code doc update

Author: gletort

src/epicure/Utils.py

@@ -1,5 +1,7 @@
 """
-    Diverse functions for EpiCure
+    **Diverse functions for EpiCure**
+
+    Proposes utility functions that do not depend on a class and can be usefull in several classes.
 """
 
 import numpy as np
@@ -53,11 +55,16 @@ def show_debug(message):
     print(message)
 
 def show_documentation():
+    """ Open browser on main EpiCure documentation page """
     import webbrowser
     webbrowser.open_new_tab("https://image-analysis-hub.github.io/Epicure/")
     return
 
 def show_documentation_page(page):
+    """ 
+        Open browser on the selected page of EpiCure documentation 
+        :param: page: name of the documentation page to go to (only the name of the page, without the full path)    
+    """
     import webbrowser
     webbrowser.open_new_tab("https://image-analysis-hub.github.io/Epicure/"+page)
     return
@@ -99,6 +106,17 @@ def get_directory(imagepath):
     return os.path.dirname(imagepath)
 
 def extract_names(imagepath, subname="epics", mkdir=True):
+    """
+        From the image file path, extracts the name of the directoties to work in
+
+        :param: imagepath: file path to the main raw movie
+        :param: subname (default: "epics"): name of the results directory where all will be saved
+        
+        :return: 
+            - name of the raw movie without the extension, that will be used to save all other files
+            - path to the directory where the raw movie is
+            - path to the results directory on which to save all outputs
+    """
     imgname = os.path.splitext(os.path.basename(imagepath))[0]
     imgdir = os.path.dirname(imagepath)
     resdir = os.path.join(imgdir, subname)

src/epicure/inspecting.py

@@ -1,3 +1,16 @@
+"""
+    ** EpiCure - Inspect panel interface **
+
+    Handle supects and events detection layer.
+    Inspection functions propose to look for user selected features to detect potential errors in the segmentration from inspecting the tracks.
+
+    Extrusion events are detected as disappearance of a track & a cell size small enough.
+    Divisions events can be detected by the tracking algorithm directly and saved in the track graph, or they can be detected by the inspection as the disappearance of one track at the same time that two new tracks appear in the same area.
+
+    Inpsection could also be performed on a static image by looking at outlier values of a selected feature.
+"""
+
+
 import numpy as np
 from skimage import filters
 from skimage.measure import regionprops
@@ -9,14 +22,12 @@
 import time
 from joblib import Parallel, delayed
 
-"""
-    EpiCure - Inspection interface
-    Handle supects, events detection layer
-"""
-
 class Inspecting(QWidget):
 
     def __init__(self, napari_viewer, epic):
+        """
+        Generate the graphical interface for the inspection panel, and initialize the events layer.
+        """
         super().__init__()
         self.viewer = napari_viewer
         self.epicure = epic
@@ -76,7 +87,7 @@ def __init__(self, napari_viewer, epic):
         self.key_binding()
 
     def key_binding(self):
-        """ active key bindings for events options """
+        """ active key bindings (keyboard and mouse shortcuts) for events options """
         sevents = self.epicure.shortcuts["Events"]
         self.epicure.overtext["events"] = "---- Events editing ---- \n"
         self.epicure.overtext["events"] += ut.print_shortcuts( sevents )
@@ -417,6 +428,7 @@ def set_colors_from_properties(self, feature):
         self.events.face_color = feature
 
     def update_display(self):
+        """ Update the display of the events layer """
         self.events.refresh()
         self.color_events()