celldetective 1.3.9.post5__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/gui/{btrack_options.py → settings/_settings_tracking.py}

@@ -1,9 +1,13 @@
-from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+"""
+Copyright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
+"""
+
+
+from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMessageBox, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QDoubleValidator
 
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
-from superqt import QLabeledDoubleSlider,QLabeledSlider
+from celldetective.gui.gui_utils import FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
+from superqt import QLabeledDoubleSlider, QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import extract_experiment_channels, get_software_location
@@ -16,9 +20,10 @@ import os
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
-from celldetective.gui import Styles
+from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
+
 
-class ConfigTracking(QMainWindow, Styles):
+class SettingsTracking(CelldetectiveSettingsPanel):
 	
 	"""
 	UI to set tracking parameters for bTrack.
@@ -27,51 +32,51 @@ class ConfigTracking(QMainWindow, Styles):
 
 	def __init__(self, parent_window=None):
 		
-		super().__init__()
 		self.parent_window = parent_window
-		self.setWindowTitle("Configure tracking")
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
-		self.floatValidator = QDoubleValidator()
-
-		if self.mode=="targets":
-			self.config_name = os.sep.join(["configs", "btrack_config_targets.json"])
-			self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs","tracking_instructions_targets.json"])
-		elif self.mode=="effectors":
-			self.config_name = os.sep.join(["configs","btrack_config_effectors.json"])
-			self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", "tracking_instructions_effectors.json"])
-		self.soft_path = get_software_location()
+
+		self.config_name = os.sep.join(["configs", f"btrack_config_{self.mode}.json"])
+		self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", f"tracking_instructions_{self.mode}.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(self.exp_dir)
 		self.channel_names = np.array(self.channel_names)
 		self.channels = np.array(self.channels)
-		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
-
-		center_window(self)
-		self.setMinimumWidth(540)
 		self.minimum_height = 300
-		# self.setMinimumHeight(int(0.3*self.screen_height))
-		# self.setMaximumHeight(int(0.8*self.screen_height))
-		self.populate_widget()
-		self.load_previous_tracking_instructions()
 
-	def populate_widget(self):
+		super().__init__(title="Configure tracking")
+		
+		self._add_to_layout()
+		self._load_previous_instructions()
+		
+		self._widget.setMinimumWidth(500)
+		self._adjustSize()
+		self.resize(int(self.width()*1.5), int(self._screen_height * 0.8))
+	
+	def _add_to_layout(self):
+		
+		tracker_hbox = QHBoxLayout()
+		tracker_hbox.setContentsMargins(15, 15, 15, 15)
+		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
+		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
+		
+		self._layout.addLayout(tracker_hbox)
+		self._layout.addWidget(self.config_frame)
+		self._layout.addWidget(self.features_frame)
+		self._layout.addWidget(self.config_trackpy_frame)
+		self._layout.addWidget(self.post_proc_frame)
+		self._layout.addWidget(self.submit_btn)
+
+
+	def _create_widgets(self):
 
 		"""
 		Create the multibox design with collapsable frames.
 
 		"""
 		
-		# Create button widget and layout
-		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
-		main_layout = QVBoxLayout()
-		self.button_widget.setLayout(main_layout)
-		main_layout.setContentsMargins(30,30,30,30)
-
-		# First collapsable Frame CONFIG
+		super()._create_widgets()
 
 		self.btrack_option = QRadioButton('bTrack')
 		self.btrack_option.setChecked(True)
@@ -85,70 +90,37 @@ class ConfigTracking(QMainWindow, Styles):
 		self.config_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_config_frame()
 
-		tracker_hbox = QHBoxLayout()
-		tracker_hbox.setContentsMargins(15,15,15,15)
-		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
-		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
-		main_layout.addLayout(tracker_hbox)
-
-		main_layout.addWidget(self.config_frame)
-
 		# Second collapsable frame FEATURES
 		self.features_frame = QFrame()
 		self.features_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_features_frame()
-		main_layout.addWidget(self.features_frame)
 
 		self.config_trackpy_frame = QFrame()
 		self.config_trackpy_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_config_trackpy_frame()
-		main_layout.addWidget(self.config_trackpy_frame)
 		self.config_trackpy_frame.hide()
 
 		# Third collapsable frame POST-PROCESSING
 		self.post_proc_frame = QFrame()
 		self.post_proc_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_post_proc_frame()
-		main_layout.addWidget(self.post_proc_frame)
-
-		self.submit_btn = QPushButton('Save')
-		self.submit_btn.setStyleSheet(self.parent_window.parent_window.parent_window.button_style_sheet)
-		self.submit_btn.clicked.connect(self.write_instructions)
-		main_layout.addWidget(self.submit_btn)
-
-		#self.populate_left_panel()
-		#grid.addLayout(self.left_side, 0, 0, 1, 1)
-		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.btrack_option.toggled.connect(self.show_tracking_options)
 		self.trackpy_option.toggled.connect(self.show_tracking_options)
 
