celldetective 1.3.9.post1__tar.gz → 1.3.9.post2__tar.gz

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Files changed (136) hide show
  1. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/PKG-INFO +1 -1
  2. celldetective-1.3.9.post2/celldetective/_version.py +1 -0
  3. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/measure_cells.py +5 -2
  4. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/PKG-INFO +1 -1
  5. celldetective-1.3.9.post1/celldetective/_version.py +0 -1
  6. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/LICENSE +0 -0
  7. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/README.md +0 -0
  8. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/__init__.py +0 -0
  9. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/__main__.py +0 -0
  10. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/datasets/segmentation_annotations/blank +0 -0
  11. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/datasets/signal_annotations/blank +0 -0
  12. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/events.py +0 -0
  13. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/extra_properties.py +0 -0
  14. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/filters.py +0 -0
  15. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/InitWindow.py +0 -0
  16. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/__init__.py +0 -0
  17. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/about.py +0 -0
  18. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/analyze_block.py +0 -0
  19. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/btrack_options.py +0 -0
  20. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/classifier_widget.py +0 -0
  21. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/configure_new_exp.py +0 -0
  22. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/control_panel.py +0 -0
  23. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/generic_signal_plot.py +0 -0
  24. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/gui_utils.py +0 -0
  25. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/DL-segmentation-strategy.json +0 -0
  26. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/Threshold-vs-DL.json +0 -0
  27. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/cell-populations.json +0 -0
  28. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/exp-structure.json +0 -0
  29. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/feature-btrack.json +0 -0
  30. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/neighborhood.json +0 -0
  31. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/prefilter-for-segmentation.json +0 -0
  32. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/preprocessing.json +0 -0
  33. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/propagate-classification.json +0 -0
  34. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/track-postprocessing.json +0 -0
  35. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/help/tracking.json +0 -0
  36. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/json_readers.py +0 -0
  37. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/layouts.py +0 -0
  38. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/measurement_options.py +0 -0
  39. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/neighborhood_options.py +0 -0
  40. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/plot_measurements.py +0 -0
  41. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/plot_signals_ui.py +0 -0
  42. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/process_block.py +0 -0
  43. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/downloader.py +0 -0
  44. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/segment_cells.py +0 -0
  45. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/track_cells.py +0 -0
  46. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/train_segmentation_model.py +0 -0
  47. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/train_signal_model.py +0 -0
  48. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/retrain_segmentation_model_options.py +0 -0
  49. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/retrain_signal_model_options.py +0 -0
  50. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/seg_model_loader.py +0 -0
  51. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/signal_annotator.py +0 -0
  52. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/signal_annotator2.py +0 -0
  53. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/signal_annotator_options.py +0 -0
  54. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/styles.py +0 -0
  55. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/survival_ui.py +0 -0
  56. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/tableUI.py +0 -0
  57. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/thresholds_gui.py +0 -0
  58. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/viewers.py +0 -0
  59. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/workers.py +0 -0
  60. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/logo-large.png +0 -0
  61. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/logo.png +0 -0
  62. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/signals_icon.png +0 -0
  63. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/splash-test.png +0 -0
  64. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/splash.png +0 -0
  65. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/splash0.png +0 -0
  66. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/survival2.png +0 -0
  67. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/vignette_signals2.png +0 -0
  68. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/icons/vignette_signals2.svg +0 -0
  69. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/io.py +0 -0
  70. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/links/zenodo.json +0 -0
  71. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/measure.py +0 -0
  72. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/pair_signal_detection/blank +0 -0
  73. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/blank +0 -0
  74. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json +0 -0
  75. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/ricm_bf_all_last/ricm_bf_all_last +0 -0
  76. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json +0 -0
  77. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/test-transfer/config_input.json +0 -0
  78. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_effectors/test-transfer/test-transfer +0 -0
  79. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_generic/blank +0 -0
  80. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/segmentation_targets/blank +0 -0
  81. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/classification_loss.png +0 -0
  82. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/classifier.h5 +0 -0
  83. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/config_input.json +0 -0
  84. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/log_classifier.csv +0 -0
  85. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/log_regressor.csv +0 -0
  86. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/regression_loss.png +0 -0
  87. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/regressor.h5 +0 -0
  88. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/scores.npy +0 -0
  89. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/test_confusion_matrix.png +0 -0
  90. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/test_regression.png +0 -0
