celldetective 1.3.9.post5__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/gui_utils.py

@@ -1,23 +1,48 @@
-import numpy as np
-from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
+import os
+
+from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
 	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
 from PyQt5.QtCore import Qt, QSize, QAbstractTableModel, QEvent, pyqtSignal
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
 
-from celldetective.gui import Styles
+from celldetective.gui import Styles, CelldetectiveWidget
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT
 import matplotlib.pyplot as plt
-import celldetective.extra_properties as extra_properties
+
+from celldetective.utils import get_software_location
+
+try:
+	import celldetective.extra_properties as extra_properties
+	extra_props = True
+except Exception as e:
+	print(f"The module extra_properties seems corrupted: {e}... Skip...")
+	extra_props = False
+
 from inspect import getmembers, isfunction
 from celldetective.filters import *
 from os import sep
 import json
 
 
+def generic_message(message, msg_type="warning"):
+	
+	print(message)
+	message_box = QMessageBox()
+	if msg_type=="warning":
+		message_box.setIcon(QMessageBox.Warning)
+	elif msg_type=="info":
+		message_box.setIcon(QMessageBox.Information)
+	elif msg_type=="critical":
+		message_box.setIcon(QMessageBox.Critical)
+	message_box.setText(message)
+	message_box.setWindowTitle(msg_type)
+	message_box.setStandardButtons(QMessageBox.Ok)
+	_ = message_box.exec()
+
 class PreprocessingLayout(QVBoxLayout, Styles):
 
 	"""
@@ -328,7 +353,7 @@ class PandasModel(QAbstractTableModel):
 		self.dataChanged.emit(ix, ix, (Qt.BackgroundRole,))
 
 
-class GenericOpColWidget(QWidget, Styles):
+class GenericOpColWidget(CelldetectiveWidget):
 
 	def __init__(self, parent_window, column=None, title=''):
 
@@ -415,7 +440,7 @@ class QuickSliderLayout(QHBoxLayout):
 		The slider widget that allows the user to select a value.
 	"""
 
-	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=1.0E-03, *args):
+	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=3, *args):
 		super().__init__(*args)
 
 		if label is not None and isinstance(label,str):
@@ -423,10 +448,11 @@ class QuickSliderLayout(QHBoxLayout):
 			self.addWidget(self.qlabel, int(100*layout_ratio[0]))
 
 		self.slider = slider
-		self.slider.setOrientation(1)
+		self.slider.setOrientation(Qt.Horizontal)
 		if decimal_option:
-			self.slider.setSingleStep(precision)
-			self.slider.setTickInterval(precision)
+			self.slider.setSingleStep(1.0*(10**(-precision)))
+			self.slider.setTickInterval(1.0*(10**(-precision)))
+			self.slider.setDecimals(precision)
 		else:
 			self.slider.setSingleStep(1)
 			self.slider.setTickInterval(1)
@@ -546,7 +572,7 @@ class QHSeperationLine(QFrame):
 		self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
 
 
-class FeatureChoice(QWidget, Styles):
+class FeatureChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -575,10 +601,11 @@ class FeatureChoice(QWidget, Styles):
 								 "intensity_min",
 								 ]
 
-		members = getmembers(extra_properties, isfunction)
-		for o in members:
-			if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
-				standard_measurements.append(o[0])
+		if extra_props:
+			members = getmembers(extra_properties, isfunction)
+			for o in members:
+				if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
+					standard_measurements.append(o[0])
 
 		self.combo_box.addItems(standard_measurements)
 
@@ -599,7 +626,7 @@ class FeatureChoice(QWidget, Styles):
 		self.close()
 
 
-class FilterChoice(QWidget, Styles):
+class FilterChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -707,7 +734,7 @@ class FilterChoice(QWidget, Styles):
 				self.arguments_labels[i].setText('')
 
 
-class OperationChoice(QWidget):
+class OperationChoice(CelldetectiveWidget):
 	"""
 	Mini window to select an operation from numpy to apply on the ROI.
 
