celldetective 1.5.0b1__py3-none-any.whl → 1.5.0b3__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.5.0b1"
+__version__ = "1.5.0b3"

celldetective/gui/InitWindow.py

@@ -21,6 +21,7 @@ from PyQt5.QtWidgets import (
     QPushButton,
     QMessageBox,
     QVBoxLayout,
+    QProgressDialog,
 )
 from fonticon_mdi6 import MDI6
 from psutil import cpu_count
@@ -57,6 +58,8 @@ class BackgroundLoader(QThread):
             import scipy.ndimage
             import tifffile
             import numpy
+            import napari
+            from celldetective.napari.utils import launch_napari_viewer
         except Exception:
             logger.error("Background packages not loaded...")
         logger.info("Background packages loaded...")
@@ -322,14 +325,18 @@ class AppInitWindow(CelldetectiveMainWindow):
     def reload_previous_experiments(self):
 
         self.recent_file_acts = []
-        if os.path.exists(os.sep.join([self.soft_path, "celldetective", "recent.txt"])):
-            recent_exps = open(
-                os.sep.join([self.soft_path, "celldetective", "recent.txt"]), "r"
-            )
-            recent_exps = recent_exps.readlines()
-            recent_exps = [r.strip() for r in recent_exps]
+        recent_path = os.sep.join([self.soft_path, "celldetective", "recent.txt"])
+        if os.path.exists(recent_path):
+            with open(recent_path, "r") as f:
+                recent_exps = [r.strip() for r in f.readlines()]
             recent_exps.reverse()
-            recent_exps = list(dict.fromkeys(recent_exps))
+            recent_exps = list(dict.fromkeys(recent_exps))[:10]
+
+            # Auto-clean the file as well
+            with open(recent_path, "w") as f:
+                for r in reversed(recent_exps):
+                    f.write(r + "\n")
+
             self.recent_file_acts = [QAction(r, self) for r in recent_exps]
             for r in self.recent_file_acts:
                 r.triggered.connect(
@@ -337,14 +344,33 @@ class AppInitWindow(CelldetectiveMainWindow):
                 )
 
     def correct_seg_annotation(self):
+
         from celldetective.napari.utils import correct_annotation
 
         self.filename, _ = QFileDialog.getOpenFileName(
             self, "Open Image", "/home/", "TIF Files (*.tif)"
         )
+
         if self.filename != "":
+            # 2. Show progress bar for opening the image in Napari
+            progress_open = QProgressDialog(
+                f"Opening {os.path.basename(self.filename)} in napari...",
+                None,
+                0,
+                0,
+                self,
+            )
+            progress_open.setWindowTitle("Please wait")
+            progress_open.setWindowModality(Qt.WindowModal)
+            progress_open.setMinimumDuration(0)
+            progress_open.show()
+            QApplication.processEvents()
+
             logger.info(f"Opening {self.filename} in napari...")
-            correct_annotation(self.filename)
+            try:
+                correct_annotation(self.filename)
+            finally:
+                progress_open.close()
         else:
             return None
 
@@ -503,10 +529,23 @@ class AppInitWindow(CelldetectiveMainWindow):
                 logger.info(f"Number of positions per well:")
                 pretty_table(number_pos)
 
-                with open(
-                    os.sep.join([self.soft_path, "celldetective", "recent.txt"]), "a+"
-                ) as f:
-                    f.write(self.exp_dir + "\n")
+                recent_path = os.sep.join(
+                    [self.soft_path, "celldetective", "recent.txt"]
+                )
+                recent_exps = []
+                if os.path.exists(recent_path):
+                    with open(recent_path, "r") as f:
+                        recent_exps = [r.strip() for r in f.readlines()]
+
+                recent_exps.append(self.exp_dir)
+                # Deduplicate (keep latest)
+                recent_exps = list(dict.fromkeys(reversed(recent_exps)))
+                recent_exps.reverse()  # Back to original order (latest at end)
+                recent_exps = recent_exps[-10:]  # Keep only last 10
+
+                with open(recent_path, "w") as f:
+                    for r in recent_exps:
+                        f.write(r + "\n")
 
