14 | 
15 |     # DCE DATA
16 |     if data == "dce_tofts_v6":
17 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_dce','tofts_v6.nii.gz'))
18 |     elif data == "dce_tofts_v6_label":
19 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_dce','tofts_v6-label.nii.gz'))
20 |     elif data == "dce_tofts_v9":
21 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_dce','tofts_v9.nii.gz'))
22 |     elif data == "dce_tofts_v9_label":
23 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_dce','tofts_v9-label.nii.gz'))
24 |     elif data == "dce_tofts_v9_aif":
25 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_dce','tofts_v9-AIF-label.nii.gz'))
26 | 
27 |     elif data == "sample_mri":
28 |         filepath = os.path.abspath(os.path.join(os.path.dirname(__file__),'test_data_features','MRHead.nii.gz'))
29 | 
30 |     # FEATURE DATA
31 |     # elif data == ''
32 | 
33 |     else:
34 |         print('There is no test data under this name. Returning an empty string.')
35 |         return []
36 | 
37 | 
38 |     if return_type == "filepath":
39 |         return filepath
40 | 
41 | if __name__ == '__main__':
42 |     pass
43 | 


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/qtim_tools/test_data/test_data_features/README.MD:
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1 | # Digital Reference Objects for Shape, Size, Intensity, and GLCM Features
2 | 
3 | These folders contain digital reference objects (DROs) for shape, size, intensity, and GLCM features. Folders prepended with the label "Phantom" are non-anatomical DROs, while folders prepended with "MRHead" are label-based DROs overlaid on sample MR data from a brain.
4 | 
5 | MRHead volumes originated as sample data in the open-source imaging Platform 3D Slicer. https://www.slicer.org/wiki/SampleData
6 | 


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/requirements.txt:
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1 | nibabel
2 | pydicom
3 | pynrrd
4 | matplotlib
5 | numpy
6 | scipy


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/setup.cfg:
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1 | [metadata]
2 | description-file = README.md


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/setup.py:
--------------------------------------------------------------------------------
 1 | from setuptools import setup, find_packages
 2 | from codecs import open
 3 | from os import path
 4 | 
 5 | # with open(path.join('./', 'README.md'), encoding='utf-8') as f:
 6 |     # long_description = f.read()
 7 | 
 8 | #with open('requirements.txt') as f:
 9 | #    required = f.read().splitlines()
10 | 
11 | setup(
12 |   name = 'qtim_tools',
13 |   # packages = ['qtim_tools'], # this must be the same as the name above
14 |   version = '0.1.13',
15 |   description = 'A library for medical imaging analysis, with an emphasis on MRI, machine learning, and neuroimaging. Created by the Quantiative Tumor Imaging Lab at the Martinos Center (Harvard-MIT Program in Health, Sciences, and Technology / Massachussets General Hospital)',
16 |   packages = find_packages(),
17 |   entry_points =  {
18 |                   "console_scripts": ['qtim = qtim_tools.__main__:main'], 
19 |                   },
20 |   author = 'Andrew Beers',
21 |   author_email = 'abeers@mgh.harvard.edu',
22 |   url = 'https://github.com/QTIM-Lab/qtim_tools', # use the URL to the github repo
23 |   download_url = 'https://github.com/QTIM-Lab/qtim_tools/tarball/0.1.13',
24 |   keywords = ['neuroimaging', 'niftis', 'nifti','mri','dce','dsc','ktrans','ve','tofts','machine learning','vision','texture','learning'], # arbitrary keywords
25 |   install_requires=['dicom','pynrrd','Pillow','configparser','pyyaml','beautifulsoup4','nibabel','scikit-image','matplotlib','scipy','numpy'],
26 |   classifiers = [],
27 | )
28 | 


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/sphinx/_build/html/.buildinfo:
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1 | # Sphinx build info version 1
2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3 | config: 27a00f668e112a0b7e62a144696e5530
4 | tags: 645f666f9bcd5a90fca523b33c5a78b7
5 | 


