celldetective 1.0.2__py3-none-any.whl → 1.1.0__py3-none-any.whl

celldetective/gui/viewers.py

@@ -0,0 +1,596 @@
+import numpy as np
+from celldetective.io import auto_load_number_of_frames, load_frames
+from celldetective.filters import *
+from celldetective.segmentation import filter_image
+from celldetective.measure import contour_of_instance_segmentation
+from celldetective.utils import _get_img_num_per_channel
+from tifffile import imread
+import matplotlib.pyplot as plt 
+from stardist import fill_label_holes
+from pathlib import Path
+from natsort import natsorted
+from glob import glob
+import os
+
+from PyQt5.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, QComboBox, QLineEdit, QListWidget
+from PyQt5.QtCore import Qt, QSize
+from celldetective.gui.gui_utils import FigureCanvas, QuickSliderLayout, center_window
+from celldetective.gui import Styles
+from superqt import QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider
+from superqt.fonticon import icon
+from fonticon_mdi6 import MDI6
+from matplotlib_scalebar.scalebar import ScaleBar
+import gc
+
+
+class StackVisualizer(QWidget, Styles):
+
+	"""
+	A widget around an imshow and accompanying sliders.
+	"""
+	def __init__(self, stack=None, stack_path=None, frame_slider=True, contrast_slider=True, channel_cb=False, channel_names=None, n_channels=1, target_channel=0, window_title='View', PxToUm=None, background_color='transparent',imshow_kwargs={}):
+		super().__init__()
+
+		#self.setWindowTitle(window_title)
+		self.window_title = window_title
+
+		self.stack = stack
+		self.stack_path = stack_path
+		self.create_frame_slider = frame_slider
+		self.background_color = background_color
+		self.create_contrast_slider = contrast_slider
+		self.create_channel_cb = channel_cb
+		self.n_channels = n_channels
+		self.channel_names = channel_names
+		self.target_channel = target_channel
+		self.imshow_kwargs = imshow_kwargs
+		self.PxToUm = PxToUm
+		self.init_contrast = False
+
+		self.load_stack() # need to get stack, frame etc
+		self.generate_figure_canvas()
+		if self.create_channel_cb:
+			self.generate_channel_cb()
+		if self.create_contrast_slider:
+			self.generate_contrast_slider()
+		if self.create_frame_slider:
+			self.generate_frame_slider()
+
+		center_window(self)
+		self.canvas.layout.setContentsMargins(15,15,15,30)
+		self.setAttribute(Qt.WA_DeleteOnClose)
+
+	def show(self):
+		self.canvas.show()
+
+	def load_stack(self):
+
+		if self.stack is not None:
+
+			if isinstance(self.stack, list):
+				self.stack = np.array(self.stack)
+
+			if self.stack.ndim==3:
+				print('No channel axis found...')
