celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/seg_model_loader.py

@@ -1,8 +1,20 @@
-from PyQt5.QtWidgets import QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
-from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, generic_message
-from celldetective.gui.layouts import ChannelNormGenerator
-from celldetective.gui import ThresholdConfigWizard, CelldetectiveWidget
+from PyQt5.QtWidgets import (
+    QGridLayout,
+    QComboBox,
+    QVBoxLayout,
+    QLabel,
+    QLineEdit,
+    QHBoxLayout,
+    QRadioButton,
+    QFileDialog,
+    QPushButton,
+    QMessageBox,
+)
+from PyQt5.QtCore import Qt, QSize, QTimer
+from celldetective.gui.base.components import generic_message
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.base.channel_norm_generator import ChannelNormGenerator
+from celldetective.gui.base.components import CelldetectiveWidget
 from PyQt5.QtGui import QDoubleValidator
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
@@ -11,475 +23,570 @@ from glob import glob
 import os
 import json
 import shutil
-from celldetective.gui import Styles
 import gc
-from cellpose.models import CellposeModel
 
 
 class SegmentationModelLoader(CelldetectiveWidget):
-	
-	"""
-	Upload a segmentation model or define a Threshold pipeline.
-	"""
-
-	def __init__(self, parent_window):
-		
-		super().__init__()
-		self.parent_window = parent_window
-		self.mode = self.parent_window.mode
-		self.target_folder = f"segmentation_{self.mode}"
-		self.setWindowTitle('Upload model')
-		self.generate_content()
-		center_window(self)
-
-	def generate_content(self):
-
-		self.layout = QGridLayout(self)
-		self.layout.addWidget(QLabel('Select:'), 0, 0, 1, 1)
-		self.layout.setSpacing(5)
-
-		option_layout = QHBoxLayout()
-		option_layout.setContentsMargins(10,10,10,10)
-
-		# Create radio buttons
-		self.stardist_button = QRadioButton('StarDist')
-		#self.stardist_button.setIcon(QIcon(abs_path+f"/icons/star.png"))
-
-		self.cellpose_button = QRadioButton('Cellpose')
-		#self.cellpose_button.setIcon(QIcon(abs_path+f"/icons/cellpose.png"))
-
-		self.threshold_button = QRadioButton('Threshold')
-
-		option_layout.addWidget(self.threshold_button)
-		option_layout.addWidget(self.stardist_button)
-		option_layout.addWidget(self.cellpose_button)
-
-		self.layout.addLayout(option_layout, 1,0,1,2, alignment=Qt.AlignCenter)
-		self.generate_base_block()
-		self.layout.addLayout(self.base_block, 2,0,1,2)
-		# self.combos = self.channel_layout.channel_cbs
-		# self.cb_labels = self.channel_layout.channel_labels
-
-		self.generate_cellpose_options()
-		self.layout.addLayout(self.cellpose_block, 3,0,1,2)
-		self.generate_threshold_options()
-
-		# Create file dialog
-		self.file_dialog = QFileDialog()
-
-		# Create button to open file dialog
-		self.open_dialog_button = QPushButton('Choose File')
-		self.open_dialog_button.clicked.connect(self.showDialog)
-		self.file_label = QLabel('No file chosen', self)
-		self.layout.addWidget(self.open_dialog_button, 9, 0, 1, 1)
-		self.layout.addWidget(self.file_label, 9, 1, 1, 1)
-
-
-		self.merge_lbl = QLabel('Merging option: ')
-		self.merge_cb = QComboBox()
-		self.merge_cb.addItems(['OR'])
-		merge_hbox = QHBoxLayout()
-		merge_hbox.addWidget(self.merge_lbl, 33)
-		merge_hbox.addWidget(self.merge_cb, 66)
-		self.layout.addLayout(merge_hbox, 10, 0, 1, 2)
-		self.merge_lbl.hide()
-		self.merge_cb.hide()
-
-		self.upload_button = QPushButton("Upload")
-		self.upload_button.clicked.connect(self.upload_model)
-		self.upload_button.setIcon(icon(MDI6.upload,color="white"))
-		self.upload_button.setIconSize(QSize(25, 25))
-		self.upload_button.setStyleSheet(self.button_style_sheet)
-		self.upload_button.setEnabled(False)
-		self.layout.addWidget(self.upload_button, 11, 0, 1, 1)
-		
-		self.base_block_options = [self.calibration_label, self.spatial_calib_le,*self.channel_layout.channel_cbs,*self.channel_layout.channel_labels,*self.channel_layout.normalization_mode_btns, *self.channel_layout.normalization_clip_btns, *self.channel_layout.normalization_min_value_lbl,
-								   *self.channel_layout.normalization_min_value_le, *self.channel_layout.normalization_max_value_lbl,*self.channel_layout.normalization_max_value_le,
-								   self.channel_layout.add_col_btn]
-
-		self.stardist_button.toggled.connect(self.show_seg_options)
-		self.cellpose_button.toggled.connect(self.show_seg_options)
-		self.threshold_button.toggled.connect(self.show_seg_options)
-
-		for cb in self.channel_layout.channel_cbs:
-			cb.activated.connect(self.unlock_upload)
-
-		self.setLayout(self.layout)
-
-		self.threshold_button.setChecked(True)
-		self.show()
-
-	def unlock_upload(self):
-		if self.stardist_button.isChecked():
-			if np.any([c.currentText()!='--' for c in self.channel_layout.channel_cbs]):
-				self.upload_button.setEnabled(True)
-			else:
-				self.upload_button.setEnabled(False)
-		elif self.cellpose_button.isChecked():
-			if np.any([c.currentText()!='--' for c in self.channel_layout.channel_cbs]):
-				self.upload_button.setEnabled(True)
-			else:
-				self.upload_button.setEnabled(False)
-
-	def generate_base_block(self):
-
-		"""
-		Create widgets common to StarDist and Cellpose.
