celldetective 1.0.2__py3-none-any.whl

celldetective/gui/neighborhood_options.py

@@ -0,0 +1,452 @@
+from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, 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 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
+
+class ConfigNeighborhoods(QMainWindow):
+	
+	"""
+	UI to set measurement instructions.
+
+	"""
+
+	def __init__(self, parent=None):
+		
+		super().__init__()
+		self.parent = parent
+		self.setWindowTitle("Configure neighborhoods")
+		#self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','mexican-hat.png'])))
+
+		self.exp_dir = self.parent.exp_dir
+		self.neigh_instructions = self.parent.exp_dir + os.sep.join(["configs","neighborhood_instructions.json"])
+		self.clear_previous = False
+		self.not_status_reference = False
+		self.not_status_neighbor = False	
+
+		exp_config = self.exp_dir +"config.ini"
+		self.channel_names, self.channels = extract_experiment_channels(exp_config)
+		self.channel_names = np.array(self.channel_names)
+		self.channels = np.array(self.channels)
+
+		self.screen_height = self.parent.parent.parent.screen_height
+		center_window(self)
+
+		self.setMinimumWidth(750)
+		self.setMinimumHeight(int(0.5*self.screen_height))
+		self.setMaximumHeight(int(0.95*self.screen_height))
+		
+		self.populate_widget()
+		self.load_previous_neighborhood_instructions()
+
+	def populate_widget(self):
+
+		"""
+		Create the multibox design.
+
+		"""
+		
+		# 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)
+
+		# second frame for ISOTROPIC MEASUREMENTS
+		pop_hbox = QHBoxLayout()
+
+		self.reference_population_frame = QFrame()
+		self.reference_population_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+		self.populate_reference_frame()
+		pop_hbox.addWidget(self.reference_population_frame, 50)
+
+		self.neigh_population_frame = QFrame()
+		self.neigh_population_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+		self.populate_neigh_frame()
+		pop_hbox.addWidget(self.neigh_population_frame, 50)
+		main_layout.addLayout(pop_hbox)
+
+		self.radii_frame = QFrame()
+		self.radii_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+		self.populate_radii_frame()
+		main_layout.addWidget(self.radii_frame)
+
+		self.clear_previous_btn = QCheckBox('clear previous neighborhoods')
+		main_layout.addWidget(self.clear_previous_btn, alignment=Qt.AlignRight)
+
+		main_layout.addWidget(QLabel(''))
+		self.submit_btn = QPushButton('Set')
+		self.submit_btn.setStyleSheet(self.parent.parent.parent.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()
+
+		QApplication.processEvents()
+		#self.adjustScrollArea()
+
+
+	def populate_reference_frame(self):
+
+		"""
+		Add widgets and layout in the reference population frame.
+		"""
+
+		grid = QVBoxLayout(self.reference_population_frame)
+		grid.setSpacing(15)
+		self.ref_lbl = QLabel("REFERENCE")
+		self.ref_lbl.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+		grid.addWidget(self.ref_lbl, 30, alignment=Qt.AlignCenter)
+		self.generate_reference_contents()
+		grid.addWidget(self.ContentsReference, 70)
+
+	def populate_neigh_frame(self):
+
+		"""
+		Add widgets and layout in the neighbor population frame.
+		"""
+
+		grid = QVBoxLayout(self.neigh_population_frame)
+		grid.setSpacing(15)
+
+		self.neigh_lbl = QLabel("NEIGHBORS")
+		self.neigh_lbl.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+		grid.addWidget(self.neigh_lbl, 30, alignment=Qt.AlignCenter)
+		self.generate_neighbors_contents()
+		grid.addWidget(self.ContentsNeigh, 70)
+
+	def populate_radii_frame(self):
+
+		"""
+		Add widgets and layout in the radii frame.
+		"""
+
+		grid = QVBoxLayout(self.radii_frame)
+
+		self.dist_lbl = QLabel("NEIGHBORHOOD CUT-DISTANCES")
+		self.dist_lbl.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+		grid.addWidget(self.dist_lbl, alignment=Qt.AlignCenter)
+		self.generate_radii_contents()
+		grid.addWidget(self.ContentsIso) #1, 0, 1, 4, alignment=Qt.AlignTop
+
+
+	def generate_radii_contents(self):
+
+		self.ContentsIso = QFrame()
+		layout = QVBoxLayout(self.ContentsIso)
+		layout.setContentsMargins(0,0,0,0)
+
+		radii_layout = QHBoxLayout()
+		self.radii_lbl = QLabel('Cut-distance radii:')
+		self.radii_lbl.setToolTip('From reference cells, in pixel units. Define radii for neighborhood computations.')
