celldetective 1.0.2__py3-none-any.whl

celldetective/gui/configure_new_exp.py

@@ -0,0 +1,532 @@
+from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QDialog, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QSlider, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
+from PyQt5.QtGui import QIntValidator, QDoubleValidator
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui.styles import Styles
+from superqt import QLabeledSlider
+from PyQt5.QtCore import Qt, QSize
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+from configparser import ConfigParser
+import os
+from shutil import copyfile
+import time
+from functools import partial
+import numpy as np
+
+class ConfigNewExperiment(QMainWindow):
+
+	def __init__(self, parent=None):
+		
+		super().__init__()
+		self.parent = parent
+		self.setWindowTitle("New experiment")
+		center_window(self)
+		self.setFixedWidth(500)
+		self.setMaximumHeight(int(0.8*self.parent.screen_height))
+		self.onlyFloat = QDoubleValidator()
+		
+		self.Styles = Styles()
+		self.button_style = self.Styles.button_add
+		self.button_style_sheet = self.Styles.button_style_sheet
+
+		self.newExpFolder = str(QFileDialog.getExistingDirectory(self, 'Select directory'))
+		self.populate_widget()
+
+	def populate_widget(self):
+		
+		# Create button widget and layout
+		self.scroll_area = QScrollArea(self)
+		button_widget = QWidget()
+		grid = QGridLayout()
+		button_widget.setLayout(grid)
+
+		grid.setContentsMargins(30,30,30,30)
+		grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
+		self.supFolder = QLineEdit()
+		self.supFolder.setAlignment(Qt.AlignLeft)	
+		self.supFolder.setEnabled(True)
+		self.supFolder.setText(self.newExpFolder)
+		grid.addWidget(self.supFolder, 1, 0, 1, 1)
+
+		self.browse_button = QPushButton("Browse...")
+		self.browse_button.clicked.connect(self.browse_experiment_folder)
+		self.browse_button.setIcon(icon(MDI6.folder, color="white"))
+		self.browse_button.setStyleSheet(self.parent.button_style_sheet)
+		#self.browse_button.setIcon(QIcon_from_svg(abs_path+f"/icons/browse.svg", color='white'))
+		grid.addWidget(self.browse_button, 1, 1, 1, 1)
+
+		grid.addWidget(QLabel("Experiment name:"), 2, 0, 1, 3)
+		
+		self.expName = QLineEdit()
+		self.expName.setPlaceholderText('folder_name_for_the_experiment')
+		self.expName.setAlignment(Qt.AlignLeft)	
+		self.expName.setEnabled(True)
+		self.expName.setFixedWidth(400)
+		self.expName.setText("Untitled_Experiment")
+		grid.addWidget(self.expName, 3, 0, 1, 3)
+
+		self.generate_movie_settings()
+		grid.addLayout(self.ms_grid,29,0,1,3)
+
+		self.generate_channel_params_box()
+		grid.addLayout(self.channel_grid,30,0,1,3)
+
+		self.validate_button = QPushButton("Submit")
+		self.validate_button.clicked.connect(self.create_config)
+		self.validate_button.setStyleSheet(self.parent.button_style_sheet)
+		#self.validate_button.setIcon(QIcon_from_svg(abs_path+f"/icons/process.svg", color='white'))
+
+		grid.addWidget(self.validate_button, 31, 0, 1, 3, alignment = Qt.AlignBottom)		
+		button_widget.adjustSize()
+
+		self.scroll_area.setAlignment(Qt.AlignCenter)
+		self.scroll_area.setWidget(button_widget)
+		self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
+		self.scroll_area.setWidgetResizable(True)
+		self.setCentralWidget(self.scroll_area)
+		self.show()
+
+		QApplication.processEvents()
+		self.adjustScrollArea()
+
+	def adjustScrollArea(self):
+		
+		"""
+		Auto-adjust scroll area to fill space 
+		(from https://stackoverflow.com/questions/66417576/make-qscrollarea-use-all-available-space-of-qmainwindow-height-axis)
+		"""
+
+		step = 5
+		while self.scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
+			self.resize(self.width(), self.height() + step)
+
+	def generate_movie_settings(self):
+		
+		"""
+		Parameters related to the movie parameters
+		"""
+
+		onlyInt = QIntValidator()
+		onlyInt.setRange(0, 100000)
+
+		self.ms_grid = QGridLayout()
+		self.ms_grid.setContentsMargins(21,30,20,30)
+
+		ms_lbl = QLabel("MOVIE SETTINGS")
+		ms_lbl.setStyleSheet("""
+			font-weight: bold;
+			""")
