celldetective 1.4.0__py3-none-any.whl → 1.4.1.post1__py3-none-any.whl

celldetective/gui/processes/track_cells.py

@@ -1,10 +1,8 @@
 from multiprocessing import Process
 import time
-import datetime
-import os
-import json
 from celldetective.io import auto_load_number_of_frames, _load_frames_to_measure, locate_labels
-from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, _mask_intensity_measurements
+from celldetective.utils import config_section_to_dict, _get_img_num_per_channel, \
+	_mask_intensity_measurements, remove_file_if_exists
 from pathlib import Path, PurePath
 from glob import glob
 from tqdm import tqdm
@@ -155,12 +153,12 @@ class TrackingProcess(Process):
 
 	def extract_experiment_parameters(self):
 
-		self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]
-		self.spatial_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["pxtoum"])
-		self.time_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["frametomin"])
-		self.len_movie = float(ConfigSectionMap(self.config,"MovieSettings")["len_movie"])
-		self.shape_x = int(ConfigSectionMap(self.config,"MovieSettings")["shape_x"])
-		self.shape_y = int(ConfigSectionMap(self.config,"MovieSettings")["shape_y"])
+		self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")["movie_prefix"]
+		self.spatial_calibration = float(config_section_to_dict(self.config, "MovieSettings")["pxtoum"])
+		self.time_calibration = float(config_section_to_dict(self.config, "MovieSettings")["frametomin"])
+		self.len_movie = float(config_section_to_dict(self.config, "MovieSettings")["len_movie"])
+		self.shape_x = int(config_section_to_dict(self.config, "MovieSettings")["shape_x"])
+		self.shape_y = int(config_section_to_dict(self.config, "MovieSettings")["shape_y"])
 
 		self.channel_names, self.channel_indices = extract_experiment_channels(self.exp_dir)
 		self.nbr_channels = len(self.channel_names)
@@ -246,7 +244,9 @@ class TrackingProcess(Process):
 
 		print('Features successfully measured...')
 
-		df = pd.concat(self.timestep_dataframes)	
+		df = pd.concat(self.timestep_dataframes)
+		df = df.replace([np.inf, -np.inf], np.nan)
+
 		df.reset_index(inplace=True, drop=True)
 		df = _mask_intensity_measurements(df, self.mask_channels)
 
@@ -280,8 +280,7 @@ class TrackingProcess(Process):
 		trajectories.to_csv(self.pos+os.sep.join(['output', 'tables', self.table_name]), index=False)
 		print(f"Trajectory table successfully exported in {os.sep.join(['output', 'tables'])}...")
 
-		if os.path.exists(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')])):
-			os.remove(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')]))
+		remove_file_if_exists(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')]))
 
 		del trajectories; del napari_data;
 		gc.collect()		

celldetective/gui/settings/__init__.py

@@ -0,0 +1,7 @@
+from ._settings_measurements import SettingsMeasurements
+from ._settings_segmentation import SettingsSegmentation
+from ._settings_tracking import SettingsTracking
+from ._settings_segmentation_model_training import SettingsSegmentationModelTraining
+from ._settings_event_model_training import SettingsEventDetectionModelTraining
+from ._settings_signal_annotator import SettingsSignalAnnotator
+from ._settings_neighborhood import SettingsNeighborhood