+		radii_layout.addWidget(self.radii_lbl, 90)
+
+		self.del_radius_btn = QPushButton("")
+		self.del_radius_btn.setStyleSheet(self.parent.parent.parent.button_select_all)
+		self.del_radius_btn.setIcon(icon(MDI6.trash_can,color="black"))
+		self.del_radius_btn.setToolTip("Remove radius")
+		self.del_radius_btn.setIconSize(QSize(20, 20))
+		radii_layout.addWidget(self.del_radius_btn, 5)
+
+		self.add_radius_btn = QPushButton("")
+		self.add_radius_btn.setStyleSheet(self.parent.parent.parent.button_select_all)
+		self.add_radius_btn.setIcon(icon(MDI6.plus,color="black"))
+		self.add_radius_btn.setToolTip("Add radius")
+		self.add_radius_btn.setIconSize(QSize(20, 20))	
+		radii_layout.addWidget(self.add_radius_btn, 5)
+		layout.addLayout(radii_layout)
+		
+		self.radii_list = ListWidget(self, DistanceChoice, initial_features=["60"], dtype=int)
+		layout.addWidget(self.radii_list)
+
+		self.del_radius_btn.clicked.connect(self.radii_list.removeSel)
+		self.add_radius_btn.clicked.connect(self.radii_list.addItem)
+
+	def generate_reference_contents(self):
+
+		self.ContentsReference = QFrame()
+		layout = QVBoxLayout(self.ContentsReference)
+		layout.setContentsMargins(15,15,15,15)
+
+		pop_hbox = QHBoxLayout()
+		pop_hbox.addWidget(QLabel('population: '),30)
+		self.ref_pop_cb = QComboBox()
+		self.ref_pop_cb.addItems(['targets','effectors'])
+		pop_hbox.addWidget(self.ref_pop_cb,70)
+		layout.addLayout(pop_hbox)
+
+		status_hbox = QHBoxLayout()
+		status_hbox.addWidget(QLabel('status: '), 30)
+		self.ref_pop_status_cb = QComboBox()
+		#self.ref_pop_status_cb.addItems(['--'])
+
+		status_cb_hbox = QHBoxLayout()
+		status_cb_hbox.setContentsMargins(0,0,0,0)
+		status_cb_hbox.addWidget(self.ref_pop_status_cb,90)
+		# replace with not gate
+
+		self.ref_not_gate_btn = QPushButton("")
+		self.ref_not_gate_btn.setStyleSheet(self.parent.parent.parent.button_select_all)
+		self.ref_not_gate_btn.setIcon(icon(MDI6.gate_not,color="black"))
+		self.ref_not_gate_btn.setToolTip("NOT (flip zeros and ones)")
+		self.ref_not_gate_btn.setIconSize(QSize(20, 20))
+		self.ref_not_gate_btn.clicked.connect(self.switch_not_reference)
+		status_cb_hbox.addWidget(self.ref_not_gate_btn, 5)
+		status_hbox.addLayout(status_cb_hbox,70)
+		layout.addLayout(status_hbox)
+
+		event_hbox = QHBoxLayout()
+		event_hbox.addWidget(QLabel('event time: '),30)
+		self.event_time_cb = QComboBox()
+		#self.event_time_cb.addItems(['--'])
+		event_hbox.addWidget(self.event_time_cb,70)
+		layout.addLayout(event_hbox)
+		
+		self.set_combo_boxes_reference()
+		self.ref_pop_cb.currentIndexChanged.connect(self.set_combo_boxes_reference)
+
+	def switch_not_reference(self):
+		self.not_status_reference = not self.not_status_reference
+		if self.not_status_reference:
+			self.ref_not_gate_btn.setIcon(icon(MDI6.gate_not,color="#1565c0"))
+			self.ref_not_gate_btn.setIconSize(QSize(20, 20))
+		else:
+			self.ref_not_gate_btn.setIcon(icon(MDI6.gate_not,color="black"))
+			self.ref_not_gate_btn.setIconSize(QSize(20, 20))
+
+	def generate_neighbors_contents(self):
+
+		self.ContentsNeigh = QFrame()
+		layout = QVBoxLayout(self.ContentsNeigh)
+		layout.setContentsMargins(15,15,15,15)
+
+		pop_hbox = QHBoxLayout()
+		pop_hbox.addWidget(QLabel('population: '),30)
+		self.neigh_pop_cb = QComboBox()
+		self.neigh_pop_cb.addItems(['targets','effectors'])