+		self.ms_grid.addWidget(ms_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
+
+		self.number_of_wells = QLabel("Number of wells:")
+		self.ms_grid.addWidget(self.number_of_wells, 1, 0, 1, 3)
+
+		self.SliderWells = QLabeledSlider(Qt.Horizontal, self)
+		self.SliderWells.setMinimum(1)
+		self.SliderWells.setMaximum(32)
+		self.ms_grid.addWidget(self.SliderWells, 2, 0, 1, 3, alignment=Qt.AlignTop)
+
+		self.number_of_positions = QLabel("Number of positions per well:")
+		self.ms_grid.addWidget(self.number_of_positions, 3, 0, 1, 3)
+
+		self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
+		self.SliderPos.setMinimum(1)
+		self.SliderPos.setMaximum(50)
+
+		self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
+
+		self.ms_grid.addWidget(QLabel("Calibration from pixel to µm:"), 5, 0, 1, 3)
+		self.PxToUm_field = QLineEdit()
+		self.PxToUm_field.setValidator(self.onlyFloat)
+		self.PxToUm_field.setPlaceholderText('1 px = XXX µm')
+		self.PxToUm_field.setAlignment(Qt.AlignLeft)	
+		self.PxToUm_field.setEnabled(True)
+		self.PxToUm_field.setFixedWidth(400)
+		self.PxToUm_field.setText("1,0")
+		self.ms_grid.addWidget(self.PxToUm_field, 6, 0, 1, 3)
+
+		self.ms_grid.addWidget(QLabel("Calibration from frame to minutes:"), 7, 0, 1, 3)
+		self.FrameToMin_field = QLineEdit()
+		self.FrameToMin_field.setAlignment(Qt.AlignLeft)	
+		self.FrameToMin_field.setEnabled(True)
+		self.FrameToMin_field.setFixedWidth(400)
+		self.FrameToMin_field.setValidator(self.onlyFloat)
+		self.FrameToMin_field.setPlaceholderText('1 frame = XXX min')
+		self.FrameToMin_field.setText("1,0")
+		self.ms_grid.addWidget(self.FrameToMin_field, 8, 0, 1, 3)
+
+		self.movie_length = QLabel("Number of frames:")
+		self.movie_length.setToolTip('Optional: depending on how the movies are encoded, the automatic extraction of the number of frames can be difficult.\nThe software will then rely on this value.')
+		self.ms_grid.addWidget(self.movie_length,9, 0, 1, 3)
+		self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
+		self.MovieLengthSlider.setMinimum(2)
+		self.MovieLengthSlider.setMaximum(128)
+		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
+
+		self.prefix_lbl = QLabel("Prefix for the movies:")
+		self.prefix_lbl.setToolTip('The stack file name must start with this prefix to be properly loaded.')
+		self.ms_grid.addWidget(self.prefix_lbl, 11, 0, 1, 3)
+		self.movie_prefix_field = QLineEdit()
+		self.movie_prefix_field.setAlignment(Qt.AlignLeft)	
+		self.movie_prefix_field.setEnabled(True)
+		self.movie_prefix_field.setFixedWidth(400)
+		self.movie_prefix_field.setText("")
+		self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
+
+		self.ms_grid.addWidget(QLabel("X shape in pixels:"), 13, 0, 1, 3)
+		self.shape_x_field = QLineEdit()
+		self.shape_x_field.setValidator(onlyInt)
+		self.shape_x_field.setAlignment(Qt.AlignLeft)	
+		self.shape_x_field.setEnabled(True)
+		self.shape_x_field.setFixedWidth(400)
+		self.shape_x_field.setText("2048")
+		self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
+
+		self.ms_grid.addWidget(QLabel("Y shape in pixels:"), 15, 0, 1, 3)
+		self.shape_y_field = QLineEdit()
+		self.shape_y_field.setValidator(onlyInt)
+		self.shape_y_field.setAlignment(Qt.AlignLeft)	
+		self.shape_y_field.setEnabled(True)
+		self.shape_y_field.setFixedWidth(400)
+		self.shape_y_field.setText("2048")
+		self.ms_grid.addWidget(self.shape_y_field, 16, 0, 1, 3)
+
+
+	def generate_channel_params_box(self):
+
+		"""
+		Parameters related to the movie channels
+		Rewrite all of it
+
+		"""
+
+		self.channel_grid = QGridLayout()
+		self.channel_grid.setContentsMargins(21,30,20,30)
+
+		channel_lbl = QLabel("CHANNELS")
+		channel_lbl.setStyleSheet("""
+			font-weight: bold;
+			""")
+		self.channel_grid.addWidget(channel_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
+
+
+		self.channels = ['brightfield', "live nuclei channel\n(Hoechst, NucSpot®)", "dead nuclei channel\n(PI)", "effector fluorescence\n(CFSE)",
+						"adhesion\n(RICM, IRM)", "fluorescence miscellaneous 1\n(LAMP-1, Actin...)", "fluorescence miscellaneous 2\n(LAMP-1, Actin...)"]