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/sphinx/_build/html/_modules/qtim_tools/qtim_features/document_test.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
 2 |   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 3 | 
 4 | 
 5 | <html xmlns="http://www.w3.org/1999/xhtml">
 6 |   <head>
 7 |     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 8 |     
 9 |     <title>qtim_tools.qtim_features.document_test &mdash; qtim_tools 0.2 documentation</title>
10 |     
11 |     <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
12 |     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
13 |     
14 |     <script type="text/javascript">
15 |       var DOCUMENTATION_OPTIONS = {
16 |         URL_ROOT:    '../../../',
17 |         VERSION:     '0.2',
18 |         COLLAPSE_INDEX: false,
19 |         FILE_SUFFIX: '.html',
20 |         HAS_SOURCE:  true
21 |       };
22 |     </script>
23 |     <script type="text/javascript" src="../../../_static/jquery.js"></script>
24 |     <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 |     <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 |     <link rel="top" title="qtim_tools 0.2 documentation" href="../../../index.html" />
27 |     <link rel="up" title="qtim_tools.qtim_features" href="../qtim_features.html" />
28 |    
29 |   
30 |   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
31 | 
32 |   </head>
33 |   <body role="document">  
34 | 
35 |     <div class="document">
36 |       <div class="documentwrapper">
37 |         <div class="bodywrapper">
38 |           <div class="body" role="main">
39 |             
40 |   <h1>Source code for qtim_tools.qtim_features.document_test</h1><div class="highlight"><pre>
41 | 
42 | 
43 | <div class="viewcode-block" id="main"><a class="viewcode-back" href="../../../qtim_tools.qtim_features.html#qtim_tools.qtim_features.document_test.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
44 |     <span class="sd">&quot;&quot;&quot;This is the entry point of the application!</span>
45 | <span class="sd">    :raises: :class:`KeyboardInterrupt`, :class:`SystemExit`</span>
46 | <span class="sd">    &quot;&quot;&quot;</span>
47 |     <span class="k">pass</span></div>
48 | 
49 | 
50 | <span class="c1"># vim:et:fdm=marker:sts=4:sw=4:ts=4</span>
51 | </pre></div>
52 | 
53 |           </div>
54 |         </div>
55 |       </div>
56 |       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
57 |         <div class="sphinxsidebarwrapper"><div class="relations">
58 | <h3>Related Topics</h3>
59 | <ul>
60 |   <li><a href="../../../index.html">Documentation overview</a><ul>
61 |   <li><a href="../../index.html">Module code</a><ul>
62 |   <li><a href="../qtim_features.html">qtim_tools.qtim_features</a><ul>
63 |   </ul></li>
64 |   </ul></li>
65 |   </ul></li>
66 | </ul>
67 | </div>
68 | <div id="searchbox" style="display: none" role="search">
69 |   <h3>Quick search</h3>
70 |     <form class="search" action="../../../search.html" method="get">
71 |       <input type="text" name="q" />
72 |       <input type="submit" value="Go" />
73 |       <input type="hidden" name="check_keywords" value="yes" />
74 |       <input type="hidden" name="area" value="default" />
75 |     </form>
76 |     <p class="searchtip" style="font-size: 90%">
77 |     Enter search terms or a module, class or function name.
78 |     </p>
79 | </div>
80 | <script type="text/javascript">$('#searchbox').show(0);</script>
81 |         </div>
82 |       </div>
83 |       <div class="clearer"></div>
84 |     </div>
85 |     <div class="footer">
86 |       &copy;2017, Andrew Beers (MGH).
87 |       
88 |       |
89 |       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
90 |       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
91 |       
92 |     </div>
93 | 
94 |     
95 | 
96 |     
97 |   </body>
98 | </html>


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/sphinx/_build/html/_sources/index.txt:
--------------------------------------------------------------------------------
 1 | ``qtim_tools`` Package
 2 | ==================
 3 | 
 4 | Contents:
 5 | 
 6 | .. automodule:: qtim_tools
 7 |     :members:
 8 | 
 9 | -------------------
10 | 
11 | **Sub-Modules:**
12 | 
13 | .. toctree::
14 | 
15 |     qtim_tools.qtim_features
16 |     qtim_tools.qtim_dce
17 | 
18 | Indices and tables
19 | ==================
20 | 
21 | * :ref:`genindex`
22 | * :ref:`modindex`
23 | * :ref:`search`
24 | 
25 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/modules.txt:
--------------------------------------------------------------------------------
1 | qtim_tools
2 | ==========
3 | 
4 | .. toctree::
5 |    :maxdepth: 4
6 | 
7 |    qtim_tools
8 | 


