celldetective 1.0.2__py3-none-any.whl

celldetective/gui/signal_annotator_options.py

@@ -0,0 +1,340 @@
+"""
+Copright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
+"""
+
+from PyQt5.QtWidgets import QMainWindow, QComboBox, QLabel, QRadioButton, QLineEdit, QApplication, QPushButton, QScrollArea, QWidget, QVBoxLayout, QHBoxLayout
+from PyQt5.QtCore import Qt, QSize
+from celldetective.gui.gui_utils import center_window, QHSeperationLine
+from superqt import QLabeledDoubleSlider, QLabeledSlider
+from celldetective.utils import extract_experiment_channels, get_software_location
+import json
+import numpy as np
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+import os
+
+class ConfigSignalAnnotator(QMainWindow):
+	
+	"""
+	UI to set normalization and animation parameters for the annotator tool. 
+
+	"""
+
+	def __init__(self, parent=None):
+		
+		super().__init__()
+		self.parent = parent
+		self.setWindowTitle("Configure signal annotator")
+		self.mode = self.parent.mode
+		self.exp_dir = self.parent.exp_dir
+		self.soft_path = get_software_location()
+		
+		if self.mode=="targets":
+			self.instructions_path = self.parent.exp_dir + "configs/signal_annotator_config_targets.json"
+		elif self.mode=="effectors":
+			self.instructions_path = self.parent.exp_dir + "configs/signal_annotator_config_effectors.json"
+				
+		exp_config = self.exp_dir +"config.ini"
+		#self.config_path = self.exp_dir + self.config_name
+		self.channel_names, self.channels = extract_experiment_channels(exp_config)
+		self.channel_names = np.array(self.channel_names)
+		self.channels = np.array(self.channels)
+		self.log_option = False
+
+		self.screen_height = self.parent.parent.parent.screen_height
+		center_window(self)
+
+		self.setMinimumHeight(int(0.4*self.screen_height))
+		self.setMaximumHeight(int(0.8*self.screen_height))
+		self.populate_widget()
+		#self.load_previous_measurement_instructions()
+
+	def populate_widget(self):
+		
+		"""
+		Create the widgets.
+		
+		"""
+
+		self.scroll_area = QScrollArea(self)
+		self.button_widget = QWidget()
+
+		main_layout = QVBoxLayout()
+		main_layout.setContentsMargins(30,30,30,30)
+
+		sub_layout = QVBoxLayout()
+		sub_layout.setContentsMargins(10,10,10,20)
+
+		self.button_widget.setLayout(main_layout)
+		sub_layout.setContentsMargins(30,30,30,30)
+
+		sub_layout.addWidget(QLabel('Modality: '))
+		
+		# Create radio buttons
+		option_layout = QHBoxLayout()
+		self.gs_btn = QRadioButton('grayscale')
+		self.gs_btn.setChecked(True)
+		option_layout.addWidget(self.gs_btn, alignment=Qt.AlignCenter)
+
+		self.rgb_btn = QRadioButton('RGB')
+		option_layout.addWidget(self.rgb_btn, alignment=Qt.AlignCenter)
+		sub_layout.addLayout(option_layout)
+
+		btn_hbox = QHBoxLayout()
+
+		self.percentile_btn = QPushButton()
+		self.percentile_btn.setIcon(icon(MDI6.percent_circle_outline,color="black"))
+		self.percentile_btn.setIconSize(QSize(20, 20))	
+		self.percentile_btn.setStyleSheet(self.parent.parent.parent.button_select_all)	
+		self.percentile_btn.setToolTip("Switch to percentile normalization values.")
+		self.percentile_btn.clicked.connect(self.switch_to_absolute_normalization_mode)
+
+		self.log_btn = QPushButton()
+		self.log_btn.setIcon(icon(MDI6.math_log,color="black"))
+		self.log_btn.setStyleSheet(self.parent.parent.parent.button_select_all)
+		self.log_btn.clicked.connect(self.switch_to_log)
+		self.log_btn.setToolTip("Log-transform the intensities.")