-		QApplication.processEvents()
-		self.adjustScrollArea()
-
 	def show_tracking_options(self):
 
 		if self.btrack_option.isChecked():
 			self.config_frame.show()
 			self.features_frame.show()
 			self.config_trackpy_frame.hide()
-			#self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
-			#self.adjustSize()
+			#self._adjustSize()
 		else:
 			self.config_frame.hide()
 			self.features_frame.hide()
 			self.config_trackpy_frame.show()
-			#self.scroll_area.setMinimumHeight(self.minimum_height)
-			#self.adjustSize()
-
+			#self._adjustSize()
+	
 
 	def populate_post_proc_frame(self):
 
@@ -172,13 +144,13 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox = QHBoxLayout()
 
 		self.collapse_post_proc_btn = QPushButton()
-		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 		self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 		self.collapse_post_proc_btn.setStyleSheet(self.button_select_all)
 		#grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
 
 		self.help_post_btn = QPushButton()
-		self.help_post_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_post_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
 		self.help_post_btn.setIconSize(QSize(20, 20))
 		self.help_post_btn.clicked.connect(self.help_post)
 		self.help_post_btn.setStyleSheet(self.button_select_all)
@@ -188,7 +160,7 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
 		title_hbox.addWidget(self.help_post_btn, 5)
 		title_hbox.addWidget(self.collapse_post_proc_btn, 5)
-		grid.addLayout(title_hbox, 0,0,1,4)
+		grid.addLayout(title_hbox, 0, 0, 1, 4)
 
 		self.generate_post_proc_panel_contents()
 		grid.addWidget(self.ContentsPostProc, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -205,15 +177,15 @@ class ConfigTracking(QMainWindow, Styles):
 		is_open = np.array([features_open, config_open, post_open])
 
 		if self.ContentsPostProc.isHidden():
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def help_post(self):
@@ -222,7 +194,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Helper for track post-processing strategy.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','track-postprocessing.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'track-postprocessing.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -246,7 +218,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Helper for track post-processing strategy.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','feature-btrack.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'feature-btrack.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -300,7 +272,7 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
 		title_hbox.addWidget(self.help_feature_btn, 5)
 		title_hbox.addWidget(self.collapse_features_btn, 5)
-		grid.addLayout(title_hbox, 0,0,1,4)		
+		grid.addLayout(title_hbox, 0, 0, 1, 4)
 
 		self.generate_feature_panel_contents()
 		grid.addWidget(self.ContentsFeatures, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -321,15 +293,15 @@ class ConfigTracking(QMainWindow, Styles):
 		is_open = np.array([features_open, config_open, post_open])
 
 		if self.ContentsFeatures.isHidden():
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def generate_post_proc_panel_contents(self):
@@ -351,7 +323,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.min_tracklength_slider.setSingleStep(1)
 		self.min_tracklength_slider.setTickInterval(1)
 		self.min_tracklength_slider.setSingleStep(1)
-		self.min_tracklength_slider.setOrientation(1)
+		self.min_tracklength_slider.setOrientation(Qt.Horizontal)
 		self.min_tracklength_slider.setRange(0,self.parent_window.parent_window.len_movie)
 		self.min_tracklength_slider.setValue(0)
 		tracklength_layout.addWidget(QLabel('Min. tracklength: '),40)
@@ -391,7 +363,6 @@ class ConfigTracking(QMainWindow, Styles):
 
 		layout.addLayout(clean_traj_sublayout)
 
-
 	def generate_feature_panel_contents(self):
 		
 		self.ContentsFeatures = QFrame()
@@ -456,10 +427,9 @@ class ConfigTracking(QMainWindow, Styles):
 
 		# Slider to set vmin & vmax
 		self.haralick_scale_slider = QLabeledDoubleSlider()
-		self.haralick_scale_slider.setSingleStep(0.05)
 		self.haralick_scale_slider.setTickInterval(0.05)
 		self.haralick_scale_slider.setSingleStep(1)
-		self.haralick_scale_slider.setOrientation(1)
+		self.haralick_scale_slider.setOrientation(Qt.Horizontal)
 		self.haralick_scale_slider.setRange(0,1)
 		self.haralick_scale_slider.setValue(0.5)
 		self.haralick_scale_lbl = QLabel('Scale: ')
@@ -621,12 +591,12 @@ class ConfigTracking(QMainWindow, Styles):
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 	def collapse_config_trackpy_advanced(self):
 