             threading.Thread(
                 target=log_position_stats, args=(wells,), daemon=True

celldetective/gui/base/components.py

@@ -11,11 +11,13 @@ from PyQt5.QtWidgets import (
     QStylePainter,
     QStyleOptionComboBox,
     QStyle,
-    QFrame,
     QSizePolicy,
     QProgressDialog,
+    QPushButton,
+    QFrame,
 )
 from PyQt5.QtCore import Qt, pyqtSignal, QEvent
+from superqt.fonticon import icon
 from celldetective.gui.base.styles import Styles
 
 
@@ -118,6 +120,8 @@ class QCheckableComboBox(QComboBox):
         actions = self.toolMenu.actions()
 
         item = self.model().itemFromIndex(index)
+        if item is None:
+            return
         if item.checkState() == Qt.Checked:
             item.setCheckState(Qt.Unchecked)
             actions[idx].setChecked(False)
@@ -247,3 +251,20 @@ class QHSeperationLine(QFrame):
         self.setFrameShape(QFrame.HLine)
         self.setFrameShadow(QFrame.Sunken)
         self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
+
+
+class HoverButton(QPushButton):
+    def __init__(self, text, icon_enum, default_color="black", hover_color="white"):
+        super().__init__(text)
+        self.icon_enum = icon_enum
+        self.default_color = default_color
+        self.hover_color = hover_color
+        self.setIcon(icon(self.icon_enum, color=self.default_color))
+
+    def enterEvent(self, event):
+        self.setIcon(icon(self.icon_enum, color=self.hover_color))
+        super().enterEvent(event)
+
+    def leaveEvent(self, event):
+        self.setIcon(icon(self.icon_enum, color=self.default_color))
+        super().leaveEvent(event)

celldetective/gui/base_annotator.py

@@ -47,6 +47,9 @@ from celldetective.gui.gui_utils import (
 from celldetective.gui.base.figure_canvas import FigureCanvas
 from celldetective.gui.base.utils import center_window
 import gc
+from celldetective import get_logger
+
+logger = get_logger(__name__)
 
 
 class BaseAnnotator(CelldetectiveMainWindow, Styles):
@@ -302,7 +305,11 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
         ]
         # self.log_btns = [QPushButton() for i in range(self.n_signals)]
 
-        signals = list(self.df_tracks.columns)
+        signals = [
+            c
+            for c in self.df_tracks.columns
+            if pd.api.types.is_numeric_dtype(self.df_tracks[c])
+        ]
 
         to_remove = [
             "FRAME",
@@ -354,7 +361,10 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
 
         for i in range(len(self.signal_choice_cb)):
             self.signal_choice_cb[i].addItems(["--"] + signals)
-            self.signal_choice_cb[i].setCurrentIndex(i + 1)
+            if i + 1 < self.signal_choice_cb[i].count():
+                self.signal_choice_cb[i].setCurrentIndex(i + 1)
+            else:
+                self.signal_choice_cb[i].setCurrentIndex(0)
             self.signal_choice_cb[i].currentIndexChanged.connect(self.plot_signals)
 
     def on_scatter_pick(self, event):
@@ -364,7 +374,7 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
         self.correct_btn.disconnect()
         self.correct_btn.clicked.connect(self.show_annotation_buttons)
 
-        print(f"{self.selection=}")
+        logger.info(f"{self.selection=}")
 
         ind = event.ind
 
@@ -711,7 +721,7 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
                 try:
                     self.df_tracks = self.df_tracks.drop([c], axis=1)
                 except Exception as e:
-                    print(e)
+                    logger.error(e)
             item_idx = self.class_choice_cb.findText(class_to_delete)
             self.class_choice_cb.removeItem(item_idx)
 