-		"""
-		
-		self.base_block = QVBoxLayout()
-		
-		pixel_calib_layout = QHBoxLayout()
-		self.calibration_label = QLabel("input spatial\ncalibration: ")
-		self.spatial_calib_le = QLineEdit("0,1")
-		self.qdv = QDoubleValidator(0.0, np.amax([self.parent_window.parent_window.shape_x, self.parent_window.parent_window.shape_y]), 8, notation=QDoubleValidator.StandardNotation)
-		self.spatial_calib_le.setValidator(self.qdv)
-		pixel_calib_layout.addWidget(self.calibration_label, 30)
-		pixel_calib_layout.addWidget(self.spatial_calib_le, 70)
-		self.base_block.addLayout(pixel_calib_layout)
-
-		self.channel_layout = ChannelNormGenerator(self, mode='channels',init_n_channels=2)
-		self.channel_layout.setContentsMargins(0,0,0,0)
-		self.base_block.addLayout(self.channel_layout)
-
-
-	def generate_cellpose_options(self):
-
-		"""
-		Create Cellpose specific fields to use the model properly when calling it from the app.
-		"""
-
-		self.cellpose_block = QVBoxLayout()
-		self.cp_diameter_label = QLabel('cell\ndiameter:   ')
-		self.cp_diameter_le = QLineEdit("30,0")
-		self.cp_diameter_le.setValidator(self.qdv)
-		diam_hbox = QHBoxLayout()
-		diam_hbox.addWidget(self.cp_diameter_label, 30)
-		diam_hbox.addWidget(self.cp_diameter_le, 70)
-		self.cellpose_block.addLayout(diam_hbox)
-
-		qdv_prob = QDoubleValidator(-6, 6, 8, notation=QDoubleValidator.StandardNotation)
-		self.cp_cellprob_label = QLabel('cellprob\nthreshold:   ')
-		self.cp_cellprob_le = QLineEdit('0,0')
-		self.cp_cellprob_le.setValidator(qdv_prob)
-		cellprob_hbox = QHBoxLayout()
-		cellprob_hbox.addWidget(self.cp_cellprob_label, 30)
-		cellprob_hbox.addWidget(self.cp_cellprob_le, 70)
-		self.cellpose_block.addLayout(cellprob_hbox)
-
-		self.cp_flow_label = QLabel('flow threshold:   ')
-		self.cp_flow_le = QLineEdit('0,4')
-		self.cp_flow_le.setValidator(qdv_prob)
-		flow_hbox = QHBoxLayout()
-		flow_hbox.addWidget(self.cp_flow_label, 30)
-		flow_hbox.addWidget(self.cp_flow_le, 70)
-		self.cellpose_block.addLayout(flow_hbox)
-
-		self.cellpose_options = [self.cp_diameter_label,self.cp_diameter_le,self.cp_cellprob_label,
-			self.cp_cellprob_le, self.cp_flow_label, self.cp_flow_le]
-		for c in self.cellpose_options:
-			c.hide()
-
-	def generate_threshold_options(self):
-
-		"""
-		Show the threshold config pipeline button.
-		"""
-
-		self.threshold_config_button = QPushButton("Threshold Config Wizard")
-		self.threshold_config_button.setIcon(icon(MDI6.auto_fix,color="#1565c0"))
-		self.threshold_config_button.setIconSize(QSize(20, 20))
-		self.threshold_config_button.setVisible(False)
-		self.threshold_config_button.setStyleSheet(self.button_style_sheet_2)
-		self.threshold_config_button.clicked.connect(self.open_threshold_config_wizard)
-		self.layout.addWidget(self.threshold_config_button,3,0,1,2)
-		self.threshold_config_button.hide()
-
-	def showDialog(self):
-
-		"""
-		Import the model in the proper folder.
-		"""
-
-		# Set the file dialog according to the option chosen
-		if self.stardist_button.isChecked():
-			self.seg_mode = "stardist"
-			self.file_dialog.setFileMode(QFileDialog.Directory)
-		elif self.cellpose_button.isChecked():
-			self.seg_mode = "cellpose"
-			self.file_dialog.setFileMode(QFileDialog.ExistingFile)
-		elif self.threshold_button.isChecked():
-			self.seg_mode = "threshold"
-			self.file_dialog.setFileMode(QFileDialog.ExistingFile)
-
-		# If accepted check validity of data
-		if self.seg_mode!='threshold':
-			if self.file_dialog.exec_() == QFileDialog.Accepted:
-				self.filename = self.file_dialog.selectedFiles()[0]
-				if self.seg_mode=="stardist":
-					subfiles = glob(self.filename+"/*")
-					subfiles = [s.replace('\\','/') for s in subfiles]
-					if self.filename+"/thresholds.json" in subfiles:
-						self.file_label.setText(self.filename.split("/")[-1])
-						self.modelname = self.filename.split("/")[-1]
-						self.destination = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
-						self.folder_dest = self.destination
-					else:
-						generic_message(
-							"StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
-						return None
-				
-				if self.seg_mode=="cellpose":
-					self.file_label.setText(self.filename.split("/")[-1])
-					self.modelname = self.filename.split("/")[-1]
-					print(f"Transferring Cellpose model {self.filename}...")
