celldetective 1.1.1.post3__py3-none-any.whl → 1.2.0__py3-none-any.whl

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 (42) hide show
  1. celldetective/__init__.py +2 -1
  2. celldetective/__main__.py +17 -0
  3. celldetective/extra_properties.py +62 -34
  4. celldetective/gui/__init__.py +1 -0
  5. celldetective/gui/analyze_block.py +2 -1
  6. celldetective/gui/classifier_widget.py +18 -10
  7. celldetective/gui/control_panel.py +57 -6
  8. celldetective/gui/layouts.py +14 -11
  9. celldetective/gui/neighborhood_options.py +21 -13
  10. celldetective/gui/plot_signals_ui.py +39 -11
  11. celldetective/gui/process_block.py +413 -95
  12. celldetective/gui/retrain_segmentation_model_options.py +17 -4
  13. celldetective/gui/retrain_signal_model_options.py +106 -6
  14. celldetective/gui/signal_annotator.py +110 -30
  15. celldetective/gui/signal_annotator2.py +2708 -0
  16. celldetective/gui/signal_annotator_options.py +3 -1
  17. celldetective/gui/survival_ui.py +15 -6
  18. celldetective/gui/tableUI.py +248 -43
  19. celldetective/io.py +598 -416
  20. celldetective/measure.py +919 -969
  21. celldetective/models/pair_signal_detection/blank +0 -0
  22. celldetective/neighborhood.py +482 -340
  23. celldetective/preprocessing.py +81 -61
  24. celldetective/relative_measurements.py +648 -0
  25. celldetective/scripts/analyze_signals.py +1 -1
  26. celldetective/scripts/measure_cells.py +28 -8
  27. celldetective/scripts/measure_relative.py +103 -0
  28. celldetective/scripts/segment_cells.py +5 -5
  29. celldetective/scripts/track_cells.py +4 -1
  30. celldetective/scripts/train_segmentation_model.py +23 -18
  31. celldetective/scripts/train_signal_model.py +33 -0
  32. celldetective/segmentation.py +67 -29
  33. celldetective/signals.py +402 -8
  34. celldetective/tracking.py +8 -2
  35. celldetective/utils.py +144 -12
  36. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/METADATA +8 -8
  37. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/RECORD +42 -38
  38. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/WHEEL +1 -1
  39. tests/test_segmentation.py +1 -1
  40. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/LICENSE +0 -0
  41. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/entry_points.txt +0 -0
  42. {celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/top_level.txt +0 -0
{celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: celldetective
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- Version: 1.1.1.post3
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+ Version: 1.2.0
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  Summary: description
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  Home-page: http://github.com/remyeltorro/celldetective
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  Author: Rémy Torro
@@ -12,14 +12,14 @@ Requires-Dist: wheel
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  Requires-Dist: nbsphinx
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  Requires-Dist: nbsphinx-link
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  Requires-Dist: sphinx-rtd-theme
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- Requires-Dist: sphinx ==5.0.2
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- Requires-Dist: jinja2 <3.1
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+ Requires-Dist: sphinx==5.0.2
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+ Requires-Dist: jinja2<3.1
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  Requires-Dist: ipykernel
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  Requires-Dist: stardist
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- Requires-Dist: cellpose <3
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+ Requires-Dist: cellpose<3
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  Requires-Dist: scikit-learn
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  Requires-Dist: btrack
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- Requires-Dist: tensorflow <=2.12.1
