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

tests/gui/test_new_project.py

@@ -0,0 +1,228 @@
+import pytest
+from PyQt5 import QtCore
+from PyQt5.QtWidgets import QApplication
+from celldetective.gui.InitWindow import AppInitWindow
+from celldetective.utils import get_software_location
+import os
+from unittest.mock import patch
+import shutil
+from pathlib import Path
+
+abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]])
+print(abs_path)
+
+@pytest.fixture
+def app(qtbot):
+	software_location = get_software_location()
+	test_app = AppInitWindow(software_location=software_location)
+	qtbot.addWidget(test_app)
+	return test_app
+
+def test_new_project(app, qtbot):
+	# app.newExpAction.trigger()
+	# qtbot.wait(1000)
+	interaction_time = 500
+	test_directory = os.path.dirname(os.path.abspath(__file__))
+	parent_directory = str(Path(test_directory).parent)
+
+	# Patch QFileDialog.getExistingDirectory to return test_directory
+	with patch('PyQt5.QtWidgets.QFileDialog.getExistingDirectory', return_value=parent_directory):
+		
+		if os.path.exists(os.sep.join([parent_directory, "ExperimentTest"])):
+			shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+		
+		app.newExpAction.trigger()
+		qtbot.wait(interaction_time*3)
+
+		app.new_exp_window.expName.setText('ExperimentTest')
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.SliderWells.setValue(10)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.SliderPos.setValue(3)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.MovieLengthSlider.setValue(1)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.PxToUm_field.setText("0,3112")
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.shape_x_field.setText("660")
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.shape_y_field.setText('682')
+		qtbot.wait(interaction_time)
+
+		# set first channel
+		app.new_exp_window.checkBoxes[0].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[0].setValue(0)
+		qtbot.wait(interaction_time)
+
+		# set second with channel index of 1
+		app.new_exp_window.checkBoxes[1].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[1].setValue(3)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.checkBoxes[2].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[2].setValue(1)
+		qtbot.wait(interaction_time)
+
+		# add extra custom channel
+		qtbot.mouseClick(app.new_exp_window.addChannelBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.name_le.setText('empty_channel')
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.createBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.checkBoxes[-1].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[-1].setValue(2)
+		qtbot.wait(interaction_time)
+
+		# Untick populations and create new one
+		for box in app.new_exp_window.population_checkboxes:
+			if box.text() == 'targets':
+				box.setChecked(True)
+			else:
+				box.setChecked(False)
+		
+		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.name_le.setText('more_cells')
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.validate_button, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.w.submit_btn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		shutil.copy(os.sep.join([parent_directory, "assets", "sample.tif"]), os.sep.join([parent_directory, "ExperimentTest", "W1", "100", "movie", "sample.tif"]))
+		qtbot.wait(interaction_time)
+
+		qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+		qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		app.control_panel.viewer.channels_cb.setCurrentIndex(1)
+		qtbot.wait(interaction_time*2)
+		
+		app.control_panel.viewer.contrast_slider.setValue([200,300])
+		qtbot.wait(interaction_time*2)
+	
+	# QApplication.closeAllWindows()
+	# try:
+	# 	shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+	# except:
+	# 	pass
+# def test_lauch_app(app, qtbot):
+# 	app.show()
+# 	qtbot.wait(1000)
+#
+# def test_open_project(app, qtbot):
+# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+#
+# def test_launch_demo(app, qtbot):
+# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+#
+# def test_preprocessing_panel(app, qtbot):
+#
+# 	app.experiment_path_selection.setText(abs_path + 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)
+#
+# def test_app(app, qtbot):
+#
+# 	# Set an experiment folder and open
+# 	app.experiment_path_selection.setText(os.sep.join([abs_path,'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].ConfigSegmentationTrain.close()
+#
+# 	# Config tracking
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].track_config_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigTracking.close()
+#
+# 	# Config measurements
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].measurements_config_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigMeasurements.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].ConfigSignalAnnotator.rgb_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigSignalAnnotator.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].SignalAnnotator.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)
+#
+#
+#
+# def test_click(app, qtbot):
+# 	qtbot.mouseClick(app.new_exp_button, QtCore.Qt.LeftButton)
+# 	qtbot.wait(10000)

tests/{test_qt.py → gui/test_project.py}

@@ -2,36 +2,38 @@ import pytest
 from PyQt5 import QtCore
 from celldetective.gui.InitWindow import AppInitWindow
 from celldetective.utils import get_software_location
-import time
 import os
 
-abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]])
-print(abs_path)
+software_location = get_software_location()
 
 @pytest.fixture
 def app(qtbot):
-	software_location = get_software_location()
 	test_app = AppInitWindow(software_location=software_location)
 	qtbot.addWidget(test_app)
 	return test_app
 
-# def test_launch_demo(app, qtbot):
-# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
-# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+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)
+
+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)
 
-# def test_preprocessing_panel(app, qtbot):
+def test_preprocessing_panel(app, qtbot):
 
-# 	app.experiment_path_selection.setText(abs_path + 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([abs_path,'examples','demo']))
+	app.experiment_path_selection.setText(os.sep.join([software_location,'examples','demo']))
 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
 
