celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

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Files changed (152) hide show
  1. celldetective/__init__.py +25 -0
  2. celldetective/__main__.py +62 -43
  3. celldetective/_version.py +1 -1
  4. celldetective/extra_properties.py +477 -399
  5. celldetective/filters.py +192 -97
  6. celldetective/gui/InitWindow.py +541 -411
  7. celldetective/gui/__init__.py +0 -15
  8. celldetective/gui/about.py +44 -39
  9. celldetective/gui/analyze_block.py +120 -84
  10. celldetective/gui/base/__init__.py +0 -0
  11. celldetective/gui/base/channel_norm_generator.py +335 -0
  12. celldetective/gui/base/components.py +249 -0
  13. celldetective/gui/base/feature_choice.py +92 -0
  14. celldetective/gui/base/figure_canvas.py +52 -0
  15. celldetective/gui/base/list_widget.py +133 -0
  16. celldetective/gui/{styles.py → base/styles.py} +92 -36
  17. celldetective/gui/base/utils.py +33 -0
  18. celldetective/gui/base_annotator.py +900 -767
  19. celldetective/gui/classifier_widget.py +6 -22
  20. celldetective/gui/configure_new_exp.py +777 -671
  21. celldetective/gui/control_panel.py +635 -524
  22. celldetective/gui/dynamic_progress.py +449 -0
  23. celldetective/gui/event_annotator.py +2023 -1662
  24. celldetective/gui/generic_signal_plot.py +1292 -944
  25. celldetective/gui/gui_utils.py +899 -1289
  26. celldetective/gui/interactions_block.py +658 -0
  27. celldetective/gui/interactive_timeseries_viewer.py +447 -0
  28. celldetective/gui/json_readers.py +48 -15
  29. celldetective/gui/layouts/__init__.py +5 -0
  30. celldetective/gui/layouts/background_model_free_layout.py +537 -0
  31. celldetective/gui/layouts/channel_offset_layout.py +134 -0
  32. celldetective/gui/layouts/local_correction_layout.py +91 -0
  33. celldetective/gui/layouts/model_fit_layout.py +372 -0
  34. celldetective/gui/layouts/operation_layout.py +68 -0
  35. celldetective/gui/layouts/protocol_designer_layout.py +96 -0
  36. celldetective/gui/pair_event_annotator.py +3130 -2435
  37. celldetective/gui/plot_measurements.py +586 -267
  38. celldetective/gui/plot_signals_ui.py +724 -506
  39. celldetective/gui/preprocessing_block.py +395 -0
  40. celldetective/gui/process_block.py +1678 -1831
  41. celldetective/gui/seg_model_loader.py +580 -473
  42. celldetective/gui/settings/__init__.py +0 -7
  43. celldetective/gui/settings/_cellpose_model_params.py +181 -0
  44. celldetective/gui/settings/_event_detection_model_params.py +95 -0
  45. celldetective/gui/settings/_segmentation_model_params.py +159 -0
  46. celldetective/gui/settings/_settings_base.py +77 -65
  47. celldetective/gui/settings/_settings_event_model_training.py +752 -526
  48. celldetective/gui/settings/_settings_measurements.py +1133 -964
  49. celldetective/gui/settings/_settings_neighborhood.py +574 -488
  50. celldetective/gui/settings/_settings_segmentation_model_training.py +779 -564
  51. celldetective/gui/settings/_settings_signal_annotator.py +329 -305
  52. celldetective/gui/settings/_settings_tracking.py +1304 -1094
  53. celldetective/gui/settings/_stardist_model_params.py +98 -0
  54. celldetective/gui/survival_ui.py +422 -312
  55. celldetective/gui/tableUI.py +1665 -1701
  56. celldetective/gui/table_ops/_maths.py +295 -0
  57. celldetective/gui/table_ops/_merge_groups.py +140 -0
  58. celldetective/gui/table_ops/_merge_one_hot.py +95 -0
  59. celldetective/gui/table_ops/_query_table.py +43 -0
  60. celldetective/gui/table_ops/_rename_col.py +44 -0
  61. celldetective/gui/thresholds_gui.py +382 -179
  62. celldetective/gui/viewers/__init__.py +0 -0
  63. celldetective/gui/viewers/base_viewer.py +700 -0
  64. celldetective/gui/viewers/channel_offset_viewer.py +331 -0
  65. celldetective/gui/viewers/contour_viewer.py +394 -0
  66. celldetective/gui/viewers/size_viewer.py +153 -0
  67. celldetective/gui/viewers/spot_detection_viewer.py +341 -0
  68. celldetective/gui/viewers/threshold_viewer.py +309 -0
  69. celldetective/gui/workers.py +403 -126
  70. celldetective/log_manager.py +92 -0
  71. celldetective/measure.py +1895 -1478
  72. celldetective/napari/__init__.py +0 -0
  73. celldetective/napari/utils.py +1025 -0
  74. celldetective/neighborhood.py +1914 -1448
  75. celldetective/preprocessing.py +1620 -1220
  76. celldetective/processes/__init__.py +0 -0