celldetective/gui/settings/_settings_base.py

@@ -0,0 +1,70 @@
+from abc import abstractmethod
+from PyQt5.QtWidgets import QApplication, QScrollArea, QSizePolicy, QVBoxLayout, QPushButton
+from PyQt5.QtCore import Qt
+from celldetective.utils import get_software_location
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
+
+class CelldetectiveSettingsPanel(CelldetectiveMainWindow):
+	
+	def __init__(self, title=""):
+		
+		super().__init__()
+		self.setWindowTitle(title)
+		
+		self._get_screen_height()
+		#self.setMinimumWidth(500)
+		self.setMaximumHeight(int(0.8 * self._screen_height))
+		self._scroll_area = QScrollArea(self)
+		self._floatValidator = QDoubleValidator()
+		self._intValidator = QIntValidator()
+		self._software_path = get_software_location()
+
+		self._create_widgets()
+		self._build_layouts()
+		self.center_window()
+	
+	def _create_widgets(self):
+		self.submit_btn: QPushButton = QPushButton("Save")
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
+		self.submit_btn.clicked.connect(self._write_instructions)
+	
+	def center_window(self):
+		return center_window(self)
+	
+	def _get_screen_height(self):
+		app = QApplication.instance()
+		screen = app.primaryScreen()
+		geometry = screen.availableGeometry()
+		self._screen_width, self._screen_height = geometry.getRect()[-2:]
+	
+	def _adjustSize(self):
+		self._widget.adjustSize()
+		self._scroll_area.adjustSize()
+		self.adjustSize()
+	
+	def _build_layouts(self):
+		
+		self._layout: QVBoxLayout = QVBoxLayout()
+		self._widget: CelldetectiveWidget = CelldetectiveWidget()
+		self._widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+		
+		# Create button widget and layout
+		self._widget.setLayout(self._layout)
+		self._layout.setContentsMargins(30, 30, 30, 30)
+		
+		self._scroll_area.setAlignment(Qt.AlignCenter)
+		self._scroll_area.setWidget(self._widget)
+		self._scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self._scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self._scroll_area.setWidgetResizable(True)
+		self.setCentralWidget(self._scroll_area)
+		
+		QApplication.processEvents()
+	
+	@abstractmethod
+	def _load_previous_instructions(self): pass
+	
+	@abstractmethod
+	def _write_instructions(self): pass

celldetective/gui/{retrain_signal_model_options.py → settings/_settings_event_model_training.py}

@@ -1,12 +1,9 @@
-from PyQt5.QtWidgets import QApplication, QDialog, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QMessageBox, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QDoubleValidator, QIntValidator, QIcon
-from celldetective.gui.gui_utils import center_window
 from celldetective.gui.layouts import ChannelNormGenerator
 from superqt import QLabeledDoubleSlider, QLabeledSlider, QSearchableComboBox
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-from celldetective.utils import get_software_location
 from celldetective.io import locate_signal_dataset, get_signal_datasets_list, load_experiment_tables
 from celldetective.signals import train_signal_model
 import numpy as np
@@ -14,12 +11,12 @@ import json
 import os
 from glob import glob
 from datetime import datetime
-from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 from pandas.api.types import is_numeric_dtype
 from celldetective.gui.processes.train_signal_model import TrainSignalModelProcess
 from celldetective.gui.workers import ProgressWindow
+from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
 
-class ConfigSignalModelTraining(CelldetectiveMainWindow):
+class SettingsEventDetectionModelTraining(CelldetectiveSettingsPanel):
 	
 	"""
 	UI to set measurement instructions.
@@ -28,87 +25,62 @@ class ConfigSignalModelTraining(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None, signal_mode='single-cells'):
 		
-		super().__init__()
 		self.parent_window = parent_window
-		self.setWindowTitle("Train signal model")
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
-		self.soft_path = get_software_location()
-		self.pretrained_model = None 
+		self.pretrained_model = None
 		self.dataset_folder = None
 		self.current_neighborhood = None
 		self.reference_population = None
 		self.neighbor_population = None
 		self.signal_mode = signal_mode
+		
+		super().__init__(title="Train event detection model")
 
 		if self.signal_mode=='single-cells':
-			self.signal_models_dir = self.soft_path+os.sep+os.sep.join(['celldetective','models','signal_detection'])
+			self.signal_models_dir = self._software_path+os.sep+os.sep.join(['celldetective','models','signal_detection'])
 		elif self.signal_mode=='pairs':
-			self.signal_models_dir = self.soft_path+os.sep+os.sep.join(['celldetective','models','pair_signal_detection'])
+			self.signal_models_dir = self._software_path+os.sep+os.sep.join(['celldetective','models','pair_signal_detection'])
 			self.mode = 'pairs'
+		
+		self._add_to_layout()
+		self._load_previous_instructions()
+		
+		self._adjustSize()
+		new_width = int(self.width()*1.2)
+		self.resize(new_width, int(self._screen_height * 0.8))
+		self.setMinimumWidth(new_width)
+	
+	def _add_to_layout(self):
+		self._layout.addWidget(self.model_frame)
+		self._layout.addWidget(self.data_frame)
+		self._layout.addWidget(self.hyper_frame)
+		self._layout.addWidget(self.submit_btn)
 
-		self.onlyFloat = QDoubleValidator()
-		self.onlyInt = QIntValidator()
-
-		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
-		center_window(self)
-
-		self.setMinimumWidth(500)
-		self.setMinimumHeight(int(0.3*self.screen_height))
-		self.setMaximumHeight(int(0.8*self.screen_height))
-		self.populate_widget()
-		#self.load_previous_measurement_instructions()
-
-	def populate_widget(self):
+	def _create_widgets(self):
 
 		"""
 		Create the multibox design.
 