-					self.folder_dest = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
-					self.destination = self.folder_dest+f"/{self.modelname}"
-
-		else:
-			self.filename, _ = QFileDialog.getOpenFileNames(
-														None,
-														"Load threshold configuration(s)...",
-														"",
-														"Json Configs (*.json)",
-														)
-			if self.filename:
-				n_files = len(self.filename)
-				print(f'You loaded {n_files} threshold configuration files...')
-				for i,filename in enumerate(self.filename):
-					print(f"Config {i}: ",filename,"...")
-
-				if n_files==1:
-					self.merge_cb.hide()
-					self.merge_lbl.hide()
-					self.file_label.setText(self.filename[0].split("/")[-1])
-				else:
-					generic_message(
-						"You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
-					self.merge_cb.show()
-					self.merge_lbl.show()
-					self.file_label.setText(f"{n_files} configs loaded...")
-
-	def show_seg_options(self):
-
-		"""
-		Show the relevant widgets, mask the others.
-		"""
-
-		self.filename = None
-		self.file_label.setText('No file chosen')
-		self.base_block_options = [self.calibration_label, self.spatial_calib_le,*self.channel_layout.channel_cbs,*self.channel_layout.channel_labels,*self.channel_layout.normalization_mode_btns, *self.channel_layout.normalization_clip_btns, *self.channel_layout.normalization_min_value_lbl,
-								   *self.channel_layout.normalization_min_value_le, *self.channel_layout.normalization_max_value_lbl,*self.channel_layout.normalization_max_value_le,
-								   self.channel_layout.add_col_btn]
-
-		if self.cellpose_button.isChecked():
-			self.spatial_calib_le.setToolTip('Cellpose rescales the images such that the cells are 30.0 pixels. You can compute the scale from the training data as\n(pixel calibration [µm] in training images)*(cell diameter [px] in training images)/(30 [px]).\nIf you pass images with a different calibration to the model, they will be rescaled automatically.\nThe rescaling is ignored if you pass a diameter different from 30 px below.')
-			self.channel_layout.channel_labels[0].setText('cyto: ')
-			self.channel_layout.channel_labels[1].setText('nuclei: ')
-			for c in [self.threshold_config_button, self.merge_lbl, self.merge_cb]:
-				c.hide()
-			for c in self.cellpose_options+self.base_block_options:
-				c.show()
-			self.unlock_upload()
-		elif self.stardist_button.isChecked():
-			self.spatial_calib_le.setToolTip('')
-			self.channel_layout.channel_labels[0].setText('channel 1: ')
-			self.channel_layout.channel_labels[1].setText('channel 2: ')
-			for c in self.base_block_options:
-				c.show()
-			for c in self.cellpose_options+[self.threshold_config_button, self.merge_lbl, self.merge_cb]:
-				c.hide()
-			self.unlock_upload()
-		else:
-			for c in self.base_block_options + self.cellpose_options:
-				c.hide()
-			self.threshold_config_button.show()
-			self.upload_button.setEnabled(True)
-
-		self.resize(self.sizeHint());
-		#self.adjustSize()
-
-	def upload_model(self):
-
-		"""
-		Upload the model.
-		"""
-		
-		channels = []
-		for i in range(len(self.channel_layout.channel_cbs)):
-			channels.append(self.channel_layout.channel_cbs[i].currentText())
-
-		if self.file_label.text()=='No file chosen':
-			generic_message('Please select a model first...')
-			return None
-
-		if not self.threshold_button.isChecked():
-			
-			if self.stardist_button.isChecked():
-				
-				try:
-					shutil.copytree(self.filename, self.destination)
-				except FileExistsError:
-					generic_message("A model with the same name already exists in the models folder. Please rename it.")
-					return None
-
-			elif self.cellpose_button.isChecked():
-
-				try:
-					if not os.path.exists(self.folder_dest):
-						os.mkdir(self.folder_dest)
-					shutil.copy(self.filename, self.destination)
-				except FileExistsError:
-					generic_message("A model with the same name already exists in the models folder. Please rename it.")
-					return None
-				try:
-					model = CellposeModel(pretrained_model=self.destination, model_type=None, nchan=len(channels))
-					self.scale_model = model.diam_mean
-					print(f'{self.scale_model=}')
-					del model
-					gc.collect()
-				except Exception as e:
-					print(e)
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Critical)
-					msgBox.setText(f"Cellpose model could not be loaded...")
-					msgBox.setWindowTitle("Error")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						return None					
-
-			self.generate_input_config()
-			self.parent_window.init_seg_model_list()
-			self.close()
-		else:
-			if not isinstance(self.filename, list):
-				if not self.filename is None:
-					self.filename = [self.filename]
-
-			idx = self.parent_window.parent_window.populations.index(self.mode)
-			self.parent_window.threshold_configs[idx] = self.filename
-			self.parent_window.seg_model_list.setCurrentText('Threshold')
-			self.close()
-
-	def generate_input_config(self):
-
-		"""
-		Check the ticked options and input parameters to create
-		a configuration to use the uploaded model properly.
