celldetective 1.4.0__py3-none-any.whl → 1.4.1.post1__py3-none-any.whl

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Files changed (78) hide show
  1. celldetective/_version.py +1 -1
  2. celldetective/exceptions.py +11 -0
  3. celldetective/filters.py +7 -1
  4. celldetective/gui/InitWindow.py +4 -1
  5. celldetective/gui/__init__.py +2 -9
  6. celldetective/gui/about.py +2 -2
  7. celldetective/gui/base_annotator.py +786 -0
  8. celldetective/gui/classifier_widget.py +18 -13
  9. celldetective/gui/configure_new_exp.py +51 -30
  10. celldetective/gui/control_panel.py +10 -7
  11. celldetective/gui/{signal_annotator.py → event_annotator.py} +473 -1437
  12. celldetective/gui/generic_signal_plot.py +2 -1
  13. celldetective/gui/gui_utils.py +5 -2
  14. celldetective/gui/help/neighborhood.json +2 -2
  15. celldetective/gui/layouts.py +21 -11
  16. celldetective/gui/{signal_annotator2.py → pair_event_annotator.py} +3 -1
  17. celldetective/gui/process_block.py +129 -91
  18. celldetective/gui/processes/downloader.py +37 -34
  19. celldetective/gui/processes/measure_cells.py +14 -8
  20. celldetective/gui/processes/segment_cells.py +438 -314
  21. celldetective/gui/processes/track_cells.py +12 -13
  22. celldetective/gui/settings/__init__.py +7 -0
  23. celldetective/gui/settings/_settings_base.py +70 -0
  24. celldetective/gui/{retrain_signal_model_options.py → settings/_settings_event_model_training.py} +35 -91
  25. celldetective/gui/{measurement_options.py → settings/_settings_measurements.py} +28 -81
  26. celldetective/gui/{neighborhood_options.py → settings/_settings_neighborhood.py} +1 -1
  27. celldetective/gui/settings/_settings_segmentation.py +49 -0
  28. celldetective/gui/{retrain_segmentation_model_options.py → settings/_settings_segmentation_model_training.py} +33 -79
  29. celldetective/gui/{signal_annotator_options.py → settings/_settings_signal_annotator.py} +73 -95
  30. celldetective/gui/{btrack_options.py → settings/_settings_tracking.py} +64 -87
  31. celldetective/gui/styles.py +2 -1
  32. celldetective/gui/survival_ui.py +1 -1
  33. celldetective/gui/tableUI.py +25 -0
  34. celldetective/gui/table_ops/__init__.py +0 -0
  35. celldetective/gui/table_ops/merge_groups.py +118 -0
  36. celldetective/gui/viewers.py +3 -5
  37. celldetective/gui/workers.py +0 -2
  38. celldetective/io.py +98 -55
  39. celldetective/links/zenodo.json +145 -144
  40. celldetective/measure.py +31 -26
  41. celldetective/preprocessing.py +34 -21
  42. celldetective/regionprops/_regionprops.py +16 -5
  43. celldetective/scripts/measure_cells.py +5 -5
  44. celldetective/scripts/measure_relative.py +16 -11
  45. celldetective/scripts/segment_cells.py +4 -4
  46. celldetective/scripts/segment_cells_thresholds.py +3 -3
  47. celldetective/scripts/track_cells.py +7 -7
  48. celldetective/scripts/train_segmentation_model.py +10 -1
  49. celldetective/tracking.py +10 -4
  50. celldetective/utils.py +59 -58
  51. {celldetective-1.4.0.dist-info → celldetective-1.4.1.post1.dist-info}/METADATA +1 -1
  52. celldetective-1.4.1.post1.dist-info/RECORD +123 -0
  53. tests/gui/__init__.py +0 -0
  54. tests/gui/test_new_project.py +228 -0
  55. tests/{test_qt.py → gui/test_project.py} +22 -26
  56. tests/test_preprocessing.py +2 -2
  57. celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json +0 -79
  58. celldetective/models/segmentation_effectors/ricm_bf_all_last/ricm_bf_all_last +0 -0
  59. celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json +0 -37
  60. celldetective/models/segmentation_effectors/test-transfer/config_input.json +0 -39
  61. celldetective/models/segmentation_effectors/test-transfer/test-transfer +0 -0
  62. celldetective/models/signal_detection/NucCond/classification_loss.png +0 -0
  63. celldetective/models/signal_detection/NucCond/classifier.h5 +0 -0
  64. celldetective/models/signal_detection/NucCond/config_input.json +0 -1
  65. celldetective/models/signal_detection/NucCond/log_classifier.csv +0 -126
  66. celldetective/models/signal_detection/NucCond/log_regressor.csv +0 -282
  67. celldetective/models/signal_detection/NucCond/regression_loss.png +0 -0
  68. celldetective/models/signal_detection/NucCond/regressor.h5 +0 -0
  69. celldetective/models/signal_detection/NucCond/scores.npy +0 -0
  70. celldetective/models/signal_detection/NucCond/test_confusion_matrix.png +0 -0
  71. celldetective/models/signal_detection/NucCond/test_regression.png +0 -0
  72. celldetective/models/signal_detection/NucCond/validation_confusion_matrix.png +0 -0
  73. celldetective/models/signal_detection/NucCond/validation_regression.png +0 -0
  74. celldetective-1.4.0.dist-info/RECORD +0 -131
  75. {celldetective-1.4.0.dist-info → celldetective-1.4.1.post1.dist-info}/WHEEL +0 -0
  76. {celldetective-1.4.0.dist-info → celldetective-1.4.1.post1.dist-info}/entry_points.txt +0 -0
  77. {celldetective-1.4.0.dist-info → celldetective-1.4.1.post1.dist-info}/licenses/LICENSE +0 -0
