celldetective 1.4.0__py3-none-any.whl → 1.4.1.post1__py3-none-any.whl

celldetective/gui/{btrack_options.py → settings/_settings_tracking.py}

@@ -1,8 +1,12 @@
-from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+"""
+Copyright © 2023 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
+"""
+
+
+from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMessageBox, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QDoubleValidator
 
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
+from celldetective.gui.gui_utils import FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
 from superqt import QLabeledDoubleSlider, QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
@@ -16,10 +20,10 @@ import os
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
-from celldetective.gui import CelldetectiveWidget, CelldetectiveMainWindow
+from celldetective.gui.settings._settings_base import CelldetectiveSettingsPanel
 
 
-class ConfigTracking(CelldetectiveMainWindow):
+class SettingsTracking(CelldetectiveSettingsPanel):
 	
 	"""
 	UI to set tracking parameters for bTrack.
@@ -28,46 +32,51 @@ class ConfigTracking(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None):
 		
-		super().__init__()
 		self.parent_window = parent_window
-		self.setWindowTitle("Configure tracking")
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
-		self.floatValidator = QDoubleValidator()
 
 		self.config_name = os.sep.join(["configs", f"btrack_config_{self.mode}.json"])
 		self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", f"tracking_instructions_{self.mode}.json"])
-		self.soft_path = get_software_location()
 		
 		self.config_path = self.exp_dir + self.config_name
 		self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
 		self.channel_names = np.array(self.channel_names)
 		self.channels = np.array(self.channels)
-		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
-
-		center_window(self)
-		self.setMinimumWidth(540)
 		self.minimum_height = 300
-		# self.setMinimumHeight(int(0.3*self.screen_height))
-		# self.setMaximumHeight(int(0.8*self.screen_height))
-		self.populate_widget()
-		self.load_previous_tracking_instructions()
 
-	def populate_widget(self):
+		super().__init__(title="Configure tracking")
+		
+		self._add_to_layout()
+		self._load_previous_instructions()
+		
+		self._widget.setMinimumWidth(500)
+		self._adjustSize()
+		self.resize(int(self.width()*1.5), int(self._screen_height * 0.8))
+	
+	def _add_to_layout(self):
+		
+		tracker_hbox = QHBoxLayout()
+		tracker_hbox.setContentsMargins(15, 15, 15, 15)
+		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
+		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
+		
+		self._layout.addLayout(tracker_hbox)
+		self._layout.addWidget(self.config_frame)
+		self._layout.addWidget(self.features_frame)
+		self._layout.addWidget(self.config_trackpy_frame)
+		self._layout.addWidget(self.post_proc_frame)
+		self._layout.addWidget(self.submit_btn)
+
+
+	def _create_widgets(self):
 
 		"""
 		Create the multibox design with collapsable frames.
 
 		"""
 		
-		# Create button widget and layout
-		self.scroll_area = QScrollArea(self)
-		self.button_widget = CelldetectiveWidget()
-		main_layout = QVBoxLayout()
-		self.button_widget.setLayout(main_layout)
-		main_layout.setContentsMargins(30, 30, 30, 30)
-
-		# First collapsable Frame CONFIG
+		super()._create_widgets()
 
 		self.btrack_option = QRadioButton('bTrack')
 		self.btrack_option.setChecked(True)
@@ -81,69 +90,37 @@ class ConfigTracking(CelldetectiveMainWindow):
 		self.config_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_config_frame()
 
-		tracker_hbox = QHBoxLayout()
-		tracker_hbox.setContentsMargins(15, 15, 15, 15)
-		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
-		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
-		main_layout.addLayout(tracker_hbox)
-
-		main_layout.addWidget(self.config_frame)
-
 		# Second collapsable frame FEATURES
 		self.features_frame = QFrame()
 		self.features_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_features_frame()
-		main_layout.addWidget(self.features_frame)
 
 		self.config_trackpy_frame = QFrame()
 		self.config_trackpy_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_config_trackpy_frame()
-		main_layout.addWidget(self.config_trackpy_frame)
 		self.config_trackpy_frame.hide()
 
 		# Third collapsable frame POST-PROCESSING
 		self.post_proc_frame = QFrame()
 		self.post_proc_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.populate_post_proc_frame()
-		main_layout.addWidget(self.post_proc_frame)
-
-		self.submit_btn = QPushButton('Save')
-		self.submit_btn.setStyleSheet(self.parent_window.parent_window.parent_window.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()
 
 		self.btrack_option.toggled.connect(self.show_tracking_options)
 		self.trackpy_option.toggled.connect(self.show_tracking_options)
 
