celldetective 1.2.0__py3-none-any.whl → 1.2.2__py3-none-any.whl

celldetective/gui/json_readers.py

@@ -1,8 +1,6 @@
-import sys
 import configparser
 from PyQt5.QtWidgets import QWidget, QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
 from PyQt5.QtCore import Qt
-import sys
 import configparser
 from celldetective.gui import Styles
 

celldetective/gui/layouts.py

@@ -1,16 +1,15 @@
 from PyQt5.QtWidgets import QCheckBox, QLineEdit, QWidget, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
-from celldetective.gui.gui_utils import ThresholdLineEdit
+from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, center_window
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIntValidator
 
-from superqt import QLabeledRangeSlider, QLabeledSlider, QLabeledDoubleRangeSlider, QSearchableComboBox
+from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider, QSearchableComboBox
 
 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
+from celldetective.gui.viewers import ThresholdedStackVisualizer, CellEdgeVisualizer, StackVisualizer, CellSizeViewer
 from celldetective.gui import Styles
-from celldetective.gui.gui_utils import QuickSliderLayout
 from celldetective.preprocessing import correct_background_model, correct_background_model_free, estimate_background_per_condition
 from functools import partial
 from glob import glob
@@ -18,6 +17,239 @@ import os
 import pandas as pd
 import numpy as np
 
+class StarDistParamsWidget(QWidget, Styles):
+
+	"""
+	A widget to configure parameters for StarDist segmentation.
+
+	This widget allows the user to select specific imaging channels for segmentation and adjust 
+	parameters for StarDist, a neural network-based image segmentation tool designed to segment 
+	star-convex shapes (typically nuclei).
+
+	Parameters
+	----------
+	parent_window : QWidget, optional
+		The parent window hosting this widget (default is None).
+	model_name : str, optional
+		The name of the StarDist model being used, typically 'SD_versatile_fluo' for versatile 
+		fluorescence or 'SD_versatile_he' for H&E-stained images (default is 'SD_versatile_fluo').
+	"""
+
+	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
+		
+		# 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 populate_widgets(self):
+
+		"""
+		Populates the widget with channel selection comboboxes and a 'set' button to configure
+		the StarDist segmentation settings. Handles different models by adjusting the number of
+		available channels.
+		"""
+		
+		# Initialize comboboxes based on the selected model
+		self.stardist_channel_cb = [QComboBox() for i in range(1)]
+		self.stardist_channel_template = ['live_nuclei_channel']
+		max_i = 1
+		
+		# If the H&E model is selected, update the combobox configuration
+		if self.model_name=="SD_versatile_he":
+			self.stardist_channel_template = ["H&E_1","H&E_2","H&E_3"]
+			self.stardist_channel_cb = [QComboBox() for i in range(3)]
+			max_i = 3
+	   
+		# Populate the comboboxes with available channels from the experiment
+		for k in range(max_i):
+			hbox_channel = QHBoxLayout()
+			hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
+			hbox_channel.addWidget(self.stardist_channel_cb[k])
+			if k==1:
+				self.stardist_channel_cb[k].addItems(list(self.attr_parent.exp_channels)+['None'])
+			else:
+				self.stardist_channel_cb[k].addItems(list(self.attr_parent.exp_channels))
+			
+			# Set the default channel based on the template or fallback to the first option
+			idx = self.stardist_channel_cb[k].findText(self.stardist_channel_template[k])
+			if idx>0:
+				self.stardist_channel_cb[k].setCurrentIndex(idx)
+			else:
+				self.stardist_channel_cb[k].setCurrentIndex(0)
+
+			self.layout.addLayout(hbox_channel)
+		
+		# Button to apply the StarDist settings
+		self.set_stardist_scale_btn = QPushButton('set')
+		self.set_stardist_scale_btn.setStyleSheet(self.button_style_sheet)
+		self.set_stardist_scale_btn.clicked.connect(self.parent_window.set_stardist_scale)
+		self.layout.addWidget(self.set_stardist_scale_btn)
+
+
+class CellposeParamsWidget(QWidget, Styles):
+
+	"""
+	A widget to configure parameters for Cellpose segmentation, allowing users to set the cell diameter, 
+	select imaging channels, and adjust flow and cell probability thresholds for cell detection.
+
+	This widget is designed for estimating cell diameters and configuring parameters for Cellpose, 
+	a deep learning-based segmentation tool. It also provides functionality to preview the image stack with a scale bar.
+
+	Parameters
+	----------
+	parent_window : QWidget, optional
+		The parent window that hosts the widget (default is None).
+	model_name : str, optional
+		The name of the Cellpose model being used, typically 'CP_cyto2' for cytoplasm or 'CP_nuclei' for nuclei segmentation 
+		(default is 'CP_cyto2').
+
+	Notes
+	-----
+	- This widget assumes that the parent window or one of its ancestor windows has access to the experiment channels
+	  and can locate the current image stack via `locate_image()`.
+	- This class integrates sliders for flow and cell probability thresholds, as well as a channel selection for running
+	  Cellpose segmentation.
+	- The `view_current_stack_with_scale_bar()` method opens a new window where the user can visually inspect the 
+	  image stack with a superimposed scale bar, to better estimate the cell diameter.
+
+	"""
+
+
+	def __init__(self, parent_window=None, model_name='CP_cyto2', *args, **kwargs):
+		
+		super().__init__(*args)
+		self.setWindowTitle('Estimate diameter')
+		self.parent_window = parent_window
+		self.model_name = model_name
+		
+		# 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
+	   
+		# Layout and widgets setup
+		self.layout = QVBoxLayout()
+		self.populate_widgets()
+		self.setLayout(self.layout)
+		center_window(self)
+
+	def populate_widgets(self):
+
+		"""
+		Populates the widget with UI elements such as buttons, sliders, and comboboxes to allow configuration
+		of Cellpose segmentation parameters.
+		"""
+
+		# 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 pixels', value_type='float')
+		
+		# Comboboxes for selecting imaging channels
+		self.cellpose_channel_cb = [QComboBox() for i in range(2)]
+		self.cellpose_channel_template = ['brightfield_channel', 'live_nuclei_channel']
+		if self.model_name=="CP_nuclei":
+			self.cellpose_channel_template = ['live_nuclei_channel', 'None']
+
+		for k in range(2):
+			hbox_channel = QHBoxLayout()
+			hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
+			hbox_channel.addWidget(self.cellpose_channel_cb[k])
+			if k==1:
+				self.cellpose_channel_cb[k].addItems(list(self.attr_parent.exp_channels)+['None'])
+			else:
+				self.cellpose_channel_cb[k].addItems(list(self.attr_parent.exp_channels))
+			idx = self.cellpose_channel_cb[k].findText(self.cellpose_channel_template[k])
+			if idx>0:
+				self.cellpose_channel_cb[k].setCurrentIndex(idx)
+			else:
+				self.cellpose_channel_cb[k].setCurrentIndex(0)
+
+			if k==1:
+				idx = self.cellpose_channel_cb[k].findText('None')
+				self.cellpose_channel_cb[k].setCurrentIndex(idx)
+
+			self.layout.addLayout(hbox_channel)
+		
+		# Layout for diameter input and button
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('diameter [px]: '), 33)
+		hbox.addWidget(self.diameter_le, 61)
+		hbox.addWidget(self.view_diameter_btn)
+		self.layout.addLayout(hbox)
+		
+		# Flow threshold slider
+		self.flow_slider = QLabeledDoubleSlider()
+		self.flow_slider.setOrientation(1)
+		self.flow_slider.setRange(-6,6)
+		self.flow_slider.setValue(0.4)
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('flow threshold: '), 33)
+		hbox.addWidget(self.flow_slider, 66)
+		self.layout.addLayout(hbox)
+
+		# Cell probability threshold slider
+		self.cellprob_slider = QLabeledDoubleSlider()
+		self.cellprob_slider.setOrientation(1)
+		self.cellprob_slider.setRange(-6,6)
+		self.cellprob_slider.setValue(0.)
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('cellprob threshold: '), 33)
+		hbox.addWidget(self.cellprob_slider, 66)
+		self.layout.addLayout(hbox)
+		
+		# Button to set the scale for Cellpose segmentation
+		self.set_cellpose_scale_btn = QPushButton('set')
+		self.set_cellpose_scale_btn.setStyleSheet(self.button_style_sheet)
+		self.set_cellpose_scale_btn.clicked.connect(self.parent_window.set_cellpose_scale)
+		self.layout.addWidget(self.set_cellpose_scale_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:
+			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,
+										 )
+			self.viewer.show()
+
 class ChannelNormGenerator(QVBoxLayout, Styles):
 	
 	"""Generator for list of channels"""
@@ -44,6 +276,8 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 	def generate_widgets(self):
 		
 		self.channel_cbs = [QSearchableComboBox() for i in range(self.init_n_channels)]
+		self.channel_labels = [QLabel() for i in range(self.init_n_channels)]
+
 		self.normalization_mode_btns = [QPushButton('') for i in range(self.init_n_channels)]
 		self.normalization_mode = [True for i in range(self.init_n_channels)]
 		self.normalization_clip_btns = [QPushButton('') for i in range(self.init_n_channels)]
@@ -127,8 +361,10 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 	def add_channel(self):
 
 		self.channel_cbs.append(QSearchableComboBox())
+		self.channel_labels.append(QLabel())
 		self.channel_cbs[-1].addItems(self.channel_items)
 		self.channel_cbs[-1].currentIndexChanged.connect(self.check_valid_channels)
+		self.channel_labels[-1].setText(f'channel {len(self.channel_cbs)-1}: ')
 
 		self.normalization_mode_btns.append(QPushButton(''))
 		self.normalization_mode.append(True)
@@ -153,18 +389,21 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 		self.normalization_max_value_le.append(QLineEdit('99.99'))
 
 		ch_layout = QHBoxLayout()
-		ch_layout.addWidget(QLabel(f'channel {len(self.channel_cbs)-1}: '), 30)
+		ch_layout.addWidget(self.channel_labels[-1], 30)
 		ch_layout.addWidget(self.channel_cbs[-1], 70)
 		self.channels_vb.addLayout(ch_layout)
 
 		channel_norm_options_layout = QHBoxLayout()
-		channel_norm_options_layout.setContentsMargins(130,0,0,0)
-		channel_norm_options_layout.addWidget(self.normalization_min_value_lbl[-1])			
-		channel_norm_options_layout.addWidget(self.normalization_min_value_le[-1])
-		channel_norm_options_layout.addWidget(self.normalization_max_value_lbl[-1])
-		channel_norm_options_layout.addWidget(self.normalization_max_value_le[-1])
-		channel_norm_options_layout.addWidget(self.normalization_clip_btns[-1])
-		channel_norm_options_layout.addWidget(self.normalization_mode_btns[-1])
+		channel_norm_options_layout.addWidget(QLabel(''),30)
+		ch_norm_sublayout = QHBoxLayout()
+		ch_norm_sublayout.addWidget(self.normalization_min_value_lbl[-1])
+		ch_norm_sublayout.addWidget(self.normalization_min_value_le[-1])
+		ch_norm_sublayout.addWidget(self.normalization_max_value_lbl[-1])
+		ch_norm_sublayout.addWidget(self.normalization_max_value_le[-1])
+		ch_norm_sublayout.addWidget(self.normalization_clip_btns[-1])
+		ch_norm_sublayout.addWidget(self.normalization_mode_btns[-1])
+		channel_norm_options_layout.addLayout(ch_norm_sublayout, 70)
+
 		self.channels_vb.addLayout(channel_norm_options_layout)
 
 
@@ -175,20 +414,24 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 		for i in range(len(self.channel_cbs)):
 			
 			ch_layout = QHBoxLayout()
-			ch_layout.addWidget(QLabel(f'channel {i}: '), 30)
+			self.channel_labels[i].setText(f'channel {i}: ')
+			ch_layout.addWidget(self.channel_labels[i], 30)
 			self.channel_cbs[i].addItems(self.channel_items)
 			self.channel_cbs[i].currentIndexChanged.connect(self.check_valid_channels)
 			ch_layout.addWidget(self.channel_cbs[i], 70)
 			self.channels_vb.addLayout(ch_layout)
 
 			channel_norm_options_layout = QHBoxLayout()
-			channel_norm_options_layout.setContentsMargins(130,0,0,0)
-			channel_norm_options_layout.addWidget(self.normalization_min_value_lbl[i])			
-			channel_norm_options_layout.addWidget(self.normalization_min_value_le[i])
-			channel_norm_options_layout.addWidget(self.normalization_max_value_lbl[i])
-			channel_norm_options_layout.addWidget(self.normalization_max_value_le[i])
-			channel_norm_options_layout.addWidget(self.normalization_clip_btns[i])
-			channel_norm_options_layout.addWidget(self.normalization_mode_btns[i])
+			#channel_norm_options_layout.setContentsMargins(130,0,0,0)
+			channel_norm_options_layout.addWidget(QLabel(''),30)
+			ch_norm_sublayout = QHBoxLayout()
+			ch_norm_sublayout.addWidget(self.normalization_min_value_lbl[i])			
+			ch_norm_sublayout.addWidget(self.normalization_min_value_le[i])
+			ch_norm_sublayout.addWidget(self.normalization_max_value_lbl[i])
+			ch_norm_sublayout.addWidget(self.normalization_max_value_le[i])
+			ch_norm_sublayout.addWidget(self.normalization_clip_btns[i])
+			ch_norm_sublayout.addWidget(self.normalization_mode_btns[i])
+			channel_norm_options_layout.addLayout(ch_norm_sublayout, 70)
 			self.channels_vb.addLayout(channel_norm_options_layout)
 
 		self.addLayout(self.channels_vb)
@@ -249,7 +492,7 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 			if np.all([cb.currentText()=='--' for cb in self.channel_cbs]):
 				self.parent_window.submit_btn.setEnabled(False)
 
-		if hasattr(self.parent_window, "spatial_calib_le"):
+		if hasattr(self.parent_window, "spatial_calib_le") and hasattr(self.parent_window, "submit_btn"):
 			if self.parent_window.spatial_calib_le.text()!='--':
 				self.parent_window.submit_btn.setEnabled(True)
 		elif hasattr(self.parent_window, "submit_btn"):
@@ -619,7 +862,6 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 		
 		for k in range(len(self.tab_layouts)):
 			wg = QWidget()
-			print('almost there',self.channel_names)
 			self.tab_layouts[k].parent_window = self
 			wg.setLayout(self.tab_layouts[k])
 			self.tabs.addTab(wg, self.tab_names[k])
@@ -635,8 +877,11 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 		self.delete_protocol_btn.clicked.connect(self.remove_protocol_from_list)
 
 	def generate_layout(self):
-		
-		self.addWidget(self.title_lbl, alignment=Qt.AlignCenter)
+
+		self.title_layout = QHBoxLayout()
+		self.title_layout.addWidget(self.title_lbl, 100, alignment=Qt.AlignCenter)
+
+		self.addLayout(self.title_layout)
 		self.addWidget(self.tabs)
 
 		list_header_layout = QHBoxLayout()
@@ -692,7 +937,6 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		from PyQt5.QtWidgets import QSlider
 		from superqt import QRangeSlider
 		self.frame_range_slider = QLabeledRangeSlider(parent=None)
-		print('here ok')
 
 		self.timeseries_rb.toggled.connect(self.activate_time_range)
 		self.tiles_rb.toggled.connect(self.activate_time_range)

celldetective/gui/measurement_options.py

@@ -1,43 +1,33 @@
-import math
 
-import skimage
 from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
-    QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, QTabWidget, \
-    QRadioButton, QButtonGroup, QSizePolicy, QListWidget, QDialog
+    QGridLayout, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIcon, QDoubleValidator, QIntValidator
-from matplotlib.patches import Circle
-from scipy import ndimage
-from skimage.draw import disk
-from skimage.morphology import disk
 
-from celldetective.filters import std_filter, gauss_filter
 from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
-    GeometryChoice, OperationChoice, ChannelChoice
-from superqt import QLabeledDoubleRangeSlider, QLabeledDoubleSlider, QLabeledSlider
+    GeometryChoice, OperationChoice
+from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
-from celldetective.gui.thresholds_gui import ThresholdNormalisation, ThresholdSpot
+from celldetective.gui.thresholds_gui import ThresholdSpot
 from celldetective.utils import extract_experiment_channels, get_software_location
-from celldetective.io import interpret_tracking_configuration, load_frames, auto_load_number_of_frames
-from celldetective.measure import compute_haralick_features, contour_of_instance_segmentation, normalise_by_cell
+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
-from shutil import copyfile
 import os
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
 from natsort import natsorted
 from tifffile import imread
-from pathlib import Path, PurePath
+from pathlib import Path
 import gc
-from stardist import fill_label_holes
 
 from celldetective.gui.viewers import CellEdgeVisualizer
-from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout, OperationLayout
+from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
 from celldetective.gui.gui_utils import ThresholdLineEdit
 from celldetective.gui import Styles
 
@@ -217,7 +207,7 @@ class ConfigMeasurements(QMainWindow, Styles):
         radii_layout.addWidget(self.add_radius_btn, 5)
         layout.addLayout(radii_layout)
 
-        self.radii_list = ListWidget(self, GeometryChoice, initial_features=["10"], dtype=int)
+        self.radii_list = ListWidget(GeometryChoice, initial_features=["10"], dtype=int)
         layout.addWidget(self.radii_list)
 
         self.del_radius_btn.clicked.connect(self.radii_list.removeSel)
@@ -244,7 +234,7 @@ class ConfigMeasurements(QMainWindow, Styles):
         operation_layout.addWidget(self.add_op_btn, 5)
         layout.addLayout(operation_layout)
 
-        self.operations_list = ListWidget(self, OperationChoice, initial_features=["mean"])
+        self.operations_list = ListWidget(OperationChoice, initial_features=["mean"])
         layout.addWidget(self.operations_list)
 
         self.del_op_btn.clicked.connect(self.operations_list.removeSel)
@@ -272,7 +262,7 @@ class ConfigMeasurements(QMainWindow, Styles):
         self.add_feature_btn.setToolTip("Add feature")
         self.add_feature_btn.setIconSize(QSize(20, 20))
 
-        self.features_list = ListWidget(self, FeatureChoice, initial_features=['area', 'intensity_mean', ])
+        self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_mean', ])
 
         self.del_feature_btn.clicked.connect(self.features_list.removeSel)
         self.add_feature_btn.clicked.connect(self.features_list.addItem)
@@ -315,7 +305,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 
         layout.addLayout(contour_layout)
 
-        self.contours_list = ListWidget(self, GeometryChoice, initial_features=[], dtype=int)
+        self.contours_list = ListWidget(GeometryChoice, initial_features=[], dtype=int)
         layout.addWidget(self.contours_list)
 
         self.del_contour_btn.clicked.connect(self.contours_list.removeSel)
@@ -797,7 +787,8 @@ class ConfigMeasurements(QMainWindow, Styles):
             self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
             self.hist_window = FigureCanvas(self.fig, title="Haralick: control digitized histogram")
             self.ax.clear()
-            self.ax.hist(norm_img.flatten(), bins=self.haralick_options['n_intensity_bins'])
+            flat = norm_img.flatten()
+            self.ax.hist(flat[flat==flat], bins=self.haralick_options['n_intensity_bins'])
             self.ax.set_xlabel('gray level value')
             self.ax.set_ylabel('#')
             plt.tight_layout()

celldetective/gui/neighborhood_options.py

@@ -1,25 +1,13 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication, QComboBox, QFrame, QCheckBox, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIcon
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, DistanceChoice, OperationChoice
-from superqt import QLabeledDoubleRangeSlider, QLabeledDoubleSlider,QLabeledSlider
+from celldetective.gui.gui_utils import center_window, ListWidget, DistanceChoice
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-from celldetective.utils import extract_experiment_channels, get_software_location
-from celldetective.io import interpret_tracking_configuration, load_frames, auto_load_number_of_frames
-from celldetective.measure import compute_haralick_features, contour_of_instance_segmentation
 import numpy as np
-from tifffile import imread
 import json
-from shutil import copyfile
 import os
-import matplotlib.pyplot as plt
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
-from natsort import natsorted
-from tifffile import imread
-from pathlib import Path, PurePath
-import gc
 import pandas as pd
 from celldetective.gui.viewers import CellSizeViewer, CellEdgeVisualizer
 from celldetective.gui import Styles
@@ -152,7 +140,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		layout.addLayout(list_header_layout)
 
-		self.measurements_list = ListWidget(self, DistanceChoice, initial_features=["60"], dtype=int)
+		self.measurements_list = ListWidget(DistanceChoice, initial_features=["60"], dtype=int)
 		self.measurements_list.setToolTip('Neighborhoods to compute.')
 		layout.addWidget(self.measurements_list)
 
@@ -230,11 +218,12 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		status_layout = QHBoxLayout()
 
-		status_layout.addWidget(QLabel('status: '), 30)
+		#status_layout.addWidget(QLabel('status: '), 30)
 
 		status_sublayout = QHBoxLayout()
 		self.reference_population_status_cb = QComboBox()
 		self.reference_population_status_cb.setToolTip('Status of the reference population.')
+		self.reference_population_status_cb.hide()
 		status_sublayout.addWidget(self.reference_population_status_cb,95)
 
 		self.reference_switch_status_btn = QPushButton("")
@@ -243,6 +232,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		self.reference_switch_status_btn.setIconSize(QSize(20, 20))
 		self.reference_switch_status_btn.clicked.connect(self.switch_not_reference)
 		self.reference_switch_status_btn.setToolTip('Invert status values.')
+		self.reference_switch_status_btn.hide()
 
 		status_sublayout.addWidget(self.reference_switch_status_btn, 5)
 

celldetective/gui/plot_measurements.py

@@ -1,40 +1,27 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QButtonGroup, QComboBox, QFrame, \
-    QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, \
-    QRadioButton, QSpacerItem, QSizePolicy
-from PyQt5.QtCore import Qt, QSize, QRect
+from PyQt5.QtWidgets import QMessageBox, QScrollArea, QButtonGroup, QComboBox, \
+    QCheckBox, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, \
+    QRadioButton, QSizePolicy
+from PyQt5.QtCore import Qt, QRect
 from PyQt5.QtGui import QIcon, QDoubleValidator
-from sklearn.preprocessing import MinMaxScaler
 
 from celldetective.gui import Styles
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
-    GeometryChoice, OperationChoice
-from superqt import QLabeledSlider
+from celldetective.gui.gui_utils import center_window, FigureCanvas
+
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-from celldetective.utils import extract_experiment_channels, get_software_location, _extract_labels_from_config
-from celldetective.io import interpret_tracking_configuration, load_frames, auto_load_number_of_frames, \
-    load_experiment_tables, get_experiment_antibodies, get_experiment_cell_types, get_experiment_concentrations, \
+from celldetective.utils import get_software_location, _extract_labels_from_config
+from celldetective.io import load_experiment_tables, get_experiment_antibodies, get_experiment_cell_types, get_experiment_concentrations, \
     get_positions_in_well, get_experiment_wells
-from celldetective.measure import compute_haralick_features, contour_of_instance_segmentation
-from celldetective.signals import columnwise_mean, mean_signal
+from celldetective.signals import mean_signal
 import numpy as np
-from tifffile import imread
 import json
-from shutil import copyfile
 import os
 import matplotlib.pyplot as plt
 
 plt.rcParams['svg.fonttype'] = 'none'
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
-from natsort import natsorted
-from tifffile import imread
-from pathlib import Path, PurePath
-import gc
 import pandas as pd
-from tqdm import tqdm
-from lifelines import KaplanMeierFitter
-from matplotlib.cm import viridis, tab10
+from matplotlib.cm import tab10
 import math
 import seaborn as sns