celldetective 1.3.7.post1__py3-none-any.whl → 1.3.8__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 (31) hide show
  1. celldetective/_version.py +1 -1
  2. celldetective/gui/btrack_options.py +8 -8
  3. celldetective/gui/classifier_widget.py +8 -0
  4. celldetective/gui/configure_new_exp.py +1 -1
  5. celldetective/gui/json_readers.py +2 -4
  6. celldetective/gui/plot_signals_ui.py +38 -29
  7. celldetective/gui/process_block.py +1 -0
  8. celldetective/gui/processes/downloader.py +108 -0
  9. celldetective/gui/processes/measure_cells.py +346 -0
  10. celldetective/gui/processes/segment_cells.py +354 -0
  11. celldetective/gui/processes/track_cells.py +298 -0
  12. celldetective/gui/processes/train_segmentation_model.py +270 -0
  13. celldetective/gui/processes/train_signal_model.py +108 -0
  14. celldetective/gui/seg_model_loader.py +71 -25
  15. celldetective/gui/signal_annotator2.py +10 -7
  16. celldetective/gui/signal_annotator_options.py +1 -1
  17. celldetective/gui/tableUI.py +252 -20
  18. celldetective/gui/viewers.py +1 -1
  19. celldetective/io.py +53 -20
  20. celldetective/measure.py +12 -144
  21. celldetective/relative_measurements.py +40 -43
  22. celldetective/segmentation.py +48 -1
  23. celldetective/signals.py +84 -305
  24. celldetective/tracking.py +23 -24
  25. celldetective/utils.py +1 -1
  26. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/METADATA +11 -2
  27. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/RECORD +31 -25
  28. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/WHEEL +1 -1
  29. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/LICENSE +0 -0
  30. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/entry_points.txt +0 -0
  31. {celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/top_level.txt +0 -0
celldetective/tracking.py CHANGED
@@ -441,9 +441,14 @@ def interpolate_per_track(group_df):
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  """
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- interpolated_group = group_df.interpolate(method='linear',limit_direction="both")
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+ for c in list(group_df.columns):
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+ group_df_new_dtype = group_df[c].infer_objects(copy=False)
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+ if group_df_new_dtype.dtype!='O':
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+ group_df[c] = group_df_new_dtype.interpolate(method='linear',limit_direction="both")
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+
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+ #interpolated_group = group_df.interpolate(method='linear',limit_direction="both")
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- return interpolated_group
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+ return group_df
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  def interpolate_nan_properties(trajectories, track_label="TRACK_ID"):
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@@ -937,18 +942,6 @@ def track_at_position(pos, mode, return_tracks=False, view_on_napari=False, thre
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  return df
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  else:
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  return None
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-
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- # # if return_labels or view_on_napari:
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- # # labels = locate_labels(pos, population=mode)
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- # # if view_on_napari:
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- # # if stack_prefix is None:
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- # # stack_prefix = ''
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- # # stack = locate_stack(pos, prefix=stack_prefix)
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- # # _view_on_napari(tracks=None, stack=stack, labels=labels)
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- # # if return_labels:
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- # # return labels
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- # # else:
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- # return None
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  def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_labels={'track': "TRACK_ID", 'time': 'FRAME', 'x': 'POSITION_X', 'y': 'POSITION_Y'}):
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@@ -972,27 +965,33 @@ def write_first_detection_class(df, img_shape=None, edge_threshold=20, column_la
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  column_labels : dict, optional
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  A dictionary mapping logical column names to actual column names in `tab`. Keys include:
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- - `'track'`: The column indicating the track ID (default: `"TRACK_ID"`).
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- - `'time'`: The column indicating the frame/time (default: `"FRAME"`).
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- - `'x'`: The column indicating the X-coordinate (default: `"POSITION_X"`).
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- - `'y'`: The column indicating the Y-coordinate (default: `"POSITION_Y"`).
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+
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+ - `'track'`: The column indicating the track ID (default: `"TRACK_ID"`).
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+ - `'time'`: The column indicating the frame/time (default: `"FRAME"`).
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+ - `'x'`: The column indicating the X-coordinate (default: `"POSITION_X"`).
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+ - `'y'`: The column indicating the Y-coordinate (default: `"POSITION_Y"`).
