patkit 0.14.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (106) hide show
  1. patkit-0.14.1/.gitignore +70 -0
  2. patkit-0.14.1/LICENSE.markdown +675 -0
  3. patkit-0.14.1/PKG-INFO +890 -0
  4. patkit-0.14.1/README.md +172 -0
  5. patkit-0.14.1/patkit/__init__.py +71 -0
  6. patkit-0.14.1/patkit/annotations/__init__.py +36 -0
  7. patkit-0.14.1/patkit/annotations/peaks.py +694 -0
  8. patkit-0.14.1/patkit/audio_processing/__init__.py +34 -0
  9. patkit-0.14.1/patkit/audio_processing/audio_processing.py +204 -0
  10. patkit-0.14.1/patkit/cli.py +68 -0
  11. patkit-0.14.1/patkit/cli_commands.py +180 -0
  12. patkit-0.14.1/patkit/configuration/__init__.py +50 -0
  13. patkit-0.14.1/patkit/configuration/configuration_models.py +635 -0
  14. patkit-0.14.1/patkit/configuration/configuration_parsers.py +520 -0
  15. patkit-0.14.1/patkit/configuration/configuration_setup.py +170 -0
  16. patkit-0.14.1/patkit/configuration/exclusion_list_functions.py +224 -0
  17. patkit-0.14.1/patkit/constants.py +291 -0
  18. patkit-0.14.1/patkit/data_import/AAA_raw_ultrasound.py +202 -0
  19. patkit-0.14.1/patkit/data_import/AAA_recordings.py +213 -0
  20. patkit-0.14.1/patkit/data_import/AAA_splines.py +312 -0
  21. patkit-0.14.1/patkit/data_import/RASL_3D_ultrasound_recordings.py +410 -0
  22. patkit-0.14.1/patkit/data_import/__init__.py +61 -0
  23. patkit-0.14.1/patkit/data_import/audio.py +109 -0
  24. patkit-0.14.1/patkit/data_import/session_import_config.py +158 -0
  25. patkit-0.14.1/patkit/data_import/spline_import_config.py +177 -0
  26. patkit-0.14.1/patkit/data_import/three_dim_ultrasound.py +131 -0
  27. patkit-0.14.1/patkit/data_import/video.py +98 -0
  28. patkit-0.14.1/patkit/data_loader.py +161 -0
  29. patkit-0.14.1/patkit/data_processor.py +140 -0
  30. patkit-0.14.1/patkit/data_structures/__init__.py +45 -0
  31. patkit-0.14.1/patkit/data_structures/base_classes.py +571 -0
  32. patkit-0.14.1/patkit/data_structures/data_structures.py +785 -0
  33. patkit-0.14.1/patkit/data_structures/metadata_classes.py +233 -0
  34. patkit-0.14.1/patkit/errors.py +68 -0
  35. patkit-0.14.1/patkit/export/__init__.py +45 -0
  36. patkit-0.14.1/patkit/export/images.py +216 -0
  37. patkit-0.14.1/patkit/export/metadata.py +313 -0
  38. patkit-0.14.1/patkit/export/modality_data.py +172 -0
  39. patkit-0.14.1/patkit/external_class_extensions/__init__.py +43 -0
  40. patkit-0.14.1/patkit/external_class_extensions/base_model_extensions.py +112 -0
  41. patkit-0.14.1/patkit/external_class_extensions/enum_extensions.py +317 -0
  42. patkit-0.14.1/patkit/gui/__init__.py +37 -0
  43. patkit-0.14.1/patkit/gui/boundary_animation.py +245 -0
  44. patkit-0.14.1/patkit/gui/dialog_template.py +83 -0
  45. patkit-0.14.1/patkit/gui/image_save_dialog.py +154 -0
  46. patkit-0.14.1/patkit/gui/list_save_dialog.py +206 -0
  47. patkit-0.14.1/patkit/gui/ofbrowse.py +173 -0
  48. patkit-0.14.1/patkit/gui/qt_annotator.ui +488 -0
  49. patkit-0.14.1/patkit/gui/qt_annotator_window.py +291 -0
  50. patkit-0.14.1/patkit/gui/qt_tiers.ui +466 -0
  51. patkit-0.14.1/patkit/gui/replace_dialog.py +92 -0
  52. patkit-0.14.1/patkit/import_formats/__init__.py +40 -0
  53. patkit-0.14.1/patkit/import_formats/avi_read.py +75 -0
  54. patkit-0.14.1/patkit/import_formats/dicom_ultra_read.py +147 -0
  55. patkit-0.14.1/patkit/import_formats/rasl_dat_to_wav.py +89 -0
  56. patkit-0.14.1/patkit/import_formats/splines_read.py +80 -0
  57. patkit-0.14.1/patkit/import_formats/ult_read.py +90 -0
  58. patkit-0.14.1/patkit/import_formats/wav_read.py +106 -0
  59. patkit-0.14.1/patkit/initialise.py +224 -0
  60. patkit-0.14.1/patkit/interpolate_raw_uti.py +225 -0
  61. patkit-0.14.1/patkit/interpreter.py +78 -0
  62. patkit-0.14.1/patkit/metrics/__init__.py +57 -0
  63. patkit-0.14.1/patkit/metrics/aggregate_image.py +210 -0
  64. patkit-0.14.1/patkit/metrics/calculate_aggregate_images.py +130 -0
  65. patkit-0.14.1/patkit/metrics/calculate_distance_matrices.py +270 -0
  66. patkit-0.14.1/patkit/metrics/calculate_intensity.py +60 -0
  67. patkit-0.14.1/patkit/metrics/calculate_pd.py +313 -0
  68. patkit-0.14.1/patkit/metrics/calculate_spline_metric.py +324 -0
  69. patkit-0.14.1/patkit/metrics/distance_matrix.py +292 -0
  70. patkit-0.14.1/patkit/metrics/downsample_metric.py +167 -0
  71. patkit-0.14.1/patkit/metrics/metrics_helpers.py +76 -0
  72. patkit-0.14.1/patkit/metrics/ofreg.py +296 -0
  73. patkit-0.14.1/patkit/metrics/pd.py +278 -0
  74. patkit-0.14.1/patkit/metrics/spline_metric.py +236 -0
  75. patkit-0.14.1/patkit/metrics/tongue_shape_analysis.py +402 -0
  76. patkit-0.14.1/patkit/modalities/__init__.py +40 -0
  77. patkit-0.14.1/patkit/modalities/recorded_metadata_classes.py +77 -0
  78. patkit-0.14.1/patkit/modalities/recorded_modalities.py +457 -0
  79. patkit-0.14.1/patkit/modalities/splines.py +157 -0
  80. patkit-0.14.1/patkit/plot_and_publish/__init__.py +44 -0
  81. patkit-0.14.1/patkit/plot_and_publish/legend_generation.py +142 -0
  82. patkit-0.14.1/patkit/plot_and_publish/plot.py +587 -0
  83. patkit-0.14.1/patkit/plot_and_publish/plot_utilities.py +69 -0
  84. patkit-0.14.1/patkit/plot_and_publish/publish.py +366 -0
  85. patkit-0.14.1/patkit/qt_annotator.py +1292 -0
  86. patkit-0.14.1/patkit/satgrid.py +534 -0
  87. patkit-0.14.1/patkit/save_and_load/__init__.py +34 -0
  88. patkit-0.14.1/patkit/save_and_load/load.py +347 -0
  89. patkit-0.14.1/patkit/save_and_load/save.py +415 -0
  90. patkit-0.14.1/patkit/save_and_load/save_and_load_schemas.py +123 -0
  91. patkit-0.14.1/patkit/simulation/__init__.py +68 -0