+				self.stack = self.stack[:,:,:,np.newaxis]
+				self.target_channel = 0
+			
+			self.mode = 'direct'
+			self.stack_length = len(self.stack)
+			self.mid_time = self.stack_length // 2
+			self.init_frame = self.stack[self.mid_time,:,:,self.target_channel]
+			self.last_frame = self.stack[-1,:,:,self.target_channel]
+		else:
+			self.mode = 'virtual'
+			assert isinstance(self.stack_path, str)
+			assert self.stack_path.endswith('.tif')
+			self.locate_image_virtual()
+
+	def locate_image_virtual(self):
+
+		self.stack_length = auto_load_number_of_frames(self.stack_path)
+		if self.stack_length is None:
+			stack = imread(self.stack_path)
+			self.stack_length = len(stack)
+			del stack
+			gc.collect()
+
+		self.mid_time = self.stack_length // 2
+		self.img_num_per_channel = _get_img_num_per_channel(np.arange(self.n_channels), self.stack_length, self.n_channels)
+
+		self.init_frame = load_frames(self.img_num_per_channel[self.target_channel, self.mid_time], 
+									  self.stack_path,
+									  normalize_input=False).astype(float)[:,:,0]
+		self.last_frame = load_frames(self.img_num_per_channel[self.target_channel, self.stack_length-1], 
+									  self.stack_path,
+									  normalize_input=False).astype(float)[:,:,0]
+
+	def generate_figure_canvas(self):
+
+		self.fig, self.ax = plt.subplots(tight_layout=True) #figsize=(5, 5)
+		self.canvas = FigureCanvas(self.fig, title=self.window_title, interactive=True)
+		self.ax.clear()
+		self.im = self.ax.imshow(self.init_frame, cmap='gray', interpolation='none', **self.imshow_kwargs)
+		if self.PxToUm is not None:
+			scalebar = ScaleBar(self.PxToUm,
+								"um",
+								length_fraction=0.25,
+								location='upper right',
+								border_pad=0.4,
+								box_alpha=0.95,
+								color='white',
+								box_color='black',
+								)
+			if self.PxToUm==1:
+				scalebar = ScaleBar(1,
+								"px",
+								dimension="pixel-length",
+								length_fraction=0.25,
+								location='upper right',
+								border_pad=0.4,
+								box_alpha=0.95,
+								color='white',
+								box_color='black',
+								)
+			self.ax.add_artist(scalebar)
+		self.ax.set_xticks([])
+		self.ax.set_yticks([])
+		self.fig.set_facecolor('none')  # or 'None'
+		self.fig.canvas.setStyleSheet(f"background-color: {self.background_color};")
+		self.canvas.canvas.draw()
+
+	def generate_channel_cb(self):
+
+		assert self.channel_names is not None
+		assert len(self.channel_names)==self.n_channels
+
+		channel_layout = QHBoxLayout()
+		channel_layout.setContentsMargins(15,0,15,0)
+		channel_layout.addWidget(QLabel('Channel: '), 25)
+
+		self.channels_cb = QComboBox()
+		self.channels_cb.addItems(self.channel_names)
+		self.channels_cb.currentIndexChanged.connect(self.set_channel_index)
+		channel_layout.addWidget(self.channels_cb, 75)
+		self.canvas.layout.addLayout(channel_layout)
+
+	def generate_contrast_slider(self):
+		
+		self.contrast_slider = QLabeledDoubleRangeSlider()
+		contrast_layout = QuickSliderLayout(
+											label='Contrast: ',
+											slider=self.contrast_slider,
+											slider_initial_value=[np.nanpercentile(self.init_frame, 1),np.nanpercentile(self.init_frame, 99.99)],
+											slider_range=(np.nanmin(self.init_frame),np.nanmax(self.init_frame)),
+											decimal_option=True,
+											precision=1.0E-05,
+											)
+		contrast_layout.setContentsMargins(15,0,15,0)
+		self.im.set_clim(vmin=np.nanpercentile(self.init_frame, 1),vmax=np.nanpercentile(self.init_frame, 99.99))
+		self.contrast_slider.valueChanged.connect(self.change_contrast)