+		self.neigh_pop_cb.currentIndexChanged.connect(self.set_combo_boxes_neigh)
+
+		pop_hbox.addWidget(self.neigh_pop_cb,70)
+		layout.addLayout(pop_hbox)
+
+		status_hbox = QHBoxLayout()
+		status_hbox.addWidget(QLabel('status: '),30)
+		self.neigh_pop_status_cb = QComboBox()
+		self.set_combo_boxes_neigh()
+
+		status_cb_hbox = QHBoxLayout()
+		status_cb_hbox.setContentsMargins(0,0,0,0)
+		status_cb_hbox.addWidget(self.neigh_pop_status_cb,90)
+		self.neigh_not_gate_btn = QPushButton("")
+		self.neigh_not_gate_btn.setStyleSheet(self.parent.parent.parent.button_select_all)
+		self.neigh_not_gate_btn.setIcon(icon(MDI6.gate_not,color="black"))
+		self.neigh_not_gate_btn.setToolTip("NOT (flip zeros and ones)")
+		self.neigh_not_gate_btn.setIconSize(QSize(20, 20))
+		self.neigh_not_gate_btn.clicked.connect(self.switch_not_neigh)
+		status_cb_hbox.addWidget(self.neigh_not_gate_btn, 5)
+		status_hbox.addLayout(status_cb_hbox, 70)
+		layout.addLayout(status_hbox)
+
+		self.cum_presence_btn = QCheckBox('cumulated presence')
+		layout.addWidget(self.cum_presence_btn)
+
+		self.symmetrize_btn = QCheckBox('symmetrize')
+		layout.addWidget(self.symmetrize_btn)
+
+	def switch_not_neigh(self):
+		self.not_status_neighbor = not self.not_status_neighbor
+		if self.not_status_neighbor:
+			self.neigh_not_gate_btn.setIcon(icon(MDI6.gate_not,color="#1565c0"))
+			self.neigh_not_gate_btn.setIconSize(QSize(20, 20))
+		else:
+			self.neigh_not_gate_btn.setIcon(icon(MDI6.gate_not,color="black"))
+			self.neigh_not_gate_btn.setIconSize(QSize(20, 20))
+
+	def set_combo_boxes_neigh(self):
+		pop = self.neigh_pop_cb.currentText()
+		class_cols, status_cols, _ = self.locate_population_columns(pop)
+		self.neigh_pop_status_cb.clear()
+		self.neigh_pop_status_cb.addItems(['--','class','status']+class_cols+status_cols)
+
+	def set_combo_boxes_reference(self):
+		pop = self.ref_pop_cb.currentText()
+		class_cols, status_cols, time_cols = self.locate_population_columns(pop)
+		self.ref_pop_status_cb.clear()
+		self.ref_pop_status_cb.addItems(['--','class', 'status']+class_cols+status_cols)
+		self.event_time_cb.addItems(['--', 't0']+time_cols)
+
+	def locate_population_columns(self, population):
+
+		# Look for all classes and times
+		tables = glob(self.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_{population}.csv']))
+		self.all_columns = []
+		for tab in tables:
+			cols = pd.read_csv(tab, nrows=1).columns.tolist()
+			self.all_columns.extend(cols)
+		self.all_columns = np.unique(self.all_columns)
+
+		class_idx = np.array([s.startswith('class_') for s in self.all_columns])
+		status_idx = np.array([s.startswith('status_') for s in self.all_columns])
+		time_idx = np.array([s.startswith('t_') for s in self.all_columns])
+
+		if len(class_idx)>0:
+			class_columns = list(self.all_columns[class_idx])
+			for c in ['class_id', 'class_color']:
+				if c in class_columns:
+					class_columns.remove(c)
+		else:
+			class_columns = []
+
+		if len(status_idx)>0:
+			status_columns = list(self.all_columns[status_idx])
+		else:
+			status_columns = []
+
+		if len(time_idx)>0:
+			time_columns = list(self.all_columns[time_idx])
+		else:
+			time_columns = []
+
+		return class_columns, status_columns, time_columns
+
+	def write_instructions(self):
+
+		"""
+		Write the selected options in a json file for later reading by the software.