@@ -738,7 +765,7 @@ class OperationChoice(QWidget):
 		self.close()
 
 
-class GeometryChoice(QWidget):
+class GeometryChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -802,7 +829,7 @@ class GeometryChoice(QWidget):
 		self.close()
 
 
-class DistanceChoice(QWidget):
+class DistanceChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -836,7 +863,7 @@ class DistanceChoice(QWidget):
 		self.close()
 
 
-class ListWidget(QWidget):
+class ListWidget(CelldetectiveWidget):
 
 	"""
 	A customizable widget for displaying and managing a list of items, with the 
@@ -963,7 +990,7 @@ class ListWidget(QWidget):
 				del self.items[idx]
 
 
-class FigureCanvas(QWidget):
+class FigureCanvas(CelldetectiveWidget):
 	"""
 	Generic figure canvas.
 	"""
@@ -1185,6 +1212,7 @@ def color_from_state(state, recently_modified=False):
 	unique_values = np.unique(state)
 	color_map={}
 	for value in unique_values:
+
 		if np.isnan(value):
 			value = "nan"
 			color_map[value] = 'k'
@@ -1219,7 +1247,7 @@ def color_from_class(cclass, recently_modified=False):
 			return 'k'
 
 
-class ChannelChoice(QWidget):
+class ChannelChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()

celldetective/gui/json_readers.py

@@ -1,10 +1,11 @@
 import configparser
-from PyQt5.QtWidgets import QWidget, QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
+from PyQt5.QtWidgets import QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
 from PyQt5.QtCore import Qt
 import configparser
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 
-class ConfigEditor(QWidget, Styles):
+
+class ConfigEditor(CelldetectiveWidget):
     
     def __init__(self, parent_window):
 
@@ -27,7 +28,7 @@ class ConfigEditor(QWidget, Styles):
         # Create a scroll area to contain the main layout
         scroll = QScrollArea()
         scroll.setWidgetResizable(True)
-        scroll_content = QWidget()
+        scroll_content = CelldetectiveWidget()
         self.scroll_layout = QVBoxLayout(scroll_content)
         scroll_content.setLayout(self.scroll_layout)
         scroll.setWidget(scroll_content)

celldetective/gui/layouts.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QCheckBox, QLineEdit, QWidget, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
+from PyQt5.QtWidgets import QCheckBox, QLineEdit, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
 from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, center_window
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIntValidator
+from PyQt5.QtGui import QIntValidator, QDoubleValidator
 
 from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider, QSearchableComboBox
 
@@ -9,15 +9,223 @@ from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import _extract_channel_indices_from_config
 from celldetective.gui.viewers import ThresholdedStackVisualizer, CellEdgeVisualizer, StackVisualizer, CellSizeViewer, ChannelOffsetViewer
-from celldetective.gui import Styles
+from celldetective.gui import Styles, CelldetectiveWidget
 from celldetective.preprocessing import correct_background_model, correct_background_model_free, estimate_background_per_condition
 from functools import partial
 from glob import glob
 import os
 import pandas as pd
 import numpy as np
+from celldetective.io import locate_segmentation_model, locate_signal_model
+import json
 