  77. celldetective/processes/background_correction.py +271 -0
  78. celldetective/processes/compute_neighborhood.py +894 -0
  79. celldetective/processes/detect_events.py +246 -0
  80. celldetective/processes/downloader.py +137 -0
  81. celldetective/processes/measure_cells.py +565 -0
  82. celldetective/processes/segment_cells.py +760 -0
  83. celldetective/processes/track_cells.py +435 -0
  84. celldetective/processes/train_segmentation_model.py +694 -0
  85. celldetective/processes/train_signal_model.py +265 -0
  86. celldetective/processes/unified_process.py +292 -0
  87. celldetective/regionprops/_regionprops.py +358 -317
  88. celldetective/relative_measurements.py +987 -710
  89. celldetective/scripts/measure_cells.py +313 -212
  90. celldetective/scripts/measure_relative.py +90 -46
  91. celldetective/scripts/segment_cells.py +165 -104
  92. celldetective/scripts/segment_cells_thresholds.py +96 -68
  93. celldetective/scripts/track_cells.py +198 -149
  94. celldetective/scripts/train_segmentation_model.py +324 -201
  95. celldetective/scripts/train_signal_model.py +87 -45
  96. celldetective/segmentation.py +844 -749
  97. celldetective/signals.py +3514 -2861
  98. celldetective/tracking.py +30 -15
  99. celldetective/utils/__init__.py +0 -0
  100. celldetective/utils/cellpose_utils/__init__.py +133 -0
  101. celldetective/utils/color_mappings.py +42 -0
  102. celldetective/utils/data_cleaning.py +630 -0
  103. celldetective/utils/data_loaders.py +450 -0
  104. celldetective/utils/dataset_helpers.py +207 -0
  105. celldetective/utils/downloaders.py +235 -0
  106. celldetective/utils/event_detection/__init__.py +8 -0
  107. celldetective/utils/experiment.py +1782 -0
  108. celldetective/utils/image_augmenters.py +308 -0
  109. celldetective/utils/image_cleaning.py +74 -0
  110. celldetective/utils/image_loaders.py +926 -0
  111. celldetective/utils/image_transforms.py +335 -0
  112. celldetective/utils/io.py +62 -0
  113. celldetective/utils/mask_cleaning.py +348 -0
  114. celldetective/utils/mask_transforms.py +5 -0
  115. celldetective/utils/masks.py +184 -0
  116. celldetective/utils/maths.py +351 -0
  117. celldetective/utils/model_getters.py +325 -0
  118. celldetective/utils/model_loaders.py +296 -0
  119. celldetective/utils/normalization.py +380 -0
  120. celldetective/utils/parsing.py +465 -0
  121. celldetective/utils/plots/__init__.py +0 -0
  122. celldetective/utils/plots/regression.py +53 -0
  123. celldetective/utils/resources.py +34 -0
  124. celldetective/utils/stardist_utils/__init__.py +104 -0
  125. celldetective/utils/stats.py +90 -0
  126. celldetective/utils/types.py +21 -0
  127. {celldetective-1.4.2.dist-info → celldetective-1.5.0b1.dist-info}/METADATA +1 -1
  128. celldetective-1.5.0b1.dist-info/RECORD +187 -0
  129. {celldetective-1.4.2.dist-info → celldetective-1.5.0b1.dist-info}/WHEEL +1 -1
  130. tests/gui/test_new_project.py +129 -117
  131. tests/gui/test_project.py +127 -79
  132. tests/test_filters.py +39 -15
  133. tests/test_notebooks.py +8 -0
  134. tests/test_tracking.py +232 -13
  135. tests/test_utils.py +123 -77
  136. celldetective/gui/base_components.py +0 -23
  137. celldetective/gui/layouts.py +0 -1602
  138. celldetective/gui/processes/compute_neighborhood.py +0 -594
  139. celldetective/gui/processes/downloader.py +0 -111
  140. celldetective/gui/processes/measure_cells.py +0 -360
  141. celldetective/gui/processes/segment_cells.py +0 -499
  142. celldetective/gui/processes/track_cells.py +0 -303
  143. celldetective/gui/processes/train_segmentation_model.py +0 -270
  144. celldetective/gui/processes/train_signal_model.py +0 -108
  145. celldetective/gui/table_ops/merge_groups.py +0 -118
  146. celldetective/gui/viewers.py +0 -1354
  147. celldetective/io.py +0 -3663
  148. celldetective/utils.py +0 -3108
  149. celldetective-1.4.2.dist-info/RECORD +0 -123
  150. {celldetective-1.4.2.dist-info → celldetective-1.5.0b1.dist-info}/entry_points.txt +0 -0
  151. {celldetective-1.4.2.dist-info → celldetective-1.5.0b1.dist-info}/licenses/LICENSE +0 -0
  152. {celldetective-1.4.2.dist-info → celldetective-1.5.0b1.dist-info}/top_level.txt +0 -0
celldetective/gui/classifier_widget.py CHANGED
@@ -21,14 +21,10 @@ import matplotlib.pyplot as plt
21
21
  import json
22
22
 
