Merge pull request #11 from gletort/epidev

Epidev - import/export TM - Shortcuts Mac

Author: gletort

docs/Inspect.md

@@ -35,7 +35,9 @@ Division events are detected based on the tracking graph. If cells has not been
 (Un)Select the option `show division` to (un)display division events. You can see the total number of divisions found written in the top of the `Inspect` panel.
 
 You can manually add a division event, or remove one.
+
 * To remove a division, the shortcut is the same as for removing any event: by default, press <kbd>Control+Alt+Right-click</kbd> on the event to remove.
+
 * To add a divison, do <kbd>Control+Shift+Left clikc</kbd> from one daughter cell to the other. EpiCure will detect automatically the most likely mother cell.
 If suspect events had been found on the two daughter cells or on the mother cell, they will be automatically removed when manually adding the division.
 

docs/Start-epicure.md

@@ -8,16 +8,20 @@ However, if some format is not correctly recongized/handled by EpiCure, you can
 
 In the `Start EpiCure` step, you have a dedicated interface in the right part of the main interface.
 
+### Raw movie
 The first file to choose is the movie containing the epithelial staining, with the `image file` parameter. 
 It should be _2D(+time/channels) file_. 3D is not handled. If a file has a Z dimension and no temporal dimension, EpiCure will swap them and use the Z axis as time.  
 
 If the file contains several chanels, the plugin should detect it and show the `junction_chanel` parameter, to choose the chanel that contains the junction staining. The plugin will display only this chanel. If you wish to also see the other chanels, use the option `show other chanels` in the [advanced parameters](#advanced-parameters) panel.
 
-The second file is the segmentation of this movie (it should only contain the segmentation), to select with the `segmentation file` parameter. It can be a binarized file of the junctions (skeletonized) or a labelled file (each cell is filled by a unique number).
+### Segmentation/Tracks
+The second file is the segmentation or tracks of this movie (it should only contain the segmentation), to select with the `segmentation file` parameter. It can be a binarized file of the junctions (skeletonized), a labelled file (each cell is filled by a unique number), or a TrackMate `.xml` file.
+
+If it is a TrackMate file, the tracks and the divisions will be loaded directly from it.
 
 _Note that if you haven't done the segmentation yet, there's an [additional option](./Segment-option.md) in EpiCure to directly run [EpySeg](https://github.com/baigouy/EPySeg) on the loaded movie._ 
 
-If the input movie file had already been processed with EpiCure previously (and saved), EpiCure will automatically propose to load the saved file and reload the previous parameters. You can directly click `START CURE` in this case.
+If the input movie file had already been processed with EpiCure previously (and saved), EpiCure will **automatically propose to load the saved file** and reload the previous parameters. You can directly click `START CURE` in this case.
 
 ![start interface](./imgs/starting.png)
 

docs/index.md

@@ -18,7 +18,7 @@ It should be _2D(+time/channel) file_.
 	Note that if your file format is not correctly handled by EpiCure, you can first open the image with other plugins and start EpiCure from the opened layer(s). See [Start EpiCure page](./Start-epicure.md#start-from-opened-layers) for more details.
 
 
-The second file is the segmentation of this movie (it should contain only the segmentation). It can be a binarized file of the junctions (skeletonized) or a labelled file (each cell is filled by a unique number).
+The second file is the segmentation of this movie (it should contain only the segmentation) or a TrackMate file (`.xml` file). It can be a binarized file of the junctions (skeletonized), a labelled file (each cell is filled by a unique number) or the `.xml` file generated by TrackMate.
 _Note that if you haven't done the segmentation yet, there's an [additional option](./Segment-option.md) in EpiCure to directly run [EpySeg](https://github.com/baigouy/EPySeg) on the loaded movie._ 
 