 		"""
+		super()._create_widgets()
 		
-		# Create button widget and layout
-		self.scroll_area = QScrollArea(self)
-		self.button_widget = CelldetectiveWidget()
-		self.main_layout = QVBoxLayout()
-		self.button_widget.setLayout(self.main_layout)
-		self.main_layout.setContentsMargins(30,30,30,30)
-
 		# first frame for FEATURES
 		self.model_frame = QFrame()
 		self.model_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_model_frame()
-		self.main_layout.addWidget(self.model_frame)
 
 		self.data_frame = QFrame()
 		self.data_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_data_frame()
-		self.main_layout.addWidget(self.data_frame)
 
 		self.hyper_frame = QFrame()
 		self.hyper_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_hyper_frame()
-		self.main_layout.addWidget(self.hyper_frame)
 
-		self.submit_btn = QPushButton('Train')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.prep_model)
-		self.main_layout.addWidget(self.submit_btn)
 		self.submit_btn.setEnabled(False)
+		self.submit_btn.setText("Train")
 
-		#self.populate_left_panel()
-		#grid.addLayout(self.left_side, 0, 0, 1, 1)
-		self.button_widget.adjustSize()
-
-		self.scroll_area.setAlignment(Qt.AlignCenter)
-		self.scroll_area.setWidget(self.button_widget)
-		self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll_area.setWidgetResizable(True)
-		self.setCentralWidget(self.scroll_area)
-		self.show()
-
-		QApplication.processEvents()
-		self.adjustScrollArea()
 
 	def populate_hyper_frame(self):
 
@@ -138,14 +110,14 @@ class ConfigSignalModelTraining(CelldetectiveMainWindow):
 		lr_layout = QHBoxLayout()
 		lr_layout.addWidget(QLabel('learning rate: '),30)
 		self.lr_le = QLineEdit('0,01')
-		self.lr_le.setValidator(self.onlyFloat)
+		self.lr_le.setValidator(self._floatValidator)
 		lr_layout.addWidget(self.lr_le, 70)
 		layout.addLayout(lr_layout)
 
 		bs_layout = QHBoxLayout()
 		bs_layout.addWidget(QLabel('batch size: '),30)
 		self.bs_le = QLineEdit('64')
-		self.bs_le.setValidator(self.onlyInt)
+		self.bs_le.setValidator(self._intValidator)
 		bs_layout.addWidget(self.bs_le, 70)
 		layout.addLayout(bs_layout)
 
@@ -378,42 +350,11 @@ class ConfigSignalModelTraining(CelldetectiveMainWindow):
 		self.dataframes = {}
 		self.neighborhood_cols = []
 		for population in self.parent_window.parent_window.populations:
-			df_pop = load_experiment_tables(self.parent_window.exp_dir, population=pop, load_pickle=True)
-			self.dataframes.update({pop: df_pop})
+			df_pop = load_experiment_tables(self.parent_window.exp_dir, population=population, load_pickle=True)
+			self.dataframes.update({population: df_pop})
 			if df_pop is not None:
 				self.neighborhood_cols.extend(
-					[f'{pop}_ref_' + c for c in list(df_pop.columns) if c.startswith('neighborhood')])
-
-		# df_targets = load_experiment_tables(self.parent_window.exp_dir, population='targets', load_pickle=True)
-		# df_effectors = load_experiment_tables(self.parent_window.exp_dir, population='effectors', load_pickle=True)
-		#
-		# self.dataframes = {
-		# 	'targets': df_targets,
-		# 	'effectors': df_effectors,
-		# }
-		#
-		# self.neighborhood_cols = []
-		# self.reference_populations = []
-		# self.neighbor_populations = []
-		# if df_targets is not None:
-		# 	self.neighborhood_cols.extend(['target_ref_'+c for c in list(df_targets.columns) if c.startswith('neighborhood')])
-		# 	self.reference_populations.extend(['targets' for c in list(df_targets.columns) if c.startswith('neighborhood')])
-		# 	for c in list(df_targets.columns):
-		# 		if c.startswith('neighborhood') and '_2_' in c:
-		# 			self.neighbor_populations.append('effectors')
-		# 		elif c.startswith('neighborhood') and 'self' in c:
-		# 			self.neighbor_populations.append('targets')
-		#
-		# if df_effectors is not None:
-		# 	self.neighborhood_cols.extend(['effector_ref_'+c for c in list(df_effectors.columns) if c.startswith('neighborhood')])
-		# 	self.reference_populations.extend(['effectors' for c in list(df_effectors.columns) if c.startswith('neighborhood')])
-		# 	for c in list(df_effectors.columns):
-		# 		if c.startswith('neighborhood') and '_2_' in c:
-		# 			self.neighbor_populations.append('targets')
-		# 		elif c.startswith('neighborhood') and 'self' in c:
-		# 			self.neighbor_populations.append('effectors')
-		#
-		# print(f"The following neighborhoods were detected: {self.neighborhood_cols=} {self.reference_populations=} {self.neighbor_populations=}")
+					[f'{population}_ref_' + c for c in list(df_pop.columns) if c.startswith('neighborhood')])
 