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  Returns
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  -------
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  pandas.DataFrame
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  The input DataFrame `df` with two additional columns:
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- - `'class_firstdetection'`: A class assigned based on detection status:
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- - `0`: Valid detection not near the edge and not at the initial frame.
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- - `2`: Detection near the edge, at the initial frame, or no detection available.
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- - `'t_firstdetection'`: The adjusted first detection time (in frame units):
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- - `-1`: Indicates no valid detection or detection near the edge.
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- - A float value representing the adjusted first detection time otherwise.
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+
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+ - `'class_firstdetection'`: A class assigned based on detection status:
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+
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+ - `0`: Valid detection not near the edge and not at the initial frame.
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+ - `2`: Detection near the edge, at the initial frame, or no detection available.
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+
984
+ - `'t_firstdetection'`: The adjusted first detection time (in frame units):
985
+
986
+ - `-1`: Indicates no valid detection or detection near the edge.
987
+ - A float value representing the adjusted first detection time otherwise.
990
988
 
991
989
  Notes
992
990
  -----
993
991
  - The function assumes that tracks are grouped and sorted by track ID and frame.
994
992
  - Detections near the edge or at the initial frame (frame 0) are considered invalid and assigned special values.
995
993
  - If `img_shape` is not provided, edge checks are skipped.
994
+
996
995
  """
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996
 
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997
  df = df.sort_values(by=[column_labels['track'],column_labels['time']])
celldetective/utils.py CHANGED
@@ -1794,7 +1794,7 @@ def ConfigSectionMap(path,section):
1794
1794
 
1795
1795
  """
1796
1796
 
1797
- Config = configparser.ConfigParser()
1797
+ Config = configparser.ConfigParser(interpolation=None)
1798
1798
  Config.read(path)
1799
1799
  dict1 = {}
1800
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  try:
{celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.2
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2
  Name: celldetective
3
- Version: 1.3.7.post1
3
+ Version: 1.3.8
4
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  Summary: description
5
5
  Home-page: http://github.com/remyeltorro/celldetective
6
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  Author: Rémy Torro
@@ -30,6 +30,7 @@ Requires-Dist: setuptools
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  Requires-Dist: scipy
31
31
  Requires-Dist: seaborn
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  Requires-Dist: opencv-python-headless==4.7.0.72
33
+ Requires-Dist: PyQt5
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  Requires-Dist: liblapack
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  Requires-Dist: gputools
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  Requires-Dist: lmfit
@@ -43,6 +44,14 @@ Requires-Dist: h5py
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  Requires-Dist: cliffs_delta
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  Requires-Dist: requests
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  Requires-Dist: trackpy
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+ Dynamic: author
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+ Dynamic: author-email
49
+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: license
53
+ Dynamic: requires-dist
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+ Dynamic: summary
46
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47