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+ Requires-Dist: tensorflow<=2.12.1
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  Requires-Dist: napari
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  Requires-Dist: tqdm
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  Requires-Dist: mahotas
@@ -29,11 +29,11 @@ Requires-Dist: lifelines
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  Requires-Dist: setuptools
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  Requires-Dist: scipy
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  Requires-Dist: seaborn
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- Requires-Dist: opencv-python-headless ==4.7.0.72
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+ Requires-Dist: opencv-python-headless==4.7.0.72
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  Requires-Dist: liblapack
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  Requires-Dist: gputools
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- Requires-Dist: lmfit ~=1.2.2
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- Requires-Dist: superqt[cmap] >=0.6.1
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+ Requires-Dist: lmfit~=1.2.2
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+ Requires-Dist: superqt[cmap]>=0.6.1
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  Requires-Dist: matplotlib-scalebar
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  # Celldetective
{celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/RECORD RENAMED
@@ -1,41 +1,43 @@
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- celldetective/__init__.py,sha256=FEZpJKcskBH2IginYzeqPWoR1lVGuyYCXhv7Hnlkoo8,49
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- celldetective/__main__.py,sha256=XFAkq_2cBEkWAVXDGSNFagoQBglyl0Y-GOO3KFc8UqM,13888
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+ celldetective/__init__.py,sha256=PH25g2_AZt7N5Jg1KB3YT9wFvfMr9lIb2WxYzmDqlX4,105
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+ celldetective/__main__.py,sha256=TQzL_FLAeEF1YIyRZXMiai40xXy21roPPV23ig4jwG0,14494
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  celldetective/events.py,sha256=s2pWnR3Z1fcB15sET5WsF2Pi6v6qv16hks_m3WiklNs,3658
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- celldetective/extra_properties.py,sha256=ZdWV046RR8jrQPYxLSVVb1cXkWYxfrrLj2tXfc358cU,4179
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+ celldetective/extra_properties.py,sha256=8DkxTvVs7gASsnnGurVZ3_zt6uR0pvvJhBKO2LC6hGk,5118
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  celldetective/filters.py,sha256=b0qKwHor1fvNA_dHovP17nQz8EsW5YlyhT2TJnayn08,3615
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- celldetective/io.py,sha256=ptaX4GadWuf0zOQ3ZWSLCzihEID-YAalPfxW1nqvgIU,80889
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- celldetective/measure.py,sha256=HDQZfSRx3daOCV5Snu1paYU5JYkwu8engO2qZqhTAUo,48089
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- celldetective/neighborhood.py,sha256=QCuhesMHGyr3c3ys9wWcNR1HM6CHdHe51R8upoolgPw,49514
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- celldetective/preprocessing.py,sha256=dpor6ry6RChzd-rdH98SQc0zvLZv95YZB5KIGym1mEY,37388
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- celldetective/segmentation.py,sha256=Hu4-lOJ4UhPw2o0Hn_NPOCHsa6Iwsw5A3PR6X3Tzbb8,29196
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- celldetective/signals.py,sha256=P7eiDZGGIAYCFBKjGCBi8gMBvJYywxlxZNzyGgw-26Y,102783
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- celldetective/tracking.py,sha256=A0mhdF4uq4m8OX1-rhtuhG69rlh_6Pb34Aebu7hIeKM,37601
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- celldetective/utils.py,sha256=f0VvWv5ZgndZiWsFFDs0O6tJlRXkRtPW0xEKM_R90yo,77581
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+ celldetective/io.py,sha256=Y6YJQr4rmQYH3wrBGD9IfHJKqH_AbsJ8Qg99b9c2KuY,86058
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+ celldetective/measure.py,sha256=kTKoGeCEYvACOf-pg11NPfyByogBMIC91lIZA-qZk1E,41344
