celldetective 1.5.0b6__py3-none-any.whl → 1.5.0b8__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.
- celldetective/_version.py +1 -1
- celldetective/event_detection_models.py +2463 -0
- celldetective/gui/base/channel_norm_generator.py +19 -3
- celldetective/gui/base/figure_canvas.py +1 -1
- celldetective/gui/base_annotator.py +2 -5
- celldetective/gui/event_annotator.py +248 -138
- celldetective/gui/pair_event_annotator.py +146 -20
- celldetective/gui/process_block.py +2 -2
- celldetective/gui/seg_model_loader.py +4 -4
- celldetective/gui/settings/_settings_event_model_training.py +32 -14
- celldetective/gui/settings/_settings_segmentation_model_training.py +5 -5
- celldetective/gui/settings/_settings_signal_annotator.py +0 -19
- celldetective/gui/viewers/base_viewer.py +17 -20
- celldetective/processes/train_signal_model.py +1 -1
- celldetective/processes/unified_process.py +16 -2
- celldetective/scripts/train_signal_model.py +1 -1
- celldetective/signals.py +4 -2426
- celldetective/utils/cellpose_utils/__init__.py +2 -2
- celldetective/utils/event_detection/__init__.py +1 -1
- celldetective/utils/stardist_utils/__init__.py +1 -2
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/METADATA +1 -5
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/RECORD +27 -26
- tests/test_signals.py +4 -4
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/WHEEL +0 -0
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/entry_points.txt +0 -0
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/licenses/LICENSE +0 -0
- {celldetective-1.5.0b6.dist-info → celldetective-1.5.0b8.dist-info}/top_level.txt +0 -0
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@@ -109,7 +109,7 @@ def _prep_cellpose_model(
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except ImportError as e:
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raise RuntimeError(
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"Torch is not installed. Please install it to use this feature.\n"
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"You can install the full package with: pip install celldetective[
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"You can install the full package with: pip install celldetective[all]\n"
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) from e
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if not use_gpu:
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@@ -122,7 +122,7 @@ def _prep_cellpose_model(
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except ImportError as e:
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raise RuntimeError(
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"Cellpose is not installed. Please install it to use this feature.\n"
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"You can install the full package with: pip install celldetective[
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"You can install the full package with: pip install celldetective[all]\n"
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"Or specifically: pip install celldetective[cellpose]"
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) from e
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@@ -48,8 +48,7 @@ def _prep_stardist_model(
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except ImportError as e:
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raise RuntimeError(
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"StarDist is not installed. Please install it to use this feature.\n"
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"You can install the full package with: pip install celldetective[
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"Or specifically: pip install celldetective[stardist]"
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"You can install the full package with: pip install celldetective[all]"
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) from e
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model = StarDist2D(None, name=model_name, basedir=path)
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.4
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Name: celldetective
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Version: 1.5.
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Version: 1.5.0b8
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Summary: description
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Home-page: http://github.com/remyeltorro/celldetective
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Author: Rémy Torro
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@@ -50,10 +50,6 @@ Requires-Dist: natsort
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Provides-Extra: tensorflow
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Requires-Dist: tensorflow~=2.15.0; extra == "tensorflow"
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Requires-Dist: stardist; extra == "tensorflow"
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Provides-Extra: process