+		self.canvas.layout.addLayout(contrast_layout)
+
+
+
+	def generate_frame_slider(self):
+	
+		self.frame_slider = QLabeledSlider()
+		frame_layout = QuickSliderLayout(
+										label='Frame: ',
+										slider=self.frame_slider,
+										slider_initial_value=int(self.mid_time),
+										slider_range=(0,self.stack_length-1),
+										decimal_option=False,
+										)
+		frame_layout.setContentsMargins(15,0,15,0)
+		self.frame_slider.valueChanged.connect(self.change_frame)
+		self.canvas.layout.addLayout(frame_layout)
+
+	def set_target_channel(self, value):
+		
+		self.target_channel = value
+		self.change_frame(self.frame_slider.value())
+
+	def change_contrast(self, value):
+
+		vmin = value[0]
+		vmax = value[1]
+		self.im.set_clim(vmin=vmin, vmax=vmax)
+		self.fig.canvas.draw_idle()
+
+	def set_channel_index(self, value):
+
+		self.target_channel = value
+		self.init_contrast = True
+		if self.mode == 'direct':
+			self.last_frame = self.stack[-1,:,:,self.target_channel]
+		elif self.mode == 'virtual':
+			self.last_frame = load_frames(self.img_num_per_channel[self.target_channel, self.stack_length-1], 
+										  self.stack_path,
+										  normalize_input=False).astype(float)[:,:,0]
+		self.change_frame(self.frame_slider.value())
+		self.init_contrast = False
+
+	def change_frame(self, value):
+		
+		if self.mode=='virtual':
+
+			self.init_frame = load_frames(self.img_num_per_channel[self.target_channel, value], 
+								self.stack_path,
+								normalize_input=False
+								).astype(float)[:,:,0]
+		elif self.mode=='direct':
+			self.init_frame = self.stack[value,:,:,self.target_channel].copy()
+		
+		self.im.set_data(self.init_frame)
+		
+		if self.init_contrast:
+			self.im.autoscale()
+			I_min, I_max = self.im.get_clim()
+			self.contrast_slider.setRange(np.nanmin([self.init_frame,self.last_frame]),np.nanmax([self.init_frame,self.last_frame]))
+			self.contrast_slider.setValue((I_min,I_max))
+
+		if self.create_contrast_slider:
+			self.change_contrast(self.contrast_slider.value())
+
+	
+	def closeEvent(self, event):
+		self.canvas.close()
+
+
+class ThresholdedStackVisualizer(StackVisualizer):
+
+	"""
+	A widget around an imshow and accompanying sliders.
+	"""
+	def __init__(self, preprocessing=None, parent_le=None, initial_threshold=5, initial_mask_alpha=0.5, *args, **kwargs):
+		
+		super().__init__(*args, **kwargs)
+		self.preprocessing = preprocessing
+		self.thresh = initial_threshold
+		self.mask_alpha = initial_mask_alpha
+		self.parent_le = parent_le
+		self.compute_mask(self.thresh)
+		self.generate_mask_imshow()
+		self.generate_threshold_slider()
+		self.generate_opacity_slider()
+		if isinstance(self.parent_le, QLineEdit):
+			self.generate_apply_btn()
+
+	def generate_apply_btn(self):
+		
+		apply_hbox = QHBoxLayout()
+		self.apply_threshold_btn = QPushButton('Apply')
+		self.apply_threshold_btn.clicked.connect(self.set_threshold_in_parent_le)
+		self.apply_threshold_btn.setStyleSheet(self.button_style_sheet)
+		apply_hbox.addWidget(QLabel(''),33)
+		apply_hbox.addWidget(self.apply_threshold_btn, 33)
+		apply_hbox.addWidget(QLabel(''),33)		
+		self.canvas.layout.addLayout(apply_hbox)
+
+	def set_threshold_in_parent_le(self):
+		self.parent_le.set_threshold(self.threshold_slider.value())
+		self.close()
+
+	def generate_mask_imshow(self):
+		
+		self.im_mask = self.ax.imshow(np.ma.masked_where(self.mask==0, self.mask), alpha=self.mask_alpha, interpolation='none')
+		self.canvas.canvas.draw()
+
+	def generate_threshold_slider(self):
+
+		self.threshold_slider = QLabeledDoubleSlider()
