celldetective 1.5.0b7__py3-none-any.whl → 1.5.0b9__py3-none-any.whl

celldetective/gui/generic_signal_plot.py

@@ -29,6 +29,7 @@ import matplotlib.pyplot as plt
 
 plt.rcParams["svg.fonttype"] = "none"
 from glob import glob
+from celldetective import get_logger
 from matplotlib.cm import tab10
 from celldetective.gui.base.components import CelldetectiveWidget
 import matplotlib.cm as mcm
@@ -36,6 +37,8 @@ import pandas as pd
 
 from lifelines.utils import qth_survival_times
 
+logger = get_logger(__name__)
+
 
 class GenericSignalPlotWidget(CelldetectiveWidget):
 
@@ -317,7 +320,7 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
         alpha = value
         try:
             alpha = float(alpha)
-        except:
+        except (ValueError, TypeError):
             return None
         if alpha > 1.0:
             alpha = 1.0
@@ -440,7 +443,7 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
             + glob(self.parent_window.exp_dir + os.sep.join([f"W*", "*metadata.txt"]))
             + glob(self.parent_window.exp_dir + "*metadata.txt")
         )
-        print(f"Found {len(self.metafiles)} metadata files...")
+        logger.debug(f"Found {len(self.metafiles)} metadata files.")
         if len(self.metafiles) > 0:
             self.metadata_found = True
 
@@ -455,17 +458,17 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
                 data = json.load(f)
                 positions = data["Summary"]["InitialPositionList"]
         except Exception as e:
-            print(f"Trouble loading metadata: error {e}...")
+            logger.debug(f"Trouble loading metadata: {e}")
             return None
 
         for k in range(len(positions)):
             pos_label = positions[k]["Label"]
             try:
                 coords = positions[k]["DeviceCoordinatesUm"]["XYStage"]
-            except:
+            except KeyError:
                 try:
                     coords = positions[k]["DeviceCoordinatesUm"]["PIXYStage"]
-                except:
+                except KeyError:
                     self.no_meta = True
 
             if not self.no_meta:
@@ -515,8 +518,8 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
             self.fig_scatter.tight_layout()
             self.fig_scatter.canvas.mpl_connect("motion_notify_event", self.hover)
             self.fig_scatter.canvas.mpl_connect("pick_event", self.unselect_position)
-        except Exception as e:
-            pass
+        except (KeyError, TypeError) as e:
+            logger.debug(f"Could not plot spatial location: {e}")
 
     def update_annot(self, ind):
 
@@ -616,19 +619,16 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
                 leg.set_visible(True)
 
     def show_hide_legend(self):
-
+        """Toggle legend visibility and replot to sync state."""
         if self.legend_visible:
-            leg = self.ax.get_legend()
-            leg.set_visible(False)
             self.legend_visible = False
             self.legend_btn.setIcon(icon(MDI6.text_box, color="black"))
         else:
-            leg = self.ax.get_legend()
-            leg.set_visible(True)
             self.legend_visible = True
             self.legend_btn.setIcon(icon(MDI6.text_box, color=self.help_color))
 
-        self.plot_widget.canvas.draw_idle()
+        # Replot to sync legend state
+        self.plot_signals(0)
 
     def switch_to_log(self):
         """
@@ -886,7 +886,7 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
         try:
             self.plot_signals(0)
         except Exception as e:
-            print(f"{e=}")
+            logger.debug(f"Error plotting signals: {e}")
 
     def switch_cell_lines(self):
 

celldetective/gui/gui_utils.py

@@ -35,11 +35,19 @@ class PreprocessingLayout(QVBoxLayout, Styles):
     A widget that allows user to choose preprocessing filters for an image
     """
 
-    def __init__(self, parent_window=None, apply_btn_option=True, *args, **kwargs):
+    def __init__(
+        self,
+        parent_window=None,
+        apply_btn_option=True,
+        extra_widget=None,
+        *args,
+        **kwargs,
+    ):
         super().__init__(*args, **kwargs)
 
         self.parent_window = parent_window
         self.apply_btn_option = apply_btn_option
+        self.extra_widget = extra_widget
         self.generate_components()
         self.add_to_layout()
 