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/sphinx/_build/html/_sources/qtim_tools.qtim_dce.txt:
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 1 | qtim_tools.qtim_dce package
 2 | ===========================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_dce.dce_util module
 8 | -----------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_dce.dce_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_dce.help module
16 | -------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_dce.help
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_dce.process_dce_file module
24 | -------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_dce.process_dce_file
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_dce.tofts_parameter_calculator module
32 | -----------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_dce.tofts_parameter_calculator
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_dce.tofts_parametric_mapper module
40 | --------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_dce.tofts_parametric_mapper
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_dce.tofts_worker module
48 | ---------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_dce.tofts_worker
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | 
56 | Module contents
57 | ---------------
58 | 
59 | .. automodule:: qtim_tools.qtim_dce
60 |     :members:
61 |     :undoc-members:
62 |     :show-inheritance:
63 | 


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/sphinx/_build/html/_sources/qtim_tools.qtim_features.txt:
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 1 | qtim_tools.qtim_features package
 2 | ================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_features.GLCM module
 8 | ------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_features.GLCM
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_features.document_test module
16 | ---------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_features.document_test
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_features.extract_features module
24 | ------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_features.extract_features
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_features.morphology module
32 | ------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_features.morphology
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_features.phantoms module
40 | ----------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_features.phantoms
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_features.statistics module
48 | ------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_features.statistics
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_features.test module
56 | ------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_features.test
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | 
64 | Module contents
65 | ---------------
66 | 
67 | .. automodule:: qtim_tools.qtim_features
68 |     :members:
69 |     :undoc-members:
70 |     :show-inheritance:
71 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_learning.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_learning package
 2 | ================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_learning.nn_preprocessing module
 8 | ------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_learning.nn_preprocessing
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_learning
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_pipelines.txt:
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 1 | qtim_tools.qtim_pipelines package
 2 | =================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_pipelines.process_dce module
 8 | --------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_pipelines.process_dce
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_pipelines
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_preprocessing.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_preprocessing package
 2 | =====================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_preprocessing.image module
 8 | ------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_preprocessing.image
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_preprocessing.normalization module
16 | --------------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_preprocessing.normalization
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_preprocessing.registration module
24 | -------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_preprocessing.registration
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_preprocessing.signal module
32 | -------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_preprocessing.signal
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_preprocessing.threshold module
40 | ----------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_preprocessing.threshold
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | 
48 | Module contents
49 | ---------------
50 | 
51 | .. automodule:: qtim_tools.qtim_preprocessing
52 |     :members:
53 |     :undoc-members:
54 |     :show-inheritance:
55 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_dce.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_dce package
 2 | ======================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_dce.dce_util module
 8 | ----------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.dce_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_tools.qtim_dce.help module
16 | ------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.help
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_tools.qtim_dce.process_dce_file module
24 | ------------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.process_dce_file
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_tools.qtim_dce.tofts_parameter_calculator module
32 | ----------------------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.tofts_parameter_calculator
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_tools.qtim_dce.tofts_parametric_mapper module
40 | -------------------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.tofts_parametric_mapper
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_tools.qtim_dce.tofts_worker module
48 | --------------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_tools.qtim_dce.tofts_worker
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | 
56 | Module contents
57 | ---------------
58 | 