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Requires-Dist: cellpose<3; extra == "process"
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Requires-Dist: stardist; extra == "process"
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Requires-Dist: tensorflow~=2.15.0; extra == "process"
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Provides-Extra: all
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Requires-Dist: cellpose<3; extra == "all"
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Requires-Dist: stardist; extra == "all"
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@@ -1,6 +1,7 @@
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celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
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celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
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celldetective/_version.py,sha256=
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celldetective/_version.py,sha256=_aQC8i0kOHSYGEkfpTecn4OzPtL_z-LVXk1dtkjlJtQ,24
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celldetective/event_detection_models.py,sha256=A7ZJFhJwfdhzfxJ-YZIj6IoI9Gc1hyAodFkKt8kNxDk,93549
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celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
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celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
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celldetective/extra_properties.py,sha256=s_2R4_El2p-gQNZ_EpgDxgrN3UnRitN7KDKHhyLuoHc,21681
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@@ -11,7 +12,7 @@ celldetective/neighborhood.py,sha256=Z5wu2nSMvabrQz91oy6DRf2o90LUY0RMXTEwgW7ORAg
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celldetective/preprocessing.py,sha256=tjAMLG4ZMfopMSFulGGjMQox7czEcReV2MzEkWlL2eQ,59948
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celldetective/relative_measurements.py,sha256=j7xIj1FiY3kn5nA_wMqHV3wvjqikjnk99kZ7v9G6I5Q,42928
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celldetective/segmentation.py,sha256=yIFZn0XDaudj9XkSjWW9k6LqZEM-OQdp98ylwQQtlTg,33583
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celldetective/signals.py,sha256=
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celldetective/signals.py,sha256=iLWpFOssWmsaZwHZvKf7bcTdFNqtd7ykaN2jMpzppEY,44653
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celldetective/tracking.py,sha256=iwN6rQ9Bmz20JPrFoewywPBrhD864NUiMaZbIINJVZc,49758
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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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@@ -19,33 +20,33 @@ celldetective/gui/InitWindow.py,sha256=uta0lqFsiwcPz3bh8hz44LrTGhzKWa_SQWbylSBZU
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celldetective/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/gui/about.py,sha256=l9SA7WnQs3ISPvZYAGMmf1A0GRXcinkyGwWJpG8akFQ,1977
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celldetective/gui/analyze_block.py,sha256=R82PVFHXfKn8BvUCpbjDOkLBNF4xRVCzYKFHitjw0kk,4114
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celldetective/gui/base_annotator.py,sha256=
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celldetective/gui/base_annotator.py,sha256=Ipk0yJ8_QyQGE8rcSQti70CcBuySJPjxAOEBtCjNc6c,32548
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celldetective/gui/classifier_widget.py,sha256=uQ9KQmUFp6qWy0Aic-AKB9DkGNpOLxaERtYBSIX9RHw,25424
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celldetective/gui/configure_new_exp.py,sha256=vgT6ozRIGDvT3R0qENlqvDn17BpKnwyJRhRhDS6ax8A,29954
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celldetective/gui/control_panel.py,sha256=dMNzgivt6GdYROPlYpEY5TTNcANenm9ifUI3W3OcpOo,24337
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celldetective/gui/dynamic_progress.py,sha256=wjTmDPy62qssY0zdteP3T9umIGGQk0UvebFIdn54CIc,16676
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celldetective/gui/event_annotator.py,sha256=
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celldetective/gui/event_annotator.py,sha256=JVd64Gch_qzXv29VJGAa2Ytk-WhxifZVgMK-hAxnGu4,41262
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celldetective/gui/generic_signal_plot.py,sha256=D3b6pG1yrSi8C2PPyYzK2yA6711CBBPRp5_OIrjayqs,49348
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celldetective/gui/gui_utils.py,sha256=t6SjEfjcaRH9a0TlbTGEiVRpCgocaCh4lgkIvRgRRwE,33497
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celldetective/gui/interactions_block.py,sha256=34VaHFrdKsq1hYuXrosmpP15JU26dSfbyx4lyt1jxNg,28440
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celldetective/gui/interactive_timeseries_viewer.py,sha256=u_amAhLdEHRpYSRwPDtVm5v-JZIz0ANTcG4YGksX1Vo,16079
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celldetective/gui/json_readers.py,sha256=t5rhtIxACj0pdwLrnPs-QjyhQo3P25UGWGgOCIBhQxs,4572
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celldetective/gui/measure_annotator.py,sha256=ljNbsKmFXQk0R9zEfBZ6XfBHzFmlL7Gt6QyPHyqh08g,38357