@@ -48,7 +56,12 @@ class PreprocessingLayout(QVBoxLayout, Styles):
         self.setContentsMargins(20, 20, 20, 20)
 
         button_layout = QHBoxLayout()
-        button_layout.addWidget(self.preprocess_lbl, 85, alignment=Qt.AlignLeft)
+        v_layout = QVBoxLayout()
+        v_layout.addWidget(self.preprocess_lbl, alignment=Qt.AlignLeft)
+        if self.extra_widget is not None:
+            v_layout.addWidget(self.extra_widget, alignment=Qt.AlignLeft)
+
+        button_layout.addLayout(v_layout, 85)
         button_layout.addWidget(self.delete_filter_btn, 5)
         button_layout.addWidget(self.add_filter_btn, 5)
         button_layout.addWidget(self.help_prefilter_btn, 5)
@@ -129,10 +142,12 @@ class PreprocessingLayout(QVBoxLayout, Styles):
 
 class PreprocessingLayout2(PreprocessingLayout):
 
-    def __init__(self, fraction=75, *args, **kwargs):
+    def __init__(self, fraction=75, extra_widget=None, *args, **kwargs):
 
         self.fraction = fraction
-        super().__init__(apply_btn_option=False, *args, **kwargs)
+        super().__init__(
+            apply_btn_option=False, extra_widget=extra_widget, *args, **kwargs
+        )
         self.preprocess_lbl.setText("Preprocessing: ")
         self.preprocess_lbl.setStyleSheet("")
         self.setContentsMargins(0, 0, 0, 0)
@@ -142,12 +157,18 @@ class PreprocessingLayout2(PreprocessingLayout):
         main_layout = QHBoxLayout()
         main_layout.setContentsMargins(0, 0, 0, 0)
         main_layout.setSpacing(5)
+        main_layout.setSpacing(5)
+
         main_layout.addWidget(self.preprocess_lbl, self.fraction, alignment=Qt.AlignTop)
 
         list_grid = QGridLayout()
         list_grid.addWidget(self.list, 0, 0, 2, 2)
         list_grid.addWidget(self.add_filter_btn, 0, 2, 1, 1)
         list_grid.addWidget(self.delete_filter_btn, 1, 2, 1, 1)
+
+        if self.extra_widget is not None:
+            list_grid.addWidget(self.extra_widget, 2, 0, 1, 3, alignment=Qt.AlignRight)
+
         main_layout.addLayout(list_grid, 100 - self.fraction)
         self.add_filter_btn.setFixedWidth(35)  # Ensure the button width is fixed
         self.delete_filter_btn.setFixedWidth(35)
@@ -449,8 +470,6 @@ class FilterChoice(CelldetectiveWidget):
     def add_current_feature(self):
 
         filtername = self.combo_box.currentText()
-        self.parent_window.list_widget.addItems([filtername])
-
         filter_instructions = [filtername.split("_")[0]]
         for a in self.arguments_le:
 
@@ -467,7 +486,9 @@ class FilterChoice(CelldetectiveWidget):
 
         print(f"You added filter {filter_instructions}.")
 
+        # Update items BEFORE adding to widget to ensure signals pick up the new state
         self.parent_window.items.append(filter_instructions)
+        self.parent_window.list_widget.addItems([filtername])
         self.close()
 
     def update_arguments(self):

celldetective/gui/pair_event_annotator.py

@@ -21,7 +21,7 @@ from celldetective.gui.base.components import (
     CelldetectiveWidget,
 )
 from celldetective.gui.base.utils import center_window
-from superqt import QLabeledDoubleRangeSlider, QSearchableComboBox
+from superqt import QLabeledDoubleRangeSlider, QSearchableComboBox, QLabeledSlider
 from celldetective import (
     get_software_location,
 )
@@ -466,11 +466,26 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         # Animation
         animation_buttons_box = QHBoxLayout()
 