+		thresh_layout = QuickSliderLayout(label='Threshold: ',
+										slider=self.threshold_slider,
+										slider_initial_value=self.thresh,
+										slider_range=(0,30),
+										decimal_option=True,
+										precision=1.0E-05,
+										)
+		thresh_layout.setContentsMargins(15,0,15,0)
+		self.threshold_slider.valueChanged.connect(self.change_threshold)
+		self.canvas.layout.addLayout(thresh_layout)
+
+	def generate_opacity_slider(self):
+
+		self.opacity_slider = QLabeledDoubleSlider()
+		opacity_layout = QuickSliderLayout(label='Opacity: ',
+										slider=self.opacity_slider,
+										slider_initial_value=0.5,
+										slider_range=(0,1),
+										decimal_option=True,
+										precision=1.0E-03
+										)
+		opacity_layout.setContentsMargins(15,0,15,0)
+		self.opacity_slider.valueChanged.connect(self.change_mask_opacity)
+		self.canvas.layout.addLayout(opacity_layout)
+
+	def change_mask_opacity(self, value):
+
+		self.mask_alpha = value
+		self.im_mask.set_alpha(self.mask_alpha)
+		self.canvas.canvas.draw_idle()
+
+	def change_threshold(self, value):
+		
+		self.thresh = value
+		self.compute_mask(self.thresh)
+		mask = np.ma.masked_where(self.mask == 0, self.mask)
+		self.im_mask.set_data(mask)
+		self.canvas.canvas.draw_idle()
+
+	def change_frame(self, value):
+		
+		super().change_frame(value)
+		self.change_threshold(self.threshold_slider.value())
+
+	def compute_mask(self, threshold_value):
+
+		self.preprocess_image()
+		self.mask = self.processed_image > threshold_value
+		self.mask = fill_label_holes(self.mask).astype(int)
+
+	def preprocess_image(self):
+		
+		if self.preprocessing is not None:
+
+			assert isinstance(self.preprocessing, list)
+			self.processed_image = filter_image(self.init_frame.copy(),filters=self.preprocessing)
+
+
+class CellEdgeVisualizer(StackVisualizer):
+
+	"""
+	A widget around an imshow and accompanying sliders.
+	"""
+	def __init__(self, cell_type="effectors", edge_range=(-30,30), invert=False, parent_list_widget=None, parent_le=None, labels=None, initial_edge=5, initial_mask_alpha=0.5, *args, **kwargs):
+		
+		super().__init__(*args, **kwargs)
+		self.edge_size = initial_edge
+		self.mask_alpha = initial_mask_alpha
+		self.cell_type = cell_type
+		self.labels = labels
+		self.edge_range = edge_range
+		self.invert = invert
+		self.parent_list_widget = parent_list_widget
+		self.parent_le = parent_le
+
+		self.load_labels()
+		self.generate_label_imshow()
+		self.generate_edge_slider()
+		self.generate_opacity_slider()
+		if isinstance(self.parent_list_widget, QListWidget):
+			self.generate_add_to_list_btn()
+		if isinstance(self.parent_le, QLineEdit):
+			self.generate_add_to_le_btn()
+
+	def load_labels(self):
+
+		if self.labels is not None:
+
+			if isinstance(self.labels, list):
+				self.labels = np.array(self.labels)
+
+			assert self.labels.ndim==3,'Wrong dimensions for the provided labels, expect TXY'
+			assert len(self.labels)==self.stack_length
+
+			self.mode = 'direct'
+			self.init_label = self.labels[self.mid_time,:,:]
+		else:
+			self.mode = 'virtual'
+			assert isinstance(self.stack_path, str)
+			assert self.stack_path.endswith('.tif')
+			self.locate_labels_virtual()
+		
+		self.compute_edge_labels()
+
+	def locate_labels_virtual(self):
+
+		labels_path = str(Path(self.stack_path).parent.parent) + os.sep + f'labels_{self.cell_type}' + os.sep
+		self.mask_paths = natsorted(glob(labels_path + '*.tif'))
+		
+		if len(self.mask_paths) == 0:
+
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Critical)
+			msgBox.setText("No labels were found for the selected cells. Abort.")