 If the input movie file had already been processed with EpiCure previously (and saved), EpiCure will automatically propose to load the saved file and reload the previous parameters. You can directly click `START CURE` in this case.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "epicure"
-version = "1.4"
+version = "1.4.5"
 description = "Napari plugin to manually correct epithelia segmentation in movies"
 license.file = "LICENSE"
 readme = "README.md"
@@ -40,7 +40,7 @@ dependencies = [
     "imagecodecs",
     "edt",
     "packaging",
-    "laptrack",
+    "laptrack>=0.15.0",
     "joblib",
 ]
 

src/epicure/Utils.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import os, sys
+from sys import platform
 import time
 import math
 from skimage.measure import label, regionprops, find_contours, regionprops_table
@@ -21,7 +22,6 @@
 from skimage.morphology import medial_axis
 import pandas as pd
 from epicure.laptrack_centroids import LaptrackCentroids
-from bioio import BioImage
 import tifffile as tif # type: ignore
 import napari
 from napari.utils import progress # type: ignore
@@ -79,6 +79,10 @@ def close_progress( viewer, progress_bar ):
     progress_bar.close()
     show_progress( viewer, False)
 
+def version_above( module, version ):
+    """ Compare if python module is above a given version """
+    return Version(module.__version__) > Version(version)
+
 #### Handle versions of napari
 def version_napari_above( compare_version ):
     """ Compare if the current version of napari is above given version """
@@ -135,6 +139,7 @@ def create_text_window( name ):
     blabla.show()
     return blabla
 
+
 def napari_shortcuts():
     """ Write main napari shortcuts list """
     text = "---- Main napari default shortcuts ----\n"
@@ -259,6 +264,7 @@ def open_image(imagepath, get_metadata=False, verbose=True):
             print("Opening Tif image "+str(imagepath)+" with bioio-tifffile")
         import bioio_tifffile
         if version_python_minor(10):
+            from bioio import BioImage
             img = BioImage(imagepath, reader=bioio_tifffile.Reader)
         else:
             ## python 3.9 or under
@@ -270,6 +276,7 @@ def open_image(imagepath, get_metadata=False, verbose=True):
         if verbose:
             print("Opening "+extension+" image "+str(imagepath)+" with bioio-bioformats")
         if version_python_minor(10):
+            from bioio import BioImage
             img = BioImage(imagepath, reader=bioio_bioformats.Reader)
         else:
             ## python 3.9 or under
@@ -1111,6 +1118,13 @@ def shortcut_click_match( shortcut, event ):
         if len(event.modifiers) > 0:
             return False
         return True
+
+def is_darwin():
+    """ Test if OS is MacOS or not """
+    try:
+        return platform.lower() == "darwin"
+    except:
+        return False
 
 def print_shortcuts( shortcut_group ):
     """ Put to text the subset of shortcuts """
@@ -1123,7 +1137,13 @@ def print_shortcuts( shortcut_group ):
             if "modifiers" in vals.keys():
                 modifiers = vals["modifiers"]
                 for mod in modifiers:
-                    modif += mod+"-"
+                    if mod == "Control":
+                        if is_darwin():
+                            modif += "Command"+"-"
+                        else:
+                            modif += mod+"-"
+                    else:
+                        modif += mod+"-"
             text += "  <"+modif+vals["button"]+"-click> "+vals["text"]+"\n"
     return text
 

src/epicure/_version.py

@@ -17,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev103+g64f1ff3.d20260123'
-__version_tuple__ = version_tuple = (0, 1, 'dev103', 'g64f1ff3.d20260123')
+__version__ = version = '0.1.dev135+g785d2b9.d20260216'
+__version_tuple__ = version_tuple = (0, 1, 'dev135', 'g785d2b9.d20260216')

src/epicure/epicuring.py

@@ -7,6 +7,7 @@
 from skimage.morphology import skeletonize
 from skimage.measure import regionprops
 from joblib import Parallel, delayed
+from pathlib import Path
 
 import epicure.Utils as ut
 from epicure.editing import Editing
@@ -15,6 +16,7 @@
 from epicure.outputing import Outputing
 from epicure.displaying import Displaying
 from epicure.preferences import Preferences
+import epicure.tm_loader as tm
 
 """
     EpiCure main
@@ -246,9 +248,28 @@ def add_other_chanels(self, chan, chanaxis):
                 mview.gamma=0.95
                 mview.visible = False
 