+		self.channel_mapping = ['brightfield_channel', 'live_nuclei_channel', 'dead_nuclei_channel', 'effector_fluo_channel',
+								'adhesion_channel', 'fluo_channel_1', 'fluo_channel_2']
+		self.checkBoxes = [QCheckBox() for i in range(len(self.channels))]
+		self.sliders = [QLabeledSlider(Qt.Orientation.Horizontal) for i in range(len(self.channels))]
+
+		for i in range(len(self.channels)):
+
+			self.checkBoxes[i].setText(self.channels[i])
+			self.checkBoxes[i].toggled.connect(partial(self.show_slider, i))
+
+			self.channel_grid.addWidget(self.checkBoxes[i], i+1, 0, 1, 1)
+
+			self.sliders[i].setMinimum(0)
+			self.sliders[i].setMaximum(len(self.channels))
+			self.sliders[i].setEnabled(False)
+
+			self.channel_grid.addWidget(self.sliders[i], i+1, 1, 1, 2, alignment = Qt.AlignRight)
+
+		# Add channel button
+		self.addChannelBtn = QPushButton('Add channel')
+		self.addChannelBtn.setIcon(icon(MDI6.plus,color="#000000"))
+		self.addChannelBtn.setIconSize(QSize(25, 25))
+		self.addChannelBtn.setStyleSheet(self.button_style)
+		self.addChannelBtn.clicked.connect(self.add_custom_channel)
+		self.channel_grid.addWidget(self.addChannelBtn, 1000, 0, 1, 1)
+
+	def add_custom_channel(self):
+
+		self.CustomChannelWidget = QWidget()
+		self.CustomChannelWidget.setWindowTitle("Custom channel")
+		layout = QVBoxLayout()
+		self.CustomChannelWidget.setLayout(layout)
+
+		self.name_le = QLineEdit('custom_channel')
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('channel name: '), 33)
+		hbox.addWidget(self.name_le, 66)
+		layout.addLayout(hbox)
+
+		self.createBtn = QPushButton('create')
+		self.createBtn.setStyleSheet(self.button_style_sheet)
+		self.createBtn.clicked.connect(self.write_custom_channel)
+		layout.addWidget(self.createBtn)
+		center_window(self.CustomChannelWidget)
+		self.CustomChannelWidget.show()
+
+		print('new channel added')
+
+	def write_custom_channel(self):
+		
+		self.new_channel_name = self.name_le.text()
+		name_map = self.new_channel_name
+		name_map = name_map.replace('_channel','')
+		name_map = name_map.replace('channel','')
+		name_map = name_map.replace(' ','')
+		if not name_map.endswith('_channel'):
+			name_map += '_channel'
+
+		self.channels.append(self.new_channel_name)
+		self.channel_mapping.append(name_map)
+		self.checkBoxes.append(QCheckBox())
+		self.sliders.append(QLabeledSlider(Qt.Orientation.Horizontal))
+		self.CustomChannelWidget.close()
+
+		self.checkBoxes[-1].setText(self.channels[-1])
+		self.checkBoxes[-1].toggled.connect(partial(self.show_slider, len(self.channels)-1))
+		self.channel_grid.addWidget(self.checkBoxes[-1], len(self.channels)+1, 0, 1, 1)
+
+		self.sliders[-1].setMinimum(0)
+		for i in range(len(self.channels)):
+			self.sliders[i].setMaximum(len(self.channels))
+		self.sliders[-1].setEnabled(False)
+		self.channel_grid.addWidget(self.sliders[-1], len(self.channels)+1, 1, 1, 2, alignment = Qt.AlignRight)
+
+	def show_slider(self, index):
+		if self.checkBoxes[index].isChecked():
+			self.sliders[index].setEnabled(True)
+		else:
+			self.sliders[index].setEnabled(False)
+
+	def browse_experiment_folder(self):
+
+		"""
+		Set a new base directory.