+        self.speed_slider = QLabeledSlider(Qt.Horizontal)
+        self.speed_slider.setRange(1, 60)
+        # Convert initial interval (ms) to FPS
+        initial_fps = int(1000 / max(1, self.anim_interval))
+        self.speed_slider.setValue(initial_fps)
+        self.speed_slider.valueChanged.connect(self.update_speed)
+        self.speed_slider.setFixedWidth(200)
+        self.speed_slider.setToolTip("Adjust animation framerate (FPS)")
+
+        speed_layout = QHBoxLayout()
+        speed_layout.addWidget(QLabel("Framerate: "))
+        speed_layout.addWidget(self.speed_slider)
+
         animation_buttons_box.addWidget(self.frame_lbl, 20, alignment=Qt.AlignLeft)
+        animation_buttons_box.addLayout(speed_layout, 20)
 
         self.first_frame_btn = QPushButton()
         self.first_frame_btn.clicked.connect(self.set_first_frame)
-        self.first_frame_btn.setShortcut(QKeySequence("f"))
+        self.first_short = QShortcut(QKeySequence("f"), self)
+        self.first_short.activated.connect(self.set_first_frame)
         self.first_frame_btn.setIcon(icon(MDI6.page_first, color="black"))
         self.first_frame_btn.setStyleSheet(self.button_select_all)
         self.first_frame_btn.setFixedSize(QSize(60, 60))
@@ -478,7 +493,8 @@ class PairEventAnnotator(CelldetectiveMainWindow):
 
         self.last_frame_btn = QPushButton()
         self.last_frame_btn.clicked.connect(self.set_last_frame)
-        self.last_frame_btn.setShortcut(QKeySequence("l"))
+        self.last_short = QShortcut(QKeySequence("l"), self)
+        self.last_short.activated.connect(self.set_last_frame)
         self.last_frame_btn.setIcon(icon(MDI6.page_last, color="black"))
         self.last_frame_btn.setStyleSheet(self.button_select_all)
         self.last_frame_btn.setFixedSize(QSize(60, 60))
@@ -499,11 +515,32 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         self.start_btn.setIconSize(QSize(30, 30))
         self.start_btn.hide()
 
+        self.toggle_short = QShortcut(Qt.Key_Space, self)
+        self.toggle_short.activated.connect(self.toggle_animation)
+
+        self.prev_frame_btn = QPushButton()
+        self.prev_frame_btn.clicked.connect(self.prev_frame)
+        self.prev_frame_btn.setIcon(icon(MDI6.chevron_left, color="black"))
+        self.prev_frame_btn.setStyleSheet(self.button_select_all)
+        self.prev_frame_btn.setFixedSize(QSize(60, 60))
+        self.prev_frame_btn.setIconSize(QSize(30, 30))
+        self.prev_frame_btn.setEnabled(False)
+
+        self.next_frame_btn = QPushButton()
+        self.next_frame_btn.clicked.connect(self.next_frame)
+        self.next_frame_btn.setIcon(icon(MDI6.chevron_right, color="black"))
+        self.next_frame_btn.setStyleSheet(self.button_select_all)
+        self.next_frame_btn.setFixedSize(QSize(60, 60))
+        self.next_frame_btn.setIconSize(QSize(30, 30))
+        self.next_frame_btn.setEnabled(False)
+
         animation_buttons_box.addWidget(
             self.first_frame_btn, 5, alignment=Qt.AlignRight
         )
+        animation_buttons_box.addWidget(self.prev_frame_btn, 5, alignment=Qt.AlignRight)
         animation_buttons_box.addWidget(self.stop_btn, 5, alignment=Qt.AlignRight)
         animation_buttons_box.addWidget(self.start_btn, 5, alignment=Qt.AlignRight)
+        animation_buttons_box.addWidget(self.next_frame_btn, 5, alignment=Qt.AlignRight)
         animation_buttons_box.addWidget(self.last_frame_btn, 5, alignment=Qt.AlignRight)
 
         self.right_panel.addLayout(animation_buttons_box, 5)
@@ -1968,10 +2005,7 @@ class PairEventAnnotator(CelldetectiveMainWindow):
                 else:
                     self.fraction = 0.25
 
