celldetective 1.0.2__py3-none-any.whl

celldetective/gui/control_panel.py

@@ -0,0 +1,438 @@
+from PyQt5.QtWidgets import QMainWindow, QComboBox, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
+	QTabWidget, QVBoxLayout, QMessageBox, QScrollArea, QDesktopWidget
+from PyQt5.QtCore import Qt, QSize
+from PyQt5.QtGui import QIcon
+from celldetective.gui.gui_utils import center_window, QHSeperationLine
+from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels
+from celldetective.gui import ConfigEditor, ProcessPanel, AnalysisPanel, NeighPanel
+from natsort import natsorted
+from glob import glob
+import os
+import numpy as np
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+import gc
+import subprocess
+
+class ControlPanel(QMainWindow):
+
+	def __init__(self, parent=None, exp_dir=""):
+		
+		super().__init__()
+		self.exp_dir = exp_dir
+		if not self.exp_dir.endswith(os.sep):
+			self.exp_dir = self.exp_dir+os.sep
+		self.setWindowTitle("celldetective")
+		self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','logo.png'])))
+		self.parent = parent
+		center_window(self)
+
+		self.init_wells_and_positions()
+		self.load_configuration()
+
+		self.w = QWidget()
+		self.grid = QGridLayout(self.w)
+		self.grid.setSpacing(5)
+		self.grid.setContentsMargins(20,20,20,20) #left top right bottom
+
+		self.to_disable = []
+		self.generate_header()
+		self.ProcessEffectors = ProcessPanel(self,'effectors')
+		self.ProcessTargets = ProcessPanel(self,'targets')
+		self.NeighPanel = NeighPanel(self)
+		
+		ProcessFrame = QFrame()
+		grid_process = QVBoxLayout(ProcessFrame)
+		grid_process.setContentsMargins(20,50,20,20)
+
+		AnalyzeFrame = QFrame()
+		grid_analyze = QVBoxLayout(AnalyzeFrame)
+		grid_analyze.setContentsMargins(20,50,20,20)
+		self.SurvivalBlock = AnalysisPanel(self,title='Survival')
+
+
+		grid_process.addWidget(self.ProcessEffectors)
+		grid_process.addWidget(self.ProcessTargets)
+		grid_process.addWidget(self.NeighPanel)
+		grid_analyze.addWidget(self.SurvivalBlock)
+
+		self.scroll=QScrollArea()
+		self.scroll.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self.scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
+		self.scroll.setWidgetResizable(True)
+		desktop = QDesktopWidget()
+		self.scroll.setMinimumHeight(500)
+		#self.scroll.setMinimumHeight(int(0.4*screen_height))
+
+		tabWidget = QTabWidget()
+		tab_index_process = tabWidget.addTab(ProcessFrame, "Process")
+		tabWidget.setTabIcon(tab_index_process, icon(MDI6.cog_outline, color='black'))
+
+		tab_index_analyze = tabWidget.addTab(AnalyzeFrame, "Analyze")
+		tabWidget.setTabIcon(tab_index_analyze, icon(MDI6.poll, color='black'))
+		tabWidget.setStyleSheet(self.parent.qtab_style)
+
+		self.grid.addWidget(tabWidget, 7,0,1,3, alignment=Qt.AlignTop)
+		self.grid.setSpacing(5)
+		self.scroll.setWidget(self.w)
+		self.setCentralWidget(self.scroll)
+		self.create_config_dir()
+		self.update_position_options()
+		#self.setMinimumHeight(int(self.sizeHint().height()))
+
+		self.initial_height = self.size().height()
+		self.initial_width = self.size().width()
+		self.screen_height = desktop.screenGeometry().height()
+		self.screen_width = desktop.screenGeometry().width()
+		self.scroll.setMinimumWidth(410)
+
+	def init_wells_and_positions(self):
+
+		"""
+		Detect the wells in the experiment folder and the associated positions.
+		"""
+		
+		self.wells = natsorted(glob(self.exp_dir + "W*" + os.sep))
+		self.positions = []
+		for w in self.wells:
+			w = os.path.split(w[:-1])
+			root = w[0]
+			w = w[1]
+			positions_path = natsorted(glob(os.sep.join([root, w, f"{w[1:]}*{os.sep}"])))
+			self.positions.append([os.path.split(pos[:-1])[1] for pos in positions_path])
+
+	def generate_header(self):
+		
+		"""
+		Show the experiment name, create two QComboBox for respectively the 
+		biological condition (well) and position of interest, access the experiment config.
