celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/settings/_settings_signal_annotator.py

@@ -2,11 +2,19 @@
 Copyright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 """
 
-from PyQt5.QtWidgets import QComboBox, QLabel, QRadioButton, QLineEdit, QApplication, QPushButton, QScrollArea, QVBoxLayout, QHBoxLayout
+from PyQt5.QtWidgets import (
+    QComboBox,
+    QLabel,
+    QRadioButton,
+    QLineEdit,
+    QPushButton,
+    QVBoxLayout,
+    QHBoxLayout,
+)
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, QHSeperationLine
+from celldetective.gui.base.components import QHSeperationLine
 from superqt import QLabeledDoubleSlider, QLabeledSlider
-from celldetective.utils import extract_experiment_channels, get_software_location
+from celldetective.utils.experiment import extract_experiment_channels
 import json
 import numpy as np
 from superqt.fonticon import icon
@@ -14,306 +22,322 @@ from fonticon_mdi6 import MDI6
 import os
 from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
 
+
 class SettingsSignalAnnotator(CelldetectiveSettingsPanel):
-	
-	"""
-	UI to set normalization and animation parameters for the annotator tool. 
-
-	"""
-
-	def __init__(self, parent_window=None):
-		
-		self.parent_window = parent_window
-		self.mode = self.parent_window.mode
-		self.exp_dir = self.parent_window.exp_dir
-		
-		self.instructions_path = self.parent_window.exp_dir + f"configs/signal_annotator_config_{self.mode}.json"
-		if self.mode == "pairs":
-			self.instructions_path = self.parent_window.exp_dir + "configs/signal_annotator_config_neighborhood.json"
-
-		self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
-		self.channel_names = np.array(self.channel_names)
-		self.channels = np.array(self.channels)
-		self.log_option = False
-		
-		super().__init__(title="Configure signal annotator")
-
-		self._add_to_layout()
-		self._load_previous_instructions()
-		
-		self._adjustSize()
-		self.resize(int(self.width()), int(self._screen_height * 0.55))
-	
-	def _add_to_layout(self):
-		
-		sub_layout = QVBoxLayout()
-		sub_layout.setContentsMargins(10,10,10,20)
-		sub_layout.setContentsMargins(30,30,30,30)
-		sub_layout.addWidget(self._modality_lbl)
-		
-		# Create radio buttons
-		option_layout = QHBoxLayout()
-		option_layout.addWidget(self.gs_btn, alignment=Qt.AlignCenter)
-		option_layout.addWidget(self.rgb_btn, alignment=Qt.AlignCenter)
-		sub_layout.addLayout(option_layout)
-		
-		btn_hbox = QHBoxLayout()
-		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)
-
-		for i in range(3):
-			hlayout = QHBoxLayout()
-			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)
-
-		sub_layout.addWidget(self.hsep)
-		hbox_frac = QHBoxLayout()
-		hbox_frac.addWidget(self._fraction_lbl, 20)
-		hbox_frac.addWidget(self.fraction_slider, 80)
-		sub_layout.addLayout(hbox_frac)
-		
-		hbox_interval = QHBoxLayout()
-		hbox_interval.addWidget(self._interval_lbl, 20)
-		hbox_interval.addWidget(self.interval_slider, 80)
-		sub_layout.addLayout(hbox_interval)
-		
-		self._layout.addLayout(sub_layout)
-
-		self._layout.addWidget(self.submit_btn)
-
-	def _create_widgets(self):
-		
-		"""
-		Create the widgets.
-		
-		"""
-		super()._create_widgets()
-		
-		self._modality_lbl = QLabel("Modality: ")
-		self._fraction_lbl = QLabel("fraction: ")
-		self._interval_lbl = QLabel('interval [ms]: ')
-		
-		self.gs_btn = QRadioButton('grayscale')
-		self.gs_btn.setChecked(True)
-		
-		self.rgb_btn = QRadioButton('RGB')
-
-
-		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.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.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))	
-
-		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):
-
-			self.channel_cbs[i].addItems(self.channel_names)
-			self.channel_cbs[i].setCurrentIndex(i)
-			self.channel_cbs_lbls[i].setText(self.rgb_text[i])
-			
-			self.min_val_les[i].setValidator(self._floatValidator)
-			self.max_val_les[i].setValidator(self._floatValidator)
-
-
-		self.enable_channels()
-		
-		self.gs_btn.toggled.connect(self.enable_channels)
-		self.rgb_btn.toggled.connect(self.enable_channels)
-
-		self.hsep = QHSeperationLine()
-
-		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(Qt.Horizontal)
-		self.fraction_slider.setRange(0.1,1)
-		self.fraction_slider.setValue(0.25)
-
-		self.interval_slider = QLabeledSlider()
-		self.interval_slider.setSingleStep(1)
-		self.interval_slider.setTickInterval(1)
-		self.interval_slider.setSingleStep(1)
-		self.interval_slider.setOrientation(Qt.Horizontal)
-		self.interval_slider.setRange(1,1000)
-		self.interval_slider.setValue(1)
-
-	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().replace(',','.')), float(self.max_val_les[i].text().replace(',','.'))])
-		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 _load_previous_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]).replace('.',','))
-						self.max_val_les[i].setText(str(channels[i][2]).replace('.',','))
-
-				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
+    """