 	# Set a position
@@ -60,17 +62,17 @@ def test_app(app, qtbot):
 	# Train model
 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].train_btn, QtCore.Qt.LeftButton)
 	qtbot.wait(1000)
-	app.control_panel.ProcessPopulations[0].ConfigSegmentationTrain.close()
+	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].ConfigTracking.close()
+	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].ConfigMeasurements.close()
+	app.control_panel.ProcessPopulations[0].settings_measurements.close()
 
 	# Classifier widget
 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].classify_btn, QtCore.Qt.LeftButton)
@@ -79,14 +81,14 @@ def test_app(app, qtbot):
 
 	# Config signal annotator
 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].config_signal_annotator_btn, QtCore.Qt.LeftButton)
-	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].ConfigSignalAnnotator.rgb_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].ConfigSignalAnnotator.close()
+	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].SignalAnnotator.close()
+	app.control_panel.ProcessPopulations[0].event_annotator.close()
 
 	# Table widget
 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].view_tab_btn, QtCore.Qt.LeftButton)
@@ -95,9 +97,3 @@ def test_app(app, qtbot):
 
 	#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)
-
-
-
-# def test_click(app, qtbot):
-# 	qtbot.mouseClick(app.new_exp_button, QtCore.Qt.LeftButton)
-#	qtbot.wait(10000)

tests/test_preprocessing.py

@@ -20,11 +20,11 @@ class TestFitPlane(unittest.TestCase):
 		self.assertTrue(np.allclose(self.img, mat))
 
 	def test_plane_is_well_fit_and_applied_with_division(self):
-		result = field_correction(self.img, threshold_on_std=1.0E05, operation='divide', model='plane', clip=False, return_bg=False, activation_protocol=[])
+		result = field_correction(self.img, threshold=1.0E05, operation='divide', model='plane', clip=False, return_bg=False, activation_protocol=[])
 		self.assertTrue(np.allclose(result, np.full((100,100), 1.0)))
 
 	def test_plane_is_well_fit_and_applied_with_subtraction(self):
-		result = field_correction(self.img, threshold_on_std=1.0E05, operation='subtract', model='plane', clip=False, return_bg=False, activation_protocol=[])
+		result = field_correction(self.img, threshold=1.0E05, operation='subtract', model='plane', clip=False, return_bg=False, activation_protocol=[])
 		self.assertTrue(np.allclose(result, np.zeros((100,100))))
 
 	def test_plane_is_well_fit_with_cell(self):

celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json

@@ -1,79 +0,0 @@
-{
-    "channels": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.2,
-    "dataset": {
-        "train": [
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_404_0066_roi_429_935_159_649.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0003_roi_457_991_5_488.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0008.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_305_0075.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0063_roi_405_865_462_937.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0066_roi_473_944_494_953.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0027_roi_557_998_3_447.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0017_roi_324_961_23_596.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0053_roi_511_996_4_433.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_403_0009_roi_554_996_460_994.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0066.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0066_roi_492_998_9_474.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0029_roi_177_746_4_533.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_203_0060_roi_369_906_119_648.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_304_0025.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0030_roi_152_661_531_998.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_105_0018_roi_510_954_13_422.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0016_roi_29_585_462_996.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_504_0066_roi_305_866_382_909.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0060_roi_6_479_351_847.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_403_0008.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0094.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0055_roi_1_514_68_597.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0023_roi_295_768_6_437.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_805_0081.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0010_roi_341_847_162_673.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_205_0002_roi_70_569_6_490.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0055_roi_99_778_341_986.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_802_0040.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0042_roi_99_515_11_394.tif"
-        ],
-        "validation": [
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0003_roi_501_957_576_1000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_603_0032.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0030_roi_323_824_488_995.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0014_roi_258_711_504_959.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0007_roi_119_611_5_451.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0030.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0055_roi_519_989_6_429.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0053_roi_190_724_13_490.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_300_0047_roi_416_985_436_972.tif"
-        ]
-    }
-}

celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json

@@ -1,37 +0,0 @@
-{
-    "model_name": "ricm_bf_all_last",
-    "model_type": "cellpose",
-    "pretrained": null,
-    "spatial_calibration": 0.2,
-    "channel_option": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "ds": [
-        "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects"
-    ],
-    "augmentation_factor": 3.0,
-    "validation_split": 0.2,
-    "learning_rate": 0.008,
-    "batch_size": 8,
-    "epochs": 3000,
-    "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
-}

celldetective/models/segmentation_effectors/test-transfer/config_input.json

@@ -1,39 +0,0 @@
-{
-    "channels": [
-        "brightfield_channel",
-        "None"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            1.0,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.36666666666666664,
-    "dataset": {
-        "train": [
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif"
-        ],
-        "validation": [
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif"
-        ]
-    }
-}

celldetective/models/signal_detection/NucCond/config_input.json

@@ -1 +0,0 @@
-{"channels": ["area"], "model_signal_length": 128, "label": "nucShrink", "normalize": true, "normalization_percentile": [true], "normalization_values": [[0.1, 99.99]], "normalization_clip": [true]}