-		"""
-		
-		if self.threshold_button.isChecked():
-			model_type = "threshold"
-			return None
-
-		channels = []
-		for i in range(len(self.channel_layout.channel_cbs)):
-			channels.append(self.channel_layout.channel_cbs[i].currentText())
-
-		slots_to_keep = np.where(np.array(channels)!='--')[0]
-		while '--' in channels:
-			channels.remove('--')
-
-		norm_values = np.array([[float(a.replace(',','.')),float(b.replace(',','.'))] for a,b in zip([l.text() for l in self.channel_layout.normalization_min_value_le],
-											[l.text() for l in self.channel_layout.normalization_max_value_le])])
-		norm_values = norm_values[slots_to_keep]
-		norm_values = [list(v) for v in norm_values]
-
-		clip_values = np.array(self.channel_layout.clip_option)
-		clip_values = list(clip_values[slots_to_keep])
-		clip_values = [bool(c) for c in clip_values]
-
-		normalization_mode = np.array(self.channel_layout.normalization_mode)
-		normalization_mode = list(normalization_mode[slots_to_keep])
-		normalization_mode = [bool(m) for m in normalization_mode]
-
-		dico = {}
-
-		# Check model option
-		if self.stardist_button.isChecked():
-			
-			# Get channels
-			# channels = []
-			# for c in self.combos:
-			# 	if c.currentText()!="--":
-			# 		channels.append(c.currentText())
-			model_type = "stardist"
-			spatial_calib = float(self.spatial_calib_le.text().replace(',','.'))
-			#normalize = self.normalize_checkbox.isChecked()
-			dico.update({"channels": channels,
-						 #"normalize": normalize,
-						 "spatial_calibration": spatial_calib,
-						 'normalization_percentile': normalization_mode,
-						 'normalization_clip': clip_values,
-						 'normalization_values': norm_values,
-						 })
-
-		elif self.cellpose_button.isChecked():
-			
-			# Get channels (cyto and nucleus)
-			# channels = []
-			# for c in self.combos[:2]:
-			# 	if c.currentText()!="--":
-			# 		channels.append(c.currentText())
-
-			model_type = "cellpose"
-			#cellpose requires at least two channels
-			if len(channels)==1:
-				channels += ['None']
-				normalization_mode += [True]
-				clip_values += [True]
-				norm_values += [[1,99]]
-
-			diameter = float(self.cp_diameter_le.text().replace(',','.'))
-			cellprob_threshold = float(self.cp_cellprob_le.text().replace(',','.'))
-			flow_threshold = float(self.cp_flow_le.text().replace(',','.'))
-			#normalize = self.normalize_checkbox.isChecked()
-			spatial_calib = float(self.spatial_calib_le.text().replace(',','.'))
-			# assume 30 px diameter in cellpose model
-			spatial_calib = spatial_calib * diameter / self.scale_model
-			diameter = 30.0
-
-			dico.update({"channels": channels,
-						 "diameter": diameter,
-						 "cellprob_threshold": cellprob_threshold,
-						 "flow_threshold": flow_threshold,
-						 #"normalize": normalize,
-						 "spatial_calibration": spatial_calib,
-						 'normalization_percentile': normalization_mode,
-						 'normalization_clip': clip_values,
-						 'normalization_values': norm_values,
-						 })
-
-
-		dico.update({"model_type": model_type})
-		print(f"{dico=}")
-		json_object = json.dumps(dico, indent=4)
-
-		# Writing to sample.json
-		# if os.path.exists(self.folder_dest):
-
-		# 	msgBox = QMessageBox()
-		# 	msgBox.setIcon(QMessageBox.Warning)
-		# 	msgBox.setText("A model with the same name already exists. Do you want to replace it?")
-		# 	msgBox.setWindowTitle("Confirm")
-		# 	msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
-		# 	returnValue = msgBox.exec()
-		# 	if returnValue == QMessageBox.No:
-		# 		return None
-		# 	elif returnValue == QMessageBox.Yes:
-		# 		shutil.rmtree(self.folder_dest)
-		#os.mkdir(self.folder_dest)
-
-		print("Configuration successfully written in ",self.folder_dest+os.sep+"config_input.json")
-		with open(self.folder_dest+os.sep+"config_input.json", "w") as outfile:
-			outfile.write(json_object)
-
-	def open_threshold_config_wizard(self):
-
-		self.parent_window.parent_window.locate_image()
-		if self.parent_window.parent_window.current_stack is None:
-			return None
-		else:
-			self.ThreshWizard = ThresholdConfigWizard(self)
-			self.ThreshWizard.show()
+    """
+    Upload a segmentation model or define a Threshold pipeline.