-		QApplication.processEvents()
-		self.adjustScrollArea()
-
 	def show_tracking_options(self):
 
 		if self.btrack_option.isChecked():
 			self.config_frame.show()
 			self.features_frame.show()
 			self.config_trackpy_frame.hide()
-			#self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
-			#self.adjustSize()
+			#self._adjustSize()
 		else:
 			self.config_frame.hide()
 			self.features_frame.hide()
 			self.config_trackpy_frame.show()
-			#self.scroll_area.setMinimumHeight(self.minimum_height)
-			#self.adjustSize()
+			#self._adjustSize()
+	
 
 	def populate_post_proc_frame(self):
 
@@ -203,12 +180,12 @@ class ConfigTracking(CelldetectiveMainWindow):
 			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def help_post(self):
@@ -319,12 +296,12 @@ class ConfigTracking(CelldetectiveMainWindow):
 			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def generate_post_proc_panel_contents(self):
@@ -614,12 +591,12 @@ class ConfigTracking(CelldetectiveMainWindow):
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 	def collapse_config_trackpy_advanced(self):
 
@@ -635,12 +612,12 @@ class ConfigTracking(CelldetectiveMainWindow):
 			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
-				self.scroll_area.setMinimumHeight(int(self.minimum_height))
-				self.adjustSize()
+				pass
+				#self._scroll_area.setMinimumHeight(int(self.minimum_height))
+				#self._adjustSize()
 		else:
 			self.collapse_config_trackpy_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_config_trackpy_btn.setIconSize(QSize(20, 20))
-			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
 
 	def generate_config_trackpy_panel_contents(self):
@@ -653,7 +630,7 @@ class ConfigTracking(CelldetectiveMainWindow):
 		self.search_range_lbl = QLabel("search range [px]: ")
 		self.search_range_le = QLineEdit('30')
 		self.search_range_le.setPlaceholderText('search distance in pixels')
-		self.search_range_le.setValidator(self.floatValidator)
+		self.search_range_le.setValidator(self._floatValidator)
 		sr_layout.addWidget(self.search_range_lbl, 30)
 		sr_layout.addWidget(self.search_range_le, 70)
 		layout.addLayout(sr_layout)
@@ -731,7 +708,7 @@ class ConfigTracking(CelldetectiveMainWindow):
 
 		self.file_dialog = QFileDialog()
 		try:
-			modelpath = os.sep.join([self.soft_path, "celldetective","models","tracking_configs"]) + os.sep
+			modelpath = os.sep.join([self._software_path, "celldetective","models","tracking_configs"]) + os.sep
 			print("Track config path: ", modelpath)
 			self.filename = self.file_dialog.getOpenFileName(None, "Load config", modelpath, "json files (*.json)")[0]
 			if self.filename!=self.config_path:
@@ -822,16 +799,16 @@ class ConfigTracking(CelldetectiveMainWindow):
 		else:
 			self.post_proc_ticked = True	
 
-	def adjustScrollArea(self):
-		
-		"""
-		Auto-adjust scroll area to fill space 
-		(from https://stackoverflow.com/questions/66417576/make-qscrollarea-use-all-available-space-of-qmainwindow-height-axis)
-		"""
-
-		step = 5
-		while self.scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
-			self.resize(self.width(), self.height() + step)
+	# def adjustScrollArea(self):
+	#
+	# 	"""
+	# 	Auto-adjust scroll area to fill space
+	# 	(from https://stackoverflow.com/questions/66417576/make-qscrollarea-use-all-available-space-of-qmainwindow-height-axis)
+	# 	"""
+	#
+	# 	step = 5
+	# 	while self._scroll_area.verticalScrollBar().isVisible() and self.height() < self.maximumHeight():
+	# 		self.resize(self.width(), self.height() + step)
 
 	def load_cell_config(self):
 
@@ -844,7 +821,7 @@ class ConfigTracking(CelldetectiveMainWindow):
 			json_data = json.load(f)
 			self.config_le.setText(json.dumps(json_data, indent=4))
 
-	def write_instructions(self):
+	def _write_instructions(self):
 
 		"""
 		Write the selected options in a json file for later reading by the software.
@@ -953,7 +930,7 @@ class ConfigTracking(CelldetectiveMainWindow):
 		else:
 			self.haralick_options = None		
 
-	def load_previous_tracking_instructions(self):
+	def _load_previous_instructions(self):
 
 		"""
 		Read the tracking options from a previously written json file.

