celldetective 1.4.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.4.1"

celldetective/exceptions.py

@@ -0,0 +1,11 @@
+class QueryError(Exception):
+    """Base class for query-related errors."""
+
+class EmptyQueryError(QueryError):
+    pass
+
+class MissingColumnsError(QueryError):
+    def __init__(self, missing_cols):
+        msg = f"The following columns are missing from the DataFrame: {missing_cols}"
+        super().__init__(msg)
+        self.missing_cols = missing_cols

celldetective/filters.py

@@ -1,4 +1,5 @@
-from skimage.filters import difference_of_gaussians, threshold_otsu, threshold_local, threshold_niblack, threshold_sauvola
+from skimage.filters import difference_of_gaussians, threshold_multiotsu, threshold_otsu, threshold_local, \
+	threshold_niblack, threshold_sauvola
 from celldetective.utils import interpolate_nan
 import scipy.ndimage as snd
 import numpy as np
@@ -102,6 +103,11 @@ def otsu_filter(img, *kwargs):
 	binary = img >= thresh
 	return binary.astype(float)
 
+def multiotsu_filter(img, classes=3, *kwargs):
+	thresholds = threshold_multiotsu(img, classes=classes)
+	regions = np.digitize(img, bins=thresholds)
+	return regions.astype(float)
+	
 def local_filter(img, *kwargs):
 	thresh = threshold_local(img.astype(float), *kwargs)
 	binary = img >= thresh

celldetective/gui/InitWindow.py

@@ -83,7 +83,10 @@ class AppInitWindow(CelldetectiveMainWindow):
 		self.experiment_path_selection.setDragEnabled(True)
 		self.experiment_path_selection.setFixedWidth(430)
 		self.experiment_path_selection.textChanged[str].connect(self.check_path_and_enable_opening)
-		self.foldername = os.getcwd()
+		try:
+			self.foldername = os.getcwd()
+		except FileNotFoundError as e:
+			self.foldername = ""
 		self.experiment_path_selection.setPlaceholderText('/path/to/experiment/folder/')
 		self.locate_exp_layout.addWidget(self.experiment_path_selection, 90)
 

celldetective/gui/__init__.py

@@ -1,22 +1,15 @@
 from .styles import Styles
 from .base_components import CelldetectiveWidget, CelldetectiveMainWindow
-from .btrack_options import ConfigTracking
 from .json_readers import ConfigEditor
 from .tableUI import TableUI
-from .measurement_options import ConfigMeasurements
-from .neighborhood_options import ConfigNeighborhoods
 from .classifier_widget import ClassifierWidget
 from .survival_ui import ConfigSurvival
 from .plot_signals_ui import ConfigSignalPlot
-from .signal_annotator_options import ConfigSignalAnnotator
-from .signal_annotator import SignalAnnotator
-from .signal_annotator2 import SignalAnnotator2
-from .retrain_signal_model_options import ConfigSignalModelTraining
-from .retrain_segmentation_model_options import ConfigSegmentationModelTraining
+from .event_annotator import EventAnnotator
+from .pair_event_annotator import PairEventAnnotator
 from .thresholds_gui import ThresholdConfigWizard
 from .seg_model_loader import SegmentationModelLoader
 from .process_block import ProcessPanel, NeighPanel, PreprocessingPanel
 from .analyze_block import AnalysisPanel
 from .control_panel import ControlPanel
 from .configure_new_exp import ConfigNewExperiment
-

celldetective/gui/about.py

@@ -17,7 +17,7 @@ class AboutWidget(CelldetectiveWidget):
 		self.setMaximumWidth(320)
 		center_window(self)
 		
-		logo = QPixmap(os.sep.join([get_software_location(), 'celldetective', 'icons', 'logo.png']))
+		logo = QPixmap(self.celldetective_logo_path)
 		
 		# Create the layout
 		layout = QVBoxLayout(self)
@@ -31,7 +31,7 @@ class AboutWidget(CelldetectiveWidget):
 									""")
 		layout.addWidget(self.soft_name, alignment=Qt.AlignCenter)
 		
-		self.version_lbl = QLabel(f"Version {__version__} <a href=\"https://github.com/remyeltorro/celldetective"
+		self.version_lbl = QLabel(f"Version {__version__} <a href=\"https://github.com/celldetective/celldetective"
 								  f"/releases\">(release notes)</a>")
 		self.version_lbl.setOpenExternalLinks(True)
 		layout.addWidget(self.version_lbl, alignment=Qt.AlignCenter)