59 | .. automodule:: qtim_tools.qtim_tools.qtim_dce
60 |     :members:
61 |     :undoc-members:
62 |     :show-inheritance:
63 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_features.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_features package
 2 | ===========================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_features.GLCM module
 8 | -----------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_features.GLCM
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_tools.qtim_features.document_test module
16 | --------------------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_tools.qtim_features.document_test
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_tools.qtim_features.extract_features module
24 | -----------------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_tools.qtim_features.extract_features
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_tools.qtim_features.morphology module
32 | -----------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_tools.qtim_features.morphology
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_tools.qtim_features.phantoms module
40 | ---------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_tools.qtim_features.phantoms
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_tools.qtim_features.statistics module
48 | -----------------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_tools.qtim_features.statistics
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_tools.qtim_features.test module
56 | -----------------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_tools.qtim_features.test
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | 
64 | Module contents
65 | ---------------
66 | 
67 | .. automodule:: qtim_tools.qtim_tools.qtim_features
68 |     :members:
69 |     :undoc-members:
70 |     :show-inheritance:
71 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_learning.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_learning package
 2 | ===========================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_learning.nn_preprocessing module
 8 | -----------------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_learning.nn_preprocessing
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_tools.qtim_learning
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_pipelines.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_pipelines package
 2 | ============================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_pipelines.process_dce module
 8 | -------------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_pipelines.process_dce
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_tools.qtim_pipelines
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_preprocessing.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_preprocessing package
 2 | ================================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_preprocessing.image module
 8 | -----------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing.image
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_tools.qtim_preprocessing.normalization module
16 | -------------------------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing.normalization
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_tools.qtim_preprocessing.registration module
24 | ------------------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing.registration
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_tools.qtim_preprocessing.signal module
32 | ------------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing.signal
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_tools.qtim_preprocessing.threshold module
40 | ---------------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing.threshold
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | 
48 | Module contents
49 | ---------------
50 | 
51 | .. automodule:: qtim_tools.qtim_tools.qtim_preprocessing
52 |     :members:
53 |     :undoc-members:
54 |     :show-inheritance:
55 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.qtim_utilities.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.qtim_utilities package
 2 | ============================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.qtim_utilities.array_util module
 8 | ------------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.array_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_tools.qtim_utilities.dicom_util module
16 | ------------------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.dicom_util
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_tools.qtim_utilities.file_util module
24 | -----------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.file_util
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_tools.qtim_utilities.format_util module
32 | -------------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.format_util
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_tools.qtim_utilities.image_util module
40 | ------------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.image_util
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_tools.qtim_utilities.nifti_util module
48 | ------------------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.nifti_util
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_tools.qtim_utilities.nrrd_util module
56 | -----------------------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.nrrd_util
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | qtim_tools.qtim_tools.qtim_utilities.scratch_util module
64 | --------------------------------------------------------
65 | 
66 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.scratch_util
67 |     :members:
68 |     :undoc-members:
69 |     :show-inheritance:
70 | 
71 | qtim_tools.qtim_tools.qtim_utilities.text_util module
72 | -----------------------------------------------------
73 | 
74 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.text_util
75 |     :members:
76 |     :undoc-members:
77 |     :show-inheritance:
78 | 
79 | qtim_tools.qtim_tools.qtim_utilities.transform_util module
80 | ----------------------------------------------------------
81 | 
82 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities.transform_util
83 |     :members:
84 |     :undoc-members:
85 |     :show-inheritance:
86 | 
87 | 
88 | Module contents
89 | ---------------
90 | 
91 | .. automodule:: qtim_tools.qtim_tools.qtim_utilities
92 |     :members:
93 |     :undoc-members:
94 |     :show-inheritance:
95 | 


