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

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):
@@ -672,7 +882,7 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 		else:
 			clip = False
 
-		corrected_stack = correct_background_model(self.attr_parent.exp_dir, 
+		corrected_stack = correct_background_model(self.attr_parent.exp_dir,
 						   well_option=self.attr_parent.well_list.getSelectedIndices(), #+1 ??
 						   position_option=self.attr_parent.position_list.getSelectedIndices(), #+1??
 						   target_channel=self.channels_cb.currentText(),
@@ -687,14 +897,18 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 						   show_progress_per_pos = False,
 							)
 
-		self.viewer = StackVisualizer(
-									  stack=corrected_stack[0],
-									  window_title='Corrected channel',
-									  target_channel=self.channels_cb.currentIndex(),
-									  frame_slider = True,
-									  contrast_slider = True
-									 )
-		self.viewer.show()
+		if corrected_stack:
+			self.viewer = StackVisualizer(
+										  stack=corrected_stack[0],
+										  window_title='Corrected channel',
+										  target_channel=self.channels_cb.currentIndex(),
+										  frame_slider = True,
+										  contrast_slider = True
+										 )
+			self.viewer.show()
+		else:
+			print("Corrected stack could not be generated... No stack available...")
+
 
 
 class LocalCorrectionLayout(BackgroundFitCorrectionLayout):
@@ -864,7 +1078,7 @@ 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])
@@ -1120,6 +1334,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		for c in self.coef_widgets:
 			c.setEnabled(False)
 
+		self.interpolate_check = QCheckBox("interpolate NaNs")
+
 	def add_to_layout(self):
 		
 		channel_layout = QHBoxLayout()
@@ -1173,13 +1389,23 @@ 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)
+
+		self.addWidget(self.interpolate_check, 10, 0, 1, 1)
 
 		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, 11, 0, 1, 3)
 
 		# verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
 		# self.addItem(verticalSpacer, 5, 0, 1, 3)
@@ -1221,6 +1447,11 @@ 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 +1463,9 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 					  "opt_coef_range": opt_coef_range,
 					  "opt_coef_nbr": opt_coef_nbr,
 					  "operation": operation,
-					  "clip": clip
+					  "clip": clip,
+					  "offset": offset,
+					  "fix_nan": self.interpolate_check.isChecked(),
 					 }
 
 	def set_target_channel(self):
@@ -1308,6 +1541,7 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 						   clip = clip,
 						   export= False,
 						   return_stacks=True,
+						   fix_nan=self.interpolate_check.isChecked(),
 						   show_progress_per_well = True,
 						   show_progress_per_pos = False,
 							)