  92. patkit-0.14.1/patkit/simulation/contour_tools.py +186 -0
  93. patkit-0.14.1/patkit/simulation/metric_calculations.py +329 -0
  94. patkit-0.14.1/patkit/simulation/perturbation_series_plots.py +228 -0
  95. patkit-0.14.1/patkit/simulation/rays_on_contours.py +319 -0
  96. patkit-0.14.1/patkit/simulation/simulate.py +218 -0
  97. patkit-0.14.1/patkit/simulation/simulation_plots.py +538 -0
  98. patkit-0.14.1/patkit/ui_callbacks.py +87 -0
  99. patkit-0.14.1/patkit/utility_functions/__init__.py +44 -0
  100. patkit-0.14.1/patkit/utility_functions/computational.py +145 -0
  101. patkit-0.14.1/patkit/utility_functions/logging_helpers.py +96 -0
  102. patkit-0.14.1/patkit/utility_functions/path.py +46 -0
  103. patkit-0.14.1/patkit/utility_functions/processing_helpers.py +79 -0
  104. patkit-0.14.1/patkit/utility_functions/string_formatters.py +73 -0
  105. patkit-0.14.1/patkit/utility_functions/types.py +60 -0
  106. patkit-0.14.1/pyproject.toml +68 -0
patkit-0.14.1/.gitignore ADDED
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+ venv/
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+ .idea/
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+
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+ #
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+ # Patkit generated files
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+ #
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+ *.meta
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+ *.npz
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+
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+ ####
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+ # Groups of files
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+ ####
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+ # pyinstaller results
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+ build/
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+ *.spec
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+
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+ # vs code line counter's files
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+ .VSCodeCounter/
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+
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+ # pyreverse byproducts
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+ *.dot
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+ *.vcg
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+
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+ # Emacs autosaves
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+ *~
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+
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+ # Python bytecode
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+ *.pyc
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+
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+ # Log files
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+ *.log
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+
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+ # Pickled output files
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+ *.pickle
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+
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+ # Apple Desktop Services Store file
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+ .DS_store
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+
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+ ####
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+ # Specific files
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+ ####
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+ # Result of test run
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+ spaghetti_plot.pdf
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+
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+ # Template for licenseheaders.py to include gpl in headers of python files.
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+ gpl-v3.tmpl
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+
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+ ####
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+ # Directories
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+ ####
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+
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+ # VSCode settings
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+ .vscode/
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+
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+ # Results of an optic flow run.
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+ of_results/
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+
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+ # Publication and conference datasets
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+ local_data/
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+ local/
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+ # in case it's a symlink
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+ local_data
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+ local
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+
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+ # Figure output files
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+ figures/
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+
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+ # Distribution and build files
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+ dist/
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+ *.egg-info