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/sphinx/_build/html/_sources/qtim_tools.qtim_tools.test_data.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools.test_data package
 2 | =======================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_tools.test_data.load module
 8 | -------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_tools.test_data.load
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_tools.test_data
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_tools.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_tools package
 2 | =============================
 3 | 
 4 | Subpackages
 5 | -----------
 6 | 
 7 | .. toctree::
 8 | 
 9 |     qtim_tools.qtim_tools.qtim_dce
10 |     qtim_tools.qtim_tools.qtim_features
11 |     qtim_tools.qtim_tools.qtim_learning
12 |     qtim_tools.qtim_tools.qtim_pipelines
13 |     qtim_tools.qtim_tools.qtim_preprocessing
14 |     qtim_tools.qtim_tools.qtim_utilities
15 |     qtim_tools.qtim_tools.qtim_visualization
16 |     qtim_tools.qtim_tools.test_data
17 | 
18 | Module contents
19 | ---------------
20 | 
21 | .. automodule:: qtim_tools.qtim_tools
22 |     :members:
23 |     :undoc-members:
24 |     :show-inheritance:
25 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.qtim_utilities.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.qtim_utilities package
 2 | =================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_utilities.array_util module
 8 | -------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_utilities.array_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_utilities.dicom_util module
16 | -------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_utilities.dicom_util
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_utilities.file_util module
24 | ------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_utilities.file_util
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_utilities.format_util module
32 | --------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_utilities.format_util
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_utilities.image_util module
40 | -------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_utilities.image_util
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_utilities.nifti_util module
48 | -------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_utilities.nifti_util
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_utilities.nrrd_util module
56 | ------------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_utilities.nrrd_util
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | qtim_tools.qtim_utilities.scratch_util module
64 | ---------------------------------------------
65 | 
66 | .. automodule:: qtim_tools.qtim_utilities.scratch_util
67 |     :members:
68 |     :undoc-members:
69 |     :show-inheritance:
70 | 
71 | qtim_tools.qtim_utilities.text_util module
72 | ------------------------------------------
73 | 
74 | .. automodule:: qtim_tools.qtim_utilities.text_util
75 |     :members:
76 |     :undoc-members:
77 |     :show-inheritance:
78 | 
79 | qtim_tools.qtim_utilities.transform_util module
80 | -----------------------------------------------
81 | 
82 | .. automodule:: qtim_tools.qtim_utilities.transform_util
83 |     :members:
84 |     :undoc-members:
85 |     :show-inheritance:
86 | 
87 | 
88 | Module contents
89 | ---------------
90 | 
91 | .. automodule:: qtim_tools.qtim_utilities
92 |     :members:
93 |     :undoc-members:
94 |     :show-inheritance:
95 | 


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/sphinx/_build/html/_sources/qtim_tools.qtim_visualization.txt:
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 1 | qtim_tools.qtim_visualization package
 2 | =====================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_visualization.image_database module
 8 | ---------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_visualization.image_database
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_visualization
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


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/sphinx/_build/html/_sources/qtim_tools.test_data.txt:
--------------------------------------------------------------------------------
 1 | qtim_tools.test_data package
 2 | ============================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.test_data.load module
 8 | --------------------------------
 9 | 
10 | .. automodule:: qtim_tools.test_data.load
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.test_data
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


--------------------------------------------------------------------------------
/sphinx/_build/html/_sources/qtim_tools.txt:
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 1 | qtim_tools package
 2 | ==================
 3 | 
 4 | Subpackages
 5 | -----------
 6 | 
 7 | .. toctree::
 8 | 
 9 |     qtim_tools.qtim_dce
10 |     qtim_tools.qtim_features
11 |     qtim_tools.qtim_learning
12 |     qtim_tools.qtim_pipelines
13 |     qtim_tools.qtim_preprocessing
14 |     qtim_tools.qtim_utilities
15 |     qtim_tools.qtim_visualization
16 |     qtim_tools.test_data
17 | 
18 | Module contents
19 | ---------------
20 | 
21 | .. automodule:: qtim_tools
22 |     :members:
23 |     :undoc-members:
24 |     :show-inheritance:
25 | 


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/sphinx/modules.rst:
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1 | qtim_tools
2 | ==========
3 | 
4 | .. toctree::
5 |    :maxdepth: 4
6 | 
7 |    qtim_tools
8 | 


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/sphinx/qtim_tools.qtim_dce.rst:
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 1 | qtim_tools.qtim_dce package
 2 | ===========================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_dce.dce_util module
 8 | -----------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_dce.dce_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_dce.help module
16 | -------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_dce.help
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_dce.process_dce_file module
24 | -------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_dce.process_dce_file
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_dce.tofts_parameter_calculator module
32 | -----------------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_dce.tofts_parameter_calculator
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_dce.tofts_parametric_mapper module
40 | --------------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_dce.tofts_parametric_mapper
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_dce.tofts_worker module
48 | ---------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_dce.tofts_worker
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | 
56 | Module contents
57 | ---------------
58 | 
59 | .. automodule:: qtim_tools.qtim_dce
60 |     :members:
61 |     :undoc-members:
62 |     :show-inheritance:
63 | 


