mediml 0.9.9__py3-none-any.whl

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Files changed (78) hide show
  1. MEDiml/MEDscan.py +1696 -0
  2. MEDiml/__init__.py +21 -0
  3. MEDiml/biomarkers/BatchExtractor.py +806 -0
  4. MEDiml/biomarkers/BatchExtractorTexturalFilters.py +840 -0
  5. MEDiml/biomarkers/__init__.py +16 -0
  6. MEDiml/biomarkers/diagnostics.py +125 -0
  7. MEDiml/biomarkers/get_oriented_bound_box.py +158 -0
  8. MEDiml/biomarkers/glcm.py +1602 -0
  9. MEDiml/biomarkers/gldzm.py +523 -0
  10. MEDiml/biomarkers/glrlm.py +1315 -0
  11. MEDiml/biomarkers/glszm.py +555 -0
  12. MEDiml/biomarkers/int_vol_hist.py +527 -0
  13. MEDiml/biomarkers/intensity_histogram.py +615 -0
  14. MEDiml/biomarkers/local_intensity.py +89 -0
  15. MEDiml/biomarkers/morph.py +1756 -0
  16. MEDiml/biomarkers/ngldm.py +780 -0
  17. MEDiml/biomarkers/ngtdm.py +414 -0
  18. MEDiml/biomarkers/stats.py +373 -0
  19. MEDiml/biomarkers/utils.py +389 -0
  20. MEDiml/filters/TexturalFilter.py +299 -0
  21. MEDiml/filters/__init__.py +9 -0
  22. MEDiml/filters/apply_filter.py +134 -0
  23. MEDiml/filters/gabor.py +215 -0
  24. MEDiml/filters/laws.py +283 -0
  25. MEDiml/filters/log.py +147 -0
  26. MEDiml/filters/mean.py +121 -0
  27. MEDiml/filters/textural_filters_kernels.py +1738 -0
  28. MEDiml/filters/utils.py +107 -0
  29. MEDiml/filters/wavelet.py +237 -0
  30. MEDiml/learning/DataCleaner.py +198 -0
  31. MEDiml/learning/DesignExperiment.py +480 -0
  32. MEDiml/learning/FSR.py +667 -0
  33. MEDiml/learning/Normalization.py +112 -0
  34. MEDiml/learning/RadiomicsLearner.py +714 -0
  35. MEDiml/learning/Results.py +2237 -0
  36. MEDiml/learning/Stats.py +694 -0
  37. MEDiml/learning/__init__.py +10 -0
  38. MEDiml/learning/cleaning_utils.py +107 -0
  39. MEDiml/learning/ml_utils.py +1015 -0
  40. MEDiml/processing/__init__.py +6 -0
  41. MEDiml/processing/compute_suv_map.py +121 -0
  42. MEDiml/processing/discretisation.py +149 -0
  43. MEDiml/processing/interpolation.py +275 -0
  44. MEDiml/processing/resegmentation.py +66 -0
  45. MEDiml/processing/segmentation.py +912 -0
  46. MEDiml/utils/__init__.py +25 -0
  47. MEDiml/utils/batch_patients.py +45 -0
  48. MEDiml/utils/create_radiomics_table.py +131 -0
  49. MEDiml/utils/data_frame_export.py +42 -0
  50. MEDiml/utils/find_process_names.py +16 -0
  51. MEDiml/utils/get_file_paths.py +34 -0
  52. MEDiml/utils/get_full_rad_names.py +21 -0
  53. MEDiml/utils/get_institutions_from_ids.py +16 -0
  54. MEDiml/utils/get_patient_id_from_scan_name.py +22 -0
  55. MEDiml/utils/get_patient_names.py +26 -0
  56. MEDiml/utils/get_radiomic_names.py +27 -0
  57. MEDiml/utils/get_scan_name_from_rad_name.py +22 -0
  58. MEDiml/utils/image_reader_SITK.py +37 -0
  59. MEDiml/utils/image_volume_obj.py +22 -0
  60. MEDiml/utils/imref.py +340 -0
  61. MEDiml/utils/initialize_features_names.py +62 -0
  62. MEDiml/utils/inpolygon.py +159 -0
  63. MEDiml/utils/interp3.py +43 -0
  64. MEDiml/utils/json_utils.py +78 -0
  65. MEDiml/utils/mode.py +31 -0
  66. MEDiml/utils/parse_contour_string.py +58 -0
  67. MEDiml/utils/save_MEDscan.py +30 -0
  68. MEDiml/utils/strfind.py +32 -0
  69. MEDiml/utils/textureTools.py +188 -0
  70. MEDiml/utils/texture_features_names.py +115 -0
  71. MEDiml/utils/write_radiomics_csv.py +47 -0
  72. MEDiml/wrangling/DataManager.py +1724 -0
  73. MEDiml/wrangling/ProcessDICOM.py +512 -0
  74. MEDiml/wrangling/__init__.py +3 -0
  75. mediml-0.9.9.dist-info/LICENSE.md +674 -0
  76. mediml-0.9.9.dist-info/METADATA +232 -0
  77. mediml-0.9.9.dist-info/RECORD +78 -0
  78. mediml-0.9.9.dist-info/WHEEL +4 -0
MEDiml/__init__.py ADDED
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+ import logging
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+
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+ from . import utils
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+ from . import processing
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+ from . import biomarkers
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+ from . import filters
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+ from . import wrangling
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+ from . import learning
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+ from .MEDscan import MEDscan
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+
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+
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+ stream_handler = logging.StreamHandler()
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+ stream_handler.setLevel(logging.WARNING)
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+ logging.getLogger(__name__).addHandler(stream_handler)
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+
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+ __author__ = "MEDomicsLab consortium"
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+ __version__ = "0.9.9"
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+ __copyright__ = "Copyright (C) MEDomicsLab consortium"
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+ __license__ = "GNU General Public License 3.0"
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+ __maintainer__ = "MAHDI AIT LHAJ LOUTFI"
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+ __email__ = "medomics.info@gmail.com"