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+ celldetective/neighborhood.py,sha256=2SV0upNfaScp1Gg9JBiDho3AozyTtC0_SXPyHmnm6Ok,52994
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+ celldetective/preprocessing.py,sha256=TKOJTc5o4rSgXqtYeZz-0ox062dD494VMiie3L-9aV4,38305
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+ celldetective/relative_measurements.py,sha256=WRTUewDZ7JKSjPZUZVQ5hUusevAYsFGHjkzCZ3yKHzg,25056
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+ celldetective/segmentation.py,sha256=L2VJKmOewC1CNZPiWCO6yUfxt78u9k1NHPr2qTyTaBM,30458
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+ celldetective/signals.py,sha256=tnqEBb0LkdUHqKQwnNBct7J5zQ_UWR8tVP70UFh22PQ,120176
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+ celldetective/tracking.py,sha256=k5CtlLqH8WjTwAu7ELwBd9VUuiVPjaNxL5h07KKgjEQ,37860
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+ celldetective/utils.py,sha256=C-hZnd09qvvdoTAwj-sw4e6Gq25QyY1mBR6Ydchwdv8,82442
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  celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- celldetective/gui/__init__.py,sha256=y2dvrUdJi17QMgPjl8WN3XFHYzJpu2ul4_8y7MQV1Bk,941
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+ celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc,989
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  celldetective/gui/about.py,sha256=i-y54Opb10pKTVNUEcJC-D6Cbiqud2EJ3ZLayXqhdqc,1715
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- celldetective/gui/analyze_block.py,sha256=WD3JQQylx_dVozFCvNqrOyR6LcNHV7R1_gGh7XqOVeI,25423
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+ celldetective/gui/analyze_block.py,sha256=vF3ORldZBZHnXUHCj4PeI6KXJ3skY0qV28LxuazGdmk,25429
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  celldetective/gui/btrack_options.py,sha256=eQEf63yTUsPCN-d1LqgAMmUQpfv2FH85FqnOSaR-9Q8,35575
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- celldetective/gui/classifier_widget.py,sha256=52a3kOfU3uMEzUYMIOHGqiy-Q5itMEvcG-3JYrO34I8,16918
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+ celldetective/gui/classifier_widget.py,sha256=cDMdg8XjT_YG08hmXqqJk2X_yLArkupBMvxkhEya1d8,17271
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  celldetective/gui/configure_new_exp.py,sha256=ANJ-Zn4sjBphtj_aoJu6m1PFEKyv9gxeh9XqS6xOGjk,18969
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- celldetective/gui/control_panel.py,sha256=wcDqe4XaDJRMmPmWKJpxd0D9V4_DrdRGnEH6D7B_IK0,17557
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+ celldetective/gui/control_panel.py,sha256=LNWixLPyR3wHb-fq-RWdRir-E1R3eLkxi3uBTDsm0WM,19845
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  celldetective/gui/gui_utils.py,sha256=PidFfdc8XASeIzZO5pfKgwqe4vROG7-KpYMcBZ42jdw,22673
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  celldetective/gui/json_readers.py,sha256=fTrNrlxv9NCae8ZJexBEHxI3yCLRqt6F0Yo1OeDycfA,3686
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- celldetective/gui/layouts.py,sha256=sHTWXsKdRoHYYrPELEW7djNetevcQ-RKW9aQQ2FvWoc,37644
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+ celldetective/gui/layouts.py,sha256=Qrs_5ugNaLWy6l72zzPegrV8idfNWEnNNA2ltH1DC_M,37768
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  celldetective/gui/measurement_options.py,sha256=i0CdAfupHJAqhOT7RsufEK919sAzQnFBkQO4IAMYZL0,47704
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- celldetective/gui/neighborhood_options.py,sha256=sdKxVRliZtuKSpcPfnFxqkW4V8rN2tzjhDxOPVmElyE,20191
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+ celldetective/gui/neighborhood_options.py,sha256=GCAAtBJb2aFQVcJUYGZAl-M6uY0UFt6IjbbIU5cwg04,20462
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  celldetective/gui/plot_measurements.py,sha256=xUoGxV6uXcen-t4yWtAmcGTUayICI-FxTVKPrWMNlfg,51799
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- celldetective/gui/plot_signals_ui.py,sha256=TwWU2u3_mkRNsM8er0kI_kwr5EoZ29YEzlr0cQzyW4A,43732
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- celldetective/gui/process_block.py,sha256=7n9glZ1ojEi1bObqwIj4giNhrteT69X1EPMQ1hK63aU,53565