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/sphinx/qtim_tools.qtim_features.rst:
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 1 | qtim_tools.qtim_features package
 2 | ================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_features.GLCM module
 8 | ------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_features.GLCM
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_features.document_test module
16 | ---------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_features.document_test
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_features.extract_features module
24 | ------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_features.extract_features
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_features.morphology module
32 | ------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_features.morphology
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_features.phantoms module
40 | ----------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_features.phantoms
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_features.statistics module
48 | ------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_features.statistics
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_features.test module
56 | ------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_features.test
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | 
64 | Module contents
65 | ---------------
66 | 
67 | .. automodule:: qtim_tools.qtim_features
68 |     :members:
69 |     :undoc-members:
70 |     :show-inheritance:
71 | 


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/sphinx/qtim_tools.qtim_learning.rst:
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 1 | qtim_tools.qtim_learning package
 2 | ================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_learning.nn_preprocessing module
 8 | ------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_learning.nn_preprocessing
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_learning
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


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/sphinx/qtim_tools.qtim_pipelines.rst:
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 1 | qtim_tools.qtim_pipelines package
 2 | =================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_pipelines.process_dce module
 8 | --------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_pipelines.process_dce
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_pipelines
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


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/sphinx/qtim_tools.qtim_preprocessing.rst:
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 1 | qtim_tools.qtim_preprocessing package
 2 | =====================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_preprocessing.image module
 8 | ------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_preprocessing.image
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_preprocessing.normalization module
16 | --------------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_preprocessing.normalization
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_preprocessing.registration module
24 | -------------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_preprocessing.registration
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_preprocessing.signal module
32 | -------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_preprocessing.signal
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_preprocessing.threshold module
40 | ----------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_preprocessing.threshold
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | 
48 | Module contents
49 | ---------------
50 | 
51 | .. automodule:: qtim_tools.qtim_preprocessing
52 |     :members:
53 |     :undoc-members:
54 |     :show-inheritance:
55 | 


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/sphinx/qtim_tools.qtim_utilities.rst:
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 1 | qtim_tools.qtim_utilities package
 2 | =================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_utilities.array_util module
 8 | -------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_utilities.array_util
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | qtim_tools.qtim_utilities.dicom_util module
16 | -------------------------------------------
17 | 
18 | .. automodule:: qtim_tools.qtim_utilities.dicom_util
19 |     :members:
20 |     :undoc-members:
21 |     :show-inheritance:
22 | 
23 | qtim_tools.qtim_utilities.file_util module
24 | ------------------------------------------
25 | 
26 | .. automodule:: qtim_tools.qtim_utilities.file_util
27 |     :members:
28 |     :undoc-members:
29 |     :show-inheritance:
30 | 
31 | qtim_tools.qtim_utilities.format_util module
32 | --------------------------------------------
33 | 
34 | .. automodule:: qtim_tools.qtim_utilities.format_util
35 |     :members:
36 |     :undoc-members:
37 |     :show-inheritance:
38 | 
39 | qtim_tools.qtim_utilities.image_util module
40 | -------------------------------------------
41 | 
42 | .. automodule:: qtim_tools.qtim_utilities.image_util
43 |     :members:
44 |     :undoc-members:
45 |     :show-inheritance:
46 | 
47 | qtim_tools.qtim_utilities.nifti_util module
48 | -------------------------------------------
49 | 
50 | .. automodule:: qtim_tools.qtim_utilities.nifti_util
51 |     :members:
52 |     :undoc-members:
53 |     :show-inheritance:
54 | 
55 | qtim_tools.qtim_utilities.nrrd_util module
56 | ------------------------------------------
57 | 
58 | .. automodule:: qtim_tools.qtim_utilities.nrrd_util
59 |     :members:
60 |     :undoc-members:
61 |     :show-inheritance:
62 | 
63 | qtim_tools.qtim_utilities.scratch_util module
64 | ---------------------------------------------
65 | 
66 | .. automodule:: qtim_tools.qtim_utilities.scratch_util
67 |     :members:
68 |     :undoc-members:
69 |     :show-inheritance:
70 | 
71 | qtim_tools.qtim_utilities.text_util module
72 | ------------------------------------------
73 | 
74 | .. automodule:: qtim_tools.qtim_utilities.text_util
75 |     :members:
76 |     :undoc-members:
77 |     :show-inheritance:
78 | 
79 | qtim_tools.qtim_utilities.transform_util module
80 | -----------------------------------------------
81 | 
82 | .. automodule:: qtim_tools.qtim_utilities.transform_util
83 |     :members:
84 |     :undoc-members:
85 |     :show-inheritance:
86 | 
87 | 
88 | Module contents
89 | ---------------
90 | 
91 | .. automodule:: qtim_tools.qtim_utilities
92 |     :members:
93 |     :undoc-members:
94 |     :show-inheritance:
95 | 


