celldetective 1.0.2__py3-none-any.whl

celldetective/gui/seg_model_loader.py

@@ -0,0 +1,460 @@
+from PyQt5.QtWidgets import QWidget, QGridLayout, QLabel, QCheckBox, QLineEdit, QHBoxLayout, QRadioButton, QComboBox, QFileDialog, QPushButton, QMessageBox
+from PyQt5.QtCore import Qt, QSize
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui import ThresholdConfigWizard
+from PyQt5.QtGui import QDoubleValidator
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+import numpy as np
+from glob import glob
+import os
+import json
+import shutil
+
+class SegmentationModelLoader(QWidget):
+	
+	"""
+	Upload a segmentation model or define a Threshold pipeline.
+	"""
+
+	def __init__(self, parent):
+		
+		super().__init__()
+		self.parent = parent
+		self.mode = self.parent.mode
+		if self.mode=="targets":
+			self.target_folder = "segmentation_targets"
+		elif self.mode=="effectors":
+			self.target_folder = "segmentation_effectors"
+		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.stardist_button.setChecked(True)
+		option_layout.addWidget(self.stardist_button)
+
+		self.cellpose_button = QRadioButton('Cellpose')
+		#self.cellpose_button.setIcon(QIcon(abs_path+f"/icons/cellpose.png"))
+		option_layout.addWidget(self.cellpose_button)
+
+		self.threshold_button = QRadioButton('Threshold')
+		option_layout.addWidget(self.threshold_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.generate_stardist_specific_block()
+		self.layout.addLayout(self.stardist_block, 3,0,1,2)
+		self.combos = [self.combo_ch1, self.combo_ch2, self.combo_ch3, self.combo_ch4]
+
+		self.normalize_checkbox = QCheckBox()
+		self.normalize_checkbox.setChecked(True)
+		self.normalize_lbl = QLabel('normalize: ')
+		self.layout.addWidget(self.normalize_lbl, 8,0,1,1)
+		self.layout.addWidget(self.normalize_checkbox,8, 1,1,2, Qt.AlignLeft)
+
+		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.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.parent.parent.parent.button_style_sheet)
+		self.upload_button.setEnabled(False)
+		self.layout.addWidget(self.upload_button, 10, 0, 1, 1)
+		
+		self.base_block_options = [self.calibration_label, self.spatial_calib_le, self.ch_1_label, self.combo_ch1, self.ch_2_label, self.combo_ch2, 
+								   self.normalize_checkbox, self.normalize_lbl,
+								   ]
+
+		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.combos:
+			cb.activated.connect(self.unlock_upload)
+
+		self.setLayout(self.layout)
+		self.show()
+
+	def unlock_upload(self):
+		if self.stardist_button.isChecked():
+			if np.any([c.currentText()!='--' for c in self.combos]):
+				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.combos[:2]]):
+				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 = QGridLayout()
+		
+		self.calibration_label = QLabel("pixel calibration: ")
+		self.base_block.addWidget(self.calibration_label,0,0,1,1, alignment=Qt.AlignLeft)
+		self.spatial_calib_le = QLineEdit("0,1")
+		self.qdv = QDoubleValidator(0.0, np.amax([self.parent.parent.shape_x, self.parent.parent.shape_y]), 8, notation=QDoubleValidator.StandardNotation)
+		self.spatial_calib_le.setValidator(self.qdv)
+		self.base_block.addWidget(self.spatial_calib_le, 0,1,1,2,alignment=Qt.AlignRight)
+
+		self.channel_options = ["--","live_nuclei_channel", "dead_nuclei_channel", "effector_fluo_channel", "brightfield_channel", "adhesion_channel", "fluo_channel_1", "fluo_channel_2"]
+		exp_channels = self.parent.parent.exp_channels
+		for ec in exp_channels:
+			if ec not in self.channel_options:
+				self.channel_options.append(ec)
+		self.channel_options += ['None']
+
+		self.ch_1_label = QLabel("channel 1: ")
+		self.base_block.addWidget(self.ch_1_label, 1, 0, 1, 1, alignment=Qt.AlignLeft)
+		self.combo_ch1 = QComboBox()
+		self.combo_ch1.addItems(self.channel_options)
+		self.base_block.addWidget(self.combo_ch1, 1, 1, 1, 2, alignment=Qt.AlignRight)
+
+		self.ch_2_label = QLabel("channel 2: ")
+		self.base_block.addWidget(self.ch_2_label, 2, 0, 1, 1, alignment=Qt.AlignLeft)
+		self.combo_ch2 = QComboBox()
+		self.combo_ch2.addItems(self.channel_options)
+		self.base_block.addWidget(self.combo_ch2, 2, 1, 1, 2, alignment=Qt.AlignRight)
+
+	def generate_stardist_specific_block(self):
+
+		"""
+		Create StarDist specific fields to use the model properly when calling it from the app.
+		"""
+
+		self.stardist_block = QGridLayout()
+		self.ch_3_label = QLabel("channel 3: ")
+		self.stardist_block.addWidget(self.ch_3_label, 0, 0, 1, 1, alignment=Qt.AlignLeft)
+		self.combo_ch3 = QComboBox()
+		self.combo_ch3.addItems(self.channel_options)
+		self.stardist_block.addWidget(self.combo_ch3, 0, 1, 1, 2, alignment=Qt.AlignRight)
+
+		self.ch_4_label = QLabel("channel 4: ")
+		self.stardist_block.addWidget(self.ch_4_label, 1, 0, 1, 1, alignment=Qt.AlignLeft)
+		self.combo_ch4 = QComboBox()
+		self.combo_ch4.addItems(self.channel_options)
+		self.stardist_block.addWidget(self.combo_ch4, 1, 1, 1, 2, alignment=Qt.AlignRight)
+
+		self.stardist_options = [self.ch_3_label, self.ch_4_label, self.combo_ch3, self.combo_ch4]
+
+	def generate_cellpose_options(self):
+
+		"""
+		Create Cellpose specific fields to use the model properly when calling it from the app.