+		"""
+
+		self.newExpFolder = str(QFileDialog.getExistingDirectory(self, 'Select directory'))
+		self.supFolder.setText(self.newExpFolder)
+
+	def create_config(self):
+
+		"""
+		Create the folder tree, the config, issue a warning if the experiment folder already exists.
+		"""
+
+		channel_indices = []
+		for i in range(len(self.channels)):
+			if self.checkBoxes[i].isChecked():
+				channel_indices.append(self.sliders[i].value())
+		if not channel_indices:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please set at least one channel before proceeding.")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+		if len(channel_indices) != len(set(channel_indices)):
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Some channel indices are repeated. Please check your configuration.")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+		sorted_list = set(channel_indices)
+		expected_list = set(np.arange(max(sorted_list)+1))
+		print(sorted_list, expected_list, sorted_list==expected_list)
+
+		if not sorted_list==expected_list:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("There is a gap in your channel indices. Please check your configuration.")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None			
+		
+		try:
+			
+			folder = self.supFolder.text()
+			folder = folder.replace('\\','/')
+			folder = rf"{folder}"
+
+			name = str(self.expName.text())
+			name = name.replace(' ','')
+
+			self.directory = os.sep.join([folder,name])
+			os.mkdir(self.directory)
+			os.chdir(self.directory)
+			self.create_subfolders()
+			self.annotate_wells()
+
+		except FileExistsError:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("This experiment already exists... Please select another name.")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+	def create_subfolders(self):
+
+		"""
+		Create the well folders and position folders within the wells.
+		"""
+		
+		self.nbr_wells = self.SliderWells.value()
+		self.nbr_positions = self.SliderPos.value()
+		for k in range(self.nbr_wells):
+			well_name = f"W{k+1}"+os.sep
+			os.mkdir(well_name)
+			for p in range(self.nbr_positions):
+				position_name = well_name+f"{k+1}0{p}"+os.sep
+				os.mkdir(position_name)
+				os.mkdir(position_name+os.sep+"movie"+os.sep)
+
+	def annotate_wells(self):
+		self.w = SetupConditionLabels(self, self.nbr_wells)
+		self.w.show()
+
+
+	def create_config_file(self):
+
+		"""
+
+		Write all user input parameters to a configuration file associated to an experiment.
+		"""
+
+		config = ConfigParser()
+
+		# add a new section and some values
+		config.add_section('MovieSettings')
+		config.set('MovieSettings', 'PxToUm', self.PxToUm_field.text().replace(',','.'))
+		config.set('MovieSettings', 'FrameToMin', self.FrameToMin_field.text().replace(',','.'))
+		config.set('MovieSettings', 'len_movie', str(self.MovieLengthSlider.value()))
+		config.set('MovieSettings', 'shape_x', self.shape_x_field.text())
+		config.set('MovieSettings', 'shape_y', self.shape_y_field.text())
+		config.set('MovieSettings', 'movie_prefix', self.movie_prefix_field.text())
+
+		config.add_section('Channels')
+		for i in range(len(self.channels)):
+			if self.checkBoxes[i].isChecked():
+				config.set('Channels', self.channel_mapping[i], str(self.sliders[i].value()))
+			else:
+				config.set('Channels', self.channel_mapping[i], "nan")
+
+		config.add_section('Labels')
+		config.set('Labels', 'cell_types', self.cell_types)
+		config.set('Labels', 'antibodies', self.antibodies)
+		config.set('Labels', 'concentrations', self.concentrations)
+		config.set('Labels', 'pharmaceutical_agents', self.pharmaceutical_agents)
+
+		# save to a file
+		with open('config.ini', 'w') as configfile:
+			config.write(configfile)
+
+		self.parent.set_experiment_path(self.directory)
+		print(f'New experiment successfully configured in folder {self.directory}...')