+    """
+
+    def __init__(self, parent_window):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.mode = self.parent_window.mode
+        self.target_folder = f"segmentation_{self.mode}"
+        self.setWindowTitle("Upload model")
+        self.generate_content()
+
+    def generate_content(self):
+
+        self.layout = QGridLayout(self)
+        self.layout.addWidget(QLabel("Select:"), 0, 0, 1, 1)
+        self.layout.setSpacing(5)
+
+        option_layout = QHBoxLayout()
+        option_layout.setContentsMargins(10, 10, 10, 10)
+
+        # Create radio buttons
+        self.stardist_button = QRadioButton("StarDist")
+        # self.stardist_button.setIcon(QIcon(abs_path+f"/icons/star.png"))
+
+        self.cellpose_button = QRadioButton("Cellpose")
+        # self.cellpose_button.setIcon(QIcon(abs_path+f"/icons/cellpose_utils.png"))
+
+        self.threshold_button = QRadioButton("Threshold")
+
+        option_layout.addWidget(self.threshold_button)
+        option_layout.addWidget(self.stardist_button)
+        option_layout.addWidget(self.cellpose_button)
+
+        self.layout.addLayout(option_layout, 1, 0, 1, 2, alignment=Qt.AlignCenter)
+        self.generate_base_block()
+        self.layout.addLayout(self.base_block, 2, 0, 1, 2)
+        # self.combos = self.channel_layout.channel_cbs
+        # self.cb_labels = self.channel_layout.channel_labels
+
+        self.generate_cellpose_options()
+        self.layout.addLayout(self.cellpose_block, 3, 0, 1, 2)
+        self.generate_threshold_options()
+
+        # Create file dialog
+        self.file_dialog = QFileDialog()
+
+        # Create button to open file dialog
+        self.open_dialog_button = QPushButton("Choose File")
+        self.open_dialog_button.clicked.connect(self.showDialog)
+        self.file_label = QLabel("No file chosen", self)
+        self.layout.addWidget(self.open_dialog_button, 9, 0, 1, 1)
+        self.layout.addWidget(self.file_label, 9, 1, 1, 1)
+
+        self.merge_lbl = QLabel("Merging option: ")
+        self.merge_cb = QComboBox()
+        self.merge_cb.addItems(["OR"])
+        merge_hbox = QHBoxLayout()
+        merge_hbox.addWidget(self.merge_lbl, 33)
+        merge_hbox.addWidget(self.merge_cb, 66)
+        self.layout.addLayout(merge_hbox, 10, 0, 1, 2)
+        self.merge_lbl.hide()
+        self.merge_cb.hide()
+
+        self.upload_button = QPushButton("Upload")
+        self.upload_button.clicked.connect(self.upload_model)
+        self.upload_button.setIcon(icon(MDI6.upload, color="white"))
+        self.upload_button.setIconSize(QSize(25, 25))
+        self.upload_button.setStyleSheet(self.button_style_sheet)
+        self.upload_button.setEnabled(False)
+        self.layout.addWidget(self.upload_button, 11, 0, 1, 1)
+
+        self.base_block_options = [
+            self.calibration_label,
+            self.spatial_calib_le,
+            *self.channel_layout.channel_cbs,
+            *self.channel_layout.channel_labels,
+            *self.channel_layout.normalization_mode_btns,
+            *self.channel_layout.normalization_clip_btns,
+            *self.channel_layout.normalization_min_value_lbl,
+            *self.channel_layout.normalization_min_value_le,
+            *self.channel_layout.normalization_max_value_lbl,
+            *self.channel_layout.normalization_max_value_le,
+            self.channel_layout.add_col_btn,
+        ]
+
+        self.stardist_button.toggled.connect(self.show_seg_options)
+        self.cellpose_button.toggled.connect(self.show_seg_options)
+        self.threshold_button.toggled.connect(self.show_seg_options)
+
+        for cb in self.channel_layout.channel_cbs:
+            cb.activated.connect(self.unlock_upload)
+
+        self.setLayout(self.layout)
+
+        self.threshold_button.setChecked(True)
+        self.show()
+
+    def unlock_upload(self):
+        if self.stardist_button.isChecked():
+            if np.any(
+                [c.currentText() != "--" for c in self.channel_layout.channel_cbs]
+            ):
+                self.upload_button.setEnabled(True)
+            else:
+                self.upload_button.setEnabled(False)
+        elif self.cellpose_button.isChecked():
+            if np.any(
+                [c.currentText() != "--" for c in self.channel_layout.channel_cbs]
+            ):
+                self.upload_button.setEnabled(True)
+            else:
+                self.upload_button.setEnabled(False)
+
+    def generate_base_block(self):
+        """
+        Create widgets common to StarDist and Cellpose.
+        """
+
+        self.base_block = QVBoxLayout()
+
+        pixel_calib_layout = QHBoxLayout()
+        self.calibration_label = QLabel("input spatial\ncalibration: ")
+        self.spatial_calib_le = QLineEdit("0,1")
+        self.qdv = QDoubleValidator(
+            0.0,
+            np.amax(
+                [
+                    self.parent_window.parent_window.shape_x,
+                    self.parent_window.parent_window.shape_y,
+                ]
+            ),
+            8,
+            notation=QDoubleValidator.StandardNotation,
+        )
+        self.spatial_calib_le.setValidator(self.qdv)
+        pixel_calib_layout.addWidget(self.calibration_label, 30)
+        pixel_calib_layout.addWidget(self.spatial_calib_le, 70)
+        self.base_block.addLayout(pixel_calib_layout)
+
+        self.channel_layout = ChannelNormGenerator(
+            self, mode="channels", init_n_channels=2
+        )
+        self.channel_layout.setContentsMargins(0, 0, 0, 0)
+        self.base_block.addLayout(self.channel_layout)
+
+    def generate_cellpose_options(self):
+        """
+        Create Cellpose specific fields to use the model properly when calling it from the app.