-                if "interval" in instructions:
-                    self.anim_interval = int(instructions["interval"])
-                else:
-                    self.anim_interval = 1
+                self.anim_interval = 33
 
                 if "log" in instructions:
                     self.log_option = instructions["log"]
@@ -1983,7 +2017,7 @@ class PairEventAnnotator(CelldetectiveMainWindow):
             self.percentile_mode = True
             self.target_channels = [[self.channel_names[0], 0.01, 99.99]]
             self.fraction = 0.25
-            self.anim_interval = 1
+            self.anim_interval = 33
 
     def prepare_stack(self):
 
@@ -2104,6 +2138,49 @@ class PairEventAnnotator(CelldetectiveMainWindow):
             idx = self.relative_class_choice_cb.findText(self.relative_class)
             self.relative_class_choice_cb.setCurrentIndex(idx)
 
+    def update_speed(self):
+        fps = self.speed_slider.value()
+        # Convert FPS to interval in ms
+        # FPS = 1000 / interval_ms => interval_ms = 1000 / FPS
+        val = int(1000 / max(1, fps))
+
+        self.anim_interval = val
+        print(
+            f"DEBUG: Speed slider moved. FPS: {fps} -> Interval: {val} ms. Recreating animation object."
+        )
+
+        # Check if animation is allowed to run (Pause button is visible means we are Playing)
+        should_play = self.stop_btn.isVisible()
+
+        if hasattr(self, "anim") and self.anim:
+            try:
+                self.anim.event_source.stop()
+            except Exception as e:
+                print(f"DEBUG: Error stopping animation: {e}")
+
+        # Recreate animation with new interval
+        try:
+            # We must disconnect the old pick event to avoid accumulating connections
+            # although mpl_connect returns a cid, we didn't store it properly before.
+            # However, the canvas clears usually handle this if we cleared axes, but we aren't clearing axes here.
+            # Ideally we should clean up, but for now let's focus on the animation object replacement.
+
+            self.anim = FuncAnimation(
+                self.fig,
+                self.draw_frame,
+                frames=self.animation_generator,
+                interval=self.anim_interval,
+                blit=True,
+                cache_frame_data=False,
+            )
+
+            # If we were NOT playing (i.e. Paused), pause the new animation immediately
+            if not should_play:
+                self.anim.event_source.stop()
+
+        except Exception as e:
+            print(f"DEBUG: Error recreating animation: {e}")
+
     def closeEvent(self, event):
 
         self.stop()
@@ -2119,6 +2196,18 @@ class PairEventAnnotator(CelldetectiveMainWindow):
 
         gc.collect()
 
+    def animation_generator(self):
+        """
+        Generator yielding frame indices for the animation,
+        starting from the current self.framedata.
+        """
+        i = self.framedata
+        while True:
+            yield i
+            i += 1
+            if i >= self.len_movie:
+                i = 0
+
     def looped_animation(self):
         """
         Load an image.
@@ -2195,9 +2284,10 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         self.anim = FuncAnimation(
             self.fig,
             self.draw_frame,
-            frames=self.len_movie,  # better would be to cast np.arange(len(movie)) in case frame column is incomplete
+            frames=self.animation_generator,
             interval=self.anim_interval,  # in ms
             blit=True,
+            cache_frame_data=False,
         )
 
         self.fig.canvas.mpl_connect("pick_event", self.on_scatter_pick)
@@ -2855,27 +2945,63 @@ class PairEventAnnotator(CelldetectiveMainWindow):
         self.stop_btn.hide()
         self.start_btn.show()
         self.anim.pause()
+        self.prev_frame_btn.setEnabled(True)
+        self.next_frame_btn.setEnabled(True)
         self.stop_btn.clicked.connect(self.start)
 
     def start(self):
         """
-        Starts interactive animation. Adds the draw frame command to the GUI
-        handler, calls show to start the event loop.
+        Starts interactive animation.
         """
-        self.start_btn.setShortcut(QKeySequence(""))
-
-        self.last_frame_btn.setEnabled(True)
-        self.last_frame_btn.clicked.connect(self.set_last_frame)
-
-        self.first_frame_btn.setEnabled(True)
-        self.first_frame_btn.clicked.connect(self.set_first_frame)
-
         self.start_btn.hide()
         self.stop_btn.show()
 
