celldetective 1.4.1.post1__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

tests/gui/test_project.py

@@ -1,99 +1,147 @@
 import pytest
 from PyQt5 import QtCore
+
+import celldetective.gui.preprocessing_block
 from celldetective.gui.InitWindow import AppInitWindow
-from celldetective.utils import get_software_location
+from celldetective import get_software_location
 import os
 
 software_location = get_software_location()
 
+
 @pytest.fixture
 def app(qtbot):
-	test_app = AppInitWindow(software_location=software_location)
-	qtbot.addWidget(test_app)
-	return test_app
+    test_app = AppInitWindow(software_location=software_location)
+    qtbot.addWidget(test_app)
+    return test_app
+
 
 def test_open_project(app, qtbot):
-	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
-	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
-	qtbot.wait(10000)
+    app.experiment_path_selection.setText(software_location + os.sep + "examples/demo")
+    qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+    qtbot.wait(10000)
+
 
 def test_launch_demo(app, qtbot):
-	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
-	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+    app.experiment_path_selection.setText(software_location + os.sep + "examples/demo")
+    qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
 
 def test_preprocessing_panel(app, qtbot):
 
-	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
-	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+    app.experiment_path_selection.setText(software_location + os.sep + "examples/demo")
+    qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
+    qtbot.mouseClick(
+        app.control_panel.PreprocessingPanel.collapse_btn,
+        QtCore.Qt.LeftButton,
+    )
+    qtbot.mouseClick(
+        app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn,
+        QtCore.Qt.LeftButton,
+    )
+    qtbot.mouseClick(
+        app.control_panel.PreprocessingPanel.collapse_btn,
+        QtCore.Qt.LeftButton,
+    )
 
-	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
-	qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
-	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
 
 def test_app(app, qtbot):
 
-	# Set an experiment folder and open
-	app.experiment_path_selection.setText(os.sep.join([software_location,'examples','demo']))
-	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
-
-	# Set a position
-	#app.control_panel.position_list.setCurrentIndex(0)
-	#app.control_panel.update_position_options()
-
-	# View stacl
-	qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
-	#qtbot.wait(1000)
-	app.control_panel.viewer.close()
-
-	# Expand process block
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)
-
-	# Use Threshold Config Wizard
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].upload_model_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].SegModelLoader.threshold_config_button, QtCore.Qt.LeftButton)
-	app.control_panel.ProcessPopulations[0].SegModelLoader.ThreshWizard.close()
-	app.control_panel.ProcessPopulations[0].SegModelLoader.close()
-
-	# Check segmentation with napari
-	#qtbot.mouseClick(app.control_panel.ProcessEffectors.check_seg_btn, QtCore.Qt.LeftButton)
-	# close napari?
-
-	# Train model
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].train_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].settings_segmentation_training.close()
-
-	# Config tracking
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].track_config_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].settings_tracking.close()
-
-	# Config measurements
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].measurements_config_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].settings_measurements.close()
-
-	# Classifier widget
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].classify_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].ClassifierWidget.close()
-
-	# Config signal annotator
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].config_signal_annotator_btn, QtCore.Qt.LeftButton)
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].settings_signal_annotator.rgb_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].settings_signal_annotator.close()
-
-	# Signal annotator widget
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].check_signals_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].event_annotator.close()
-
-	# Table widget
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].view_tab_btn, QtCore.Qt.LeftButton)
-	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].tab_ui.close()
-
-	#qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)
+    # Set an experiment folder and open
+    app.experiment_path_selection.setText(
+        os.sep.join([software_location, "examples", "demo"])
+    )
+    qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
+    # Set a position
+    # app.control_panel.position_list.setCurrentIndex(0)
+    # app.control_panel.update_position_options()
+
+    # View stacl
+    qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+    # qtbot.wait(1000)
+    app.control_panel.viewer.close()
+
+    # Expand process block
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton
+    )
+
+    # Use Threshold Config Wizard
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].upload_model_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[
+            0
+        ].seg_model_loader.threshold_config_button,
+        QtCore.Qt.LeftButton,
+    )
+    app.control_panel.ProcessPopulations[0].seg_model_loader.thresh_wizard.close()
+    app.control_panel.ProcessPopulations[0].seg_model_loader.close()
+
+    # Check segmentation with napari
+    # qtbot.mouseClick(app.control_panel.ProcessEffectors.check_seg_btn, QtCore.Qt.LeftButton)
+    # close napari?
+
+    # Train model
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].train_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].settings_segmentation_training.close()
+
+    # Config tracking
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].track_config_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].settings_tracking.close()
+
+    # Config measurements
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].measurements_config_btn,
+        QtCore.Qt.LeftButton,
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].settings_measurements.close()
+
+    # Classifier widget
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].classify_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].classifier_widget.close()
+
+    # Config signal annotator
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].config_signal_annotator_btn,
+        QtCore.Qt.LeftButton,
+    )
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].settings_signal_annotator.rgb_btn,
+        QtCore.Qt.LeftButton,
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].settings_signal_annotator.close()
+
+    # Signal annotator widget
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].check_signals_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].event_annotator.close()
+
+    # Table widget
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].view_tab_btn, QtCore.Qt.LeftButton
+    )
+    qtbot.wait(1000)
+    app.control_panel.ProcessPopulations[0].tab_ui.close()
+
+    # qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
+    qtbot.mouseClick(
+        app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton
+    )

