celldetective 1.5.0b10__tar.gz → 1.5.0b11__tar.gz

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b10
+Version: 1.5.0b11
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.5.0b11/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.5.0b11"

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/base/list_widget.py

@@ -89,7 +89,7 @@ class ListWidget(CelldetectiveWidget):
         """
         Retrieves and returns the items from the list widget.
 
-        This method parses any items that contain a range (formatted as 'min-max')
+        This method parses any items that contain a range (formatted as '(min,max)')
         into a list of two values, and casts all items to the specified `dtype`.
 
         Returns
@@ -97,18 +97,33 @@ class ListWidget(CelldetectiveWidget):
         list
                 A list of the items in the list widget, with ranges split into two values.
         """
+        import re
+
+        # Pattern for tuple format: "(min,max)" with optional negative numbers and decimals
+        tuple_pattern = re.compile(r"^\((-?\d+(?:\.\d+)?),\s*(-?\d+(?:\.\d+)?)\)$")
 
         items = []
         for x in range(self.list_widget.count()):
-            if len(self.list_widget.item(x).text().split("-")) == 2:
-                if self.list_widget.item(x).text()[0] == "-":
-                    items.append(self.dtype(self.list_widget.item(x).text()))
-                else:
-                    minn, maxx = self.list_widget.item(x).text().split("-")
-                    to_add = [self.dtype(minn), self.dtype(maxx)]
-                    items.append(to_add)
-            else:
-                items.append(self.dtype(self.list_widget.item(x).text()))
+            text = self.list_widget.item(x).text().strip()
+
+            # Try tuple format first: (min,max)
+            tuple_match = tuple_pattern.match(text)
+            if tuple_match:
+                try:
+                    minn = self.dtype(float(tuple_match.group(1)))
+                    maxx = self.dtype(float(tuple_match.group(2)))
+                    items.append([minn, maxx])
+                    continue
+                except ValueError:
+                    pass
+
+            # Single value
+            try:
+                items.append(self.dtype(text))
+            except ValueError:
+                print(
+                    f"Warning: Could not convert '{text}' to {self.dtype.__name__}, skipping..."
+                )
         return items
 
     def clear(self):

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/event_annotator.py

@@ -850,11 +850,40 @@ class EventAnnotator(BaseAnnotator):
 
         try:
             self.stop()
-            del self.stack
-            gc.collect()
-        except:
+        except Exception:
             pass
 
+        # Stop and delete animation to break reference cycles
+        if hasattr(self, "anim") and self.anim:
+            try:
+                self.anim.event_source.stop()
+            except Exception:
+                pass
+            del self.anim
+
+        # Close matplotlib figures
+        if hasattr(self, "fig"):
+            try:
+                plt.close(self.fig)
+            except Exception:
+                pass
+
+        if hasattr(self, "cell_fig"):
+            try:
+                plt.close(self.cell_fig)
+            except Exception:
+                pass
+
+        # Delete large objects
+        if hasattr(self, "stack"):
+            del self.stack
+
+        if hasattr(self, "df_tracks"):
+            del self.df_tracks
+
+        gc.collect()
+        super().closeEvent(event)
+
     def animation_generator(self):
         """
         Generator yielding frame indices for the animation,

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/interactions_block.py

@@ -684,5 +684,14 @@ class NeighPanel(QFrame, Styles):
 
         test = self.parent_window.locate_selected_position()
         if test:
-            self.pair_event_annotator = PairEventAnnotator(self)
-            self.pair_event_annotator.show()
+            try:
+                self.pair_event_annotator = PairEventAnnotator(self)
+                self.pair_event_annotator.show()
+            except ValueError as e:
+                # Show useful feedback if no neighborhood detected
+                msg = QMessageBox()
+                msg.setIcon(QMessageBox.Warning)
+                msg.setText(str(e))
+                msg.setWindowTitle("Warning")
+                msg.exec_()
+                return

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/pair_event_annotator.py

@@ -172,6 +172,10 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         print(
             f"The following neighborhoods were detected: {self.neighborhood_cols=}..."
         )
+        if len(self.neighborhood_cols) == 0:
+            raise ValueError(
+                "No neighborhoods detected. Please compute neighborhoods first."
+            )
 
         self.locate_relative_tracks()
 