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  # Celldetective
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{celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/RECORD RENAMED
@@ -1,48 +1,48 @@
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  celldetective/__init__.py,sha256=bi3SGTMo6s2qQBsJAaKy-a4xaGcTQVW8zsqaiX5XKeY,139
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  celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
3
- celldetective/_version.py,sha256=Yd44UrL9S8sic_5qacvIYizakEn80iQg_uqOQxs_-vo,28
3
+ celldetective/_version.py,sha256=47xEhOdVR5Y8-pZH8aVP6Z2UhhY8jGWTQ-rJHt5fIeU,22
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  celldetective/events.py,sha256=UkjY_-THo6WviWWCLnDbma7jWOd_O9a60C4IOX2htG8,8254
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  celldetective/extra_properties.py,sha256=y556D6EMjLGhtjDqRoOTRGa85XxTIe0K1Asb26VZXmo,5643
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  celldetective/filters.py,sha256=DT3MyqNBSj3EMtb74oZUirdonKcwcowjtehTT72mrrk,4181
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- celldetective/io.py,sha256=Rzwl51e0a77HzBCKG1r9M2kIHZekJ9NhdJ5Wl3RPyQA,123115
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- celldetective/measure.py,sha256=qepAEl4XHcS0Jx6zeoRlPBG_pjYjfid2gLBRMhiyDyo,64445
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+ celldetective/io.py,sha256=kD8jvaZJHndlYXM-NwVjesKs8tRQNYiZJCH5VHmk2uA,123067
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+ celldetective/measure.py,sha256=IfmyRaGzYjlTKh6uVBdn4qLEm6LgXQstb5NlB_Blc8I,58291
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  celldetective/neighborhood.py,sha256=s-zVsfGnPlqs6HlDJCXRh21lLiPKbA_S1JC6uZvfG_0,56712
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  celldetective/preprocessing.py,sha256=Wlt_PJua97CpMuWe_M65znUmz_yjYPqWIcs2ZK_RLgk,44109
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- celldetective/relative_measurements.py,sha256=ZviXp6-z_SB60e7z3GznqfEngv70waOK0sMxm_q-JJA,30546
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- celldetective/segmentation.py,sha256=ONuAioeU4qGX7n_LoUVQuv8iHHD9N0D8Bjv2kDdMOrk,29411
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- celldetective/signals.py,sha256=VYaJHJdLSJa8cyamTW0tvoX9nSH1V8BS687HOAwJKb4,121739
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- celldetective/tracking.py,sha256=babNFkxtYDwoAl_WJcZC-GYItafKShV2PLSWimxM6oA,40361
15
- celldetective/utils.py,sha256=MP2bGjb_XUIhT397TJQjcggJPgpGksyRcHJpu9VTW8Q,108422
11
+ celldetective/relative_measurements.py,sha256=-GWig0lC5UWAcJSPlo9Sp45khGj80fxuQfFk-bdBca0,30117
12
+ celldetective/segmentation.py,sha256=ul8E-cjjaWxaMZfjAtbrH7joUjxbZSeb77GL3Alp5Os,30779
13
+ celldetective/signals.py,sha256=nMyyGUpla8D2sUYKY1zjbWsAueVPI_gUalY0KXfWteI,111595
14
+ celldetective/tracking.py,sha256=VBJLd-1EeJarOVPBNEomhVBh9UYAMdSnH0tmUiUoTrY,40242
15
+ celldetective/utils.py,sha256=lX9W8H7y4z8B5DajUDqAoXlycJbIIzOmX7O-2b7eb04,108440
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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/InitWindow.py,sha256=TPKWYczhPHvPKWg654sXnE9xCEx6U-oWX0_OJgLTWbU,15044
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  celldetective/gui/__init__.py,sha256=2_r2xfOj4_2xj0yBkCTIfzlF94AHKm-j6Pvpd7DddQc,989
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  celldetective/gui/about.py,sha256=FJZrj6C-p6uqp_3UaprKosuW-Sw9_HPNQAvFbis9Gdk,1749
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  celldetective/gui/analyze_block.py,sha256=h0sp7Tk3hZFM8w0yTidwIjZX4WRI-lQF3JCFObrLCPo,2761
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- celldetective/gui/btrack_options.py,sha256=tY0XiDcsI4KDgwZtcaP7HWLJ_isxamM-7sFX-m5Dcwk,44662
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- celldetective/gui/classifier_widget.py,sha256=UyElqL9Rq5cKcM6i8ZLGCqkMqqnSDaw6i_hRoV_7WSE,19817
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- celldetective/gui/configure_new_exp.py,sha256=sRBGhMoQUP8-XchmfV6VvuFHceS4Q8qPY2ua7DQOaHI,20754
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+ celldetective/gui/btrack_options.py,sha256=ZXaJuCdqB_BK1CFRbgZErlAlXMbzDF2DP7opLSd6III,44682
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+ celldetective/gui/classifier_widget.py,sha256=nHWmaWXse2CxxRFmR4mA0JRADr5i0MsWldaqJQIQ-i8,19992