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celldetective/gui/pair_event_annotator.py,sha256=
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celldetective/gui/pair_event_annotator.py,sha256=9PT67-8FJxcL7lSDIAZcZmrW75G_R-fpRellMOsgets,128788
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celldetective/gui/plot_measurements.py,sha256=a_Mks-5XUTn2QEYih0PlXGp2lX3C34zuhK9ozzE1guM,56593
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celldetective/gui/plot_signals_ui.py,sha256=9VmA1yaTcNf1jY7drtK41R1q87dhEk7bXBCq_cQ94fs,28133
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celldetective/gui/preprocessing_block.py,sha256=cgUBv-eQBwfidK48-cTWJi0PS62wlXhsNLnsKhy6MQY,14967
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celldetective/gui/process_block.py,sha256=
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celldetective/gui/seg_model_loader.py,sha256=
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celldetective/gui/process_block.py,sha256=KVfXnC55EYGlgKVDXDSMGu_MZbxjbQaQz4Ulyl5iqSE,76881
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celldetective/gui/seg_model_loader.py,sha256=CqcyT1ZeQ27R54RmOHjAt1pfRwjtvS-Psw29PpFsT5A,23549
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celldetective/gui/survival_ui.py,sha256=IwdRm1gRvhkWdMtrQk04OIKKksW3NZSGYtZO_2GptrA,16034
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celldetective/gui/tableUI.py,sha256=kZP2lp9NwHtbWEqIyaDwohX42tRkhI0Hlf_8O5w5BD0,61267
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celldetective/gui/thresholds_gui.py,sha256=w6ke2TyIEi71LxbuFGz0UrwH8h21N_ESU-o6xq_NNKo,33346
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celldetective/gui/workers.py,sha256=WAtVxFEvHApBSAZMVyYsya_DHL_bYo8b57dbgUJQHc4,14890
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celldetective/gui/base/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/gui/base/channel_norm_generator.py,sha256=
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celldetective/gui/base/channel_norm_generator.py,sha256=HJ57wBMdBIvca92V477T-aPuxvvC2aC5BDMssKSQKCQ,14592
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celldetective/gui/base/components.py,sha256=jNUsCU_QE7QUFR0_xEvEPFEBYolMJt7YXGUKMjF7uOE,8155
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celldetective/gui/base/feature_choice.py,sha256=n1T2fPoNLiTDS_6fa_GuGReDhBW11HdUrKy2RywotF8,2800
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celldetective/gui/base/figure_canvas.py,sha256=
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celldetective/gui/base/figure_canvas.py,sha256=mSiIYvEfz7MYMgdPDf6RKSMpKN8FkeZL7lugDNnDpnM,2245
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celldetective/gui/base/list_widget.py,sha256=_WU3ZRU7UcJZIxm8qx_5HF7IK7dUu8IU1FY2AaW_qgo,4694
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celldetective/gui/base/styles.py,sha256=3Kz1eXw6OLr90wtErhK0KPJyJbyhAlqkniqm0JNGwFc,7407
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celldetective/gui/base/utils.py,sha256=KojauRKGM9XKNhaWn211p6mJNZWIHLH75yeLpDd7pvA,1103
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celldetective/gui/settings/_event_detection_model_params.py,sha256=f3jkh6f3oE-_5pCaf44yKSA-hs9YoSZoFQU7v9pJLKI,3683
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celldetective/gui/settings/_segmentation_model_params.py,sha256=YooEXRlkmOlHCyReiFynagrxBQn2y-dTB0FgowqZno0,6471
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celldetective/gui/settings/_settings_base.py,sha256=_Yfq6vLkwm4FW5n0-SjVQjdhfL3hR5pUGBc0ttq_YXE,2576
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celldetective/gui/settings/_settings_event_model_training.py,sha256=
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celldetective/gui/settings/_settings_event_model_training.py,sha256=hpA5DTCPIMe1aVZDqO_6FudEP3a-IO6SVPfys-gdfXY,30346
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celldetective/gui/settings/_settings_measurements.py,sha256=nrVR1dG3B7iyJayRql1yierhKvgXZiu6qVtfkxI1ABA,47947
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celldetective/gui/settings/_settings_neighborhood.py,sha256=ws6H99bKU4NYd2IYyaJj7g9-MScr5W6UB2raP88ytfE,23767
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celldetective/gui/settings/_settings_segmentation.py,sha256=6DihD1mk-dN4Sstdth1iJ-0HR34rTVlTHP-pXUh_rY0,1901
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celldetective/gui/settings/_settings_segmentation_model_training.py,sha256=
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celldetective/gui/settings/_settings_signal_annotator.py,sha256=
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celldetective/gui/settings/_settings_segmentation_model_training.py,sha256=g-y5ZTZDwGaaevm6eI3XK_QU8PbZOY0jBdFyb1kAsqA,30440
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celldetective/gui/settings/_settings_signal_annotator.py,sha256=9LRAgOn3qcbHctAXpTDlySGSCm6kMX2Qwqpeuwz384E,11601
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celldetective/gui/settings/_settings_tracking.py,sha256=5ZxJp3o3stD2NKdhqZofIgsUNp73oAN_pIi_bDFAd0Y,53293