@@ -1449,6 +1453,7 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         self.reference_population = self.neighborhood_choice_cb.currentText().split(
             "_"
         )[0]
+        self.neighbor_population = self.reference_population
 
         if "_(" in self.current_neighborhood and ")_" in self.current_neighborhood:
             self.neighbor_population = (
@@ -1457,9 +1462,6 @@ class PairEventAnnotator(CelldetectiveMainWindow):
             self.reference_population = (
                 self.current_neighborhood.split("_(")[-1].split(")_")[0].split("-")[0]
             )
-        else:
-            if "self" in self.current_neighborhood:
-                self.neighbor_population = self.reference_population
 
         print(f"Current neighborhood: {self.current_neighborhood}")
         print(f"New reference population: {self.reference_population}")
@@ -2183,18 +2185,44 @@ class PairEventAnnotator(CelldetectiveMainWindow):
 
     def closeEvent(self, event):
 
-        self.stop()
-        # result = QMessageBox.question(self,
-        # 			  "Confirm Exit...",
-        # 			  "Are you sure you want to exit ?",
-        # 			  QMessageBox.Yes| QMessageBox.No,
-        # 			  )
         try:
-            del self.stack
-        except:
+            self.stop()
+        except Exception:
             pass
 
+        # Stop and delete animation to break reference cycles
+        if hasattr(self, "anim") and self.anim:
+            try:
+                self.anim.event_source.stop()
+            except Exception:
+                pass
+            del self.anim
+
+        # Close matplotlib figures
+        if hasattr(self, "fig"):
+            try:
+                plt.close(self.fig)
+            except Exception:
+                pass
+
+        if hasattr(self, "cell_fig"):
+            try:
+                plt.close(self.cell_fig)
+            except Exception:
+                pass
+
+        # Delete large objects
+        if hasattr(self, "stack"):
+            del self.stack
+
+        if hasattr(self, "dataframes"):
+            self.dataframes.clear()
+
+        if hasattr(self, "df_relative"):
+            del self.df_relative
+
         gc.collect()
+        super().closeEvent(event)
 
     def animation_generator(self):
         """
@@ -2982,26 +3010,6 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         self.draw_frame(self.framedata)
         self.fcanvas.canvas.draw()
 
-    def set_first_frame(self):
-        self.stop()
-        self.framedata = 0
-        self.draw_frame(self.framedata)
-        self.fcanvas.canvas.draw()
-
-    def set_last_frame(self):
-        self.stop()
-        self.framedata = len(self.stack) - 1
-        while len(np.where(self.stack[self.framedata].flatten() == 0)[0]) > 0.99 * len(
-            self.stack[self.framedata].flatten()
-        ):
-            self.framedata -= 1
-            if self.framedata < 0:
-                self.framedata = 0
-                break
-
-        self.draw_frame(self.framedata)
-        self.fcanvas.canvas.draw()
-
     def give_reference_cell_information(self):
 
         df_reference = self.dataframes[self.reference_population]

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/settings/_settings_measurements.py

@@ -680,16 +680,15 @@ class SettingsMeasurements(CelldetectiveSettingsPanel):
                     border_distances = measurement_instructions["border_distances"]
                     if border_distances is not None:
                         if isinstance(border_distances, int):
-                            distances = [border_distances]
+                            distances = [str(border_distances)]
                         elif isinstance(border_distances, list):
                             distances = []
                             for d in border_distances:
-                                if isinstance(d, int) | isinstance(d, float):
+                                if isinstance(d, (int, float)):
                                     distances.append(str(int(d)))
                                 elif isinstance(d, list):
-                                    distances.append(
-                                        str(int(d[0])) + "-" + str(int(d[1]))
-                                    )
+                                    # Use (min,max) tuple format to match CellEdgeVisualizer output
+                                    distances.append(f"({int(d[0])},{int(d[1])})")
                         self.contours_list.list_widget.clear()
                         self.contours_list.list_widget.addItems(distances)
 

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/settings/_settings_neighborhood.py

@@ -213,6 +213,7 @@ class SettingsNeighborhood(CelldetectiveWidget):
                 channel_names=self.attr_parent.exp_channels,
                 n_channels=self.attr_parent.nbr_channels,
                 PxToUm=1,
+                single_value_mode=True,
             )
             self.viewer.show()
 

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/gui/viewers/contour_viewer.py

@@ -72,6 +72,7 @@ class CellEdgeVisualizer(StackVisualizer):
         labels=None,
         initial_edge=5,
         initial_mask_alpha=0.5,
+        single_value_mode=False,
         *args,
         **kwargs,
     ):
@@ -86,6 +87,7 @@ class CellEdgeVisualizer(StackVisualizer):
         self.invert = invert
         self.parent_list_widget = parent_list_widget
         self.parent_le = parent_le
+        self.single_value_mode = single_value_mode
 