+		self.log_btn.setIconSize(QSize(20, 20))	
+
+		btn_hbox.addWidget(QLabel(''), 90)
+		btn_hbox.addWidget(self.log_btn, 5,alignment=Qt.AlignRight)
+		btn_hbox.addWidget(self.percentile_btn, 5,alignment=Qt.AlignRight)
+		sub_layout.addLayout(btn_hbox)
+
+		self.channel_cbs = [QComboBox() for i in range(3)]
+		self.channel_cbs_lbls = [QLabel() for i in range(3)]
+
+		self.min_val_les = [QLineEdit('0') for i in range(3)]
+		self.min_val_lbls = [QLabel('Min value: ') for i in range(3)]
+		self.max_val_les = [QLineEdit('10000') for i in range(3)]
+		self.max_val_lbls = [QLabel('Max value: ') for i in range(3)]
+		self.percentile_mode = False
+
+		self.rgb_text = ['R: ', 'G: ', 'B: ']
+
+		for i in range(3):
+
+			hlayout = QHBoxLayout()
+			self.channel_cbs[i].addItems(self.channel_names)
+			self.channel_cbs[i].setCurrentIndex(i)
+			self.channel_cbs_lbls[i].setText(self.rgb_text[i])
+			hlayout.addWidget(self.channel_cbs_lbls[i], 20)
+			hlayout.addWidget(self.channel_cbs[i], 80)
+			sub_layout.addLayout(hlayout)
+
+			hlayout2 = QHBoxLayout()
+			hlayout2.addWidget(self.min_val_lbls[i], 20)
+			hlayout2.addWidget(self.min_val_les[i], 80)			
+			sub_layout.addLayout(hlayout2)
+
+			hlayout3 = QHBoxLayout()
+			hlayout3.addWidget(self.max_val_lbls[i], 20)
+			hlayout3.addWidget(self.max_val_les[i], 80)			
+			sub_layout.addLayout(hlayout3)
+
+		self.enable_channels()
+		
+		self.gs_btn.toggled.connect(self.enable_channels)
+		self.rgb_btn.toggled.connect(self.enable_channels)
+
+		self.hsep = QHSeperationLine()
+		sub_layout.addWidget(self.hsep)
+
+		hbox_frac = QHBoxLayout()
+		hbox_frac.addWidget(QLabel('fraction: '), 20)
+
+		self.fraction_slider = QLabeledDoubleSlider()
+		self.fraction_slider.setSingleStep(0.05)
+		self.fraction_slider.setTickInterval(0.05)
+		self.fraction_slider.setSingleStep(1)
+		self.fraction_slider.setOrientation(1)
+		self.fraction_slider.setRange(0.1,1)
+		self.fraction_slider.setValue(0.25)
+
+		hbox_frac.addWidget(self.fraction_slider, 80)
+		sub_layout.addLayout(hbox_frac)
+
+
+		hbox_interval = QHBoxLayout()
+		hbox_interval.addWidget(QLabel('interval [ms]: '), 20)
+
+		self.interval_slider = QLabeledSlider()
+		self.interval_slider.setSingleStep(1)
+		self.interval_slider.setTickInterval(1)
+		self.interval_slider.setSingleStep(1)
+		self.interval_slider.setOrientation(1)
+		self.interval_slider.setRange(1,1000)
+		self.interval_slider.setValue(1)
+		hbox_interval.addWidget(self.interval_slider, 80)
+		sub_layout.addLayout(hbox_interval)
+
+		main_layout.addLayout(sub_layout)
+
+		self.submit_btn = QPushButton('Save')
+		self.submit_btn.setStyleSheet(self.parent.parent.parent.button_style_sheet)
+		self.submit_btn.clicked.connect(self.write_instructions)
+		main_layout.addWidget(self.submit_btn)
+
+
+		self.button_widget.adjustSize()
+		self.scroll_area.setAlignment(Qt.AlignCenter)
+		self.scroll_area.setWidget(self.button_widget)
+		self.scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self.scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self.scroll_area.setWidgetResizable(True)
+		self.setCentralWidget(self.scroll_area)
+		self.show()
+
+		self.read_instructions()
+
+		QApplication.processEvents()
+
+	def enable_channels(self):
+
+		"""
+		Enable three channels when RGB mode is checked.
+		
+		"""
+
+		if self.gs_btn.isChecked():
+
+			self.log_btn.setEnabled(True)
+			self.percentile_btn.setEnabled(False)
+
+			for k in range(1,3):
+				self.channel_cbs[k].setEnabled(False)
+				self.channel_cbs_lbls[k].setEnabled(False)
+
+			for k in range(3):
+
+				self.min_val_les[k].setEnabled(False)
+				self.min_val_lbls[k].setEnabled(False)
+				self.max_val_les[k].setEnabled(False)
+				self.max_val_lbls[k].setEnabled(False)
+
+		elif self.rgb_btn.isChecked():
+
+			self.log_btn.setEnabled(False)
+			self.percentile_btn.setEnabled(True)
+
+			for k in range(3):
+
+				self.channel_cbs[k].setEnabled(True)
+				self.channel_cbs_lbls[k].setEnabled(True)
+
+				self.min_val_les[k].setEnabled(True)
+				self.min_val_lbls[k].setEnabled(True)
+				self.max_val_les[k].setEnabled(True)
+				self.max_val_lbls[k].setEnabled(True)
+
+	def switch_to_absolute_normalization_mode(self):
+
+		"""
+		Use absolute or percentile values for the normalization of each individual channel.