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celldetective/gui/settings/_stardist_model_params.py,sha256=dEKhaLcJ4r8VxgBU2DI-hcTaTk5S181O-_CN0j7JSgE,4020
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celldetective/gui/table_ops/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/gui/table_ops/_query_table.py,sha256=K-XHSZ1I4v2wwqWjyQAgyFRZJbem3CmTfHmO0vijh9g,1345
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celldetective/gui/table_ops/_rename_col.py,sha256=UAgDSpXJo_h4pLJpHaNc2w2VhbaW4D2JZTgJ3cYC4-g,1457
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celldetective/gui/viewers/base_viewer.py,sha256=
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celldetective/gui/viewers/base_viewer.py,sha256=Wn4na79xRL1R6PSXIoE_UabxJNtNQ-Y5l9Q-HSb508c,32013
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celldetective/gui/viewers/channel_offset_viewer.py,sha256=cywBkxyMPyKIuwZTGA03DBSS4a-H1SAohMJYOPISLEE,16289
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celldetective/gui/viewers/contour_viewer.py,sha256=riHj03LKXLoa-Ys2o2EhCE5nULfcHMohx9LFoXbI6zU,14720
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celldetective/gui/viewers/size_viewer.py,sha256=uXITjaxg5dhQ09Q6TNUxwLxi-ZglyGFcxEH1RtGIZWw,6020
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celldetective/processes/segment_cells.py,sha256=klGl5y3tHbLbQFNAQz0PV1FspmiPC-GHVGWYLgyLqwc,26500
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celldetective/processes/track_cells.py,sha256=ndKZpVXonnooOVnHK5AVED5i_i2bZ4FefTt1_dEZS48,15188
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celldetective/processes/train_segmentation_model.py,sha256=j1aPgR4CzF2OR-9njriNmUStVViiWaiicQA9YWRWOTo,25411
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celldetective/processes/train_signal_model.py,sha256=
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celldetective/processes/unified_process.py,sha256=
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celldetective/processes/train_signal_model.py,sha256=ntA3xeQtWkiNa2B48uj0MG3duZNximEgRPNkGe9A8qY,9513
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celldetective/processes/unified_process.py,sha256=xvNrYtZaRgpjEWzrPSYoY6dmqJbC81udDojkHuT4iTc,12251
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celldetective/regionprops/__init__.py,sha256=ohe9vC7j4lnpKnGXidVo1PVfoQfC8TqCuHTNo8rXmdg,44
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celldetective/regionprops/_regionprops.py,sha256=spq_Mb43HjHiKqot7yjLJl_jrMTNfIP8NLrPnCEm8Nc,13306
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celldetective/regionprops/props.json,sha256=sCwACmbh0n-JAw9eve9yV85REukoMBJLsRjxCwTRMm8,2424
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celldetective/scripts/segment_cells_thresholds.py,sha256=eeVr4mH_OMPogtp_8VaH7B7wfDVZ1G7vUcqIws7HX70,5557
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celldetective/scripts/track_cells.py,sha256=h6ZhkeM73w_ziVjH7jJBejhZYZhf_Vpeg-9G6xQtmDE,9670
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celldetective/scripts/train_segmentation_model.py,sha256=IKZGXf8i74xrc-wQ_oGgdE30FSO8eh2dhZDZfnBjkEk,12740
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celldetective/scripts/train_signal_model.py,sha256=
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celldetective/scripts/train_signal_model.py,sha256=RFSnwdj3yBhqs-4wbF83ezsuZEIIZhdRFrMlUwtVHV0,3726
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celldetective/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/utils/color_mappings.py,sha256=yarqOTSrTsnOPPiPrrN_vLoPCbgWqF3wjqFwpbp-KsU,1007
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celldetective/utils/data_cleaning.py,sha256=K-2gScxLreX7QkrM0h3dZdP0IsmvCzcxNh2-M9PALZY,22025
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@@ -161,12 +162,12 @@ celldetective/utils/parsing.py,sha256=1zpIH9tyULCRmO5Kwzy6yA01fqm5uE_mZKYtondy-V
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celldetective/utils/resources.py,sha256=3Fz_W0NYWl_Ixc2AjEmkOv5f7ejXerCLJ2z1iWhGWUI,1153
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celldetective/utils/stats.py,sha256=4TVHRqi38Y0sed-izaMI51sMP0fd5tC5M68EYyfJjkE,3636
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celldetective/utils/types.py,sha256=lRfWSMVzTkxgoctGGp0NqD551akuxu0ygna7zVGonTg,397
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celldetective/utils/cellpose_utils/__init__.py,sha256=
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celldetective/utils/event_detection/__init__.py,sha256=
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celldetective/utils/cellpose_utils/__init__.py,sha256=g41EiR6p29bHkXQN-SFHymoeaoTEfuozEFSGMuTd30Q,5991
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celldetective/utils/event_detection/__init__.py,sha256=GvsdyQLMTXJj1S_FfRXjrpOxEGODvvktzaaz6cURj-c,338
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celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
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celldetective/utils/stardist_utils/__init__.py,sha256=
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celldetective-1.5.