@@ -642,12 +612,12 @@ class ConfigTracking(QMainWindow, Styles):
 			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def generate_config_trackpy_panel_contents(self):
@@ -660,7 +630,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.search_range_lbl = QLabel("search range [px]: ")
 		self.search_range_le = QLineEdit('30')
 		self.search_range_le.setPlaceholderText('search distance in pixels')
-		self.search_range_le.setValidator(self.floatValidator)
+		self.search_range_le.setValidator(self._floatValidator)
 		sr_layout.addWidget(self.search_range_lbl, 30)
 		sr_layout.addWidget(self.search_range_le, 70)
 		layout.addLayout(sr_layout)
@@ -671,7 +641,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.memory_slider.setSingleStep(1)
 		self.memory_slider.setTickInterval(1)
 		self.memory_slider.setSingleStep(1)
-		self.memory_slider.setOrientation(1)
+		self.memory_slider.setOrientation(Qt.Horizontal)
 		self.memory_slider.setRange(0,self.parent_window.parent_window.len_movie)
 		self.memory_slider.setValue(0)
 		memory_layout.addWidget(self.memory_lbl, 30)
@@ -738,14 +708,14 @@ class ConfigTracking(QMainWindow, Styles):
 
 		self.file_dialog = QFileDialog()
 		try:
-			modelpath = os.sep.join([self.soft_path, "celldetective","models","tracking_configs"]) + os.sep
+			modelpath = os.sep.join([self._software_path, "celldetective","models","tracking_configs"]) + os.sep
 			print("Track config path: ", modelpath)
 			self.filename = self.file_dialog.getOpenFileName(None, "Load config", modelpath, "json files (*.json)")[0]
 			if self.filename!=self.config_path:
 				copyfile(self.filename, self.config_path)
 			self.load_cell_config()
 		except Exception as e:
-			print(e, modelpath)
+			print(e)
 			return None
 
 	def reset_btrack_config(self):
@@ -829,16 +799,16 @@ class ConfigTracking(QMainWindow, Styles):
 		else:
 			self.post_proc_ticked = True	
 
-	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 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 load_cell_config(self):
 
@@ -851,7 +821,7 @@ class ConfigTracking(QMainWindow, Styles):
 			json_data = json.load(f)
 			self.config_le.setText(json.dumps(json_data, indent=4))
 
-	def write_instructions(self):
+	def _write_instructions(self):
 
 		"""
 		Write the selected options in a json file for later reading by the software.
@@ -960,7 +930,7 @@ class ConfigTracking(QMainWindow, Styles):
 		else:
 			self.haralick_options = None		
 
-	def load_previous_tracking_instructions(self):
+	def _load_previous_instructions(self):
 
 		"""
 		Read the tracking options from a previously written json file.
@@ -994,7 +964,7 @@ class ConfigTracking(QMainWindow, Styles):
 				if 'search_range' in tracking_instructions:
 					search_range = tracking_instructions['search_range']
 					if search_range is not None:
-						self.search_range_le.setText(str(search_range).replace('.',','))				
+						self.search_range_le.setText(str(search_range).replace('.', ','))
 				if 'memory' in tracking_instructions:
 					memory = tracking_instructions['memory']
 					if memory is not None:
@@ -1072,7 +1042,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Load the first frame of the first movie found in the experiment folder as a sample.
 		"""
 
-		movies = glob(self.parent_window.parent_window.exp_dir + os.sep.join(["*","*","movie",self.parent_window.parent_window.movie_prefix+"*.tif"]))
+		movies = glob(self.parent_window.parent_window.exp_dir + os.sep.join(["*", "*", "movie", self.parent_window.parent_window.movie_prefix+"*.tif"]))
 		if len(movies)==0:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
@@ -1088,7 +1058,6 @@ class ConfigTracking(QMainWindow, Styles):
 			n_channels = len(self.channels)
 			self.test_frame = load_frames(np.arange(n_channels), stack0, scale=None, normalize_input=False)
 
-
 	def control_haralick_digitalization(self):
 
 		"""

celldetective/gui/styles.py

@@ -14,7 +14,8 @@ class Styles(object):
 
 		
 		self.celldetective_blue = "#1565c0"
-		self.celldetective_icon = QIcon(os.sep.join([get_software_location(),'celldetective','icons','logo.png']))
+		self.celldetective_logo_path = os.sep.join([get_software_location(),'celldetective','icons','logo.png'])
+		self.celldetective_icon = QIcon(self.celldetective_logo_path)
 
 		self.action_lbl_style_sheet = """
 			font-size: 10px;