23
23
  from celldetective.exceptions import EmptyQueryError, MissingColumnsError, QueryError
24
- from celldetective.gui.gui_utils import (
25
- FigureCanvas,
26
- center_window,
27
- color_from_status,
28
- help_generic,
29
- )
30
- from celldetective.gui.base_components import CelldetectiveWidget
31
- from celldetective.utils import get_software_location
24
+ from celldetective.gui.gui_utils import color_from_status, help_generic
25
+ from celldetective.gui.base.figure_canvas import FigureCanvas
26
+ from celldetective.gui.base.components import CelldetectiveWidget
27
+ from celldetective import get_software_location
32
28
  from celldetective.measure import (
33
29
  classify_cells_from_query,
34
30
  interpret_track_classification,
@@ -53,24 +49,12 @@ class ClassifierWidget(CelldetectiveWidget):
53
49
  self.mode = self.parent_window.mode
54
50
  self.df = self.parent_window.df
55
51
 
56
- def _is_numeric_dtype(x):
57
- try:
58
- return np.issubdtype(x, np.number)
59
- except TypeError:
60
- # Extension dtypes like StringDtype cannot be interpreted by np.issubdtype
61
- return False
62
-
63
- is_number = np.vectorize(_is_numeric_dtype)
64
- is_number_test = is_number(self.df.dtypes)
65
- self.cols = [col for t, col in zip(is_number_test, self.df.columns) if t]
52
+ self.cols = self.df.select_dtypes(include=[np.number]).columns.tolist()
66
53
 
67
54
  self.class_name = "custom"
68
55
  self.name_le = QLineEdit(self.class_name)
69
56
  self.init_class()
70
57
 
71
- # Create the QComboBox and add some items
72
- center_window(self)
73
-
74
58
  layout = QVBoxLayout(self)
75
59
  layout.setContentsMargins(30, 30, 30, 30)
76
60
 
@@ -153,7 +137,7 @@ class ClassifierWidget(CelldetectiveWidget):
153
137
  )
154
138
  self.property_query_le.textChanged.connect(self.activate_submit_btn)
155
139
  hbox_classify.addWidget(self.property_query_le, 70)
156
- self.submit_query_btn = QPushButton("Submit...")
140
+ self.submit_query_btn = QPushButton("Preview")
157
141
  self.submit_query_btn.clicked.connect(self.apply_property_query)
158
142
  self.submit_query_btn.setEnabled(False)
159
143
  hbox_classify.addWidget(self.submit_query_btn, 20)