+		
+		"""
+
+		if self.percentile_mode:
+			self.percentile_mode = False
+			self.percentile_btn.setIcon(icon(MDI6.percent_circle_outline,color="black"))
+			self.percentile_btn.setIconSize(QSize(20, 20))		
+			self.percentile_btn.setToolTip("Switch to percentile normalization values.")	
+			for k in range(3):
+				self.min_val_lbls[k].setText('Min value: ')	
+				self.min_val_les[k].setText('0')	
+				self.max_val_lbls[k].setText('Max value: ')	
+				self.max_val_les[k].setText('10000')
+		else:
+			self.percentile_mode = True
+			self.percentile_btn.setIcon(icon(MDI6.percent_circle,color="black"))
+			self.percentile_btn.setIconSize(QSize(20, 20))
+			self.percentile_btn.setToolTip("Switch to absolute normalization values.")	
+			for k in range(3):
+				self.min_val_lbls[k].setText('Min percentile: ')
+				self.min_val_les[k].setText('0.01')	
+				self.max_val_lbls[k].setText('Max percentile: ')	
+				self.max_val_les[k].setText('99.99')
+
+	def write_instructions(self):
+
+		"""
+		Save the current configuration.
+		
+		"""
+
+		instructions = {'rgb_mode': self.rgb_btn.isChecked(), 'percentile_mode': self.percentile_mode, 'fraction': float(self.fraction_slider.value()), 'interval': int(self.interval_slider.value()), 'log': self.log_option}
+		max_i = 3 if self.rgb_btn.isChecked() else 1
+		channels = []
+		for i in range(max_i):
+			channels.append([self.channel_cbs[i].currentText(), float(self.min_val_les[i].text()), float(self.max_val_les[i].text())])
+		instructions.update({'channels': channels})
+		
+		print('Instructions: ', instructions)
+		file_name = self.instructions_path
+		with open(file_name, 'w') as f:
+			json.dump(instructions, f, indent=4)
+		print('Done.')
+		self.close()
+
+	def read_instructions(self):
+		
+		"""
+		Read and set the widgets to the last configuration.
+
+		"""
+
+		print('Reading instructions..')
+		if os.path.exists(self.instructions_path):
+			with open(self.instructions_path, 'r') as f:
+				instructions = json.load(f)
+				print(instructions)
+				
+				if 'rgb_mode' in instructions:
+					rgb_mode = instructions['rgb_mode']
+					if rgb_mode:
+						self.rgb_btn.setChecked(True)
+						self.gs_btn.setChecked(False)
+
+				if 'percentile_mode' in instructions:
+					percentile_mode = instructions['percentile_mode']
+					if percentile_mode:
+						self.percentile_btn.click()
+
+				if 'channels' in instructions:
+					channels = instructions['channels']
+					
+					if len(channels)==1:
+						max_iter = 1
+					else:
+						max_iter = 3
+
+					for i in range(max_iter):
+						idx = self.channel_cbs[i].findText(channels[i][0])
+						self.channel_cbs[i].setCurrentIndex(idx)					
+						self.min_val_les[i].setText(str(channels[i][1]))
+						self.max_val_les[i].setText(str(channels[i][2]))
+
+				if 'fraction' in instructions:
+					fraction = instructions['fraction']
+					self.fraction_slider.setValue(fraction)
+
+				if 'interval' in instructions:
+					interval = instructions['interval']
+					self.interval_slider.setValue(interval)
+
+				if 'log' in instructions:
+					self.log_option = not instructions['log']
+					self.switch_to_log()
+
+	def switch_to_log(self):
+
+		"""
+		Switch threshold histogram to log scale. Auto adjust.