 		self.neighborhood_choice_cb.addItems(self.neighborhood_cols)
 
@@ -519,7 +460,7 @@ class ConfigSignalModelTraining(CelldetectiveMainWindow):
 		while self.scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
 			self.resize(self.width(), self.height() + step)
 
-	def prep_model(self):
+	def _write_instructions(self):
 
 		model_name = self.modelname_le.text()
 		pretrained_model = self.pretrained_model
@@ -597,4 +538,7 @@ class ConfigSignalModelTraining(CelldetectiveMainWindow):
 		# 	return None	
 
 		train_signal_model(model_folder+"training_instructions.json")
-		self.parent_window.refresh_signal_models()
+		self.parent_window.refresh_signal_models()
+	
+	def _load_previous_instructions(self):
+		pass

celldetective/gui/{measurement_options.py → settings/_settings_measurements.py}

@@ -1,11 +1,10 @@
 from subprocess import Popen
 
-from PyQt5.QtWidgets import QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
+from PyQt5.QtWidgets import QMessageBox, QComboBox, QFrame, QCheckBox, \
 	QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
+from celldetective.gui.gui_utils import FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
 	GeometryChoice, OperationChoice
 from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
@@ -27,10 +26,10 @@ from pathlib import Path
 from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
 from celldetective.gui.gui_utils import PreprocessingLayout2
-from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
 
 
-class ConfigMeasurements(CelldetectiveMainWindow):
+class SettingsMeasurements(CelldetectiveSettingsPanel):
 	"""
 	UI to set measurement instructions.
 
@@ -38,49 +37,33 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None):
 
-		super().__init__()
-
 		self.parent_window = parent_window
-		self.setWindowTitle("Configure measurements")
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
 		self.background_correction = []
 		self.config_name = f"btrack_config_{self.mode}.json"
 		self.measure_instructions_path = self.parent_window.exp_dir + f"configs/measurement_instructions_{self.mode}.json"
-		self.soft_path = get_software_location()
 		self.clear_previous = False
-
-		exp_config = self.exp_dir + "config.ini"
 		self.config_path = self.exp_dir + self.config_name
 		self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
 		self.channel_names = np.array(self.channel_names)
 		self.channels = np.array(self.channels)
+		
+		super().__init__("Configure measurements")
 
-		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
-		center_window(self)
-
-		self.onlyFloat = QDoubleValidator()
-		self.onlyInt = QIntValidator()
-
-		self.setMinimumWidth(500)
-		self.setMinimumHeight(int(0.3 * self.screen_height))
-		self.setMaximumHeight(int(0.8 * self.screen_height))
-		self.populate_widget()
-		self.load_previous_measurement_instructions()
-
-	def populate_widget(self):
+		self._add_to_layout()
+		self._load_previous_instructions()
+		
+		self._adjustSize()
+		self.resize(int(self.width()), int(self._screen_height * 0.8))
+	
+	def _create_widgets(self):
 
 		"""
 		Create the multibox design.
 