@@ -755,7 +765,7 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
                 self.log_btn.setIcon(icon(MDI6.math_log, color="black"))
                 self.log_scale = False
         except Exception as e:
-            print(e)
+            logger.error(e)
 
         # self.cell_ax.autoscale()
         self.cell_fcanvas.canvas.draw_idle()
@@ -839,9 +849,9 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
                 pathsave += ".npy"
             try:
                 np.save(pathsave, training_set)
-                print(f"File successfully written in {pathsave}.")
+                logger.info(f"File successfully written in {pathsave}.")
             except Exception as e:
-                print(f"Error {e}...")
+                logger.error(f"Error {e}...")
 
     def create_new_event_class(self):
 
@@ -897,10 +907,11 @@ class BaseAnnotator(CelldetectiveMainWindow, Styles):
 
     def save_trajectories(self):
         # specific to signal/static annotator
-        print("Save trajectory function not implemented for BaseAnnotator class...")
+        logger.info(
+            "Save trajectory function not implemented for BaseAnnotator class..."
+        )
 
     def cancel_selection(self):
-        print("we are in cancel selection...")
         self.hide_annotation_buttons()
         self.correct_btn.setEnabled(False)
         self.correct_btn.setText("correct")

celldetective/gui/control_panel.py

@@ -58,14 +58,15 @@ logger = logging.getLogger(__name__)
 
 
 class BackgroundLoader(QThread):
-     def run(self):
-         logger.info("Loading background packages...")
-         try:
-             from celldetective.gui.viewers.base_viewer import StackVisualizer
-             self.StackVisualizer = StackVisualizer
-         except Exception:
-             logger.error("Background packages not loaded...")
-         logger.info("Background packages loaded...")
+    def run(self):
+        logger.info("Loading background packages...")
+        try:
+            from celldetective.gui.viewers.base_viewer import StackVisualizer
+
+            self.StackVisualizer = StackVisualizer
+        except Exception:
+            logger.error("Background packages not loaded...")
+        logger.info("Background packages loaded...")
 
 
 class ControlPanel(CelldetectiveMainWindow):
@@ -179,9 +180,11 @@ class ControlPanel(CelldetectiveMainWindow):
 
         name = self.exp_dir.split(os.sep)[-2]
         experiment_label = QLabel(f"Experiment:")
-        experiment_label.setStyleSheet("""
+        experiment_label.setStyleSheet(
+            """
 			font-weight: bold;
-			""")
+			"""
+        )
 
         self.folder_exp_btn = QPushButton()
         self.folder_exp_btn.setIcon(icon(MDI6.folder, color="black"))
@@ -553,16 +556,18 @@ class ControlPanel(CelldetectiveMainWindow):
             for p in self.ProcessPopulations:
                 p.check_seg_btn.setEnabled(False)
                 p.check_tracking_result_btn.setEnabled(False)
-                p.view_tab_btn.setEnabled(True)
-                p.signal_analysis_action.setEnabled(True)
+                p.view_tab_btn.setEnabled(self.position_list.isAnySelected())
+                p.signal_analysis_action.setEnabled(self.position_list.isAnySelected())
                 p.check_seg_btn.setEnabled(False)
                 p.check_tracking_result_btn.setEnabled(False)
-                p.check_measurements_btn.setEnabled(False)
-                p.check_signals_btn.setEnabled(False)
+                p.check_measurements_btn.setEnabled(self.position_list.isAnySelected())
+                p.check_signals_btn.setEnabled(self.position_list.isAnySelected())
                 p.delete_tracks_btn.hide()
 
-            self.NeighPanel.view_tab_btn.setEnabled(True)
-            self.NeighPanel.check_signals_btn.setEnabled(False)
+            self.NeighPanel.view_tab_btn.setEnabled(self.position_list.isAnySelected())
+            self.NeighPanel.check_signals_btn.setEnabled(
+                self.position_list.isAnySelected()
+            )
             self.view_stack_btn.setEnabled(False)
 
         elif self.well_list.isMultipleSelection():