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celldetective/utils/stardist_utils/__init__.py,sha256=SY2kxFNXSRjXN4ncs3heDdXT3UNk8M3dELJQySysAf4,4231
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celldetective-1.5.0b8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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tests/test_cellpose_fallback.py,sha256=BJZTDFF8sFR1x7rDbvZQ2RQOB1OP6wuFBRfc8zbl5zw,3513
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tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
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@@ -178,7 +179,7 @@ tests/test_notebooks.py,sha256=7HVmYiytsz0QIJ11iRkGGs4_hzNjofXAUs_OZou3Gm0,301
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tests/test_partial_install.py,sha256=G69-GNcJ9YNgs6K2bVTEZO0Jpb14xMRQWTm8A6VuIco,2841
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tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
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tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
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tests/test_signals.py,sha256=
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tests/test_signals.py,sha256=DWDRGpw_k2VE5pWnqJexsa313YEi8c2KzC51DFzykco,3641
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tests/test_tracking.py,sha256=_YLjwQ3EChQssoHDfEnUJ7fI1yC5KEcJsFnAVR64L70,18909
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tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
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tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -186,8 +187,8 @@ tests/gui/test_enhancements.py,sha256=3x9au_rkQtMZ94DRj3OaEHKPr511RrWqBAUAcNQn1y
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tests/gui/test_measure_annotator_bugfix.py,sha256=tPfgWNKC0UkvrVssSrUcVDC1qgpzx6l2yCqvKtKYkM4,4544
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tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
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tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
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celldetective-1.5.
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celldetective-1.5.0b8.dist-info/METADATA,sha256=hUsQY-GrHvD70Htr2XKBXkJlHwv3B4dBe5hQ9sFQonw,11523
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celldetective-1.5.0b8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
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celldetective-1.5.0b8.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
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celldetective-1.5.0b8.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
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celldetective-1.5.0b8.dist-info/RECORD,,
|
tests/test_signals.py
CHANGED
|
@@ -73,9 +73,9 @@ class TestCreateSignalModel(unittest.TestCase):
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73
73
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74
74
|
def test_create_model(self):
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75
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from celldetective.
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from celldetective.event_detection_models import SignalDetectionModel
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77
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78
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+
model = SignalDetectionModel(
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79
79
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channel_option=["signal"],
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80
80
|
model_signal_length=128,
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81
81
|
n_channels=1,
|
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@@ -92,9 +92,9 @@ class TestTrainSignalModel(unittest.TestCase):
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92
92
|
@classmethod
|
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93
93
|
def setUpClass(self):
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94
94
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95
|
-
from celldetective.
|
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95
|
+
from celldetective.event_detection_models import SignalDetectionModel
|
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96
96
|
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|
97
|
-
|
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97
|
+
self.trajectories = generate_fake_signal_data(300)
|
|
98
98
|
if not os.path.exists('temp'):
|
|
99
99
|
os.mkdir('temp')
|
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100
100
|
export_set(self.trajectories, name='set.npy', output_folder='temp')
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File without changes
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File without changes
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File without changes
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File without changes
|