 		"""
-
-		# Create button widget and layout
-		self.scroll_area = QScrollArea(self)
-		self.button_widget = CelldetectiveWidget()
-		main_layout = QVBoxLayout()
-		self.button_widget.setLayout(main_layout)
-		main_layout.setContentsMargins(30, 30, 30, 30)
+		super()._create_widgets()
 
 		self.normalisation_frame = QFrame()
 		self.normalisation_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
@@ -98,48 +81,31 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		self.normalisation_frame.setLayout(self.protocol_layout)
 
 		#self.populate_normalisation_tabs()
-		main_layout.addWidget(self.normalisation_frame)
 
 		# first frame for FEATURES
 		self.features_frame = QFrame()
 		self.features_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_features_frame()
-		main_layout.addWidget(self.features_frame)
 
 		# second frame for ISOTROPIC MEASUREMENTS
 		self.iso_frame = QFrame()
 		self.iso_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_iso_frame()
-		main_layout.addWidget(self.iso_frame)
 
 		self.spot_detection_frame = QFrame()
 		self.spot_detection_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_spot_detection()
-		main_layout.addWidget(self.spot_detection_frame)
 
 		self.clear_previous_btn = QCheckBox('clear previous measurements')
-		main_layout.addWidget(self.clear_previous_btn)
-
-		self.submit_btn = QPushButton('Save')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.write_instructions)
-		main_layout.addWidget(self.submit_btn)
-
-		# self.populate_left_panel()
-		# grid.addLayout(self.left_side, 0, 0, 1, 1)
-		self.button_widget.adjustSize()
-
-		self.scroll_area.setAlignment(Qt.AlignCenter)
-		self.scroll_area.setWidget(self.button_widget)
-		self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll_area.setWidgetResizable(True)
-		self.setCentralWidget(self.scroll_area)
-		self.show()
-
-		QApplication.processEvents()
-		self.adjustScrollArea()
 
+	def _add_to_layout(self):
+		self._layout.addWidget(self.normalisation_frame)
+		self._layout.addWidget(self.features_frame)
+		self._layout.addWidget(self.iso_frame)
+		self._layout.addWidget(self.spot_detection_frame)
+		self._layout.addWidget(self.clear_previous_btn)
+		self._layout.addWidget(self.submit_btn)
+	
 	def populate_iso_frame(self):
 
 		"""
@@ -431,7 +397,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 
 	def go_to_extraprops(self):
 		
-		path = os.sep.join([self.soft_path,'celldetective',os.sep,'extra_properties.py'])
+		path = os.sep.join([self._software_path,'celldetective',os.sep,'extra_properties.py'])
 		try:
 			Popen(f'explorer {os.path.realpath(path)}')
 		except:
@@ -487,7 +453,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		while self.scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
 			self.resize(self.width(), self.height() + step)
 
-	def write_instructions(self):
+	def _write_instructions(self):
 
 		"""
 		Write the selected options in a json file for later reading by the software.
@@ -566,7 +532,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		else:
 			self.haralick_options = None
 
-	def load_previous_measurement_instructions(self):
+	def _load_previous_instructions(self):
 
 		"""
 		Read the measurmeent options from a previously written json file and format properly for the UI.
@@ -685,18 +651,6 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 					else:
 						self.operations_list.list_widget.clear()
 
-				# if 'radial_intensity' in measurement_instructions:
-				#     radial_intensity = measurement_instructions['radial_intensity']
-				#     if radial_intensity is not None:
-				#         self.radial_intensity_btn.setChecked(True)
-				#         self.step_size.setText(str(radial_intensity['radial_step']))
-				#         self.step_size.setEnabled(True)
-				#         self.step_lbl.setEnabled(True)
-				#         for checkbox in self.channel_chechkboxes:
-				#             checkbox.setEnabled(True)
-				#             if checkbox.text() in radial_intensity['radial_channels']:
-				#                 checkbox.setChecked(True)
-
 				if 'clear_previous' in measurement_instructions:
 					self.clear_previous = measurement_instructions['clear_previous']
 					self.clear_previous_btn.setChecked(self.clear_previous)
@@ -718,6 +672,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.Ok:
 				self.current_stack = None
+				self.test_frame = None
 				return None
 		else:
 			self.current_stack = movies[0]
@@ -946,7 +901,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		diam_hbox = QHBoxLayout()
 		self.diameter_lbl = QLabel('Spot diameter: ')
 		self.diameter_value = QLineEdit()
-		self.diameter_value.setValidator(self.onlyFloat)
+		self.diameter_value.setValidator(self._floatValidator)
 		self.diameter_value.setText('7')
 		self.diameter_value.textChanged.connect(self.enable_spot_preview)
 