-        self.anim.event_source.start()
+        self.prev_frame_btn.setEnabled(False)
+        self.next_frame_btn.setEnabled(False)
+
+        self.anim.resume()
         self.stop_btn.clicked.connect(self.stop)
 
+    def toggle_animation(self):
+        if self.stop_btn.isVisible():
+            self.stop()
+        else:
+            self.start()
+
+    def next_frame(self):
+        self.framedata += 1
+        if self.framedata >= self.len_movie:
+            self.framedata = 0
+        self.draw_frame(self.framedata)
+        self.fcanvas.canvas.draw()
+
+    def prev_frame(self):
+        self.framedata -= 1
+        if self.framedata < 0:
+            self.framedata = self.len_movie - 1
+        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/gui/plot_signals_ui.py

@@ -28,6 +28,7 @@ import matplotlib.pyplot as plt
 
 plt.rcParams["svg.fonttype"] = "none"
 from glob import glob
+from celldetective import get_logger
 from natsort import natsorted
 import math
 from celldetective.gui.base.components import CelldetectiveWidget
@@ -36,6 +37,8 @@ import matplotlib.cm
 from celldetective.relative_measurements import expand_pair_table
 from celldetective.neighborhood import extract_neighborhood_in_pair_table
 
+logger = get_logger(__name__)
+
 
 class ConfigSignalPlot(CelldetectiveWidget):
     """
@@ -173,7 +176,7 @@ class ConfigSignalPlot(CelldetectiveWidget):
             if hasattr(matplotlib.cm, str(cm).lower()):
                 try:
                     self.cbs[-1].addColormap(cm.lower())
-                except:
+                except Exception:
                     pass
 
         self.cbs[0].setCurrentIndex(1)
@@ -257,7 +260,9 @@ class ConfigSignalPlot(CelldetectiveWidget):
                 )
             )
             if not tables_pairs:
-                print("No pair table found... please compute the pair measurements...")
+                logger.warning(
+                    "No pair table found. Please compute the pair measurements."
+                )
                 return None
             self.cols_pairs = extract_cols_from_table_list(tables_pairs)
 
@@ -333,7 +338,9 @@ class ConfigSignalPlot(CelldetectiveWidget):
             time_idx = np.array(
                 [s.startswith("t_") or s.startswith("t0_") for s in self.all_columns]
             )
-            print(f"{class_idx=} {time_idx=} {self.all_columns=}")
+            logger.debug(
+                f"class_idx={class_idx}, time_idx={time_idx}, columns={self.all_columns}"
+            )
 
             try:
                 if len(class_idx) > 0:
@@ -345,7 +352,7 @@ class ConfigSignalPlot(CelldetectiveWidget):
                 else:
                     time_columns = []
             except Exception as e:
-                print(f"L266 columns not found {e}")
+                logger.warning(f"Columns not found: {e}")
                 self.auto_close = True
                 return None
 
@@ -435,8 +442,20 @@ class ConfigSignalPlot(CelldetectiveWidget):
                 query_text = self.query_le.text()
                 if query_text != "":
                     self.df = self.df.query(query_text)
+            except pd.errors.UndefinedVariableError as e:
+                logger.warning(f"Query failed - undefined variable: {e}")
+                generic_message(
+                    f"Query error: column not found.\n{e}\n\nPlease check your column names."
+                )
+                return None
+            except SyntaxError as e:
+                logger.warning(f"Query failed - syntax error: {e}")
+                generic_message(f"Query syntax error: {e}\n\nCheck your query format.")
+                return None
             except Exception as e:
-                print(e, " The query is misunderstood and will not be applied...")
+                logger.warning(f"Query not applied: {e}")
+                generic_message(f"Query could not be applied: {e}")
+                return None
 
             self.feature_selected = self.feature_cb.currentText()
             self.feature_choice_widget.close()
@@ -454,17 +473,17 @@ class ConfigSignalPlot(CelldetectiveWidget):
                     )
                     self.plot_window.show()
                 except Exception as e:
-                    print(f"{e=}")
+                    logger.debug(f"Error creating plot widget: {e}")
 
     def process_signal(self):
 
         self.FrameToMin = float(self.time_calibration_le.text().replace(",", "."))
-        print(f"Time calibration set to 1 frame =  {self.FrameToMin} min...")
+        logger.info(f"Time calibration set to 1 frame = {self.FrameToMin} min")
 