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- celldetective/gui/retrain_segmentation_model_options.py,sha256=VixtKZTjoJFJy8X6aDbAf0zgK46aXj3I6oPP_92yqhA,22457
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- celldetective/gui/retrain_signal_model_options.py,sha256=gdK1ITuaTPNvnQWXYuUBcP_pH5cvaEEns5XejjTi_Eo,17854
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+ celldetective/gui/plot_signals_ui.py,sha256=96iMud47aDGErVht_kQdUS9f0uQAIYeAg3OaGk4XBVw,44551
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+ celldetective/gui/process_block.py,sha256=oT0bmZqqOjSZvdthqBKoy9MejButRrqdmZQRnUWfJy8,67366
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+ celldetective/gui/retrain_segmentation_model_options.py,sha256=8mZpW5fb5ts6HjKPzRpG0_tIOQgtsQth_h7ruLdKVss,22954
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+ celldetective/gui/retrain_signal_model_options.py,sha256=6OqiulBk4Rn709jyENl5rHKpOHJoUsEzslxSxhRugHw,22478
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  celldetective/gui/seg_model_loader.py,sha256=uKp8oab-4QdTGqb-tb6bOD-FLD_154GOvgWFYz97BwY,17350
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- celldetective/gui/signal_annotator.py,sha256=4ymMpo_GjSBsJSRkyNKrWRLy0EFXHINbFtp9ykDqfGE,84864
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- celldetective/gui/signal_annotator_options.py,sha256=-Q7f8eCwniqbgLJqMCa91Wc-V3VHAZidwt7LPd4Z5yU,10879
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+ celldetective/gui/signal_annotator.py,sha256=CjVqWq6WTKdMkeVT4s5yRu1Vh9QgONxxbXSVbs8_XIk,87534
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+ celldetective/gui/signal_annotator2.py,sha256=-LW6rgmzYcnNvfz1MGBGOJb-aPpnI8tf9JDL5BFb52E,109578
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+ celldetective/gui/signal_annotator_options.py,sha256=ztFFgA70SJ0QkntxYGsgDNCvSuSR5GjF7_J6pYVYc1g,11020
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  celldetective/gui/styles.py,sha256=Vw4wr6MQ4iBwhOY-ZWAxFDZZ3CNohmEnuPPazwhJaho,4129
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- celldetective/gui/survival_ui.py,sha256=2JGLC5m6D_gVLwnBAM7uEvuCKw1Cli8nM9i5s7TIpGg,33612
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- celldetective/gui/tableUI.py,sha256=7QSvkvVpglcluLxqhKjehmYDwHoyZs0R7uLcJK_9fhs,34268
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+ celldetective/gui/survival_ui.py,sha256=sWY5rsxLaNHgfUCB0fphBM2c8J4LLY9q5cdSxF1aq1Q,33792
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+ celldetective/gui/tableUI.py,sha256=c0svHoiLNyFlNXcAnXYyqSqBXCR-V6RCl-26HBWIuaQ,42001
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  celldetective/gui/thresholds_gui.py,sha256=b8SkG4DlfxBRjacKTe1NSNkq7rJm8lnSLifH-mg846k,49529
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  celldetective/gui/viewers.py,sha256=buBholjAieaVVb6YinVhxPshEHxBEU3er_N0UrkwAew,27734
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  celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
@@ -48,6 +50,7 @@ celldetective/icons/survival2.png,sha256=8zsualD7d9VPAecoFA4Om9TFARErqpJzMg6U7XA
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  celldetective/links/zenodo.json,sha256=7WKRuZY7MHTR-IChWBbU0i47H_479NtlxsCGaJn9-xM,22728
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+ celldetective/models/pair_signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  celldetective/models/segmentation_effectors/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  celldetective/models/segmentation_effectors/primNK_cfse/config_input.json,sha256=gwEGP5wc6iVcwLrR5IbEb-9lTbdQuPyLLFYXh00374U,509
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  celldetective/models/segmentation_effectors/primNK_cfse/cp-cfse-transfer,sha256=ps4BAzGxr2i2R0uBGJqfF9wjg5bIeSeBGQb0YcUChhY,26559970
@@ -58,13 +61,14 @@ celldetective/models/signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
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- celldetective/scripts/analyze_signals.py,sha256=23TXGNw-j5xT3ss4mXlnKdBgFLnQ50JUEQOC6_H7Q_0,2203