  78. {celldetective-1.4.0.dist-info → celldetective-1.4.1.post1.dist-info}/top_level.txt +0 -0
celldetective/gui/processes/measure_cells.py CHANGED
@@ -6,7 +6,7 @@ import json
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  from pathlib import Path, PurePath
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  from celldetective.io import auto_load_number_of_frames, load_frames, locate_labels
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- from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel
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+ from celldetective.utils import extract_experiment_channels, config_section_to_dict, _get_img_num_per_channel
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  from celldetective.utils import remove_trajectory_measurements, _extract_coordinates_from_features, _remove_invalid_cols
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  from celldetective.measure import drop_tonal_features, measure_features, measure_isotropic_intensity, measure_radial_distance_to_center, center_of_mass_to_abs_coordinates
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@@ -17,9 +17,14 @@ import concurrent.futures
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  import pandas as pd
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  from natsort import natsorted
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  from art import tprint
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+ from typing import Optional, Union
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  class MeasurementProcess(Process):
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+
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+ pos: Optional[Union[str,Path]] = None
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+ mode: Optional[str] = None
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+ n_threads: int = 1
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  def __init__(self, queue=None, process_args=None):
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@@ -173,12 +178,12 @@ class MeasurementProcess(Process):
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  def extract_experiment_parameters(self):
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- self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]
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- self.spatial_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["pxtoum"])
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- self.time_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["frametomin"])
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- self.len_movie = float(ConfigSectionMap(self.config,"MovieSettings")["len_movie"])
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- self.shape_x = int(ConfigSectionMap(self.config,"MovieSettings")["shape_x"])
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- self.shape_y = int(ConfigSectionMap(self.config,"MovieSettings")["shape_y"])
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+ self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")["movie_prefix"]
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+ self.spatial_calibration = float(config_section_to_dict(self.config, "MovieSettings")["pxtoum"])
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+ self.time_calibration = float(config_section_to_dict(self.config, "MovieSettings")["frametomin"])
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+ self.len_movie = float(config_section_to_dict(self.config, "MovieSettings")["len_movie"])
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+ self.shape_x = int(config_section_to_dict(self.config, "MovieSettings")["shape_x"])
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+ self.shape_y = int(config_section_to_dict(self.config, "MovieSettings")["shape_y"])
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  self.channel_names, self.channel_indices = extract_experiment_channels(self.exp_dir)
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  self.nbr_channels = len(self.channel_names)
@@ -331,7 +336,8 @@ class MeasurementProcess(Process):
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  df = df.reset_index(drop=True)
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  df = _remove_invalid_cols(df)
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-
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+ df = df.replace([np.inf, -np.inf], np.nan)
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+
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  df.to_csv(self.pos+os.sep.join(["output", "tables", self.table_name]), index=False)
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  print(f'Measurement table successfully exported in {os.sep.join(["output", "tables"])}...')
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  print('Done.')