-class StarDistParamsWidget(QWidget, Styles):
+
+class SignalModelParamsWidget(CelldetectiveWidget):
+	
+	def __init__(self, parent_window=None, model_name=None, *args, **kwargs):
+		
+		super().__init__(*args)
+		self.setWindowTitle('Signals')
+		self.parent_window = parent_window
+		self.model_name = model_name
+		self.locate_model_path()
+		self.required_channels = self.input_config["channels"]
+		self.onlyFloat = QDoubleValidator()
+
+		# Setting up references to parent window attributes
+		if hasattr(self.parent_window.parent_window, 'locate_image'):
+			self.attr_parent = self.parent_window.parent_window
+		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
+			self.attr_parent = self.parent_window.parent_window.parent_window
+		else:
+			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
+		
+		# Set up layout and widgets
+		self.layout = QVBoxLayout()
+		self.populate_widgets()
+		self.setLayout(self.layout)
+		center_window(self)
+
+	def locate_model_path(self):
+
+		self.model_complete_path = locate_signal_model(self.model_name)
+		if self.model_complete_path is None:
+			print('Model could not be found. Abort.')
+			self.abort_process()
+		else:
+			print(f'Model path: {self.model_complete_path}...')
+		
+		if not os.path.exists(self.model_complete_path+"config_input.json"):
+			print('The configuration for the inputs to the model could not be located. Abort.')
+			self.abort_process()
+
+		with open(self.model_complete_path+"config_input.json") as config_file:
+			self.input_config = json.load(config_file)
+
+	def populate_widgets(self):
+
+		self.n_channels = len(self.required_channels)
+		self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
+
+		self.parent_window.load_available_tables()
+		available_channels = list(self.parent_window.signals)+['None']
+		# Populate the comboboxes with available channels from the experiment
+		for k in range(self.n_channels):
+			hbox_channel = QHBoxLayout()
+			hbox_channel.addWidget(QLabel(f'channel {k+1}: '), 33)
+
+			ch_vbox = QVBoxLayout()
+			ch_vbox.addWidget(QLabel(f'Req: {self.required_channels[k]}'), alignment=Qt.AlignLeft)
+			ch_vbox.addWidget(self.channel_cbs[k])
+
+			self.channel_cbs[k].addItems(available_channels) #Give none option for more than one channel input
+			idx = self.channel_cbs[k].findText(self.required_channels[k])
+
+			if idx>=0:
+				self.channel_cbs[k].setCurrentIndex(idx)
+			else:
+				self.channel_cbs[k].setCurrentIndex(len(available_channels)-1)
+
+			hbox_channel.addLayout(ch_vbox, 66)
+			self.layout.addLayout(hbox_channel)
+		
+		# Button to apply the StarDist settings
+		self.set_btn = QPushButton('set')
+		self.set_btn.setStyleSheet(self.button_style_sheet)
+		self.set_btn.clicked.connect(self.parent_window.set_selected_signals_for_event_detection)
+		self.layout.addWidget(self.set_btn)
+
+
+
+class SegModelParamsWidget(CelldetectiveWidget):
+	
+	def __init__(self, parent_window=None, model_name='SD_versatile_fluo', *args, **kwargs):
+		
+		super().__init__(*args)
+		self.setWindowTitle('Channels')
+		self.parent_window = parent_window
+		self.model_name = model_name
+		self.locate_model_path()
+		self.required_channels = self.input_config["channels"]
+		self.onlyFloat = QDoubleValidator()
+
+		# Setting up references to parent window attributes
+		if hasattr(self.parent_window.parent_window, 'locate_image'):
+			self.attr_parent = self.parent_window.parent_window
+		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
+			self.attr_parent = self.parent_window.parent_window.parent_window
+		else:
+			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
+		
+		# Set up layout and widgets
+		self.layout = QVBoxLayout()
+		self.populate_widgets()
+		self.setLayout(self.layout)
+		center_window(self)
+
+	def locate_model_path(self):
+
+		self.model_complete_path = locate_segmentation_model(self.model_name)
+		if self.model_complete_path is None:
+			print('Model could not be found. Abort.')