         # SDF cache (stores label + dist_in + dist_out + voronoi)
         self.sdf_cache = OrderedDict()
@@ -201,8 +203,18 @@ class CellEdgeVisualizer(StackVisualizer):
 
     def set_measurement_in_parent_list(self):
         # Add the edge size to the parent QListWidget
-
-        self.parent_list_widget.addItems([str(self.edge_slider.value())])
+        # edge_slider is a QLabeledRangeSlider returning (min, max) tuple
+        slider_val = self.edge_slider.value()
+        if isinstance(slider_val, tuple):
+            if self.single_value_mode:
+                # For neighborhood: just output the max absolute distance
+                edge_value = str(max(abs(slider_val[0]), abs(slider_val[1])))
+            else:
+                # For contour measurements: output as "(min,max)" tuple format
+                edge_value = f"({slider_val[0]},{slider_val[1]})"
+        else:
+            edge_value = str(abs(slider_val))
+        self.parent_list_widget.addItems([edge_value])
         self.close()
 
     def generate_label_imshow(self):

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/measure.py

@@ -544,10 +544,19 @@ def measure_features(
         df_props = df_props[[c for c in df_props.columns if not c.endswith("_delme")]]
 
     if border_dist is not None:
+        # Get the names of extra properties that were actually requested by the user
+        # (these were moved from features to extra_props_list earlier)
+        requested_extra_names = []
+        if extra_props_list:
+            for prop_func in extra_props_list:
+                if hasattr(prop_func, "__name__"):
+                    requested_extra_names.append(prop_func.__name__)
+
         # Filter for features containing "intensity" but not "centroid" or "peripheral"
+        # Only use user-requested features, not all available extra properties
         intensity_features = [
             f
-            for f in (features + extra)
+            for f in (features + requested_extra_names)
             if "intensity" in f and "centroid" not in f and "peripheral" not in f
         ]
 
@@ -558,7 +567,7 @@ def measure_features(
 
         clean_intensity_features = []
         for s in intensity_features:
-            if s in extra:
+            if s in requested_extra_names:
                 intensity_extra.append(getattr(extra_props, s))
             else:
                 clean_intensity_features.append(s)

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective/utils/masks.py

@@ -49,8 +49,10 @@ def contour_of_instance_segmentation(label, distance, sdf=None, voronoi_map=None
     """
     from scipy.ndimage import distance_transform_edt
 
-    # helper to parse string "rad1-rad2"
+    # helper to parse string "rad1-rad2" or "-12-13" or "-5--2"
     if isinstance(distance, str):
+        import re
+
         try:
             # Check for stringified tuple "(a, b)"
             distance = distance.strip()
@@ -74,13 +76,18 @@ def contour_of_instance_segmentation(label, distance, sdf=None, voronoi_map=None
                         min_r = val
                         max_r = 0
                 except ValueError:
-                    # It's a range string "5-10"
-                    parts = distance.split("-")
-                    # Assumption: "A-B" where A, B positive radii for OUTER annulus.
-                    r1 = float(parts[0])
-                    r2 = float(parts[1])
-                    min_r = -max(r1, r2)
-                    max_r = -min(r1, r2)
+                    # It's a range string like "5-10", "-12-13", or "-5--2"
+                    # Use regex to parse range with potentially negative numbers
+                    range_pattern = re.compile(r"^(-?\d+(?:\.\d+)?)-(-?\d+(?:\.\d+)?)$")
+                    match = range_pattern.match(distance)
+                    if match:
+                        r1 = float(match.group(1))
+                        r2 = float(match.group(2))
+                        # Use the values directly as specified (min, max in SDF space)
+                        min_r = min(r1, r2)
+                        max_r = max(r1, r2)
+                    else:
+                        raise ValueError(f"Could not parse range string: {distance}")
 
         except Exception:
             logger.warning(

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b10
+Version: 1.5.0b11
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.5.0b10 → celldetective-1.5.0b11}/celldetective.egg-info/SOURCES.txt

@@ -179,6 +179,7 @@ celldetective/utils/plots/regression.py
 celldetective/utils/stardist_utils/__init__.py
 tests/__init__.py
 tests/test_cellpose_fallback.py
+tests/test_contour_format.py
 tests/test_events.py
 tests/test_filters.py
 tests/test_io.py
@@ -193,6 +194,7 @@ tests/test_tracking.py
 tests/test_utils.py
 tests/gui/__init__.py
 tests/gui/test_enhancements.py
+tests/gui/test_event_annotator_cleanup.py
 tests/gui/test_measure_annotator_bugfix.py
 tests/gui/test_new_project.py
 tests/gui/test_project.py