@@ -957,7 +912,7 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		thresh_hbox = QHBoxLayout()
 		self.threshold_lbl = QLabel('Spot threshold: ')
 		self.threshold_value = QLineEdit()
-		self.threshold_value.setValidator(self.onlyFloat)
+		self.threshold_value.setValidator(self._floatValidator)
 		self.threshold_value.setText('0')
 		self.threshold_value.textChanged.connect(self.enable_spot_preview)
 
@@ -965,14 +920,6 @@ class ConfigMeasurements(CelldetectiveMainWindow):
 		thresh_hbox.addWidget(self.threshold_value, 70)
 		layout.addLayout(thresh_hbox)
 
-		# #invert_layout = QHBoxLayout()
-		# self.invert_check = QCheckBox('invert')
-		# self.invert_value_le = QLineEdit('65535')
-		# self.invert_value_le.setValidator(self.onlyFloat)
-		# layout.addWidget(self.invert_check, 6, 0)
-		# layout.addWidget(self.invert_value_le, 6, 1)
-		# #layout.addLayout(invert_layout, 5, 1, 1, 1)
-
 		self.spot_detection_widgets = [self.spot_channel, 
 									   self.spot_channel_lbl,
 									   self.diameter_value,

celldetective/gui/{neighborhood_options.py → settings/_settings_neighborhood.py}

@@ -12,7 +12,7 @@ from celldetective.gui.viewers import CellSizeViewer, CellEdgeVisualizer
 from celldetective.gui import CelldetectiveWidget
 
 
-class ConfigNeighborhoods(CelldetectiveWidget):
+class SettingsNeighborhood(CelldetectiveWidget):
 	
 	"""
 	Widget to configure neighborhood measurements.

celldetective/gui/settings/_settings_segmentation.py

@@ -0,0 +1,49 @@
+from PyQt5.QtWidgets import QCheckBox
+from PyQt5.QtCore import QSize
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
+import json
+import os
+
+class SettingsSegmentation(CelldetectiveSettingsPanel):
+	
+	def __init__(self, parent_window=None):
+		
+		super().__init__(title="Configure segmentation")
+		self.parent_window = parent_window
+		self.mode = self.parent_window.mode
+		self.exp_dir = self.parent_window.exp_dir
+		self._instructions_path = self.parent_window.exp_dir + f"configs/segmentation_instructions_{self.mode}.json"
+		self._add_to_layout()
+		self._load_previous_instructions()
+		
+	def _create_widgets(self):
+		super()._create_widgets()
+		
+		self.flip_segmentation_checkbox: QCheckBox = QCheckBox("Segment frames in reverse order")
+		self.flip_segmentation_checkbox.setIcon(icon(MDI6.camera_flip_outline,color="black"))
+		self.flip_segmentation_checkbox.setIconSize(QSize(20, 20))
+		self.flip_segmentation_checkbox.setStyleSheet(self.button_select_all)
+		self.flip_segmentation_checkbox.setToolTip("Flip the order of the frames for segmentation.")
+	
+	def _add_to_layout(self):
+		self._layout.addWidget(self.flip_segmentation_checkbox)
+		self._layout.addWidget(self.submit_btn)
+		#self._widget.adjustSize()
+
+	def _load_previous_instructions(self):
+		if os.path.exists(self._instructions_path):
+			with open(self._instructions_path, "r") as f:
+				instructions = json.load(f)
+			if isinstance(instructions.get("flip"),bool):
+				self.flip_segmentation_checkbox.setChecked(instructions.get("flip"))
+	
+	def _write_instructions(self):
+		instructions = {"flip": self.flip_segmentation_checkbox.isChecked()}
+		print('Segmentation instructions: ', instructions)
+		file_name = self._instructions_path
+		with open(file_name, 'w') as f:
+			json.dump(instructions, f, indent=4)
+		print('Done.')
+		self.close()