+        """
+
+        self.cellpose_block = QVBoxLayout()
+        self.cp_diameter_label = QLabel("cell\ndiameter:   ")
+        self.cp_diameter_le = QLineEdit("30,0")
+        self.cp_diameter_le.setValidator(self.qdv)
+        diam_hbox = QHBoxLayout()
+        diam_hbox.addWidget(self.cp_diameter_label, 30)
+        diam_hbox.addWidget(self.cp_diameter_le, 70)
+        self.cellpose_block.addLayout(diam_hbox)
+
+        qdv_prob = QDoubleValidator(
+            -6, 6, 8, notation=QDoubleValidator.StandardNotation
+        )
+        self.cp_cellprob_label = QLabel("cellprob\nthreshold:   ")
+        self.cp_cellprob_le = QLineEdit("0,0")
+        self.cp_cellprob_le.setValidator(qdv_prob)
+        cellprob_hbox = QHBoxLayout()
+        cellprob_hbox.addWidget(self.cp_cellprob_label, 30)
+        cellprob_hbox.addWidget(self.cp_cellprob_le, 70)
+        self.cellpose_block.addLayout(cellprob_hbox)
+
+        self.cp_flow_label = QLabel("flow threshold:   ")
+        self.cp_flow_le = QLineEdit("0,4")
+        self.cp_flow_le.setValidator(qdv_prob)
+        flow_hbox = QHBoxLayout()
+        flow_hbox.addWidget(self.cp_flow_label, 30)
+        flow_hbox.addWidget(self.cp_flow_le, 70)
+        self.cellpose_block.addLayout(flow_hbox)
+
+        self.cellpose_options = [
+            self.cp_diameter_label,
+            self.cp_diameter_le,
+            self.cp_cellprob_label,
+            self.cp_cellprob_le,
+            self.cp_flow_label,
+            self.cp_flow_le,
+        ]
+        for c in self.cellpose_options:
+            c.hide()
+
+    def generate_threshold_options(self):
+        """
+        Show the threshold config pipeline button.
+        """
+
+        self.threshold_config_button = QPushButton("Threshold Config Wizard")
+        self.threshold_config_button.setIcon(icon(MDI6.auto_fix, color="#1565c0"))
+        self.threshold_config_button.setIconSize(QSize(20, 20))
+        self.threshold_config_button.setVisible(False)
+        self.threshold_config_button.setStyleSheet(self.button_style_sheet_2)
+        self.threshold_config_button.clicked.connect(self.open_threshold_config_wizard)
+        self.layout.addWidget(self.threshold_config_button, 3, 0, 1, 2)
+        self.threshold_config_button.hide()
+
+    def showDialog(self):
+        """
+        Import the model in the proper folder.
+        """
+
+        # Set the file dialog according to the option chosen
+        if self.stardist_button.isChecked():
+            self.seg_mode = "stardist"
+            self.file_dialog.setFileMode(QFileDialog.Directory)
+        elif self.cellpose_button.isChecked():
+            self.seg_mode = "cellpose"
+            self.file_dialog.setFileMode(QFileDialog.ExistingFile)
+        elif self.threshold_button.isChecked():
+            self.seg_mode = "threshold"
+            self.file_dialog.setFileMode(QFileDialog.ExistingFile)
+
+        # If accepted check validity of data
+        if self.seg_mode != "threshold":
+            if self.file_dialog.exec_() == QFileDialog.Accepted:
+                self.filename = self.file_dialog.selectedFiles()[0]
+                if self.seg_mode == "stardist":
+                    subfiles = glob(self.filename + "/*")
+                    subfiles = [s.replace("\\", "/") for s in subfiles]
+                    if self.filename + "/thresholds.json" in subfiles:
+                        self.file_label.setText(self.filename.split("/")[-1])
+                        self.modelname = self.filename.split("/")[-1]
+                        self.destination = (
+                            os.path.split(os.path.dirname(os.path.realpath(__file__)))[
+                                0
+                            ]
+                            + f"/models/{self.target_folder}/"
+                            + self.modelname
+                        )
+                        self.folder_dest = self.destination
+                    else:
+                        generic_message(
+                            "StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model..."
+                        )
+                        return None
+
+                if self.seg_mode == "cellpose":
+                    self.file_label.setText(self.filename.split("/")[-1])
+                    self.modelname = self.filename.split("/")[-1]
+                    print(f"Transferring Cellpose model {self.filename}...")
+                    self.folder_dest = (
+                        os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]
+                        + f"/models/{self.target_folder}/"
+                        + self.modelname
+                    )
+                    self.destination = self.folder_dest + f"/{self.modelname}"
+
+        else:
+            start_dir = self.parent_window.exp_dir
+            if os.path.isdir(os.path.join(start_dir, "configs")):
+                start_dir = os.path.join(start_dir, "configs")
+
+            self.filename, _ = QFileDialog.getOpenFileNames(
+                None,
+                "Load threshold configuration(s)...",
+                start_dir,
+                "Json Configs (*.json)",
+            )
+            if self.filename:
+                n_files = len(self.filename)
+                print(f"You loaded {n_files} threshold configuration files...")