+		"""
+
+		self.cellpose_block = QGridLayout()
+		self.cp_diameter_label = QLabel('diameter:   ')
+		self.cp_diameter_le = QLineEdit("30,0")
+		self.cp_diameter_le.setValidator(self.qdv)
+		self.cellpose_block.addWidget(self.cp_diameter_label, 0, 0, 1, 2)
+		self.cellpose_block.addWidget(self.cp_diameter_le, 0, 1, 1, 2)
+
+		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)
+		self.cellpose_block.addWidget(self.cp_cellprob_label, 1, 0, 1, 2)
+		self.cellpose_block.addWidget(self.cp_cellprob_le, 1, 1, 1, 2)
+
+		self.cp_flow_label = QLabel('flow threshold:   ')
+		self.cp_flow_le = QLineEdit('0,4')
+		self.cp_flow_le.setValidator(qdv_prob)
+		self.cellpose_block.addWidget(self.cp_flow_label, 2, 0, 1, 2)
+		self.cellpose_block.addWidget(self.cp_flow_le, 2, 1, 1, 2)
+
+		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.parent.parent.parent.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.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:
+					msgBox = QMessageBox()
+					msgBox.setIcon(QMessageBox.Warning)
+					msgBox.setText("StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
+					msgBox.setWindowTitle("Warning")
+					msgBox.setStandardButtons(QMessageBox.Ok)
+					returnValue = msgBox.exec()
+					if returnValue == QMessageBox.Ok:
+						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}"
+
+			if self.seg_mode=="threshold":
+				self.file_label.setText(self.filename.split("/")[-1])
+
+	def show_seg_options(self):
+
+		"""
+		Show the relevant widgets, mask the others.
+		"""
+
+		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.ch_1_label.setText('cyto: ')
+			self.ch_2_label.setText('nuclei: ')
+			for c in self.stardist_options+[self.threshold_config_button]:
+				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.ch_1_label.setText('channel 1: ')
+			self.ch_2_label.setText('channel 2: ')
+			for c in self.stardist_options+self.base_block_options:
+				c.show()
+			for c in self.cellpose_options+[self.threshold_config_button]:
+				c.hide()
+			self.unlock_upload()
+		else:
+			for c in self.stardist_options+self.cellpose_options+self.base_block_options:
+				c.hide()
+			self.threshold_config_button.show()
+			self.upload_button.setEnabled(True)
+		self.adjustSize()
+
+	def upload_model(self):
+
+		"""
+		Upload the model.
+		"""
+
+		if self.file_label.text()=='No file chosen':
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please select a model first.")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+		if not self.threshold_button.isChecked():
+			
+			if self.stardist_button.isChecked():
+				
+				try:
+					shutil.copytree(self.filename, self.destination)
+				except FileExistsError:
+					msgBox = QMessageBox()
+					msgBox.setIcon(QMessageBox.Warning)
+					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
+					msgBox.setWindowTitle("Warning")
+					msgBox.setStandardButtons(QMessageBox.Ok)
+					returnValue = msgBox.exec()
+					if returnValue == QMessageBox.Ok:
+						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:
+					msgBox = QMessageBox()
+					msgBox.setIcon(QMessageBox.Warning)
+					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
+					msgBox.setWindowTitle("Warning")
+					msgBox.setStandardButtons(QMessageBox.Ok)
+					returnValue = msgBox.exec()
+					if returnValue == QMessageBox.Ok:
+						return None
+
+			self.generate_input_config()
+			self.parent.init_seg_model_list()
+			self.close()
+		else:
+			if self.mode=="targets":	
+				self.parent.threshold_config_targets = self.filename
+				print('Path to threshold configuration successfully set in the software')
+				self.close()
+			elif self.mode=="effectors":
+				self.parent.threshold_config_effectors = self.filename
+				print('Path to threshold configuration successfully set in the software')
+				self.close()	
+
+	def generate_input_config(self):
+
+		"""
+		Check the ticked options and input parameters to create
+		a configuration to use the uploaded model properly.
+		"""
+		
+		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': norm_percentile,
+						 'normalization_clip': norm_clip,
+						 'normalization_values': normalization_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']
+
+			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(',','.'))
+			if normalize:
+				norm_percentile = [True]*len(channels)
+				norm_clip = [True]*len(channels)
+			else:
+				norm_percentile = [False]*len(channels)
+				norm_clip = [False]*len(channels)
+			normalization_values = [[1.0,99.0]]*len(channels)
+
+			dico.update({"channels": channels,
+						 "diameter": diameter,
+						 "cellprob_threshold": cellprob_threshold,
+						 "flow_threshold": flow_threshold,
+						 "normalize": normalize,
+						 "spatial_calibration": spatial_calib,
+						 'normalization_percentile': norm_percentile,
+						 'normalization_clip': norm_clip,
+						 'normalization_values': normalization_values,
+						 })
+
+		elif self.threshold_button.isChecked():
+			model_type = "threshold"
+			return None
+
+		dico.update({"model_type": model_type})
+		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+"/config_input.json")
+		with open(self.folder_dest+"/config_input.json", "w") as outfile:
+			outfile.write(json_object)
+
+	def open_threshold_config_wizard(self):
+
+		if isinstance(self.parent.parent.pos, str):
+			self.ThreshWizard = ThresholdConfigWizard(self)
+			self.ThreshWizard.show()
+		else:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please select a unique position before launching the wizard...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None