cellects 0.1.3__py3-none-any.whl → 0.2.6__py3-none-any.whl

cellects/__main__.py

@@ -1,23 +1,45 @@
 #!/usr/bin/env python3
-"""Launcher of cellects software.
+"""
+Launcher for the Cellects software.
+
+This module initializes logging configuration, creates the Qt application instance,
+loads Cellects icon, and launches the main GUI interface.
+"""
 
- """
-import logging
 import sys
+import logging
 import coloredlogs
 from PySide6 import QtWidgets, QtGui
 from cellects.core.cellects_paths import ICONS_DIR
 
-# These two lines allow the taskbar icon to be cellects_icon instead if python icon.
 if sys.platform.startswith('win'):
-    import ctypes
-    ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID('company.app.1')
-
+    try:
+        import ctypes
+        ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID('company.app.1')
+    except Exception as e:
+        logging.getLogger(__name__).debug(f"Windows taskbar icon setup failed: {e}")
 
-LOGLEVEL = "INFO" #"DEBUG"
+LOGLEVEL = "INFO" # Set to DEBUG for development
 
 def _initialize_coloredlogs(loglevel: str = 'DEBUG') -> None:
-    """Initialize logging parameters with coloredlogs library."""
+
+    """Initialize colored console logging with custom format.
+
+    Parameters
+    ----------
+    loglevel : str, optional
+        Logging threshold level (default is DEBUG). Accepts standard Python
+        logging level strings like 'DEBUG', 'INFO', or 'WARNING'.
+
+    Notes
+    -----
+    This function must be called before any other logging setup to ensure proper
+    configuration of colored output.
+    """
+    # Configure basic logging before applying colored logs
+    logging.basicConfig(level=loglevel)
+
+    # Apply colored formatting to the root logger
     coloredlogs.install(
         logger=logging.basicConfig(),
         level=loglevel,
@@ -26,23 +48,41 @@ def _initialize_coloredlogs(loglevel: str = 'DEBUG') -> None:
 
 
 def run_cellects():
-    """Entry point of cellects software."""
+    """Run the Cellects application entry point.
+
+        This function initializes the Qt application, loads platform-specific icons,
+        creates and displays the main window widget, then starts the event loop.
+
+        Raises
+        ------
+        ImportError
+            If required GUI components cannot be loaded
+        """
     _initialize_coloredlogs(LOGLEVEL)
-    from cellects.gui.cellects import CellectsMainWidget
-    app = QtWidgets.QApplication([])
-
-    # Add the icon file to the app
-    icon = QtGui.QIcon()
-    if sys.platform.startswith('win'):
-        icon.addPixmap(QtGui.QPixmap(ICONS_DIR / "cellects_icon.ico"))
-    else:
-        icon.addPixmap(QtGui.QPixmap(ICONS_DIR / "cellects_icon.icns"))
-    app.setWindowIcon(icon)
-    # Start session
-    session = CellectsMainWidget()
-    session.instantiate()
-    session.show()
-    sys.exit(app.exec())
+
+    try:
+        from cellects.gui.cellects import CellectsMainWidget
+
+        # Initialize application
+        app = QtWidgets.QApplication([])
+
+        # Set custom window icon for taskbar (platform-specific handling)
+        icon = QtGui.QIcon()
+        platform_icon_path = (
+            ICONS_DIR / "cellects_icon.ico" if sys.platform.startswith('win')
+            else ICONS_DIR / "cellects_icon.icns"
+        )
+        icon.addPixmap(QtGui.QPixmap(str(platform_icon_path)))
+        app.setWindowIcon(icon)
+
+        # Create and display main window
+        session = CellectsMainWidget()
+        session.instantiate()
+        session.show()
+        sys.exit(app.exec())
+    except Exception as e:
+        logging.getLogger(__name__).critical("Application failed to start", exc_info=True)
+        raise
 
 
 if __name__ == "__main__":

cellects/config/all_vars_dict.py

@@ -41,7 +41,6 @@ class DefaultDicts:
             'extract_time_interval': True,
             'do_multiprocessing': False,
             'extension': '.tif',
-            'first_detection_frame': 1,
             'folder_number': 1,
             'first_folder_sample_number': 1,
             'first_move_threshold_in_mm²': 10,
@@ -64,11 +63,15 @@ class DefaultDicts:
             'set_spot_shape': True,
             'set_spot_size': True,
             'starting_blob_hsize_in_mm': 15,
-            'starting_blob_shape': None
+            'starting_blob_shape': None,
+            'auto_mesh_side_length': True,
+            'auto_mesh_step_length': True,
+            'auto_mesh_min_int_var': True,
         }
 
         self.vars = {
-            'analyzed_individuals': np.empty(0, dtype=np.uint16),
+            'video_list': None,
+            'analyzed_individuals': np.array([1], dtype=np.uint16),
             'arena_shape': 'rectangle', # 'circle',
             'bio_label': 1,
             'bio_label2': 1,
@@ -83,16 +86,19 @@ class DefaultDicts:
             'first_move_threshold': None,
             'img_number': 0,
             'iso_digi_analysis': True,
+            'first_detection_frame': 0,
             'luminosity_threshold': 127,
             'max_size_for_connection': 300,
             'min_size_for_connection': 20,
             'origin_state': 'fluctuating',
             'oscilacyto_analysis': False,
-            'network_analysis': False,
-            'graph_extraction': False,
-            'network_detection_threshold': 20,
-            'network_mesh_side_length': 8,
-            'network_mesh_step_length': 2,
+
+            'rolling_window_segmentation': {'do': False, 'side_len': None, 'step': None, 'min_int_var': None},
+            'grid_segmentation': False,
+            'mesh_side_length': 4,
+            'mesh_step_length': 2,
+            'mesh_min_int_var': 20,
+
             'fractal_analysis': False,
             'fractal_box_side_threshold': 32,
             'fractal_zoom_step': 0,
@@ -115,11 +121,12 @@ class DefaultDicts:
             'maximal_growth_factor': 0.05,
             'min_ram_free': 0.87,
             'expected_oscillation_period': 2,  # (min)
-            'minimal_oscillating_cluster_size': 10,  # (pixels)
+            'minimal_oscillating_cluster_size': 50,  # (pixels)
             'output_in_mm': True,
             'save_processed_videos': True,
             'several_blob_per_arena': False,
             'time_step': 1,
+            'time_step_is_arbitrary': True,
             'true_if_use_light_AND_slope_else_OR': False,
             'do_fading': False,
             'fading': 0,
@@ -128,13 +135,12 @@ class DefaultDicts:
             'exif': [],
             'lose_accuracy_to_save_memory': True,
             'save_coord_specimen': False,
-            'save_coord_contour': False,
+            'save_graph': False,
             'save_coord_thickening_slimming': False,
             'save_coord_network': False,
-            'grid_segmentation': False,
             # Data stored during analysis:
             'descriptors': descriptors,
-            'filter_spec': {'filter1_type': "", 'filter1_param': [1., 1.], 'filter2_type': "", 'filter2_param': [1., 1.]},
+            'filter_spec': {'filter1_type': "", 'filter1_param': [.5, 1.], 'filter2_type': "", 'filter2_param': [.5, 1.]},
         }
 
     def save_as_pkl(self, po=None):
@@ -148,8 +154,3 @@ class DefaultDicts:
             po.all = self.all
             po.vars = self.vars
             po.save_variable_dict()
-
-
-
-if __name__ == "__main__":
-    DefaultDicts().save_as_pkl()