+		self.close()
+
+class SetupConditionLabels(QWidget):
+	def __init__(self, parent, n_wells):
+		super().__init__()
+		self.parent = parent
+		self.n_wells = n_wells
+		self.setWindowTitle("Well conditions")
+		self.layout = QVBoxLayout()
+		self.layout.setContentsMargins(30,30,30,30)
+		self.setLayout(self.layout)
+		self.onlyFloat = QDoubleValidator()
+		self.populate()
+		center_window(self)
+
+	def populate(self):
+
+		self.cell_type_cbs = [QLineEdit() for i in range(self.n_wells)]
+		self.antibodies_cbs = [QLineEdit() for i in range(self.n_wells)]
+		self.concentrations_cbs = [QLineEdit() for i in range(self.n_wells)]
+		self.pharmaceutical_agents_cbs = [QLineEdit() for i in range(self.n_wells)]
+
+		for i in range(self.n_wells):
+			hbox = QHBoxLayout()
+			hbox.setContentsMargins(15,5,15,5)
+			hbox.addWidget(QLabel(f'well {i+1}'), 5, alignment=Qt.AlignLeft)
+			hbox.addWidget(QLabel('cell type: '), 5)
+			hbox.addWidget(self.cell_type_cbs[i], 10)
+			self.cell_type_cbs[i].setPlaceholderText('e.g. T-cell, NK')
+
+			hbox.addWidget(QLabel('antibody: '), 5)
+			hbox.addWidget(self.antibodies_cbs[i], 10)
+			self.antibodies_cbs[i].setPlaceholderText('e.g. anti-CD4')
+			
+			hbox.addWidget(QLabel('concentration: '), 5)
+			hbox.addWidget(self.concentrations_cbs[i], 10)
+			self.concentrations_cbs[i].setPlaceholderText('e.g. 100 (pM)')
+			self.concentrations_cbs[i].setValidator(self.onlyFloat)
+			
+			hbox.addWidget(QLabel('pharmaceutical agents: '), 5)
+			hbox.addWidget(self.pharmaceutical_agents_cbs[i], 10)
+			self.pharmaceutical_agents_cbs[i].setPlaceholderText('e.g. dextran')
+
+			self.layout.addLayout(hbox)
+
+		btn_hbox = QHBoxLayout()
+		btn_hbox.setContentsMargins(0,20,0,0)
+		self.skip_btn = QPushButton('Skip')
+		self.skip_btn.setStyleSheet(self.parent.parent.button_style_sheet_2)
+		self.skip_btn.clicked.connect(self.set_default_values)
+		btn_hbox.addWidget(self.skip_btn)
+
+		self.submit_btn = QPushButton('Submit')
+		self.submit_btn.setStyleSheet(self.parent.parent.button_style_sheet)
+		self.submit_btn.clicked.connect(self.set_user_values)
+		btn_hbox.addWidget(self.submit_btn)
+		self.layout.addLayout(btn_hbox)
+
+	def set_default_values(self):
+		
+		for i in range(self.n_wells):
+			self.cell_type_cbs[i].setText(str(i))
+			self.antibodies_cbs[i].setText(str(i))
+			self.concentrations_cbs[i].setText(str(i))
+			self.pharmaceutical_agents_cbs[i].setText(str(i))
+		self.set_attributes()
+		self.parent.create_config_file()
+		self.close()
+
+	def set_user_values(self):
+		for i in range(self.n_wells):
+			if self.cell_type_cbs[i].text()=='':
+				self.cell_type_cbs[i].setText(str(i))
+			if self.antibodies_cbs[i].text()=='':
+				self.antibodies_cbs[i].setText(str(i))
+			if self.concentrations_cbs[i].text()=='':
+				self.concentrations_cbs[i].setText(str(i))
+			if self.pharmaceutical_agents_cbs[i].text()=='':
+				self.pharmaceutical_agents_cbs[i].setText(str(i))
+		self.set_attributes()
+		self.parent.create_config_file()
+		self.close()
+
+	def set_attributes(self):
+
+		cell_type_text = [c.text() for c in self.cell_type_cbs]
+		self.parent.cell_types = ','.join(cell_type_text)
+
+		antibodies_text = [c.text() for c in self.antibodies_cbs]
+		self.parent.antibodies = ','.join(antibodies_text)
+
+		concentrations_text = [c.text() for c in self.concentrations_cbs]
+		self.parent.concentrations = ','.join(concentrations_text)
+
+		pharamaceutical_text = [c.text() for c in self.pharmaceutical_agents_cbs]
+		self.parent.pharmaceutical_agents = ','.join(pharamaceutical_text)
+
+
+
+
+