celldetective 1.5.0b8__tar.gz → 1.5.0b10__tar.gz

{celldetective-1.5.0b8 → celldetective-1.5.0b10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b8
+Version: 1.5.0b10
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.5.0b10/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.5.0b10"

{celldetective-1.5.0b8 → celldetective-1.5.0b10}/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-1.5.0b8 → celldetective-1.5.0b10}/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-1.5.0b8 → celldetective-1.5.0b10}/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-1.5.0b8 → celldetective-1.5.0b10}/celldetective/gui/settings/_settings_measurements.py

@@ -838,7 +838,6 @@ class SettingsMeasurements(CelldetectiveSettingsPanel):
             self.imshow_digit_window.canvas.draw()
             self.imshow_digit_window.show()
 
-
     def control_haralick_intensity_histogram(self):
         """
         Load an image for the first experiment movie found.
@@ -1123,7 +1122,9 @@ class SettingsMeasurements(CelldetectiveSettingsPanel):
                 # else:
                 # 	invert_value = None
 
-                from celldetective.gui.viewers.spot_detection_viewer import SpotDetectionVisualizer
+                from celldetective.gui.viewers.spot_detection_viewer import (
+                    SpotDetectionVisualizer,
+                )
 
                 self.spot_visual = SpotDetectionVisualizer(
                     frame_slider=True,
@@ -1139,6 +1140,13 @@ class SettingsMeasurements(CelldetectiveSettingsPanel):
                     parent_diameter_le=self.diameter_value,
                     parent_threshold_le=self.threshold_value,
                     parent_preprocessing_list=self.spot_preprocessing.list,
+                    initial_diameter=self.diameter_value.text(),
+                    initial_threshold=self.threshold_value.text(),
+                    initial_preprocessing=(
+                        self.spot_preprocessing.list.items
+                        if self.spot_preprocessing.list.items
+                        else None
+                    ),
                     # parent_invert_check=self.invert_check,
                     # invert = self.invert_check.isChecked(),
                     # invert_value = self.invert_value_le.text().replace(',','.'),

{celldetective-1.5.0b8 → celldetective-1.5.0b10}/celldetective/gui/survival_ui.py

@@ -19,11 +19,13 @@ from celldetective.utils.data_cleaning import extract_cols_from_table_list
 from celldetective.utils.parsing import _extract_labels_from_config
 from celldetective.utils.data_loaders import load_experiment_tables
 import numpy as np
+import pandas as pd
 import os
 import matplotlib.pyplot as plt
 
 plt.rcParams["svg.fonttype"] = "none"
 from glob import glob
+from celldetective import get_logger
 from celldetective.gui.base.styles import Styles
 from celldetective.gui.base.components import CelldetectiveWidget
 from matplotlib import colormaps
@@ -32,6 +34,8 @@ from celldetective.relative_measurements import expand_pair_table
 import matplotlib.cm
 from celldetective.neighborhood import extract_neighborhood_in_pair_table
 
+logger = get_logger(__name__)
+
 
 class ConfigSurvival(CelldetectiveWidget):
     """
@@ -225,7 +229,9 @@ class ConfigSurvival(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)
 
@@ -264,7 +270,7 @@ class ConfigSurvival(CelldetectiveWidget):
                     and str(self.population_neigh) not in c
                 ]
 
-            print(f"{self.neighborhood_keys=}")
+            logger.debug(f"Neighborhood keys: {self.neighborhood_keys}")
 
             time_idx = np.array(
                 [s.startswith("t_") or s.startswith("t0") for s in self.cols_pairs]
@@ -281,8 +287,8 @@ class ConfigSurvival(CelldetectiveWidget):
 
             try:
                 time_columns = list(self.all_columns[time_idx])
-            except:
-                print("no column starts with t")
+            except (IndexError, KeyError):
+                logger.warning("No column starts with 't_' for time reference.")
                 self.auto_close = True
                 return None
 
@@ -295,8 +301,15 @@ class ConfigSurvival(CelldetectiveWidget):
 
     def process_survival(self):
 
+        # Validate that reference time and time of interest are different
+        time_of_reference = self.cbs[1].currentText()
+        time_of_interest = self.cbs[2].currentText()
+        if time_of_reference == time_of_interest:
+            generic_message("Reference time and time of interest must be different.")
+            return None
+
         self.FrameToMin = float(self.time_calibration_le.text().replace(",", "."))
-        self.time_of_interest = self.cbs[2].currentText()
+        self.time_of_interest = time_of_interest
         if self.time_of_interest == "t0":
             self.class_of_interest = "class"
         elif self.time_of_interest.startswith("t0"):
@@ -312,8 +325,22 @@ class ConfigSurvival(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 (e.g., 'column > 100')."
+                )
+                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.interpret_pos_location()
 
@@ -391,11 +418,12 @@ class ConfigSurvival(CelldetectiveWidget):
                     / self.FrameToMin
                 )
                 if not 0 < cut_observation_time <= (self.df["FRAME"].max()):
-                    print("Invalid cut time (larger than movie length)... Not applied.")
+                    logger.warning(
+                        "Invalid cut time (larger than movie length). Not applied."
+                    )
                     cut_observation_time = None
         except Exception as e:
-            print(f"{e=}")
-            pass
+            logger.debug(f"Cut time parsing error: {e}")
 
         pairs = False
         if self.neighborhood_keys is not None:
@@ -403,7 +431,7 @@ class ConfigSurvival(CelldetectiveWidget):
 
         # Per position survival
         for block, movie_group in self.df.groupby(["well", "position"]):
-            print(f"{block=}")
+            logger.debug(f"Processing block: {block}")
             ks = compute_survival(
                 movie_group,
                 self.class_of_interest,
@@ -413,7 +441,7 @@ class ConfigSurvival(CelldetectiveWidget):
                 cut_observation_time=cut_observation_time,
                 pairs=pairs,
             )
-            print(f"{ks=}")
+            logger.debug(f"Survival fit result: {ks}")
             if ks is not None:
                 self.df_pos_info.loc[
                     self.df_pos_info["pos_path"] == block[1], "survival_fit"