celldetective/gui/styles.py

@@ -14,7 +14,8 @@ class Styles(object):
 
 		
 		self.celldetective_blue = "#1565c0"
-		self.celldetective_icon = QIcon(os.sep.join([get_software_location(),'celldetective','icons','logo.png']))
+		self.celldetective_logo_path = os.sep.join([get_software_location(),'celldetective','icons','logo.png'])
+		self.celldetective_icon = QIcon(self.celldetective_logo_path)
 
 		self.action_lbl_style_sheet = """
 			font-size: 10px;

celldetective/gui/survival_ui.py

@@ -1,4 +1,4 @@
-from PyQt5.QtWidgets import QMessageBox, QComboBox, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QComboBox, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QDoubleValidator
 from celldetective.gui.gui_utils import center_window, generic_message

celldetective/gui/tableUI.py

@@ -3,6 +3,9 @@ from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QBrush, QColor, QDoubleValidator
 import pandas as pd
 import matplotlib.pyplot as plt
+
+from celldetective.gui.table_ops.merge_groups import MergeGroupWidget
+
 plt.rcParams['svg.fonttype'] = 'none'
 from celldetective.gui.gui_utils import FigureCanvas, center_window, QHSeperationLine, GenericOpColWidget, PandasModel
 from celldetective.utils import differentiate_per_track, collapse_trajectories_by_status, test_2samp_generic, safe_log
@@ -650,11 +653,17 @@ class TableUI(CelldetectiveMainWindow):
 		self.calibrate_action.triggered.connect(self.calibrate_selected_feature)
 		self.calibrate_action.setShortcut("Ctrl+C")
 		self.mathMenu.addAction(self.calibrate_action)
+		
+		self.merge_classification_action = QAction('&Merge states...', self)
+		self.merge_classification_action.triggered.connect(self.merge_classification_features)
+		self.mathMenu.addAction(self.merge_classification_action)
 
 		self.derivative_action = QAction('&Differentiate...', self)
 		self.derivative_action.triggered.connect(self.differenciate_selected_feature)
 		self.derivative_action.setShortcut("Ctrl+D")
 		self.mathMenu.addAction(self.derivative_action)
+		if not self.tracks:
+			self.derivative_action.setEnabled(False)
 
 		self.abs_action = QAction('&Absolute value...', self)
 		self.abs_action.triggered.connect(self.take_abs_of_selected_feature)
@@ -993,6 +1002,22 @@ class TableUI(CelldetectiveMainWindow):
 
 		self.LogWidget = LogColWidget(self, selected_col)
 		self.LogWidget.show()
+		
+	def merge_classification_features(self):
+		
+		x = self.table_view.selectedIndexes()
+		col_idx = np.unique(np.array([l.column() for l in x]))
+		
+		col_selection = []
+		if isinstance(col_idx, (list, np.ndarray)):
+			cols = np.array(list(self.data.columns))
+			if len(col_idx) > 0:
+				selected_cols = cols[col_idx]
+				col_selection.extend(selected_cols)
+		
+		self.merge_classification_widget = MergeGroupWidget(self, columns = col_selection)
+		self.merge_classification_widget.show()
+
 
 	def calibrate_selected_feature(self):
 		

celldetective/gui/table_ops/merge_groups.py

@@ -0,0 +1,118 @@
+from typing import List
+
+import numpy as np
+from PyQt5.QtCore import QSize, Qt
+from PyQt5.QtWidgets import QComboBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QVBoxLayout
+from fonticon_mdi6 import MDI6
+from superqt.fonticon import icon
+
+from celldetective.gui import CelldetectiveWidget
+from celldetective.gui.gui_utils import PandasModel, center_window
+
+
+class MergeGroupWidget(CelldetectiveWidget):
+	def __init__(self, parent_window, columns: List[str] = [], n_cols_init: int = 3):
+		
+		super().__init__()
+		self.parent_window = parent_window
+
+		self.setWindowTitle("Merge classifications")
+		self.group_cols = [c for c in list(self.parent_window.data.columns) if c.startswith("group_") or c.startswith("status_")]
+		self.group_cols.insert(0, "--")
+		if len(columns) > n_cols_init:
+			n_cols_init = len(columns)
+		
+		center_window(self)
+		
+		layout = QVBoxLayout(self)
+		layout.setContentsMargins(30, 10, 30, 30)
+		
+		label = QLabel(
+			"Merge several binary or multi-label classification features into a multi-label classification feature where each state is one of the possible combinations.\n")
+		
+		label.setWordWrap(True)  # enables automatic line breaking
+		label.setTextInteractionFlags(Qt.TextSelectableByMouse)  # optional, to allow copy
+		label.setStyleSheet("color: gray;")  # optional style
+		
+		layout.addWidget(label)
+		
+		
+		self.name_le = QLineEdit("group_multilabel")
+		name_layout = QHBoxLayout()
+		name_layout.addWidget(QLabel("name: "), 25)
+		name_layout.addWidget(self.name_le, 75)
+		layout.addLayout(name_layout)
+		
+		self.cbs_layout = QVBoxLayout()
+		self.cbs_layout.setContentsMargins(0,10,0,0)
+		
+		self.cbs = []
+		for i in range(n_cols_init):
+			cb_i = QComboBox()
+			cb_i.addItems(self.group_cols)
+			if i < len(columns):
+				selection = columns[i]
+				idx = cb_i.findText(selection)
+				if idx>=0:
+					cb_i.setCurrentIndex(idx)
+				else:
+					cb_i.setCurrentIndex(0)
+			self.cbs.append(cb_i)
+			
+			col_layout = QHBoxLayout()
+			col_layout.addWidget(QLabel(f'state {i}: '), 25)
+			col_layout.addWidget(cb_i, 75)
+			self.cbs_layout.addLayout(col_layout)
+		
+		layout.addLayout(self.cbs_layout)
+		
+		self.add_feature_btn = QPushButton()
+		self.add_feature_btn.setIcon(icon(MDI6.plus, color=self.help_color))
+		self.add_feature_btn.setIconSize(QSize(20, 20))
+		self.add_feature_btn.clicked.connect(self.add_col)
+		self.add_feature_btn.setStyleSheet(self.button_select_all)
+		layout.addWidget(self.add_feature_btn, alignment=Qt.AlignRight)
+		
+		self.submit_btn = QPushButton('Compute')
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
+		self.submit_btn.clicked.connect(self.compute)
+		layout.addWidget(self.submit_btn, 30)
+
+		self.setAttribute(Qt.WA_DeleteOnClose)
+	
+	def add_col(self):
+		cb_i = QComboBox()
+		cb_i.addItems(self.group_cols)
+		self.cbs.append(cb_i)
+	
+		col_layout = QHBoxLayout()
+		col_layout.addWidget(QLabel(f'state {len(self.cbs)}: '), 25)
+		col_layout.addWidget(cb_i, 75)
+	
+		self.cbs_layout.addLayout(col_layout)
+	
+	def compute(self):
+		
+		cols_to_merge = [cb_i.currentText() for cb_i in self.cbs if cb_i.currentText() != "--"]
+		name = self.name_le.text()
+		if " " in name:
+			name.replace(" ","_")
+		if name == '':
+			name = "multilabel"
+		if not name.startswith("group_"):
+			name = "group_" + name
+		
+		if len(cols_to_merge) > 1:
+			print("Computing a multi-label classification from the classification feature sources...")
+			bases = [int(self.parent_window.data[c].max()) + 1 for c in cols_to_merge]
+			multipliers = np.concatenate(([1], np.cumprod(bases[:-1])))
+			self.parent_window.data[name] = (self.parent_window.data[cols_to_merge] * multipliers).sum(axis=1)
+			self.parent_window.data.loc[self.parent_window.data[cols_to_merge].isna().any(axis=1), name] = np.nan
+	
+			self.parent_window.model = PandasModel(self.parent_window.data)
+			self.parent_window.table_view.setModel(self.parent_window.model)
+			self.close()
+		elif len(cols_to_merge) == 1:
+			print("Only one classification feature was selected, nothing to merge...")
+		else:
+			print("No classification feature was selected...")

celldetective/gui/viewers.py

@@ -1,4 +1,3 @@
-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, threshold_image
@@ -11,17 +10,16 @@ from natsort import natsorted
 from glob import glob
 import os
 
-from PyQt5.QtWidgets import QHBoxLayout, QPushButton, QLabel, QComboBox, QLineEdit, QListWidget, QShortcut
+from PyQt5.QtWidgets import QHBoxLayout, QMessageBox, QPushButton, QLabel, QComboBox, QLineEdit, QListWidget, QShortcut
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QKeySequence, QDoubleValidator
-from celldetective.gui.gui_utils import FigureCanvas, center_window, QuickSliderLayout, QHSeperationLine, ThresholdLineEdit, PreprocessingLayout2
-from celldetective.gui import Styles, CelldetectiveWidget
+from celldetective.gui.gui_utils import FigureCanvas, QuickSliderLayout, QHSeperationLine, ThresholdLineEdit, PreprocessingLayout2
+from celldetective.gui import CelldetectiveWidget
 from superqt import QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from matplotlib_scalebar.scalebar import ScaleBar
 import gc
-from celldetective.utils import mask_edges
 from scipy.ndimage import shift
 
 class StackVisualizer(CelldetectiveWidget):

celldetective/gui/workers.py

@@ -4,8 +4,6 @@ from PyQt5.QtCore import QRunnable, QObject, pyqtSignal, QThreadPool, QSize, Qt
 
 from celldetective.gui.base_components import CelldetectiveDialog
 from celldetective.gui.gui_utils import center_window
-from celldetective.gui import Styles
-import time
 import math
 
 class ProgressWindow(CelldetectiveDialog):