+    UI to set normalization and animation parameters for the annotator tool.
+
+    """
+
+    def __init__(self, parent_window=None):
+
+        self.parent_window = parent_window
+        self.mode = self.parent_window.mode
+        self.exp_dir = self.parent_window.exp_dir
+        self.percentile_mode = False
+
+        self.instructions_path = (
+            self.parent_window.exp_dir
+            + f"configs/signal_annotator_config_{self.mode}.json"
+        )
+        if self.mode == "pairs":
+            self.instructions_path = (
+                self.parent_window.exp_dir
+                + "configs/signal_annotator_config_neighborhood.json"
+            )
+
+        self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
+        self.channel_names = np.array(self.channel_names)
+        self.channels = np.array(self.channels)
+        self.log_option = False
+
+        super().__init__(title="Configure signal annotator")
+
+        self._add_to_layout()
+        self._load_previous_instructions()
+
+        self._adjust_size()
+        self.resize(int(self.width() * 1.4), int(self._screen_height * 0.65))
+
+    def _add_to_layout(self):
+
+        sub_layout = QVBoxLayout()
+        sub_layout.setContentsMargins(10, 10, 10, 20)
+        sub_layout.setContentsMargins(30, 30, 30, 30)
+        sub_layout.addWidget(self._modality_lbl)
+
+        # Create radio buttons
+        option_layout = QHBoxLayout()
+        option_layout.addWidget(self.gs_btn, alignment=Qt.AlignCenter)
+        option_layout.addWidget(self.rgb_btn, alignment=Qt.AlignCenter)
+        sub_layout.addLayout(option_layout)
+
+        btn_hbox = QHBoxLayout()
+        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)
+
+        for i in range(3):
+            hlayout = QHBoxLayout()
+            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)
+
+        sub_layout.addWidget(self.hsep)
+        hbox_frac = QHBoxLayout()
+        hbox_frac.addWidget(self._fraction_lbl, 20)
+        hbox_frac.addWidget(self.fraction_slider, 80)
+        sub_layout.addLayout(hbox_frac)
+
+        hbox_interval = QHBoxLayout()
+        hbox_interval.addWidget(self._interval_lbl, 20)
+        hbox_interval.addWidget(self.interval_slider, 80)
+        sub_layout.addLayout(hbox_interval)
+
+        self._layout.addLayout(sub_layout)
+
+        self._layout.addWidget(self.submit_btn)
+
+    def _create_widgets(self):
+        """
+        Create the widgets.
+
+        """
+        super()._create_widgets()
+
+        self._modality_lbl = QLabel("Modality: ")
+        self._fraction_lbl = QLabel("fraction: ")
+        self._interval_lbl = QLabel("interval [ms]: ")
+
+        self.gs_btn = QRadioButton("grayscale")
+        self.gs_btn.setChecked(True)
+
+        self.rgb_btn = QRadioButton("RGB")
+
+        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.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.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))
+
+        self.channel_cbs = [QComboBox() for _ in range(3)]
+        self.channel_cbs_lbls = [QLabel() for _ in range(3)]
+
+        self.min_val_les = [QLineEdit("0") for _ in range(3)]
+        self.min_val_lbls = [QLabel("Min value: ") for _ in range(3)]
+        self.max_val_les = [QLineEdit("10000") for _ in range(3)]
+        self.max_val_lbls = [QLabel("Max value: ") for _ in range(3)]
+
+        self.rgb_text = ["R: ", "G: ", "B: "]
+
+        for i in range(3):
+
+            self.channel_cbs[i].addItems(self.channel_names)
+            self.channel_cbs[i].setCurrentIndex(i)
+            self.channel_cbs_lbls[i].setText(self.rgb_text[i])
+
+            self.min_val_les[i].setValidator(self._floatValidator)
+            self.max_val_les[i].setValidator(self._floatValidator)
+
+        self.enable_channels()
+
+        self.gs_btn.toggled.connect(self.enable_channels)
+        self.rgb_btn.toggled.connect(self.enable_channels)
+
+        self.hsep = QHSeperationLine()
+
+        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(Qt.Horizontal)
+        self.fraction_slider.setRange(0.1, 1)
+        self.fraction_slider.setValue(0.25)
+
+        self.interval_slider = QLabeledSlider()
+        self.interval_slider.setSingleStep(1)
+        self.interval_slider.setTickInterval(1)
+        self.interval_slider.setSingleStep(1)
+        self.interval_slider.setOrientation(Qt.Horizontal)
+        self.interval_slider.setRange(1, 1000)
+        self.interval_slider.setValue(1)
+
+    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().replace(",", ".")),
+                    float(self.max_val_les[i].text().replace(",", ".")),
+                ]
+            )
+        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 _load_previous_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]).replace(".", ",")
+                        )
+                        self.max_val_les[i].setText(
+                            str(channels[i][2]).replace(".", ",")
+                        )
+
+                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