+			msgBox.setWindowTitle("Critical")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			self.close()
+
+		self.init_label = imread(self.mask_paths[self.frame_slider.value()])
+
+	def generate_add_to_list_btn(self):
+		
+		add_hbox = QHBoxLayout()
+		self.add_measurement_btn = QPushButton('Add measurement')
+		self.add_measurement_btn.clicked.connect(self.set_measurement_in_parent_list)
+		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="white"))
+		self.add_measurement_btn.setIconSize(QSize(20, 20))
+		self.add_measurement_btn.setStyleSheet(self.button_style_sheet)
+		add_hbox.addWidget(QLabel(''),33)
+		add_hbox.addWidget(self.add_measurement_btn, 33)
+		add_hbox.addWidget(QLabel(''),33)		
+		self.canvas.layout.addLayout(add_hbox)
+
+	def generate_add_to_le_btn(self):
+		
+		add_hbox = QHBoxLayout()
+		self.set_measurement_btn = QPushButton('Set')
+		self.set_measurement_btn.clicked.connect(self.set_measurement_in_parent_le)
+		self.set_measurement_btn.setStyleSheet(self.button_style_sheet)
+		add_hbox.addWidget(QLabel(''),33)
+		add_hbox.addWidget(self.set_measurement_btn, 33)
+		add_hbox.addWidget(QLabel(''),33)		
+		self.canvas.layout.addLayout(add_hbox)
+
+	def set_measurement_in_parent_le(self):
+		
+		self.parent_le.setText(str(int(self.edge_slider.value())))
+		self.close()
+
+	def set_measurement_in_parent_list(self):
+		
+		self.parent_list_widget.addItems([str(self.edge_slider.value())])
+		self.close()
+
+	def generate_label_imshow(self):
+		
+		self.im_mask = self.ax.imshow(np.ma.masked_where(self.edge_labels==0, self.edge_labels), alpha=self.mask_alpha, interpolation='none', cmap="viridis")
+		self.canvas.canvas.draw()
+
+	def generate_edge_slider(self):
+
+		self.edge_slider = QLabeledSlider()
+		edge_layout = QuickSliderLayout(label='Edge: ',
+										slider=self.edge_slider,
+										slider_initial_value=self.edge_size,
+										slider_range=self.edge_range,
+										decimal_option=False,
+										)
+		edge_layout.setContentsMargins(15,0,15,0)
+		self.edge_slider.valueChanged.connect(self.change_edge_size)
+		self.canvas.layout.addLayout(edge_layout)
+
+	def generate_opacity_slider(self):
+
+		self.opacity_slider = QLabeledDoubleSlider()
+		opacity_layout = QuickSliderLayout(label='Opacity: ',
+										slider=self.opacity_slider,
+										slider_initial_value=0.5,
+										slider_range=(0,1),
+										decimal_option=True,
+										precision=1.0E-03
+										)
+		opacity_layout.setContentsMargins(15,0,15,0)
+		self.opacity_slider.valueChanged.connect(self.change_mask_opacity)
+		self.canvas.layout.addLayout(opacity_layout)
+
+	def change_mask_opacity(self, value):
+
+		self.mask_alpha = value
+		self.im_mask.set_alpha(self.mask_alpha)
+		self.canvas.canvas.draw_idle()
+
+	def change_edge_size(self, value):
+		
+		self.edge_size = value
+		self.compute_edge_labels()
+		mask = np.ma.masked_where(self.edge_labels == 0, self.edge_labels)
+		self.im_mask.set_data(mask)
+		self.canvas.canvas.draw_idle()
+
+	def change_frame(self, value):
+		
+		super().change_frame(value)
+
+		if self.mode=='virtual':
+			self.init_label = imread(self.mask_paths[value])
+		elif self.mode=='direct':
+			self.init_label = self.labels[value,:,:]
+		
+		self.compute_edge_labels()
+		mask = np.ma.masked_where(self.edge_labels == 0, self.edge_labels)
+		self.im_mask.set_data(mask)
+
+	def compute_edge_labels(self):
+		
+		if self.invert:
+			edge_size = - self.edge_size
+		else:
+			edge_size = self.edge_size
+
+		self.edge_labels = contour_of_instance_segmentation(self.init_label, edge_size)
+
+class CellSizeViewer(StackVisualizer):
+
+	"""
+	A widget around an imshow and accompanying sliders.