+                for i, filename in enumerate(self.filename):
+                    print(f"Config {i}: ", filename, "...")
+
+                if n_files == 1:
+                    self.merge_cb.hide()
+                    self.merge_lbl.hide()
+                    self.file_label.setText(self.filename[0].split("/")[-1])
+                else:
+                    generic_message(
+                        "You selected more than one pipeline. Please set a merging procedure for the resulting masks..."
+                    )
+                    self.merge_cb.show()
+                    self.merge_lbl.show()
+                    self.file_label.setText(f"{n_files} configs loaded...")
+
+    def show_seg_options(self):
+        """
+        Show the relevant widgets, mask the others.
+        """
+
+        self.filename = None
+        self.file_label.setText("No file chosen")
+        self.base_block_options = [
+            self.calibration_label,
+            self.spatial_calib_le,
+            *self.channel_layout.channel_cbs,
+            *self.channel_layout.channel_labels,
+            *self.channel_layout.normalization_mode_btns,
+            *self.channel_layout.normalization_clip_btns,
+            *self.channel_layout.normalization_min_value_lbl,
+            *self.channel_layout.normalization_min_value_le,
+            *self.channel_layout.normalization_max_value_lbl,
+            *self.channel_layout.normalization_max_value_le,
+            self.channel_layout.add_col_btn,
+        ]
+
+        if self.cellpose_button.isChecked():
+            self.spatial_calib_le.setToolTip(
+                "Cellpose rescales the images such that the cells are 30.0 pixels. You can compute the scale from the training data as\n(pixel calibration [µm] in training images)*(cell diameter [px] in training images)/(30 [px]).\nIf you pass images with a different calibration to the model, they will be rescaled automatically.\nThe rescaling is ignored if you pass a diameter different from 30 px below."
+            )
+            self.channel_layout.channel_labels[0].setText("cyto: ")
+            self.channel_layout.channel_labels[1].setText("nuclei: ")
+            for c in [self.threshold_config_button, self.merge_lbl, self.merge_cb]:
+                c.hide()
+            for c in self.cellpose_options + self.base_block_options:
+                c.show()
+            self.unlock_upload()
+        elif self.stardist_button.isChecked():
+            self.spatial_calib_le.setToolTip("")
+            self.channel_layout.channel_labels[0].setText("channel 1: ")
+            self.channel_layout.channel_labels[1].setText("channel 2: ")
+            for c in self.base_block_options:
+                c.show()
+            for c in self.cellpose_options + [
+                self.threshold_config_button,
+                self.merge_lbl,
+                self.merge_cb,
+            ]:
+                c.hide()
+            self.unlock_upload()
+        else:
+            for c in self.base_block_options + self.cellpose_options:
+                c.hide()
+            self.threshold_config_button.show()
+            self.upload_button.setEnabled(True)
+
+        self.resize(self.sizeHint())
+        # self.adjustSize()
+
+    def upload_model(self):
+        """
+        Upload the model.
+        """
+
+        channels = []
+        for i in range(len(self.channel_layout.channel_cbs)):
+            channels.append(self.channel_layout.channel_cbs[i].currentText())
+
+        if self.file_label.text() == "No file chosen":
+            generic_message("Please select a model first...")
+            return None
+
+        if not self.threshold_button.isChecked():
+
+            if self.stardist_button.isChecked():
+
+                try:
+                    shutil.copytree(self.filename, self.destination)
+                except FileExistsError:
+                    generic_message(
+                        "A model with the same name already exists in the models folder. Please rename it."
+                    )
+                    return None
+
+            elif self.cellpose_button.isChecked():
+
+                try:
+                    if not os.path.exists(self.folder_dest):
+                        os.mkdir(self.folder_dest)
+                    shutil.copy(self.filename, self.destination)
+                except FileExistsError:
+                    generic_message(
+                        "A model with the same name already exists in the models folder. Please rename it."
+                    )
+                    return None
+                try:
+                    from cellpose.models import CellposeModel
+
+                    model = CellposeModel(
+                        pretrained_model=self.destination,
+                        model_type=None,
+                        nchan=len(channels),
+                    )
+                    self.scale_model = model.diam_mean
+                    print(f"{self.scale_model=}")
+                    del model
+                    gc.collect()
+                except Exception as e:
+                    print(e)
+                    msgBox = QMessageBox()
+                    msgBox.setIcon(QMessageBox.Critical)
+                    msgBox.setText(f"Cellpose model could not be loaded...")
+                    msgBox.setWindowTitle("Error")
+                    msgBox.setStandardButtons(QMessageBox.Ok)
+                    returnValue = msgBox.exec()
+                    if returnValue == QMessageBox.Ok:
+                        return None
+
+            self.generate_input_config()
+            self.parent_window.init_seg_model_list()
+            self.close()
+        else:
+            if not isinstance(self.filename, list):
+                if not self.filename is None:
+                    self.filename = [self.filename]
+
+            idx = self.parent_window.parent_window.populations.index(self.mode)
+            self.parent_window.threshold_configs[idx] = self.filename
+            self.parent_window.seg_model_list.setCurrentText("Threshold")
+            self.close()
+
+    def generate_input_config(self):
+        """
+        Check the ticked options and input parameters to create
+        a configuration to use the uploaded model properly.
