celldetective 1.5.0b1__py3-none-any.whl → 1.5.0b2__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.5.0b1"
+__version__ = "1.5.0b2"

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...")
@@ -337,14 +340,33 @@ 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
 

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
 
 
@@ -247,3 +249,20 @@ 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):
@@ -364,7 +367,7 @@ 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 +714,7 @@ 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 +758,7 @@ 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 +842,9 @@ 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 +900,11 @@ 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")