+    def import_trackmate(self, segpath, verbose=0):
+        """ Load segmentation and tracks from TrackMate XML file """
+        if verbose > 1:
+            print("Importing segmentation and tracks from TrackMate XML file")
+        np.set_printoptions(suppress=True, floatmode="maxprec_equal")
+
+        img_data_tag = tm._get_ImageData_tag(segpath)
+        metadata = tm._get_metadata(img_data_tag)
+        seg_shape = (int(metadata["nframes"]), int(metadata["height"]), int(metadata["width"]))
+        segmentation = np.zeros(seg_shape, dtype=np.uint16)-1
+        positions, tracks = tm._parse_Model_tag(segpath, metadata, segmentation)
+        label_mapping = tm._build_label_mapping(positions, tracks)
+        positions = tm.relabel_positions(label_mapping, positions)
+        tracks = tm.relabel_tracks(label_mapping, tracks)
+        segmentation = tm.relabel_segmentation(label_mapping, segmentation)
+        return segmentation, tracks
+
+
     def load_segmentation(self, seg_input):
         """Load the segmentation file"""
         start_time = ut.start_time()
+        self.graph = None ## no loaded graph
         ## compatibility to string input, the path to the image or a dictionnary
         if isinstance(seg_input, dict):
             segpath = seg_input["File"]
@@ -260,7 +281,11 @@ def load_segmentation(self, seg_input):
             self.seg = seg_input["Layer"].data
             ut.remove_layer(self.viewer, seg_input["Layer"])
         else:
-            self.seg, _, _, _, _, _ = ut.open_image(segpath, get_metadata=False, verbose=self.verbose > 1)
+            if str(segpath).endswith(".xml"):
+                ## import a TrackMate file
+                self.seg, self.graph = self.import_trackmate(segpath, verbose=self.verbose>1)
+            else:
+                self.seg, _, _, _, _, _ = ut.open_image(segpath, get_metadata=False, verbose=self.verbose > 1)
         self.seg = np.uint32(self.seg)
         ## transform static image to movie (add temporal dimension)
         if len(self.seg.shape) == 2:
@@ -279,12 +304,6 @@ def load_segmentation(self, seg_input):
 
         ## define a reference size of the movie to scale default parameters
         self.reference_size = np.max(self.imgshape2D)
-        ## define the average cell radius
-        # self.cell_avg_radius = int( math.sqrt( ut.average_area( self.seg[0])/math.pi ) )
-        # on cell area ut.summary_labels( self.seg[0] )
-        # if self.verbose > 1:
-        #    print("Reference size of the movie: "+str(self.reference_size))
-
         self.epi_metadata["Reloading"] = True  ## has been formatted to EpiCure format
 
         # display the segmentation file movie
@@ -299,13 +318,16 @@ def load_segmentation(self, seg_input):
         if self.verbose > 0:
             ut.show_duration(start_time, header="Segmentation loaded in ")
 
+
     def load_tracks(self, progress_bar):
         """From the segmentation, get all the metadata"""
         tracked = "tracked"
         self.tracking.init_tracks()
         if self.tracked == 0:
             tracked = "untracked"
         else:
+            if self.graph is not None:
+                self.tracking.set_graph(self.graph)
             if self.forbid_gaps:
                 progress_bar.set_description("check and fix track gaps")
                 self.handle_gaps(track_list=None, verbose=1)
@@ -562,13 +584,17 @@ def get_summary(self):
         summ += "Average track lengths: " + str(mean_duration) + " frames\n"
         summ += "Average cell area: " + str(mean_area) + " pixels^2\n"
         summ += "Nb suspect events: " + str(self.inspecting.nb_events(only_suspect=True)) + "\n"
-        summ += "Nb divisions: " + str(self.inspecting.nb_type("division")) + "\n"
+        summ += "Nb divisions: " + str(self.nb_divisions()) + "\n"
         summ += "Nb extrusions: " + str(self.inspecting.nb_type("extrusion")) + "\n"
         summ += "\n"
         summ += "--- Parameter infos \n"
         summ += "Junction thickness: " + str(self.thickness) + "\n"
         return summ
 