+		"""
+
+		condition_label = QLabel("condition: ")
+		position_label = QLabel("position: ")
+
+		name = self.exp_dir.split(os.sep)[-2]
+		experiment_label = QLabel(f"Experiment:")
+		experiment_label.setStyleSheet("""
+			font-weight: bold;
+			""")
+
+		self.folder_exp_btn = QPushButton()
+		self.folder_exp_btn.setIcon(icon(MDI6.folder,color="black"))
+		self.folder_exp_btn.setIconSize(QSize(20, 20))
+		self.folder_exp_btn.setToolTip("Experiment folder")
+		self.folder_exp_btn.clicked.connect(self.open_experiment_folder)
+		self.folder_exp_btn.setStyleSheet(self.parent.button_select_all)
+
+
+		self.edit_config_button = QPushButton()
+		self.edit_config_button.setIcon(icon(MDI6.cog_outline,color="black"))
+		self.edit_config_button.setIconSize(QSize(20, 20))
+		self.edit_config_button.setToolTip("Configuration file")
+		self.edit_config_button.clicked.connect(self.open_config_editor)
+		self.edit_config_button.setStyleSheet(self.parent.button_select_all)
+
+		self.exp_options_layout = QHBoxLayout()
+		self.exp_options_layout.addWidget(experiment_label, 32, alignment=Qt.AlignRight)
+		self.exp_options_layout.addWidget(QLabel(name), 65, alignment=Qt.AlignLeft)
+		self.exp_options_layout.addWidget(self.folder_exp_btn, 5, alignment=Qt.AlignRight)
+		self.exp_options_layout.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
+		self.grid.addLayout(self.exp_options_layout, 0,0,1,3)
+
+		self.well_list = QComboBox()
+		thresh = 40
+		self.well_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.well_labels]		
+		self.well_list.addItems(self.well_truncated) #self.well_labels
+		for i in range(len(self.well_labels)):
+			self.well_list.setItemData(i, self.well_labels[i], Qt.ToolTipRole)
+		self.well_list.addItems(["*"])
+		self.well_list.activated.connect(self.display_positions)
+		self.to_disable.append(self.well_list)
+
+		self.position_list = QComboBox()
+		self.position_list.addItems(["*"])
+		self.position_list.addItems(self.positions[0])
+		self.position_list.activated.connect(self.update_position_options)
+		self.to_disable.append(self.position_list)
+		#self.locate_selected_position()
+
+		self.grid.addWidget(QLabel("Well:"), 1, 0, 1,1, alignment=Qt.AlignRight)
+		self.grid.addWidget(self.well_list, 1, 1, 1, 2)
+
+		self.grid.addWidget(QLabel("Position:"),2,0,1,1, alignment=Qt.AlignRight)
+		self.grid.addWidget(self.position_list, 2,1,1,2)
+
+		
+		hsep = QHSeperationLine()
+		self.grid.addWidget(hsep, 5, 0, 1, 3)
+
+	def open_experiment_folder(self):
+
+		try:
+			subprocess.Popen(f'explorer {os.path.realpath(self.exp_dir)}')
+		except:
+			try:
+				os.system('xdg-open "%s"' % self.exp_dir)
+			except:
+				return None		
+
+	def load_configuration(self):
+
+		'''
+		This methods load the configuration read in the config.ini file of the experiment.