+		"""
+
+		print('Writing instructions...')
+		
+		neighborhood_options = {}
+		pop = [self.ref_pop_cb.currentText(), self.neigh_pop_cb.currentText()]
+		neighborhood_options.update({'population': pop})
+		
+		status_options = [self.ref_pop_status_cb.currentText(), self.neigh_pop_status_cb.currentText()]
+		for k in range(2):
+			if status_options[k]=='--':
+				status_options[k] = None
+		if pop[0]!=pop[1]:
+			mode = 'two-pop'
+		else:
+			mode = 'self'
+
+		distances = self.radii_list.getItems()
+		neighborhood_options.update({'distance': distances})	
+		neighborhood_options.update({'clear_neigh': self.clear_previous_btn.isChecked()})
+		event_time_col = self.event_time_cb.currentText()
+		if event_time_col=='--':
+			event_time_col = None
+		neighborhood_options.update({'event_time_col': event_time_col})		
+
+
+		neighborhood_kwargs = {'mode': mode, 'status': status_options, 'not_status_option': [self.not_status_reference, self.not_status_neighbor], 
+							  'compute_cum_sum': self.cum_presence_btn.isChecked(), 'attention_weight': True, 'symmetrize': self.symmetrize_btn.isChecked(),
+							  'include_dead_weight': True}
+
+		neighborhood_options.update({'neighborhood_kwargs': neighborhood_kwargs})
+
+		print('Neighborhood instructions: ', neighborhood_options)
+		file_name = self.neigh_instructions
+		with open(file_name, 'w') as f:
+			json.dump(neighborhood_options, f, indent=4)
+		print('Done.')
+		self.close()
+		
+
+	def load_previous_neighborhood_instructions(self):
+
+		"""
+		Read the measurmeent options from a previously written json file and format properly for the UI.
+		"""
+
+		print('Reading instructions..')
+		if os.path.exists(self.neigh_instructions):
+			with open(self.neigh_instructions, 'r') as f:
+				neigh_instructions = json.load(f)
+				print(neigh_instructions)
+
+				if 'distance' in neigh_instructions:
+					distances = neigh_instructions['distance']
+					distances = [str(d) for d in distances]
+					self.radii_list.list_widget.clear()
+					self.radii_list.list_widget.addItems(distances)
+
+				if 'population' in neigh_instructions:
+
+					pop = neigh_instructions['population']
+					idx0 = self.ref_pop_cb.findText(pop[0])
+					self.ref_pop_cb.setCurrentIndex(idx0)
+					idx1 = self.neigh_pop_cb.findText(pop[1])
+					self.neigh_pop_cb.setCurrentIndex(idx1)
+
+				if 'clear_neigh' in neigh_instructions:
+					clear_neigh = neigh_instructions['clear_neigh']
+					self.clear_previous_btn.setChecked(clear_neigh)
+
+				if 'event_time_col' in neigh_instructions:
+					event_time_col = neigh_instructions['event_time_col']
+					if event_time_col is None:
+						event_time_col = '--'
+					idx = self.event_time_cb.findText(event_time_col)
+					self.event_time_cb.setCurrentIndex(idx)
+
+				if 'neighborhood_kwargs' in neigh_instructions:
+					neighborhood_kwargs = neigh_instructions['neighborhood_kwargs']
+					if 'compute_cum_sum' in neighborhood_kwargs:
+						self.cum_presence_btn.setChecked(neighborhood_kwargs['compute_cum_sum'])
+					if 'symmetrize' in neighborhood_kwargs:
+						self.symmetrize_btn.setChecked(neighborhood_kwargs['symmetrize'])
+					if 'status' in neighborhood_kwargs:
+						status_options = neighborhood_kwargs['status']
+						status_options = ['--' if s is None else s for s in status_options]
+						idx0 = self.ref_pop_status_cb.findText(status_options[0])
+						self.ref_pop_status_cb.setCurrentIndex(idx0)
+						idx1 = self.neigh_pop_status_cb.findText(status_options[1])
+						self.neigh_pop_status_cb.setCurrentIndex(idx1)
+					if 'not_status_option' in neighborhood_kwargs:
+						not_status_option = neighborhood_kwargs['not_status_option']
+						if not_status_option[0]:
+							self.ref_not_gate_btn.click()
+						if not_status_option[1]:
+							self.neigh_not_gate_btn.click()
+
+
+