+	"""
+	def __init__(self, initial_diameter=40, set_radius_in_list=False, diameter_slider_range=(0,200), parent_le=None, parent_list_widget=None, *args, **kwargs):
+		
+		super().__init__(*args, **kwargs)
+		self.diameter = initial_diameter
+		self.parent_le = parent_le
+		self.diameter_slider_range = diameter_slider_range
+		self.parent_list_widget = parent_list_widget
+		self.set_radius_in_list = set_radius_in_list
+		self.generate_circle()
+		self.generate_diameter_slider()
+
+		if isinstance(self.parent_le, QLineEdit):
+			self.generate_set_btn()
+		if isinstance(self.parent_list_widget, QListWidget):
+			self.generate_add_to_list_btn()
+
+	def generate_circle(self):
+
+		self.circ = plt.Circle((self.init_frame.shape[0]//2,self.init_frame.shape[1]//2), self.diameter//2, ec="tab:red",fill=False)
+		self.ax.add_patch(self.circ)
+
+		self.ax.callbacks.connect('xlim_changed',self.on_xlims_or_ylims_change)
+		self.ax.callbacks.connect('ylim_changed', self.on_xlims_or_ylims_change)
+
+	def generate_add_to_list_btn(self):
+		
+		add_hbox = QHBoxLayout()
+		self.add_measurement_btn = QPushButton('Add measurement')
+		self.add_measurement_btn.clicked.connect(self.set_measurement_in_parent_list)
+		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="white"))
+		self.add_measurement_btn.setIconSize(QSize(20, 20))
+		self.add_measurement_btn.setStyleSheet(self.button_style_sheet)
+		add_hbox.addWidget(QLabel(''),33)
+		add_hbox.addWidget(self.add_measurement_btn, 33)
+		add_hbox.addWidget(QLabel(''),33)		
+		self.canvas.layout.addLayout(add_hbox)
+
+	def set_measurement_in_parent_list(self):
+		if self.set_radius_in_list:
+			val = int(self.diameter_slider.value()//2)
+		else:
+			val = int(self.diameter_slider.value())
+		
+		self.parent_list_widget.addItems([str(val)])
+		self.close()
+
+	def on_xlims_or_ylims_change(self, event_ax):
+
+		xmin,xmax = event_ax.get_xlim()
+		ymin,ymax = event_ax.get_ylim()
+		self.circ.center = np.mean([xmin,xmax]), np.mean([ymin,ymax])
+
+	def generate_set_btn(self):
+		
+		apply_hbox = QHBoxLayout()
+		self.apply_threshold_btn = QPushButton('Set')
+		self.apply_threshold_btn.clicked.connect(self.set_threshold_in_parent_le)
+		self.apply_threshold_btn.setStyleSheet(self.button_style_sheet)
+		apply_hbox.addWidget(QLabel(''),33)
+		apply_hbox.addWidget(self.apply_threshold_btn, 33)
+		apply_hbox.addWidget(QLabel(''),33)		
+		self.canvas.layout.addLayout(apply_hbox)
+
+	def set_threshold_in_parent_le(self):
+		self.parent_le.set_threshold(self.diameter_slider.value())
+		self.close()
+
+	def generate_diameter_slider(self):
+
+		self.diameter_slider = QLabeledDoubleSlider()
+		diameter_layout = QuickSliderLayout(label='Diameter: ',
+										slider=self.diameter_slider,
+										slider_initial_value=self.diameter,
+										slider_range=self.diameter_slider_range,
+										decimal_option=True,
+										precision=1.0E-05,
+										)
+		diameter_layout.setContentsMargins(15,0,15,0)
+		self.diameter_slider.valueChanged.connect(self.change_diameter)
+		self.canvas.layout.addLayout(diameter_layout)
+
+	def change_diameter(self, value):
+		
+		self.diameter = value
+		self.circ.set_radius(self.diameter//2)
+		self.canvas.canvas.draw_idle()