+    def nb_divisions(self):
+        """ Return the number of divisions """
+        return self.inspecting.nb_type("division")
+
     def set_contour(self, width):
         self.seglayer.contour = width
 

src/epicure/preferences.py

@@ -54,6 +54,12 @@ class Preferences():
     def __init__( self ):
         """ Initialise file path, load current preferences"""
         self.build_preferences_path()
+        print("Running on "+platform.lower())
+        
+        self.ctl = "Control"
+        #self.alt = "Alt"
+        if platform.lower() == "darwin":
+            self.ctl = "Command"
 
         self.load_default_shortcuts()
         self.load_default_settings()
@@ -133,7 +139,8 @@ def add_click_shortcut( self, main_type, shortname, fulltext, button, modifiers=
         sc["text"] = fulltext
         sc["button"] = button
         if modifiers is not None:
-            sc["modifiers"] = modifiers
+            sc["modifiers"] = ["Control" if item=="Command" else item for item in modifiers] 
+
 
     def load_default_shortcuts( self ):
         """ Load all default shortcuts """
@@ -149,7 +156,7 @@ def load_default_shortcuts( self ):
         ## Labels edition (static) shortcuts
         self.add_key_shortcut( "Labels", shortname="unused paint", fulltext="set the current label to unused value and go to paint mode", key="n" )
         self.add_key_shortcut( "Labels", shortname="unused fill", fulltext="set the current label to unused value and go to fill mode", key="Shift-n" )
-        self.add_key_shortcut( "Labels", shortname="swap mode", fulltext="then <Control>+Left click on one cell to another to swap their values", key="w" )
+        self.add_key_shortcut( "Labels", shortname="swap mode", fulltext="then <"+self.ctl+">+Left click on one cell to another to swap their values", key="w" )
 
         self.add_click_shortcut( "Labels", shortname="erase", fulltext="erase the cell under the click", button="Right", modifiers=None )
         self.add_click_shortcut( "Labels", shortname="merge", fulltext="drag-click from one cell to another to merge them", button="Left", modifiers=["Control"] )
@@ -200,7 +207,7 @@ def load_default_shortcuts( self ):
         self.add_key_shortcut( "Display", shortname="decrease", fulltext="decrease label contour size", key="Control-d" )
 
         ## Info shortcuts
-        self.add_key_shortcut( "Info", shortname="measure length", fulltext="draw and measure a line length", key="Control-i" )
+        self.add_key_shortcut( "Info", shortname="measure length", fulltext="draw and measure a line length", key="Control"+"-i" )
 
 
     def load_default_settings( self ):
@@ -241,6 +248,10 @@ def __init__( self, napari_viewer, pref ):
         super().__init__()
 
         layout = QVBoxLayout()
+        self.ctl = "Control"
+        #self.alt = "Alt"
+        if platform.lower() == "darwin":
+            self.ctl = "Command"
 
         self.sc = pref.get_shortcuts()
         ## choice list to choose which shortcuts to edit
@@ -284,9 +295,8 @@ def create_sc_type( self, sc_type ):
                         cur_modif.addItem("Control")
                         cur_modif.addItem("Shift")
                         cur_modif.addItem("Alt")
-                        if platform == "darwin":
+                        if platform.lower() == "darwin":
                             cur_modif.addItem("Command")
-                        cur_modif.addItem("Alt")
                         new_line.addWidget( cur_modif )
                         cur_modif.setCurrentText( modif )
                         self.sc_guis[sc_type][ shortname+"modifiers"+str(ind) ] = cur_modif

src/epicure/start_epicuring.py

@@ -174,6 +174,8 @@ def launch_napari_epyseg():
             scale_xy = {"widget_type": "LiteralEvalLineEdit"},
             timeframe = {"widget_type": "LiteralEvalLineEdit"},
             __ = {"widget_type": "Label"},
+            _____ = {"widget_type": "Label"},
+            ______ = {"widget_type": "Label"},
             segment_with_epyseg = {"widget_type": "PushButton", "label": "Segment now with EpySeg"},
             ___ = {"widget_type": "Label"},
             junction_half_thickness={"widget_type": "LiteralEvalLineEdit"},
@@ -188,8 +190,10 @@ def get_files(
                    unit_xy = "um",
                    timeframe = 1,
                    unit_t = "min",
-                   __ = "Segmentation",
+                   __ = "\nSegmentation\n",
+                   _____ = "Load segmentation or TrackMateXML file",
                    segmentation_file = pathlib.Path(cdir),
+                   ______ = "OR\t",
                    segment_with_epyseg = False,
                    ___ = "",
                    advanced_parameters = False,