itasc 0.2.0.dev0__py3-none-any.whl

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Files changed (162) hide show
  1. itasc/__init__.py +16 -0
  2. itasc/cellpose/__init__.py +31 -0
  3. itasc/cellpose/cellpose_runner.py +334 -0
  4. itasc/cellpose/divergence_maps.py +380 -0
  5. itasc/cellpose/flow_following.py +283 -0
  6. itasc/cellpose/joint.py +98 -0
  7. itasc/cellpose/napari.yaml +10 -0
  8. itasc/cellpose/native_masks.py +313 -0
  9. itasc/cellpose/retrack.py +232 -0
  10. itasc/cellpose/shape.py +51 -0
  11. itasc/cellpose/track_laptrack.py +279 -0
  12. itasc/contact_analysis/__init__.py +61 -0
  13. itasc/contact_analysis/_provenance.py +29 -0
  14. itasc/contact_analysis/catalog.py +393 -0
  15. itasc/contact_analysis/config.py +155 -0
  16. itasc/contact_analysis/contacts/__init__.py +24 -0
  17. itasc/contact_analysis/contacts/batch.py +158 -0
  18. itasc/contact_analysis/contacts/build.py +837 -0
  19. itasc/contact_analysis/contacts/contact_labels.py +136 -0
  20. itasc/contact_analysis/contacts/neighborhood.py +146 -0
  21. itasc/contact_analysis/contacts/reader.py +58 -0
  22. itasc/contact_analysis/contacts/signed_contact_length.py +143 -0
  23. itasc/contact_analysis/curation.py +185 -0
  24. itasc/contact_analysis/dynamics/__init__.py +43 -0
  25. itasc/contact_analysis/dynamics/collective.py +206 -0
  26. itasc/contact_analysis/dynamics/kinematics.py +278 -0
  27. itasc/contact_analysis/dynamics/msd.py +165 -0
  28. itasc/contact_analysis/dynamics/store.py +251 -0
  29. itasc/contact_analysis/dynamics/trajectories.py +100 -0
  30. itasc/contact_analysis/frame_interval.py +85 -0
  31. itasc/contact_analysis/napari.yaml +10 -0
  32. itasc/contact_analysis/pipeline.py +313 -0
  33. itasc/contact_analysis/pixel_size.py +166 -0
  34. itasc/contact_analysis/quantifier.py +204 -0
  35. itasc/contact_analysis/quantifiers/__init__.py +7 -0
  36. itasc/contact_analysis/quantifiers/_contacts_derived.py +42 -0
  37. itasc/contact_analysis/quantifiers/cell_density.py +65 -0
  38. itasc/contact_analysis/quantifiers/cell_dynamics.py +81 -0
  39. itasc/contact_analysis/quantifiers/cell_shape.py +32 -0
  40. itasc/contact_analysis/quantifiers/contacts.py +72 -0
  41. itasc/contact_analysis/quantifiers/neighbor_count.py +26 -0
  42. itasc/contact_analysis/quantifiers/nucleus_dynamics.py +77 -0
  43. itasc/contact_analysis/quantifiers/nucleus_shape.py +35 -0
  44. itasc/contact_analysis/quantifiers/shape_relational.py +34 -0
  45. itasc/contact_analysis/quantifiers/signed_contact_length.py +44 -0
  46. itasc/contact_analysis/records.py +129 -0
  47. itasc/contact_analysis/shape/__init__.py +19 -0
  48. itasc/contact_analysis/shape/core.py +141 -0
  49. itasc/contact_analysis/shape/relational.py +134 -0
  50. itasc/contact_analysis/shape_tables.py +387 -0
  51. itasc/core/__init__.py +0 -0
  52. itasc/core/cancellation.py +15 -0
  53. itasc/core/commit.py +61 -0
  54. itasc/core/imageops.py +34 -0
  55. itasc/core/label_store.py +53 -0
  56. itasc/core/lineage.py +113 -0
  57. itasc/core/logging.py +51 -0
  58. itasc/core/paths.py +34 -0
  59. itasc/core/tiff.py +13 -0
  60. itasc/correction/__init__.py +25 -0
  61. itasc/correction/labels.py +983 -0
  62. itasc/napari/__init__.py +7 -0
  63. itasc/napari/_experiments_panel.py +1091 -0
  64. itasc/napari/_flow_layout.py +98 -0
  65. itasc/napari/_icons.py +126 -0
  66. itasc/napari/_napari_compat.py +118 -0
  67. itasc/napari/_paths.py +231 -0
  68. itasc/napari/_preview_cache.py +60 -0
  69. itasc/napari/_spotlight.py +46 -0
  70. itasc/napari/_stage_loader.py +146 -0
  71. itasc/napari/_stage_status.py +110 -0
  72. itasc/napari/_standalone_paths.py +89 -0
  73. itasc/napari/_state.py +146 -0
  74. itasc/napari/_status_rail.py +128 -0
  75. itasc/napari/_track_render.py +114 -0
  76. itasc/napari/_widget_helpers.py +236 -0
  77. itasc/napari/aggregate_widget.py +339 -0
  78. itasc/napari/candidate_gallery_controller.py +285 -0
  79. itasc/napari/cell_workflow_widget.py +1405 -0
  80. itasc/napari/cellpose_segment_track_widget.py +1253 -0
  81. itasc/napari/cellpose_widget.py +1034 -0
  82. itasc/napari/contact_analysis/__init__.py +6 -0
  83. itasc/napari/contact_analysis/curation_controller.py +94 -0
  84. itasc/napari/contact_analysis/plugins/__init__.py +102 -0
  85. itasc/napari/contact_analysis/plugins/catalog_summary.py +56 -0
  86. itasc/napari/contact_analysis/plugins/curation.py +247 -0
  87. itasc/napari/contact_analysis/plugins/visualize_contacts.py +64 -0
  88. itasc/napari/contact_analysis_widget.py +951 -0
  89. itasc/napari/contact_visualization.py +895 -0
  90. itasc/napari/correction/__init__.py +8 -0