+		'''
+
+		self.exp_config = self.exp_dir + "config.ini"
+		self.PxToUm = float(ConfigSectionMap(self.exp_config,"MovieSettings")["pxtoum"])
+		self.FrameToMin = float(ConfigSectionMap(self.exp_config,"MovieSettings")["frametomin"])
+		self.len_movie = int(ConfigSectionMap(self.exp_config,"MovieSettings")["len_movie"])
+		self.shape_x = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_x"])
+		self.shape_y = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_y"])
+		self.movie_prefix = ConfigSectionMap(self.exp_config,"MovieSettings")["movie_prefix"]
+
+		# Read channels
+		self.exp_channels, channel_indices = extract_experiment_channels(self.exp_config)
+		self.nbr_channels = len(self.exp_channels)
+
+		number_of_wells = len(self.wells)
+		self.well_labels = _extract_labels_from_config(self.exp_config,number_of_wells)
+
+		self.concentrations = ConfigSectionMap(self.exp_config,"Labels")["concentrations"].split(",")
+		if number_of_wells != len(self.concentrations):
+			self.concentrations = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]		
+
+		#self.antibodies = extract_labels_from_config(config, number_of_wells)
+
+		self.cell_types = ConfigSectionMap(self.exp_config,"Labels")["cell_types"].split(",")
+		if number_of_wells != len(self.cell_types):
+			self.cell_types = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]		
+
+		try:
+			self.antibodies = ConfigSectionMap(self.exp_config,"Labels")["antibodies"].split(",")
+			if number_of_wells != len(self.antibodies):
+				self.antibodies = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
+		except:
+			print("Warning... antibodies not found...")
+			self.antibodies = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
+
+		try:
+			self.pharmaceutical_agents = ConfigSectionMap(self.exp_config,"Labels")["pharmaceutical_agents"].split(",")
+			if number_of_wells != len(self.pharmaceutical_agents):
+				self.pharmaceutical_agents = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
+		except:
+			print("Warning... pharmaceutical agents not found...")
+			self.pharmaceutical_agents = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
+
+
+	def closeEvent(self, event):
+
+		"""
+		Close child windows if closed.
+		"""
+		
+		try:
+			if self.cfg_editor:
+				self.cfg_editor.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessTargets.SegModelLoader:
+				self.ProcessTargets.SegModelLoader.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessEffectors.SegModelLoader:
+				self.ProcessEffectors.SegModelLoader.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessTargets.ConfigTracking:
+				self.ProcessTargets.ConfigTracking.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessEffectors.ConfigTracking:
+				self.ProcessEffectors.ConfigTracking.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessTargets.ConfigSignalTrain:
+				self.ProcessTargets.ConfigSignalTrain.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessEffectors.ConfigSignalTrain:
+				self.ProcessEffectors.ConfigSignalTrain.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessTargets.ConfigMeasurements:
+				self.ProcessTargets.ConfigMeasurements.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessEffectors.ConfigMeasurements:
+				self.ProcessEffectors.ConfigMeasurements.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessTargets.ConfigSignalAnnotator:
+				self.ProcessTargets.ConfigSignalAnnotator.close()
+		except:
+			pass
+
+		try:
+			if self.ProcessEffectors.ConfigSignalAnnotator:
+				self.ProcessEffectors.ConfigSignalAnnotator.close()
+		except:
+			pass
+
+		gc.collect()
+
+
+	def display_positions(self):
+
+		"""
+		Show the positions as the well is changed.
+		"""
+
+		if self.well_list.currentText()=="*":
+			self.position_list.clear()
+			self.position_list.addItems(["*"])
+			position_linspace = np.linspace(0,len(self.positions[0])-1,len(self.positions[0]),dtype=int)
+			position_linspace = [str(s) for s in position_linspace]
+			self.position_list.addItems(position_linspace)
+		else:
+			pos_index = self.well_list.currentIndex()
+			self.position_list.clear()
+			self.position_list.addItems(["*"])
+			self.position_list.addItems(self.positions[pos_index])
+	
+	def open_config_editor(self):
+		self.cfg_editor = ConfigEditor(self)
+		self.cfg_editor.show()
+
+	def locate_selected_position(self):
+
+		"""
+		Set the current position if the option one well, one positon is selected
+		Display error messages otherwise.
+
+		"""
+
+		if self.well_list.currentText()=="*":
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Critical)
+			msgBox.setText("Please select a single well...")
+			msgBox.setWindowTitle("Error")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return False
+		else:
+			self.well_index = [self.well_list.currentIndex()]
+
+		for w_idx in self.well_index:
+
+			pos = self.positions[w_idx]
+			if self.position_list.currentText()=="*":
+				msgBox = QMessageBox()
+				msgBox.setIcon(QMessageBox.Critical)
+				msgBox.setText("Please select a single position...")
+				msgBox.setWindowTitle("Error")
+				msgBox.setStandardButtons(QMessageBox.Ok)
+				returnValue = msgBox.exec()
+				if returnValue == QMessageBox.Ok:
+					return False
+			else:
+				pos_indices = natsorted([pos.index(self.position_list.currentText())])
+
+			well = self.wells[w_idx]
+
+			for pos_idx in pos_indices:
+				self.pos = natsorted(glob(well+f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*{os.sep}"))[pos_idx]
+				if not os.path.exists(self.pos + 'output'):
+					os.mkdir(self.pos + 'output')
+				if not os.path.exists(self.pos + os.sep.join(['output','tables'])):
+					os.mkdir(self.pos + os.sep.join(['output','tables']))
+
+		return True
+
+	def create_config_dir(self):
+		self.config_folder = self.exp_dir+'configs'+os.sep
+		if not os.path.exists(self.config_folder):
+			os.mkdir(self.config_folder)
+
+	def update_position_options(self):
+		
+		self.pos = self.position_list.currentText()
+		panels = [self.ProcessEffectors, self.ProcessTargets]
+		if self.position_list.currentText()=="*":
+			for p in panels:
+				p.check_seg_btn.setEnabled(False)
+				p.check_tracking_result_btn.setEnabled(False)
+			self.ProcessTargets.view_tab_btn.setEnabled(True)
+			self.ProcessEffectors.view_tab_btn.setEnabled(True)
+			self.ProcessTargets.check_seg_btn.setEnabled(False)
+			self.ProcessEffectors.check_seg_btn.setEnabled(False)
+			self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
+			self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
+			self.ProcessEffectors.check_measurements_btn.setEnabled(False)
+			self.ProcessTargets.check_measurements_btn.setEnabled(False)
+			#self.ProcessTargets.signal_analysis_action.setEnabled(False)
+			#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
+			self.ProcessTargets.check_signals_btn.setEnabled(False)
+			self.ProcessEffectors.check_signals_btn.setEnabled(False)
+		elif self.well_list.currentText()=='*':
+			self.ProcessTargets.view_tab_btn.setEnabled(True)
+			self.ProcessEffectors.view_tab_btn.setEnabled(True)			
+		else:
+			if not self.well_list.currentText()=="*":
+				self.locate_selected_position()
+				# if os.path.exists(os.sep.join([self.pos,'labels_effectors', os.sep])):
+				self.ProcessEffectors.check_seg_btn.setEnabled(True)
+				# if os.path.exists(os.sep.join([self.pos,'labels_targets', os.sep])):
+				self.ProcessTargets.check_seg_btn.setEnabled(True)
+				
+				if os.path.exists(os.sep.join([self.pos,'output','tables','napari_target_trajectories.npy'])):
+					self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
+				else:
+					self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
+				if os.path.exists(os.sep.join([self.pos,'output','tables','napari_effector_trajectories.npy'])):
+					self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
+				else:
+					self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
+
+				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv'])):
+					self.ProcessEffectors.check_measurements_btn.setEnabled(True)
+					self.ProcessEffectors.check_signals_btn.setEnabled(True)
+					#self.ProcessEffectors.signal_analysis_action.setEnabled(True)
+					self.ProcessEffectors.view_tab_btn.setEnabled(True)
+
+				else:
+					self.ProcessEffectors.check_measurements_btn.setEnabled(False)
+					self.ProcessEffectors.check_signals_btn.setEnabled(False)
+					#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
+					self.ProcessEffectors.view_tab_btn.setEnabled(False)
+
+				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_targets.csv'])):
+					self.ProcessTargets.check_measurements_btn.setEnabled(True)
+					self.ProcessTargets.check_signals_btn.setEnabled(True)
+					#self.ProcessTargets.signal_analysis_action.setEnabled(True)
+					self.ProcessTargets.view_tab_btn.setEnabled(True)
+
+				else:
+					self.ProcessTargets.check_measurements_btn.setEnabled(False)
+					self.ProcessTargets.check_signals_btn.setEnabled(False)
+					#self.ProcessTargets.signal_analysis_action.setEnabled(False)
+					self.ProcessTargets.view_tab_btn.setEnabled(False)
+