+		"""
+
+		if not self.log_option:
+			self.log_btn.setIcon(icon(MDI6.math_log,color="#1565c0"))
+			self.log_option = True
+		else:
+			self.log_btn.setIcon(icon(MDI6.math_log,color="black"))
+			self.log_option = False

celldetective/gui/styles.py

@@ -0,0 +1,217 @@
+class Styles(object):
+
+	def __init__(self):
+
+		self.init_button_styles()
+		self.init_tab_styles()
+
+	def init_button_styles(self):
+
+		self.button_style_sheet = '''
+			QPushButton {
+				background-color: #1565c0;
+				color: white;
+				border-radius: 13px;
+				padding: 7px;
+				font-weight: bold;
+				font-size: 12px;
+			}
+			QPushButton:hover {
+				background-color: #2070EB;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+
+			QPushButton:!enabled {
+				background-color: #92a8c0;
+				color: white;
+				border-radius: 13px;
+				padding: 7px;
+				font-weight: bold;
+				font-size: 12px;
+			}
+		'''
+
+		self.button_style_sheet_2 = '''
+			QPushButton {
+				background-color: transparent;
+				border: 3px solid #1565c0;
+				color: #1565c0;
+				border-radius: 15px;
+				padding: 7px;
+				font-weight: bold;
+				font-size: 12px;
+			}
+			QPushButton:hover {
+				background-color: #ecf0f1;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+
+			QPushButton:disabled {
+				border: 3px solid rgba(21, 101, 192, 0.50);
+				color: rgba(21, 101, 192, 0.50);
+			}
+
+		'''
+
+		self.button_style_sheet_2_not_done = '''
+			QPushButton {
+				background-color: transparent;
+				border: 3px solid #d14334;
+				color: #d14334;
+				border-radius: 15px;
+				padding: 7px;
+				font-weight: bold;
+				font-size: 12px;
+			}
+			QPushButton:hover {
+				background-color: #ecf0f1;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+		'''
+
+		self.button_style_sheet_3 = '''
+			QPushButton {
+				background-color: #eeeeee;
+				color: black;
+				border-radius: 10px;
+				padding: 7px;
+				font-size: 8px;
+			}
+			QPushButton:hover {
+				background-color: #2070EB;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+		'''
+
+		self.button_select_all = '''
+			QPushButton {
+				background-color: transparent;
+				color: black;
+				border-radius: 15px;
+				padding: 7px;
+				font-size: 9px;
+			}
+			QPushButton:hover {
+				background-color: #bdbdbd;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+		'''
+
+		self.button_add = '''
+			QPushButton {
+				background-color: transparent;
+				color: black;
+				border-radius: 13px;
+				padding: 7px;
+				font-size: 12px;
+				Text-align: left;
+			}
+			QPushButton:hover {
+				background-color: #bdbdbd;
+			}
+			QPushButton:pressed {
+				background-color: #ff8a00;
+			}
+		'''
+
+	def init_tab_styles(self):
+
+		self.qtab_style = """
+			QTabWidget::pane {
+			border: 1px solid #B8B8B8;
+			background: white;
+		}
+
+		QTabWidget::tab-bar:top {
+			top: 1px;
+		}
+
+		QTabWidget::tab-bar:bottom {
+			bottom: 3px solid blue;
+		}
+
+		QTabWidget::tab-bar:left {
+			right: 1px;
+		}
+
+		QTabWidget::tab-bar:right {
+			left: 1px;
+		}
+
+		QTabBar::tab {
+			border: 1px solid #B8B8B8;
+		}
+
+		QTabBar::tab:selected {
+			background: white;
+		}
+
+		QTabBar::tab:!selected {
+			background: silver;
+		}
+
+		QTabBar::tab:!selected:hover {
+			background: #999;
+		}
+
+		QTabBar::tab:top:!selected {
+			margin-top: 3px;
+		}
+
+		QTabBar::tab:bottom:!selected {
+			margin-bottom: 3px;
+		}
+
+		QTabBar::tab:top, QTabBar::tab:bottom {
+			min-width: 8ex;
+			margin-right: -1px;
+			padding: 5px 10px 5px 10px;
+		}
+
+		QTabBar::tab:top:selected {
+			border-bottom: 4px solid #1565c0;
+		}
+
+
+		QTabBar::tab:top:last, QTabBar::tab:bottom:last,
+		QTabBar::tab:top:only-one, QTabBar::tab:bottom:only-one {
+			margin-right: 0;
+		}
+
+		QTabBar::tab:left:!selected {
+			margin-right: 3px;
+		}
+
+		QTabBar::tab:right:!selected {
+			margin-left: 3px;
+		}
+
+		QTabBar::tab:left, QTabBar::tab:right {
+			min-height: 8ex;
+			margin-bottom: -1px;
+			padding: 10px 5px 10px 5px;
+		}
+
+		QTabBar::tab:left:selected {
+			border-left-color: none;
+		}
+
+		QTabBar::tab:right:selected {
+			border-right-color: none;
+		}
+
+		QTabBar::tab:left:last, QTabBar::tab:right:last,
+		QTabBar::tab:left:only-one, QTabBar::tab:right:only-one {
+			margin-bottom: 0;
+		}
+		"""