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+ celldetective/gui/configure_new_exp.py,sha256=N4SdL-4Xo0XbTAkCtt1ywr74HmHc5eaPlHGv1XgxAX0,20772
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  celldetective/gui/control_panel.py,sha256=1TWUCvEif19ZLy4pDUupPrGzIKnG6Tg6kWGp_R8OSG4,22045
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  celldetective/gui/generic_signal_plot.py,sha256=Gv4KhA5vhbgVSj5jteE42T0aNCoQZtmIAUkEsMi6JNA,36309
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  celldetective/gui/gui_utils.py,sha256=n9JVXBantJK3RFt8fQ7HJYKdCC4ezBMBwlgT5QT2I9o,39343
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- celldetective/gui/json_readers.py,sha256=Su3angSobroeGrrumGgQcs3Cr_9l9p52-Hfm3qneVcI,3664
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+ celldetective/gui/json_readers.py,sha256=SkI_bR1MlAKd8NLBmQUVjJfZ7mKiU_FEjgC4dUwBACk,3698
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  celldetective/gui/layouts.py,sha256=XsqiHR58DXsG5SSD5S8KOtUv4yw-y-s2_wZx_XsHeJs,52013
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  celldetective/gui/measurement_options.py,sha256=cfiC4lq-XqY4Sa4Vkw5mys7JKaa9tE2BgeN8_k-SIDY,40355
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  celldetective/gui/neighborhood_options.py,sha256=FBNDvlzMPKp8s0Grxds90pCPHG1s27XrpMN0HV2gf0I,19839
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  celldetective/gui/plot_measurements.py,sha256=n0pDUcYcsKlSMaUaBSVplGziuWp_7jKaeXdREs-MqyI,50848
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- celldetective/gui/plot_signals_ui.py,sha256=-yKpmmWi0CDKazn3v49ArvykdQbtGIXx0ZwQ4yO8-eY,16641
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- celldetective/gui/process_block.py,sha256=l16GS_xTeSqWIxYZj1lc4EwC3WOhZsE4k-GOTBKZR0o,71188
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+ celldetective/gui/plot_signals_ui.py,sha256=u7b36pmjF8sf0Ctb9KCrnRcvAD3vlNaaIVkX3-rHCA0,17332
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+ celldetective/gui/process_block.py,sha256=3v4q5kAq5uY6w0f3zyImXi_iTp8Qv2EFvzNjTEvqG9E,71210
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  celldetective/gui/retrain_segmentation_model_options.py,sha256=7iawDN4kwq56Z-dX9kQe9tLW8B3YMrIW_D85LMAAYwk,23906
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  celldetective/gui/retrain_signal_model_options.py,sha256=GCa0WKKsgmH2CFDHAKxPGbHtCE19p1_bbcWNasyZw5o,22482
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- celldetective/gui/seg_model_loader.py,sha256=vWvPMU6nkTiQfI-x2WjQHrdJGFdV4a4Ne-4YIOq_YZ8,18153
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+ celldetective/gui/seg_model_loader.py,sha256=b1BiHuAf_ZqroE4jSEVCo7ASQv-xyWMPWU799alpbNM,19727
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  celldetective/gui/signal_annotator.py,sha256=9l_qbIO9V862eGk6mVOCXo0jsG8Z3WP9kx7wCBFGvKU,89014
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- celldetective/gui/signal_annotator2.py,sha256=1OTGc6wKUDHitpRUOHuDMSoJbubLvh1sGR2YRN7oDeU,106289
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- celldetective/gui/signal_annotator_options.py,sha256=ztFFgA70SJ0QkntxYGsgDNCvSuSR5GjF7_J6pYVYc1g,11020
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+ celldetective/gui/signal_annotator2.py,sha256=qBDPk3UHmMoY4_i5KJt3Nr8kxjLOkYay_xNc6xrn_pE,106340
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+ celldetective/gui/signal_annotator_options.py,sha256=ekxy7Qtw5EGqXa82KdZezaSlmprSAGMW2ZZoE1SObRM,11013
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  celldetective/gui/styles.py,sha256=SZy_ACkA6QB_4ANyY1V0m1QF66C0SVGssOrwW1Qt1Aw,5076
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  celldetective/gui/survival_ui.py,sha256=J4ZYjX8ne0wT0ruQu9WL3WfLnRIAQalkaAR8ngb7PkI,14170
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- celldetective/gui/tableUI.py,sha256=89TB_U2l4rhYCpEr3RicratMOp74Spx3ioBeM5lnbHA,51021
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+ celldetective/gui/tableUI.py,sha256=Yz_pHk1ERXRb0QsBPrvLEwAGpvVlawgn1b6uzz5wL_0,58022
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  celldetective/gui/thresholds_gui.py,sha256=VjCVBCDsNh_LoXfEqUn32nsYQwO9-Elh3Gl1RBv7acc,48756