         # read instructions from combobox options
         self.load_available_tables()
         class_col = self.class_columns[self.cbs[1].currentIndex()]
-        print(f"{class_col=}")
+        logger.debug(f"Selected class column: {class_col}")
 
         if self.df is not None:
 
@@ -512,8 +531,8 @@ class ConfigSignalPlot(CelldetectiveWidget):
             )
 
         if self.df is None:
-            print("No table could be found...")
-            generic_message("No table could be found to compute survival...")
+            logger.warning("No table could be found.")
+            generic_message("No table could be found to compute signals.")
             self.close()
             return None
         else:
@@ -533,9 +552,7 @@ class ConfigSignalPlot(CelldetectiveWidget):
         # Per position signal
         self.df = self.df.dropna(subset=["FRAME"])
         if len(self.df) == 0:
-            print(
-                "Warning... The dataset is empty. Please check your filters. Abort..."
-            )
+            logger.warning("The dataset is empty. Please check your filters.")
             return None
 
         pairs = False
@@ -714,7 +731,7 @@ class ConfigSignalPlot(CelldetectiveWidget):
                     ):
 
                         if "area" in list(track_group.columns):
-                            print("area in list")
+                            logger.debug("Using 'area' column for first detection")
                             feat = track_group["area"].values
                         else:
                             feat = feature
@@ -731,7 +748,7 @@ class ConfigSignalPlot(CelldetectiveWidget):
                         matrix[cid, loc_t + 1] = second_feature
 
                     cid += 1
-                except:
+                except (KeyError, IndexError, ValueError):
                     pass
         return matrix
 

celldetective/gui/process_block.py

@@ -1361,12 +1361,12 @@ class ProcessPanel(QFrame, Styles):
                     msgBox = QMessageBox()
                     msgBox.setIcon(QMessageBox.Question)
                     msgBox.setText(
-                        "A measurement table already exists. Previously annotated data for\nthis position will be lost. Do you want to proceed?"
+                        "A measurement table already exists. Previously annotated data for this position will be lost. Do you want to proceed?"
                     )
                     msgBox.setWindowTitle("Info")
                     msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
                     if msgBox.exec() == QMessageBox.No:
-                        run_tracking = False
+                        return None
 
             if run_tracking:
                 track_args = {"mode": self.mode, "n_threads": self.n_threads}

celldetective/gui/seg_model_loader.py

@@ -129,14 +129,14 @@ class SegmentationModelLoader(CelldetectiveWidget):
     def unlock_upload(self):
         if self.stardist_button.isChecked():
             if np.any(
-                [c.currentText() != "--" for c in self.channel_layout.channel_cbs]
+                [c.currentData() != "--" for c in self.channel_layout.channel_cbs]
             ):
                 self.upload_button.setEnabled(True)
             else:
                 self.upload_button.setEnabled(False)
         elif self.cellpose_button.isChecked():
             if np.any(
-                [c.currentText() != "--" for c in self.channel_layout.channel_cbs]
+                [c.currentData() != "--" for c in self.channel_layout.channel_cbs]
             ):
                 self.upload_button.setEnabled(True)
             else:
@@ -373,7 +373,7 @@ class SegmentationModelLoader(CelldetectiveWidget):
 
         channels = []
         for i in range(len(self.channel_layout.channel_cbs)):
-            channels.append(self.channel_layout.channel_cbs[i].currentText())
+            channels.append(self.channel_layout.channel_cbs[i].currentData())
 
         if self.file_label.text() == "No file chosen":
             generic_message("Please select a model first...")
@@ -450,7 +450,7 @@ class SegmentationModelLoader(CelldetectiveWidget):
 
         channels = []
         for i in range(len(self.channel_layout.channel_cbs)):
-            channels.append(self.channel_layout.channel_cbs[i].currentText())
+            channels.append(self.channel_layout.channel_cbs[i].currentData())
 
         slots_to_keep = np.where(np.array(channels) != "--")[0]
         while "--" in channels: