celldetective 1.0.2__py3-none-any.whl → 1.1.0__py3-none-any.whl

celldetective/gui/configure_new_exp.py

@@ -12,23 +12,20 @@ from shutil import copyfile
 import time
 from functools import partial
 import numpy as np
+from celldetective.gui import Styles
 
-class ConfigNewExperiment(QMainWindow):
+class ConfigNewExperiment(QMainWindow, Styles):
 
-	def __init__(self, parent=None):
+	def __init__(self, parent_window=None):
 		
 		super().__init__()
-		self.parent = parent
+		self.parent_window = parent_window
 		self.setWindowTitle("New experiment")
 		center_window(self)
 		self.setFixedWidth(500)
-		self.setMaximumHeight(int(0.8*self.parent.screen_height))
+		self.setMaximumHeight(int(0.8*self.parent_window.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()
 
@@ -37,25 +34,25 @@ class ConfigNewExperiment(QMainWindow):
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
 		button_widget = QWidget()
-		grid = QGridLayout()
-		button_widget.setLayout(grid)
+		self.grid = QGridLayout()
+		button_widget.setLayout(self.grid)
 
-		grid.setContentsMargins(30,30,30,30)
-		grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
+		self.grid.setContentsMargins(30,30,30,30)
+		self.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.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.setStyleSheet(self.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)
+		self.grid.addWidget(self.browse_button, 1, 1, 1, 1)
 
-		grid.addWidget(QLabel("Experiment name:"), 2, 0, 1, 3)
+		self.grid.addWidget(QLabel("Experiment name:"), 2, 0, 1, 3)
 		
 		self.expName = QLineEdit()
 		self.expName.setPlaceholderText('folder_name_for_the_experiment')
@@ -63,20 +60,20 @@ class ConfigNewExperiment(QMainWindow):
 		self.expName.setEnabled(True)
 		self.expName.setFixedWidth(400)
 		self.expName.setText("Untitled_Experiment")
-		grid.addWidget(self.expName, 3, 0, 1, 3)
+		self.grid.addWidget(self.expName, 3, 0, 1, 3)
 
 		self.generate_movie_settings()
-		grid.addLayout(self.ms_grid,29,0,1,3)
+		self.grid.addLayout(self.ms_grid,29,0,1,3)
 
 		self.generate_channel_params_box()
-		grid.addLayout(self.channel_grid,30,0,1,3)
+		self.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.setStyleSheet(self.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)		
+		self.grid.addWidget(self.validate_button, 31, 0, 1, 3, alignment = Qt.AlignBottom)		
 		button_widget.adjustSize()
 
 		self.scroll_area.setAlignment(Qt.AlignCenter)
@@ -233,9 +230,9 @@ class ConfigNewExperiment(QMainWindow):
 
 		# Add channel button
 		self.addChannelBtn = QPushButton('Add channel')
-		self.addChannelBtn.setIcon(icon(MDI6.plus,color="#000000"))
+		self.addChannelBtn.setIcon(icon(MDI6.plus,color="white"))
 		self.addChannelBtn.setIconSize(QSize(25, 25))
-		self.addChannelBtn.setStyleSheet(self.button_style)
+		self.addChannelBtn.setStyleSheet(self.button_style_sheet)
 		self.addChannelBtn.clicked.connect(self.add_custom_channel)
 		self.channel_grid.addWidget(self.addChannelBtn, 1000, 0, 1, 1)
 
@@ -427,14 +424,14 @@ class ConfigNewExperiment(QMainWindow):
 		with open('config.ini', 'w') as configfile:
 			config.write(configfile)
 
-		self.parent.set_experiment_path(self.directory)
+		self.parent_window.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):
+class SetupConditionLabels(QWidget, Styles):
+	def __init__(self, parent_window, n_wells):
 		super().__init__()
-		self.parent = parent
+		self.parent_window = parent_window
 		self.n_wells = n_wells
 		self.setWindowTitle("Well conditions")
 		self.layout = QVBoxLayout()
@@ -477,12 +474,12 @@ class SetupConditionLabels(QWidget):
 		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.setStyleSheet(self.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.setStyleSheet(self.button_style_sheet)
 		self.submit_btn.clicked.connect(self.set_user_values)
 		btn_hbox.addWidget(self.submit_btn)
 		self.layout.addLayout(btn_hbox)
@@ -495,7 +492,7 @@ class SetupConditionLabels(QWidget):
 			self.concentrations_cbs[i].setText(str(i))
 			self.pharmaceutical_agents_cbs[i].setText(str(i))
 		self.set_attributes()
-		self.parent.create_config_file()
+		self.parent_window.create_config_file()
 		self.close()
 
 	def set_user_values(self):
@@ -509,22 +506,22 @@ class SetupConditionLabels(QWidget):
 			if self.pharmaceutical_agents_cbs[i].text()=='':
 				self.pharmaceutical_agents_cbs[i].setText(str(i))
 		self.set_attributes()
-		self.parent.create_config_file()
+		self.parent_window.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)
+		self.parent_window.cell_types = ','.join(cell_type_text)
 
 		antibodies_text = [c.text() for c in self.antibodies_cbs]
-		self.parent.antibodies = ','.join(antibodies_text)
+		self.parent_window.antibodies = ','.join(antibodies_text)
 
 		concentrations_text = [c.text() for c in self.concentrations_cbs]
-		self.parent.concentrations = ','.join(concentrations_text)
+		self.parent_window.concentrations = ','.join(concentrations_text)
 
 		pharamaceutical_text = [c.text() for c in self.pharmaceutical_agents_cbs]
-		self.parent.pharmaceutical_agents = ','.join(pharamaceutical_text)
+		self.parent_window.pharmaceutical_agents = ','.join(pharamaceutical_text)
 
 
 

celldetective/gui/control_panel.py

@@ -4,7 +4,7 @@ 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 celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
 from natsort import natsorted
 from glob import glob
 import os
@@ -13,18 +13,22 @@ from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import gc
 import subprocess
+from celldetective.gui.viewers import StackVisualizer
+from celldetective.utils import extract_experiment_channels
+from celldetective.gui import Styles
 
-class ControlPanel(QMainWindow):
+class ControlPanel(QMainWindow, Styles):
 
-	def __init__(self, parent=None, exp_dir=""):
+	def __init__(self, parent_window=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
+		self.parent_window = parent_window
 		center_window(self)
 
 		self.init_wells_and_positions()
@@ -33,24 +37,25 @@ class ControlPanel(QMainWindow):
 		self.w = QWidget()
 		self.grid = QGridLayout(self.w)
 		self.grid.setSpacing(5)
-		self.grid.setContentsMargins(20,20,20,20) #left top right bottom
+		self.grid.setContentsMargins(10,10,10,10) #left top right bottom
 
 		self.to_disable = []
 		self.generate_header()
 		self.ProcessEffectors = ProcessPanel(self,'effectors')
 		self.ProcessTargets = ProcessPanel(self,'targets')
 		self.NeighPanel = NeighPanel(self)
+		self.PreprocessingPanel = PreprocessingPanel(self)
 		
 		ProcessFrame = QFrame()
 		grid_process = QVBoxLayout(ProcessFrame)
-		grid_process.setContentsMargins(20,50,20,20)
+		grid_process.setContentsMargins(15,30,15,15)
 
 		AnalyzeFrame = QFrame()
 		grid_analyze = QVBoxLayout(AnalyzeFrame)
-		grid_analyze.setContentsMargins(20,50,20,20)
+		grid_analyze.setContentsMargins(15,30,15,15)
 		self.SurvivalBlock = AnalysisPanel(self,title='Survival')
 
-
+		grid_process.addWidget(self.PreprocessingPanel)
 		grid_process.addWidget(self.ProcessEffectors)
 		grid_process.addWidget(self.ProcessTargets)
 		grid_process.addWidget(self.NeighPanel)
@@ -61,7 +66,7 @@ class ControlPanel(QMainWindow):
 		self.scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
 		self.scroll.setWidgetResizable(True)
 		desktop = QDesktopWidget()
-		self.scroll.setMinimumHeight(500)
+		self.scroll.setMinimumHeight(550)
 		#self.scroll.setMinimumHeight(int(0.4*screen_height))
 
 		tabWidget = QTabWidget()
@@ -70,7 +75,7 @@ class ControlPanel(QMainWindow):
 
 		tab_index_analyze = tabWidget.addTab(AnalyzeFrame, "Analyze")
 		tabWidget.setTabIcon(tab_index_analyze, icon(MDI6.poll, color='black'))
-		tabWidget.setStyleSheet(self.parent.qtab_style)
+		tabWidget.setStyleSheet(self.qtab_style)
 
 		self.grid.addWidget(tabWidget, 7,0,1,3, alignment=Qt.AlignTop)
 		self.grid.setSpacing(5)
@@ -84,7 +89,7 @@ class ControlPanel(QMainWindow):
 		self.initial_width = self.size().width()
 		self.screen_height = desktop.screenGeometry().height()
 		self.screen_width = desktop.screenGeometry().width()
-		self.scroll.setMinimumWidth(410)
+		self.scroll.setMinimumWidth(425)
 
 	def init_wells_and_positions(self):
 
@@ -122,7 +127,7 @@ class ControlPanel(QMainWindow):
 		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.folder_exp_btn.setStyleSheet(self.button_select_all)
 
 
 		self.edit_config_button = QPushButton()
@@ -130,7 +135,7 @@ class ControlPanel(QMainWindow):
 		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.edit_config_button.setStyleSheet(self.button_select_all)
 
 		self.exp_options_layout = QHBoxLayout()
 		self.exp_options_layout.addWidget(experiment_label, 32, alignment=Qt.AlignRight)
@@ -139,8 +144,9 @@ class ControlPanel(QMainWindow):
 		self.exp_options_layout.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
 		self.grid.addLayout(self.exp_options_layout, 0,0,1,3)
 
+		well_layout = QHBoxLayout()
 		self.well_list = QComboBox()
-		thresh = 40
+		thresh = 32
 		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)):
@@ -149,6 +155,7 @@ class ControlPanel(QMainWindow):
 		self.well_list.activated.connect(self.display_positions)
 		self.to_disable.append(self.well_list)
 
+		position_layout = QHBoxLayout()
 		self.position_list = QComboBox()
 		self.position_list.addItems(["*"])
 		self.position_list.addItems(self.positions[0])
@@ -156,16 +163,73 @@ class ControlPanel(QMainWindow):
 		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)
+		self.view_stack_btn = QPushButton()
+		self.view_stack_btn.setStyleSheet(self.button_select_all)
+		self.view_stack_btn.setIcon(icon(MDI6.image_check, color="black"))
+		self.view_stack_btn.setToolTip("View stack.")
+		self.view_stack_btn.setIconSize(QSize(20, 20))
+		self.view_stack_btn.clicked.connect(self.view_current_stack)
+		self.view_stack_btn.setEnabled(False)
+
+		well_layout.setContentsMargins(0,0,0,0)
+		well_lbl = QLabel('Well: ')
+		well_lbl.setAlignment(Qt.AlignRight)
+		well_layout.addWidget(well_lbl, 32)
+		well_layout.addWidget(self.well_list, 68)
+		self.grid.addLayout(well_layout, 1, 0, 1, 3)
+
+		position_layout.setContentsMargins(0,0,0,0)
+		pos_lbl = QLabel('Position: ')
+		pos_lbl.setAlignment(Qt.AlignRight)
+		position_layout.addWidget(pos_lbl, 32)
+
+		subposition_layout = QHBoxLayout()
+		subposition_layout.addWidget(self.position_list, 95)
+		subposition_layout.addWidget(self.view_stack_btn, 5)
+		position_layout.addLayout(subposition_layout, 68)
+		self.grid.addLayout(position_layout, 2, 0, 1, 3)
 
 		
 		hsep = QHSeperationLine()
 		self.grid.addWidget(hsep, 5, 0, 1, 3)
 
+	def locate_image(self):
+
+		"""
+		Load the first frame of the first movie found in the experiment folder as a sample.
+		"""
+
+		movies = glob(self.pos + os.sep.join(['movie', f"{self.movie_prefix}*.tif"]))
+
+		if len(movies) == 0:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please select a position containing a movie...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				self.current_stack = None
+				return None
+		else:
+			self.current_stack = movies[0]
+
+	def view_current_stack(self):
+		
+		self.locate_image()
+		if self.current_stack is not None:
+			self.viewer = StackVisualizer(
+										  stack_path=self.current_stack,
+										  window_title=f'Position {self.position_list.currentText()}',
+										  frame_slider = True,
+										  contrast_slider = True,
+										  channel_cb = True,
+										  channel_names = self.exp_channels,
+										  n_channels = self.nbr_channels,
+										  PxToUm = self.PxToUm,
+										 )
+			self.viewer.show()
+
 	def open_experiment_folder(self):
 
 		try:
@@ -223,79 +287,45 @@ class ControlPanel(QMainWindow):
 			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.
 		"""
 		
+		for process_block in [self.ProcessTargets, self.ProcessEffectors]:
+			try:
+				if process_block.SegModelLoader:
+					process_block.SegModelLoader.close()
+			except:
+				pass
+			try:
+				if process_block.ConfigTracking:
+					process_block.ConfigTracking.close()
+			except:
+				pass
+			try:
+				if process_block.ConfigSignalTrain:
+					process_block.ConfigSignalTrain.close()
+			except:
+				pass
+			try:
+				if process_block.ConfigMeasurements:
+					process_block.ConfigMeasurements.close()
+			except:
+				pass
+			try:
+				if process_block.ConfigSignalAnnotator:
+					process_block.ConfigSignalAnnotator.close()
+			except:
+				pass
+
 		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()
 
 
@@ -316,6 +346,7 @@ class ControlPanel(QMainWindow):
 			self.position_list.clear()
 			self.position_list.addItems(["*"])
 			self.position_list.addItems(self.positions[pos_index])
+		self.update_position_options()
 	
 	def open_config_editor(self):
 		self.cfg_editor = ConfigEditor(self)
@@ -392,12 +423,15 @@ class ControlPanel(QMainWindow):
 			#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
 			self.ProcessTargets.check_signals_btn.setEnabled(False)
 			self.ProcessEffectors.check_signals_btn.setEnabled(False)
+			self.view_stack_btn.setEnabled(False)
 		elif self.well_list.currentText()=='*':
 			self.ProcessTargets.view_tab_btn.setEnabled(True)
-			self.ProcessEffectors.view_tab_btn.setEnabled(True)			
+			self.ProcessEffectors.view_tab_btn.setEnabled(True)	
+			self.view_stack_btn.setEnabled(False)	
 		else:
 			if not self.well_list.currentText()=="*":
 				self.locate_selected_position()
+				self.view_stack_btn.setEnabled(True)
 				# 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])):