  91. itasc/napari/correction/_correction_anchor.py +54 -0
  92. itasc/napari/correction/_correction_candidate_panel.py +259 -0
  93. itasc/napari/correction/_correction_candidates.py +169 -0
  94. itasc/napari/correction/_correction_centroids.py +132 -0
  95. itasc/napari/correction/_correction_commit.py +71 -0
  96. itasc/napari/correction/_correction_events.py +39 -0
  97. itasc/napari/correction/_correction_keymap.py +80 -0
  98. itasc/napari/correction/_correction_layer_lifecycle.py +137 -0
  99. itasc/napari/correction/_correction_layer_loader.py +86 -0
  100. itasc/napari/correction/_correction_navigation.py +97 -0
  101. itasc/napari/correction/_correction_paint.py +46 -0
  102. itasc/napari/correction/_correction_playback.py +68 -0
  103. itasc/napari/correction/_correction_protection.py +44 -0
  104. itasc/napari/correction/_correction_takeover.py +64 -0
  105. itasc/napari/correction/_correction_track_accordion.py +566 -0
  106. itasc/napari/correction/_correction_track_path.py +388 -0
  107. itasc/napari/correction/_correction_ui.py +367 -0
  108. itasc/napari/correction/_correction_ui_nucleus.py +393 -0
  109. itasc/napari/correction/_correction_utils.py +204 -0
  110. itasc/napari/correction/_correction_validation.py +83 -0
  111. itasc/napari/correction/cell_correction_widget.py +1190 -0
  112. itasc/napari/correction/correction_widget.py +1363 -0
  113. itasc/napari/correction/nucleus_correction_widget.py +2185 -0
  114. itasc/napari/divergence_maps_widget.py +795 -0
  115. itasc/napari/lineage_canvas_controller.py +351 -0
  116. itasc/napari/main_widget.py +1184 -0
  117. itasc/napari/nucleus_atom_extraction_widget.py +648 -0
  118. itasc/napari/nucleus_db_browser_widget.py +1442 -0
  119. itasc/napari/nucleus_pipeline_widget.py +579 -0
  120. itasc/napari/nucleus_segmentation_inputs_widget.py +21 -0
  121. itasc/napari/nucleus_tracking_inputs_widget.py +248 -0
  122. itasc/napari/nucleus_workflow_widget.py +963 -0
  123. itasc/napari/track_path_controller.py +387 -0
  124. itasc/napari/ui_gate.py +266 -0
  125. itasc/napari/ui_style.py +503 -0
  126. itasc/napari/validated_overlay_controller.py +254 -0
  127. itasc/napari/widgets.py +616 -0
  128. itasc/napari.yaml +45 -0
  129. itasc/segmentation/__init__.py +60 -0
  130. itasc/segmentation/cell_divergence_segmentation.py +433 -0
  131. itasc/segmentation/cell_label_icm.py +637 -0
  132. itasc/segmentation/contour_filtering.py +128 -0
  133. itasc/segmentation/lineage.py +18 -0
  134. itasc/segmentation/nucleus_segmentation.py +35 -0
  135. itasc/tracking_ultrack/__init__.py +12 -0
  136. itasc/tracking_ultrack/_node_geometry.py +191 -0
  137. itasc/tracking_ultrack/atoms.py +470 -0
  138. itasc/tracking_ultrack/config.py +76 -0
  139. itasc/tracking_ultrack/corrections.py +1213 -0
  140. itasc/tracking_ultrack/db_build.py +492 -0
  141. itasc/tracking_ultrack/db_query.py +952 -0
  142. itasc/tracking_ultrack/export.py +133 -0
  143. itasc/tracking_ultrack/extend.py +243 -0
  144. itasc/tracking_ultrack/ingest.py +83 -0
  145. itasc/tracking_ultrack/linking.py +286 -0
  146. itasc/tracking_ultrack/multi_threshold.py +46 -0
  147. itasc/tracking_ultrack/napari.yaml +10 -0
  148. itasc/tracking_ultrack/reseed.py +456 -0
  149. itasc/tracking_ultrack/retracker.py +153 -0
  150. itasc/tracking_ultrack/scoring.py +74 -0
  151. itasc/tracking_ultrack/seed_prior.py +175 -0
  152. itasc/tracking_ultrack/solve.py +52 -0
  153. itasc/tracking_ultrack/swap_candidate.py +171 -0
  154. itasc/tracking_ultrack/track_quality.py +142 -0
  155. itasc/tracking_ultrack/validation_nodes.py +315 -0
  156. itasc/tracking_ultrack/validation_state.py +430 -0
  157. itasc-0.2.0.dev0.data/data/itasc/napari.yaml +45 -0
  158. itasc-0.2.0.dev0.dist-info/METADATA +186 -0
  159. itasc-0.2.0.dev0.dist-info/RECORD +162 -0
  160. itasc-0.2.0.dev0.dist-info/WHEEL +4 -0
  161. itasc-0.2.0.dev0.dist-info/entry_points.txt +2 -0
  162. itasc-0.2.0.dev0.dist-info/licenses/LICENSE +661 -0
itasc/napari/__init__.py ADDED
@@ -0,0 +1,7 @@
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+ from itasc.napari._napari_compat import patch_napari_layer_delegate
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+
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+ patch_napari_layer_delegate()
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+
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+ from itasc.napari.main_widget import ITASCMainWidget as ITASCWidget # noqa: E402
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+
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+ __all__ = ["ITASCWidget"]