+			self.abort_process()
+		else:
+			print(f'Model path: {self.model_complete_path}...')
+		
+		if not os.path.exists(self.model_complete_path+"config_input.json"):
+			print('The configuration for the inputs to the model could not be located. Abort.')
+			self.abort_process()
+
+		with open(self.model_complete_path+"config_input.json") as config_file:
+			self.input_config = json.load(config_file)
+
+	def populate_widgets(self):
+
+		self.n_channels = len(self.required_channels)
+		self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
+		
+		# Button to view the current stack with a scale bar
+		self.view_diameter_btn = QPushButton()
+		self.view_diameter_btn.setStyleSheet(self.button_select_all)
+		self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
+		self.view_diameter_btn.setToolTip("View stack.")
+		self.view_diameter_btn.setIconSize(QSize(20, 20))
+		self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
+
+		# Line edit for entering cell diameter
+		self.diameter_le = ThresholdLineEdit(init_value=40, connected_buttons=[self.view_diameter_btn],placeholder='cell diameter in µm', value_type='float')
+
+		available_channels = list(self.attr_parent.exp_channels)+['None']
+		# Populate the comboboxes with available channels from the experiment
+		for k in range(self.n_channels):
+			hbox_channel = QHBoxLayout()
+			hbox_channel.addWidget(QLabel(f'channel {k+1}: '), 33)
+
+			ch_vbox = QVBoxLayout()
+			ch_vbox.addWidget(QLabel(f'Req: {self.required_channels[k]}'), alignment=Qt.AlignLeft)
+			ch_vbox.addWidget(self.channel_cbs[k])
+
+			self.channel_cbs[k].addItems(available_channels) #Give none option for more than one channel input
+			idx = self.channel_cbs[k].findText(self.required_channels[k])
+
+			if idx>=0:
+				self.channel_cbs[k].setCurrentIndex(idx)
+			else:
+				self.channel_cbs[k].setCurrentIndex(len(available_channels)-1)
+
+			hbox_channel.addLayout(ch_vbox, 66)
+			self.layout.addLayout(hbox_channel)
+
+		if 'cell_size_um' in self.input_config:
+
+			# Layout for diameter input and button
+			hbox = QHBoxLayout()
+			hbox.addWidget(QLabel('cell size [µm]: '), 33)
+			hbox.addWidget(self.diameter_le, 61)
+			hbox.addWidget(self.view_diameter_btn)
+			self.layout.addLayout(hbox)
+
+			self.diameter_le.set_threshold(self.input_config['cell_size_um'])
+
+			# size_hbox = QHBoxLayout()
+			# size_hbox.addWidget(QLabel('cell size [µm]: '), 33)
+			# self.size_le = QLineEdit(str(self.input_config['cell_size_um']).replace('.',','))
+			# self.size_le.setValidator(self.onlyFloat)
+			# size_hbox.addWidget(self.size_le, 66)
+			# self.layout.addLayout(size_hbox)
+		
+		# Button to apply the StarDist settings
+		self.set_btn = QPushButton('set')
+		self.set_btn.setStyleSheet(self.button_style_sheet)
+		self.set_btn.clicked.connect(self.parent_window.set_selected_channels_for_segmentation)
+		self.layout.addWidget(self.set_btn)
+
+	def view_current_stack_with_scale_bar(self):
+
+		"""
+		Displays the current image stack with a scale bar, allowing users to visually estimate cell diameters.
+		"""
+
+		self.attr_parent.locate_image()
+		if self.attr_parent.current_stack is not None:
+			max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
+			self.viewer = CellSizeViewer(
+										  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
+										  parent_le = self.diameter_le,
+										  stack_path=self.attr_parent.current_stack,
+										  window_title=f'Position {self.attr_parent.position_list.currentText()}',
+										  diameter_slider_range=(0,max_size*self.attr_parent.PxToUm),
+										  frame_slider = True,
+										  contrast_slider = True,
+										  channel_cb = True,
+										  channel_names = self.attr_parent.exp_channels,
+										  n_channels = self.attr_parent.nbr_channels,
+										  PxToUm = self.attr_parent.PxToUm,
+										 )
+			self.viewer.show()
+
+
+class StarDistParamsWidget(CelldetectiveWidget):
 