  91. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/validation_confusion_matrix.png +0 -0
  92. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/NucCond/validation_regression.png +0 -0
  93. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/signal_detection/blank +0 -0
  94. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/tracking_configs/biased_motion.json +0 -0
  95. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/tracking_configs/mcf7.json +0 -0
  96. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/tracking_configs/no_z_motion.json +0 -0
  97. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/tracking_configs/ricm.json +0 -0
  98. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/models/tracking_configs/ricm2.json +0 -0
  99. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/neighborhood.py +0 -0
  100. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/preprocessing.py +0 -0
  101. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/regionprops/__init__.py +0 -0
  102. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/regionprops/_regionprops.py +0 -0
  103. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/regionprops/props.json +0 -0
  104. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/relative_measurements.py +0 -0
  105. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/analyze_signals.py +0 -0
  106. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/measure_cells.py +0 -0
  107. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/measure_relative.py +0 -0
  108. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/segment_cells.py +0 -0
  109. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/segment_cells_thresholds.py +0 -0
  110. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/track_cells.py +0 -0
  111. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/train_segmentation_model.py +0 -0
  112. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/scripts/train_signal_model.py +0 -0
  113. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/segmentation.py +0 -0
  114. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/signals.py +0 -0
  115. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/tracking.py +0 -0
  116. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/utils.py +0 -0
  117. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/SOURCES.txt +0 -0
  118. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/dependency_links.txt +0 -0
  119. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/entry_points.txt +0 -0
  120. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/not-zip-safe +0 -0
  121. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/requires.txt +0 -0
  122. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/top_level.txt +0 -0
  123. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/setup.cfg +0 -0
  124. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/setup.py +0 -0
  125. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/__init__.py +0 -0
  126. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_events.py +0 -0
  127. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_filters.py +0 -0
  128. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_io.py +0 -0
  129. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_measure.py +0 -0
  130. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_neighborhood.py +0 -0
  131. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_preprocessing.py +0 -0
  132. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_qt.py +0 -0
  133. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_segmentation.py +0 -0
  134. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_signals.py +0 -0
  135. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_tracking.py +0 -0
  136. {celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/tests/test_utils.py +0 -0
{celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: celldetective
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- Version: 1.3.9.post1
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+ Version: 1.3.9.post2
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  Summary: description
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  Home-page: http://github.com/remyeltorro/celldetective
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  Author: Rémy Torro
celldetective-1.3.9.post2/celldetective/_version.py ADDED
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+ __version__ = "1.3.9.post2"
{celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective/gui/processes/measure_cells.py RENAMED
@@ -193,17 +193,20 @@ class MeasurementProcess(Process):
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  # Load trajectories, add centroid if not in trajectory
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  self.trajectories = self.pos+os.sep.join(['output','tables', self.table_name])
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  if os.path.exists(self.trajectories):
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- print('trajectory exists...')
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+ print('Previous table detected...')
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  self.trajectories = pd.read_csv(self.trajectories)
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  if 'TRACK_ID' not in list(self.trajectories.columns):
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+ print('Non-tracked cells detected...')
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  self.do_iso_intensities = False
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  self.intensity_measurement_radii = None
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  if self.clear_previous:
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- print('No TRACK_ID... Clear previous measurements...')
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+ print('Clear previous measurements...')
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  self.trajectories = None #remove_trajectory_measurements(trajectories, column_labels)
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  self.do_features = True
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  self.features += ['centroid']
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+ self.column_labels.update({'track': 'ID'})
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  else:
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+ print('Tracked cells detected...')
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  if self.clear_previous:
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  print('TRACK_ID found... Clear previous measurements...')
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  self.trajectories = remove_trajectory_measurements(self.trajectories, self.column_labels)
{celldetective-1.3.9.post1 → celldetective-1.3.9.post2}/celldetective.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: celldetective
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- Version: 1.3.9.post1
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+ Version: 1.3.9.post2
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  Summary: description
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  Home-page: http://github.com/remyeltorro/celldetective
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  Author: Rémy Torro
celldetective-1.3.9.post1/celldetective/_version.py DELETED
@@ -1 +0,0 @@
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- __version__ = "1.3.9.post1"