+        """
+
+        if self.threshold_button.isChecked():
+            model_type = "threshold"
+            return None
+
+        channels = []
+        for i in range(len(self.channel_layout.channel_cbs)):
+            channels.append(self.channel_layout.channel_cbs[i].currentText())
+
+        slots_to_keep = np.where(np.array(channels) != "--")[0]
+        while "--" in channels:
+            channels.remove("--")
+
+        norm_values = np.array(
+            [
+                [float(a.replace(",", ".")), float(b.replace(",", "."))]
+                for a, b in zip(
+                    [l.text() for l in self.channel_layout.normalization_min_value_le],
+                    [l.text() for l in self.channel_layout.normalization_max_value_le],
+                )
+            ]
+        )
+        norm_values = norm_values[slots_to_keep]
+        norm_values = [list(v) for v in norm_values]
+
+        clip_values = np.array(self.channel_layout.clip_option)
+        clip_values = list(clip_values[slots_to_keep])
+        clip_values = [bool(c) for c in clip_values]
+
+        normalization_mode = np.array(self.channel_layout.normalization_mode)
+        normalization_mode = list(normalization_mode[slots_to_keep])
+        normalization_mode = [bool(m) for m in normalization_mode]
+
+        dico = {}
+
+        # Check model option
+        if self.stardist_button.isChecked():
+
+            # Get channels
+            # channels = []
+            # for c in self.combos:
+            # 	if c.currentText()!="--":
+            # 		channels.append(c.currentText())
+            model_type = "stardist"
+            spatial_calib = float(self.spatial_calib_le.text().replace(",", "."))
+            # normalize = self.normalize_checkbox.isChecked()
+            dico.update(
+                {
+                    "channels": channels,
+                    # "normalize": normalize,
+                    "spatial_calibration": spatial_calib,
+                    "normalization_percentile": normalization_mode,
+                    "normalization_clip": clip_values,
+                    "normalization_values": norm_values,
+                }
+            )
+
+        elif self.cellpose_button.isChecked():
+
+            # Get channels (cyto and nucleus)
+            # channels = []
+            # for c in self.combos[:2]:
+            # 	if c.currentText()!="--":
+            # 		channels.append(c.currentText())
+
+            model_type = "cellpose"
+            # cellpose_utils requires at least two channels
+            if len(channels) == 1:
+                channels += ["None"]
+                normalization_mode += [True]
+                clip_values += [True]
+                norm_values += [[1, 99]]
+
+            diameter = float(self.cp_diameter_le.text().replace(",", "."))
+            cellprob_threshold = float(self.cp_cellprob_le.text().replace(",", "."))
+            flow_threshold = float(self.cp_flow_le.text().replace(",", "."))
+            # normalize = self.normalize_checkbox.isChecked()
+            spatial_calib = float(self.spatial_calib_le.text().replace(",", "."))
+            # assume 30 px diameter in cellpose_utils model
+            spatial_calib = spatial_calib * diameter / self.scale_model
+            diameter = 30.0
+
+            dico.update(
+                {
+                    "channels": channels,
+                    "diameter": diameter,
+                    "cellprob_threshold": cellprob_threshold,
+                    "flow_threshold": flow_threshold,
+                    # "normalize": normalize,
+                    "spatial_calibration": spatial_calib,
+                    "normalization_percentile": normalization_mode,
+                    "normalization_clip": clip_values,
+                    "normalization_values": norm_values,
+                }
+            )
+
+        dico.update({"model_type": model_type})
+        print(f"{dico=}")
+        json_object = json.dumps(dico, indent=4)
+
+        # Writing to sample.json
+        # if os.path.exists(self.folder_dest):
+
+        # 	msgBox = QMessageBox()
+        # 	msgBox.setIcon(QMessageBox.Warning)
+        # 	msgBox.setText("A model with the same name already exists. Do you want to replace it?")
+        # 	msgBox.setWindowTitle("Confirm")
+        # 	msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+        # 	returnValue = msgBox.exec()
+        # 	if returnValue == QMessageBox.No:
+        # 		return None
+        # 	elif returnValue == QMessageBox.Yes:
+        # 		shutil.rmtree(self.folder_dest)
+        # os.mkdir(self.folder_dest)
+
+        print(
+            "Configuration successfully written in ",
+            self.folder_dest + os.sep + "config_input.json",
+        )
+        with open(self.folder_dest + os.sep + "config_input.json", "w") as outfile:
+            outfile.write(json_object)
+
+    def open_threshold_config_wizard(self):
+
+        self.parent_window.parent_window.locate_image()
+        if self.parent_window.parent_window.current_stack is None:
+            return None
+        else:
+            from celldetective.gui.thresholds_gui import ThresholdConfigWizard
+
+            self.thresh_wizard = ThresholdConfigWizard(self)
+            self.thresh_wizard.show()
+
+            def safe_resize():
+                try:
+                    self.thresh_wizard.resize(
+                        self.thresh_wizard.width() + 1,
+                        self.thresh_wizard.height() + 1,
+                    )
+                except RuntimeError:
+                    pass
+
+            try:
+                QTimer.singleShot(100, safe_resize)
+                center_window(self.thresh_wizard)
+            except:
+                pass