 	"""
 	A widget to configure parameters for StarDist segmentation.
@@ -101,7 +309,7 @@ class StarDistParamsWidget(QWidget, Styles):
 		self.layout.addWidget(self.set_stardist_scale_btn)
 
 
-class CellposeParamsWidget(QWidget, Styles):
+class CellposeParamsWidget(CelldetectiveWidget):
 
 	"""
 	A widget to configure parameters for Cellpose segmentation, allowing users to set the cell diameter, 
@@ -204,7 +412,7 @@ class CellposeParamsWidget(QWidget, Styles):
 		
 		# Flow threshold slider
 		self.flow_slider = QLabeledDoubleSlider()
-		self.flow_slider.setOrientation(1)
+		self.flow_slider.setOrientation(Qt.Horizontal)
 		self.flow_slider.setRange(-6,6)
 		self.flow_slider.setValue(0.4)
 		hbox = QHBoxLayout()
@@ -214,7 +422,7 @@ class CellposeParamsWidget(QWidget, Styles):
 
 		# Cell probability threshold slider
 		self.cellprob_slider = QLabeledDoubleSlider()
-		self.cellprob_slider.setOrientation(1)
+		self.cellprob_slider.setOrientation(Qt.Horizontal)
 		self.cellprob_slider.setRange(-6,6)
 		self.cellprob_slider.setValue(0.)
 		hbox = QHBoxLayout()
@@ -236,18 +444,20 @@ class CellposeParamsWidget(QWidget, Styles):
 
 		self.attr_parent.locate_image()
 		if self.attr_parent.current_stack is not None:
+			max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
 			self.viewer = CellSizeViewer(
-										  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-										  parent_le = self.diameter_le,
-										  stack_path=self.attr_parent.current_stack,
-										  window_title=f'Position {self.attr_parent.position_list.currentText()}',
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  channel_names = self.attr_parent.exp_channels,
-										  n_channels = self.attr_parent.nbr_channels,
-										  PxToUm = 1,
-										 )
+										initial_diameter = float(self.diameter_le.text().replace(',', '.')),
+										parent_le = self.diameter_le,
+										stack_path=self.attr_parent.current_stack,
+										window_title=f'Position {self.attr_parent.position_list.currentText()}',
+										diameter_slider_range=(0, max_size),
+										frame_slider = True,
+										contrast_slider = True,
+										channel_cb = True,
+										channel_names = self.attr_parent.exp_channels,
+										n_channels = self.attr_parent.nbr_channels,
+										PxToUm = 1,
+										)
 			self.viewer.show()
 
 class ChannelNormGenerator(QVBoxLayout, Styles):
@@ -864,7 +1074,7 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 		self.tabs.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
 		
 		for k in range(len(self.tab_layouts)):
-			wg = QWidget()
+			wg = CelldetectiveWidget()
 			self.tab_layouts[k].parent_window = self
 			wg.setLayout(self.tab_layouts[k])
 			self.tabs.addTab(wg, self.tab_names[k])
@@ -1173,13 +1383,21 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		coef_nbr_layout.addWidget(self.nbr_coef_le, 75)
 		self.addLayout(coef_nbr_layout, 7,0,1,3)
 
+		offset_layout = QHBoxLayout()
+		offset_layout.addWidget(QLabel("Offset: "), 25)
+		self.camera_offset_le = QLineEdit("0")
+		self.camera_offset_le.setPlaceholderText('camera black level')
+		self.camera_offset_le.setValidator(QDoubleValidator())
+		offset_layout.addWidget(self.camera_offset_le, 75)
+		self.addLayout(offset_layout, 8, 0, 1, 3)
+
 		self.operation_layout = OperationLayout()
-		self.addLayout(self.operation_layout, 8, 0, 1, 3)
+		self.addLayout(self.operation_layout, 9, 0, 1, 3)
 
 		correction_layout = QHBoxLayout()
 		correction_layout.addWidget(self.add_correction_btn, 95)
 		correction_layout.addWidget(self.corrected_stack_viewer_btn, 5)
-		self.addLayout(correction_layout, 9, 0, 1, 3)
+		self.addLayout(correction_layout, 10, 0, 1, 3)
 
 		# verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
 		# self.addItem(verticalSpacer, 5, 0, 1, 3)
@@ -1221,6 +1439,11 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 			clip = True
 		else:
 			clip = False
+		
+		if self.camera_offset_le.text()=="":
+			offset = None
+		else:
+			offset = float(self.camera_offset_le.text().replace(",","."))
 