tests/test_filters.py

@@ -1,24 +1,48 @@
 import unittest
 import numpy as np
-from celldetective.filters import gauss_filter, abs_filter
+from celldetective.filters import gauss_filter, abs_filter, filter_image
 
 
 class TestFilters(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
-		self.img = np.ones((256,256),dtype=int)
-		self.img[100:110,100:110] = 0
-		self.gauss_sigma = 1.6
+    @classmethod
+    def setUpClass(self):
+        self.img = np.ones((256, 256), dtype=int)
+        self.img[100:110, 100:110] = 0
+        self.gauss_sigma = 1.6
 
-	def test_gauss_filter_is_float(self):
-		self.assertIsInstance(gauss_filter(self.img, self.gauss_sigma)[0,0], float)
-	
-	def test_gauss_filter_has_same_shape(self):
-		self.assertEqual(gauss_filter(self.img, self.gauss_sigma).shape, self.img.shape)
+    def test_gauss_filter_is_float(self):
+        self.assertIsInstance(gauss_filter(self.img, self.gauss_sigma)[0, 0], float)
 
-	def test_abs_filter_is_positive(self):
-		self.assertTrue(np.all(abs_filter(self.img) >= 0.))
+    def test_gauss_filter_has_same_shape(self):
+        self.assertEqual(gauss_filter(self.img, self.gauss_sigma).shape, self.img.shape)
 
-if __name__=="__main__":
-	unittest.main()
+    def test_abs_filter_is_positive(self):
+        self.assertTrue(np.all(abs_filter(self.img) >= 0.0))
+
+    def test_filter_image_none(self):
+        # Should return original image if filters is None
+        res = filter_image(self.img, filters=None)
+        np.testing.assert_array_equal(res, self.img)
+
+    def test_filter_image_single(self):
+        # Test with a single filter: e.g. abs
+        # Create an image with negatives
+        img_neg = self.img.copy() * -1
+        res = filter_image(img_neg, filters=[("abs",)])
+        self.assertTrue(np.all(res >= 0))
+        np.testing.assert_array_almost_equal(res, np.abs(img_neg))
+
+    def test_filter_image_chain(self):
+        # Test chaining: subtract 10 then abs
+        # Start with ones. Subtract 10 -> -9. Abs -> 9.
+        img = np.ones((5, 5), dtype=float)
+        filters = [("subtract", 10), ("abs",)]
+        res = filter_image(img, filters=filters)
+        expected = np.abs(img - 10)
+        np.testing.assert_array_almost_equal(res, expected)
+        self.assertTrue(np.allclose(res, 9.0))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_notebooks.py

@@ -0,0 +1,8 @@
+# test_notebooks.py
+import nbformat
+from nbclient import NotebookClient
+
+def test_notebook_runs():
+    nb = nbformat.read("../demos/ADCC_analysis_demo.ipynb", as_version=4)
+    client = NotebookClient(nb, timeout=600, kernel_name="python3")
+    client.execute()  # raises exception if any cell fails