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- celldetective/gui/viewers.py,sha256=mne5GLFAjv-vxMABXP7I9VhrJGtPnZj560HLdlwDZSU,47806
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+ celldetective/gui/viewers.py,sha256=HDLB6j1FJwgKR6dQwzeHmcDvDMbDIYwD2svd-VZhJFE,47806
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  celldetective/gui/workers.py,sha256=P4qUMXuCtGcggGmJr3VitAPSfRG30wkJ1B0pfcdGbKg,4225
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  celldetective/gui/help/DL-segmentation-strategy.json,sha256=PZD9xXjrwbX3TiudHJPuvcyZD28o4k-fVgeTd7dBKzI,1583
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  celldetective/gui/help/Threshold-vs-DL.json,sha256=rrFnZT2DhyS7g1nIDWeUV8-HH7M2Sv8D7sDCGBU1M_0,934
@@ -55,6 +55,12 @@ celldetective/gui/help/preprocessing.json,sha256=M-AxW6zYB5oDiQdoc9wcky8C5p0m6uv
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  celldetective/gui/help/propagate-classification.json,sha256=F7Ir1mtgRVTXWLN7n3ny3vrU01LFNeDh5dN2QBIXHqE,1227
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  celldetective/gui/help/track-postprocessing.json,sha256=VaGd8EEkA33OL-EI3NXWZ8yHeWWyUeImDF5yAjsVYGA,3990
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  celldetective/gui/help/tracking.json,sha256=yIAoOToqCSQ_XF4gwEZCcyXcvQ3mROju263ZPDvlUyY,776
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+ celldetective/gui/processes/downloader.py,sha256=SuMTuM82QOZBqLfj36I14fhZ2k3NmLp0PBcGUHxnpXI,3287
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+ celldetective/gui/processes/measure_cells.py,sha256=1nJNHhLKHBL7kVsmmPbWv0NHcar0D8Gihjj_AD1UxnI,12851
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+ celldetective/gui/processes/segment_cells.py,sha256=AVdRGuDnoQcrevk7itiEu5xluBeqaqXRSFVZAd7q91g,11313
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+ celldetective/gui/processes/track_cells.py,sha256=og23iqc7WyVbpqsdygltVjejLGUVIb5ocxAForGnhl0,9947
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+ celldetective/gui/processes/train_segmentation_model.py,sha256=bvcPG19hBjhNY9hd6Ch5_wk2FOJYQg97Azoz4RKeP-0,10776
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+ celldetective/gui/processes/train_signal_model.py,sha256=qqqkq9gdvNyvycYkmzWgRXWvsbEozyzNWP_POGvnlIs,3816
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  celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
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  celldetective/icons/logo.png,sha256=wV2OS8_dU5Td5cgdPbCOU3JpMpTwNuYLnfVcnQX0tJA,2437
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  celldetective/icons/signals_icon.png,sha256=vEiKoqWTtN0-uJgVqtAlwCuP-f4QeWYOlO3sdp2tg2w,3969
@@ -100,9 +106,9 @@ tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,34
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  tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
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  tests/test_tracking.py,sha256=8hebWSqEIuttD1ABn-6dKCT7EXKRR7-4RwyFWi1WPFo,8800
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  tests/test_utils.py,sha256=NKRCAC1d89aBK5cWjTb7-pInYow901RrT-uBlIdz4KI,3692
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- celldetective-1.3.7.post1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
104
- celldetective-1.3.7.post1.dist-info/METADATA,sha256=HWoXnuZNCWSAXVbN9dyKLFOJHnt4lX-QjsFLtYSHB10,10563
105
- celldetective-1.3.7.post1.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
106
- celldetective-1.3.7.post1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
107
- celldetective-1.3.7.post1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
108
- celldetective-1.3.7.post1.dist-info/RECORD,,
109
+ celldetective-1.3.8.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
110
+ celldetective-1.3.8.dist-info/METADATA,sha256=z9xNWbdnrXwtyVXG_C8WjV8GR3bCl3Ivs8T9erqRwDs,10747
111
+ celldetective-1.3.8.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
112
+ celldetective-1.3.8.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
113
+ celldetective-1.3.8.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
114
+ celldetective-1.3.8.dist-info/RECORD,,
{celldetective-1.3.7.post1.dist-info → celldetective-1.3.8.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (75.7.0)
2
+ Generator: setuptools (75.8.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5