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/sphinx/qtim_tools.qtim_visualization.rst:
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 1 | qtim_tools.qtim_visualization package
 2 | =====================================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.qtim_visualization.image_database module
 8 | ---------------------------------------------------
 9 | 
10 | .. automodule:: qtim_tools.qtim_visualization.image_database
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.qtim_visualization
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


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/sphinx/qtim_tools.rst:
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 1 | qtim_tools package
 2 | ==================
 3 | 
 4 | Subpackages
 5 | -----------
 6 | 
 7 | .. toctree::
 8 | 
 9 |     qtim_tools.qtim_dce
10 |     qtim_tools.qtim_features
11 |     qtim_tools.qtim_learning
12 |     qtim_tools.qtim_pipelines
13 |     qtim_tools.qtim_preprocessing
14 |     qtim_tools.qtim_utilities
15 |     qtim_tools.qtim_visualization
16 |     qtim_tools.test_data
17 | 
18 | Module contents
19 | ---------------
20 | 
21 | .. automodule:: qtim_tools
22 |     :members:
23 |     :undoc-members:
24 |     :show-inheritance:
25 | 


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/sphinx/qtim_tools.test_data.rst:
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 1 | qtim_tools.test_data package
 2 | ============================
 3 | 
 4 | Submodules
 5 | ----------
 6 | 
 7 | qtim_tools.test_data.load module
 8 | --------------------------------
 9 | 
10 | .. automodule:: qtim_tools.test_data.load
11 |     :members:
12 |     :undoc-members:
13 |     :show-inheritance:
14 | 
15 | 
16 | Module contents
17 | ---------------
18 | 
19 | .. automodule:: qtim_tools.test_data
20 |     :members:
21 |     :undoc-members:
22 |     :show-inheritance:
23 | 


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/sphinx/requirements.txt:
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1 | sphinx
2 | numpydoc


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/test_script.py:
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 1 | """ This is a continuously evolving test script for de-bugging purposes.
 2 | """
 3 | 
 4 | import qtim_tools
 5 | 
 6 | import os
 7 | import numpy as np
 8 | import fnmatch
 9 | from shutil import copy
10 | 
11 | from qtim_tools.qtim_utilities.dicom_util import dcm_2_numpy, dcm_2_nifti
12 | 
13 | folder = 'C:/Users/azb22/Documents/Scripting/Prostate_Texture/Test'
14 | outfile1 = 'C:/Users/azb22/Documents/Scripting/Prostate_Texture/no_normalize.csv'
15 | outfile2 = 'C:/Users/azb22/Documents/Scripting/Prostate_Texture/normalize.csv'
16 | 
17 | qtim_tools.qtim_features.generate_feature_list_batch(folder, outfile=outfile1, labels=True, features=['GLCM','morphology', 'statistics'], levels = 100, mask_value = 0, erode = [0,0,0], overwrite = True, label_suffix='-label', set_label='', file_regex='*.nii*', recursive=False, normalize_intensities=False)
18 | qtim_tools.qtim_features.generate_feature_list_batch(folder, outfile=outfile2, labels=True, features=['GLCM','morphology', 'statistics'], levels = 100, mask_value = 0, erode = [0,0,0], overwrite = True, label_suffix='-label', set_label='', file_regex='*.nii*', recursive=False, normalize_intensities=False)


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/tests/initial_test.py:
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1 | import qtim_tools


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