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- celldetective/scripts/measure_cells.py,sha256=4uRG6Dg0WsO-N8ZaBJ4loWOvX6FdHaCblIFXq6Dtirc,11000
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- celldetective/scripts/segment_cells.py,sha256=55hM3JbMoW5TB43uENgtvADL8BziI17B3GjG4axsj6s,8291
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+ celldetective/scripts/analyze_signals.py,sha256=c_vdd6Z0yAcuNAQJioVH5k6WmOnQBuvRqdWkn6fnCjg,2204
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+ celldetective/scripts/measure_cells.py,sha256=ex9fOcc8CP7RTVBbSyNHX5yHozhhl1XhTmHJXvtIr1Y,11870
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+ celldetective/scripts/measure_relative.py,sha256=lGW3zxtXcr4jEPMMkhLbc--OE6vE5GGlLnxa9ma7yfY,4296
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+ celldetective/scripts/segment_cells.py,sha256=YtTVPjaaLuIqBaV3hlpa__fMeDB3trTPOFJRfEl0jQs,8231
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- celldetective/scripts/track_cells.py,sha256=AaNiYEW4osYKKR2kbdVLOUnQEBbcZIA-D0mkhcxPWTY,7985
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- celldetective/scripts/train_segmentation_model.py,sha256=rw5LD70PrE_SCBvaFt0ri1uSa-YI5DM5exH_BGVlw5Y,8515
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- celldetective/scripts/train_signal_model.py,sha256=9-dmPCLKJ9ypjsV9AwFd-Sb6B6YaHS0QGT218H5hUPo,1861
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+ celldetective/scripts/track_cells.py,sha256=qATUotwsFrINe_uBMGlcCZbFU0iT1J9K8bEZ3TVouIg,8173
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+ celldetective/scripts/train_segmentation_model.py,sha256=Fm-46uhn5zd_1iwRiunBq_ziqiO4Fv-bzS5OgS0B_2c,9284
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+ celldetective/scripts/train_signal_model.py,sha256=LNLIViFEMzyDZvbdfU2L1p90uu2Bha5FLH2qCKSX424,3234
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@@ -72,13 +76,13 @@ tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
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- tests/test_segmentation.py,sha256=-3b7o_fUVMYxfVwX5VHFqRF0dDXObSTtylf5XQGcq1A,3493
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+ tests/test_segmentation.py,sha256=_HB8CCq-Ci6amf0xAmDIUuwtBUU_EGpgqLvcvSHrGug,3427
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- celldetective-1.1.1.post3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
80
- celldetective-1.1.1.post3.dist-info/METADATA,sha256=r2-IaTUiO4VxRyIFdQJbsYx_MJltOPt76Emkf8XqAtk,12418
81
- celldetective-1.1.1.post3.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
82
- celldetective-1.1.1.post3.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
83
- celldetective-1.1.1.post3.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
84
- celldetective-1.1.1.post3.dist-info/RECORD,,
83
+ celldetective-1.2.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
84
+ celldetective-1.2.0.dist-info/METADATA,sha256=hFfaLqmAoHCysOuQXDEC7QT7rjkTZHP1_OPuV2INxrY,12405
85
+ celldetective-1.2.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
86
+ celldetective-1.2.0.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
87
+ celldetective-1.2.0.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
88
+ celldetective-1.2.0.dist-info/RECORD,,
{celldetective-1.1.1.post3.dist-info → celldetective-1.2.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (70.2.0)
2
+ Generator: setuptools (72.1.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5
 
tests/test_segmentation.py CHANGED
@@ -44,7 +44,7 @@ class TestDLMCF7Segmentation(unittest.TestCase):
44
44
  def test_correct_segmentation_with_transferred_model(self):
45
45
 
46
46
  labels = segment(self.stack, "MCF7_h_versatile", channels=self.channels, spatial_calibration=self.spatial_calibration, view_on_napari=False,
47
- use_gpu=True, time_flat_normalization=False, time_flat_percentiles=(0.0,99.99))
47
+ use_gpu=True)
48
48
  np.testing.assert_array_equal(labels[0], labels[1])
49
49
 
50
50
  self.binary_label_true = self.label_true.copy().astype(float)