 		self.instructions = {
 					  "target_channel": self.channels_cb.currentText(),
@@ -1232,7 +1455,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 					  "opt_coef_range": opt_coef_range,
 					  "opt_coef_nbr": opt_coef_nbr,
 					  "operation": operation,
-					  "clip": clip
+					  "clip": clip,
+					  "offset": offset
 					 }
 
 	def set_target_channel(self):

celldetective/gui/measurement_options.py

@@ -1,8 +1,9 @@
+from subprocess import Popen
 
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
-	QGridLayout, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
+	QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIcon, QDoubleValidator, QIntValidator
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
 from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
 	GeometryChoice, OperationChoice
@@ -10,12 +11,10 @@ from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
-#from celldetective.gui.thresholds_gui import ThresholdSpot
 from celldetective.utils import extract_experiment_channels, get_software_location
 from celldetective.io import load_frames, auto_load_number_of_frames
 from celldetective.measure import compute_haralick_features
 import numpy as np
-from tifffile import imread
 import json
 import os
 import matplotlib.pyplot as plt
@@ -27,11 +26,11 @@ from pathlib import Path
 
 from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
-from celldetective.gui.gui_utils import ThresholdLineEdit, PreprocessingLayout2
-from celldetective.gui import Styles
+from celldetective.gui.gui_utils import PreprocessingLayout2
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
 
-class ConfigMeasurements(QMainWindow, Styles):
+class ConfigMeasurements(CelldetectiveMainWindow):
 	"""
 	UI to set measurement instructions.
 
@@ -43,16 +42,11 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		self.parent_window = parent_window
 		self.setWindowTitle("Configure measurements")
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective', 'icons', 'mexican-hat.png'])))
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
 		self.background_correction = []
-		if self.mode == "targets":
-			self.config_name = "btrack_config_targets.json"
-			self.measure_instructions_path = self.parent_window.exp_dir + "configs/measurement_instructions_targets.json"
-		elif self.mode == "effectors":
-			self.config_name = "btrack_config_effectors.json"
-			self.measure_instructions_path = self.parent_window.exp_dir + "configs/measurement_instructions_effectors.json"
+		self.config_name = f"btrack_config_{self.mode}.json"
+		self.measure_instructions_path = self.parent_window.exp_dir + f"configs/measurement_instructions_{self.mode}.json"
 		self.soft_path = get_software_location()
 		self.clear_previous = False
 
@@ -83,7 +77,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
+		self.button_widget = CelldetectiveWidget()
 		main_layout = QVBoxLayout()
 		self.button_widget.setLayout(main_layout)
 		main_layout.setContentsMargins(30, 30, 30, 30)
@@ -264,12 +258,21 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_mean', ])
 
+		self.create_feature_btn = QPushButton("")
+		self.create_feature_btn.setStyleSheet(self.button_select_all)
+		self.create_feature_btn.setIcon(icon(MDI6.file_cog, color="black"))
+		self.create_feature_btn.setToolTip("Create new feature")
+		self.create_feature_btn.setIconSize(QSize(20, 20))
+
 		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
 		self.add_feature_btn.clicked.connect(self.features_list.addItem)
+		self.create_feature_btn.clicked.connect(self.go_to_extraprops)
 
 		feature_layout.addWidget(self.feature_lbl, 90)
 		feature_layout.addWidget(self.del_feature_btn, 5)
 		feature_layout.addWidget(self.add_feature_btn, 5)
+		feature_layout.addWidget(self.create_feature_btn, 5)
+
 		layout.addLayout(feature_layout)
 		layout.addWidget(self.features_list)
 
@@ -334,7 +337,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 		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: ')
@@ -426,6 +429,18 @@ class ConfigMeasurements(QMainWindow, Styles):
 		self.haralick_normalization_mode_btn.clicked.connect(self.switch_to_absolute_normalization_mode)
 		layout.addLayout(self.haralick_layout)
 
+	def go_to_extraprops(self):
+		
+		path = os.sep.join([self.soft_path,'celldetective',os.sep,'extra_properties.py'])
+		try:
+			Popen(f'explorer {os.path.realpath(path)}')
+		except:
+
+			try:
+				os.system('xdg-open "%s"' % path)
+			except:
+				return None		
+
 	def switch_to_absolute_normalization_mode(self):
 
 		if self.percentile_mode: