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

celldetective/gui/processes/measure_cells.py

@@ -6,7 +6,7 @@ import json
 from pathlib import Path, PurePath
 
 from celldetective.io import auto_load_number_of_frames, load_frames, locate_labels
-from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel
+from celldetective.utils import extract_experiment_channels, config_section_to_dict, _get_img_num_per_channel
 from celldetective.utils import remove_trajectory_measurements, _extract_coordinates_from_features, _remove_invalid_cols
 from celldetective.measure import drop_tonal_features, measure_features, measure_isotropic_intensity, measure_radial_distance_to_center, center_of_mass_to_abs_coordinates
 
@@ -17,9 +17,14 @@ import concurrent.futures
 import pandas as pd
 from natsort import natsorted
 from art import tprint
+from typing import Optional, Union
 
 
 class MeasurementProcess(Process):
+	
+	pos: Optional[Union[str,Path]] = None
+	mode: Optional[str] = None
+	n_threads: int = 1
 
 	def __init__(self, queue=None, process_args=None):
 		
@@ -166,14 +171,19 @@ class MeasurementProcess(Process):
 			self.table_name = "trajectories_effectors.csv"
 			self.instruction_file = os.sep.join(["configs","measurement_instructions_effectors.json"])
 
+		else:
+			self.label_folder = f"labels_{self.mode}"
+			self.table_name = f"trajectories_{self.mode}.csv"
+			self.instruction_file = os.sep.join(["configs",f"measurement_instructions_{self.mode}.json"])			
+
 	def extract_experiment_parameters(self):
 
-		self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]
-		self.spatial_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["pxtoum"])
-		self.time_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["frametomin"])
-		self.len_movie = float(ConfigSectionMap(self.config,"MovieSettings")["len_movie"])
-		self.shape_x = int(ConfigSectionMap(self.config,"MovieSettings")["shape_x"])
-		self.shape_y = int(ConfigSectionMap(self.config,"MovieSettings")["shape_y"])
+		self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")["movie_prefix"]
+		self.spatial_calibration = float(config_section_to_dict(self.config, "MovieSettings")["pxtoum"])
+		self.time_calibration = float(config_section_to_dict(self.config, "MovieSettings")["frametomin"])
+		self.len_movie = float(config_section_to_dict(self.config, "MovieSettings")["len_movie"])
+		self.shape_x = int(config_section_to_dict(self.config, "MovieSettings")["shape_x"])
+		self.shape_y = int(config_section_to_dict(self.config, "MovieSettings")["shape_y"])
 
 		self.channel_names, self.channel_indices = extract_experiment_channels(self.exp_dir)
 		self.nbr_channels = len(self.channel_names)
@@ -326,7 +336,8 @@ class MeasurementProcess(Process):
 
 			df = df.reset_index(drop=True)
 			df = _remove_invalid_cols(df)
-			
+			df = df.replace([np.inf, -np.inf], np.nan)
+
 			df.to_csv(self.pos+os.sep.join(["output", "tables", self.table_name]), index=False)
 			print(f'Measurement table successfully exported in  {os.sep.join(["output", "tables"])}...')
 			print('Done.')

celldetective/gui/processes/segment_cells.py

@@ -5,7 +5,7 @@ import os
 import json
 import numpy as np
 from celldetective.io import extract_position_name, locate_segmentation_model, auto_load_number_of_frames, load_frames, _check_label_dims, _load_frames_to_segment
-from celldetective.utils import _rescale_labels, _segment_image_with_stardist_model, _segment_image_with_cellpose_model, _prep_stardist_model, _prep_cellpose_model, _get_normalize_kwargs_from_config, extract_experiment_channels, _estimate_scale_factor, _extract_channel_indices_from_config, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel
+from celldetective.utils import _rescale_labels, _segment_image_with_stardist_model, _segment_image_with_cellpose_model, _prep_stardist_model, _prep_cellpose_model, _get_normalize_kwargs_from_config, extract_experiment_channels, _estimate_scale_factor, _extract_channel_indices_from_config, config_section_to_dict, _extract_nbr_channels_from_config, _get_img_num_per_channel
 
 from pathlib import Path, PurePath
 from glob import glob
@@ -39,19 +39,30 @@ class BaseSegmentProcess(Process):
 		print(f"Position: {extract_position_name(self.pos)}...")
 		print("Configuration file: ",self.config)
 		print(f"Population: {self.mode}...")
-
+		self.instruction_file = os.sep.join(["configs", f"segmentation_instructions_{self.mode}.json"])
+		
+		self.read_instructions()
 		self.extract_experiment_parameters()
 		self.detect_movie_length()
 		self.write_folders()
+	
+	def read_instructions(self):
+		print('Looking for instruction file...')
+		instr_path = PurePath(self.exp_dir,Path(f"{self.instruction_file}"))
+		if os.path.exists(instr_path):
+			with open(instr_path, 'r') as f:
+				_instructions = json.load(f)
+				print(f"Measurement instruction file successfully loaded...")
+				print(f"Instructions: {_instructions}...")
+			self.flip = _instructions.get("flip", False)
+		else:
+			self.flip = False
+
 
 	def write_folders(self):
 
 		self.mode = self.mode.lower()
-
-		if self.mode=="target" or self.mode=="targets":
-			self.label_folder = "labels_targets"
-		elif self.mode=="effector" or self.mode=="effectors":
-			self.label_folder = "labels_effectors"
+		self.label_folder = f"labels_{self.mode}"
 
 		if os.path.exists(self.pos+self.label_folder):
 			print('Erasing the previous labels folder...')
@@ -62,9 +73,9 @@ class BaseSegmentProcess(Process):
 
 	def extract_experiment_parameters(self):
 
-		self.spatial_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["pxtoum"])
-		self.len_movie = float(ConfigSectionMap(self.config,"MovieSettings")["len_movie"])
-		self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]
+		self.spatial_calibration = float(config_section_to_dict(self.config, "MovieSettings")["pxtoum"])
+		self.len_movie = float(config_section_to_dict(self.config, "MovieSettings")["len_movie"])
+		self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")["movie_prefix"]
 		self.nbr_channels = _extract_nbr_channels_from_config(self.config)
 		self.channel_names, self.channel_indices = extract_experiment_channels(self.exp_dir)
 
@@ -123,6 +134,14 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 	def extract_model_input_parameters(self):
 
 		self.required_channels = self.input_config["channels"]
+		if 'selected_channels' in self.input_config:
+			self.required_channels = self.input_config['selected_channels']
+		
+		self.target_cell_size = None
+		if 'target_cell_size_um' in self.input_config and 'cell_size_um' in self.input_config:
+			self.target_cell_size = self.input_config['target_cell_size_um']
+			self.cell_size = self.input_config['cell_size_um']
+
 		self.normalize_kwargs = _get_normalize_kwargs_from_config(self.input_config)
 
 		self.model_type = self.input_config['model_type']
@@ -152,6 +171,14 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 		self.scale = _estimate_scale_factor(self.spatial_calibration, self.required_spatial_calibration)
 		print(f"Scale: {self.scale}...")
 
+		if self.target_cell_size is not None and self.scale is not None:
+			self.scale *= self.cell_size / self.target_cell_size
+		elif self.target_cell_size is not None:
+			if self.target_cell_size != self.cell_size:
+				self.scale = self.cell_size / self.target_cell_size
+
+		print(f"Scale accounting for expected cell size: {self.scale}...")
+
 	def locate_model_path(self):
 
 		self.model_complete_path = locate_segmentation_model(self.model_name)
@@ -183,7 +210,11 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 			elif self.model_type=='cellpose':
 				model, scale_model = _prep_cellpose_model(self.model_name, self.model_complete_path, use_gpu=self.use_gpu, n_channels=len(self.required_channels), scale=self.scale)
 
-			for t in tqdm(range(self.len_movie),desc="frame"):
+			list_indices = range(self.len_movie)
+			if self.flip:
+				list_indices = reversed(list_indices)
+
+			for t in tqdm(list_indices,desc="frame"):
 				
 				f = _load_frames_to_segment(self.file, self.img_num_channels[:,t], scale_model=scale_model, normalize_kwargs=self.normalize_kwargs)
 
@@ -219,6 +250,7 @@ class SegmentCellDLProcess(BaseSegmentProcess):
 			pass		
 		
 		gc.collect()
+		print("Done.")
 
 		# Send end signal
 		self.queue.put("finished")
@@ -339,6 +371,9 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 	def run(self):
 
 		self.indices = list(range(self.img_num_channels.shape[1]))
+		if self.flip:
+			self.indices = np.array(list(reversed(self.indices)))
+		
 		chunks = np.array_split(self.indices, self.n_threads)
 
 		with concurrent.futures.ThreadPoolExecutor(max_workers=self.n_threads) as executor:
@@ -349,6 +384,7 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 			except Exception as e:
 				print("Exception: ", e)
 
+		print('Done.')
 		# Send end signal
 		self.queue.put("finished")
 		self.queue.close()

celldetective/gui/processes/track_cells.py

@@ -1,10 +1,8 @@
 from multiprocessing import Process
 import time
-import datetime
-import os
-import json
 from celldetective.io import auto_load_number_of_frames, _load_frames_to_measure, locate_labels
-from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, _mask_intensity_measurements
+from celldetective.utils import config_section_to_dict, _get_img_num_per_channel, \
+	_mask_intensity_measurements, remove_file_if_exists
 from pathlib import Path, PurePath
 from glob import glob
 from tqdm import tqdm
@@ -147,14 +145,20 @@ class TrackingProcess(Process):
 			self.napari_name = "napari_effector_trajectories.npy"
 			self.table_name = "trajectories_effectors.csv"
 
+		else:
+			self.label_folder = f"labels_{self.mode}"
+			self.instruction_file = os.sep.join(["configs",f"tracking_instructions_{self.mode}.json"])
+			self.napari_name = f"napari_{self.mode}_trajectories.npy"
+			self.table_name = f"trajectories_{self.mode}.csv"			
+
 	def extract_experiment_parameters(self):
 
-		self.movie_prefix = ConfigSectionMap(self.config,"MovieSettings")["movie_prefix"]
-		self.spatial_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["pxtoum"])
-		self.time_calibration = float(ConfigSectionMap(self.config,"MovieSettings")["frametomin"])
-		self.len_movie = float(ConfigSectionMap(self.config,"MovieSettings")["len_movie"])
-		self.shape_x = int(ConfigSectionMap(self.config,"MovieSettings")["shape_x"])
-		self.shape_y = int(ConfigSectionMap(self.config,"MovieSettings")["shape_y"])
+		self.movie_prefix = config_section_to_dict(self.config, "MovieSettings")["movie_prefix"]
+		self.spatial_calibration = float(config_section_to_dict(self.config, "MovieSettings")["pxtoum"])
+		self.time_calibration = float(config_section_to_dict(self.config, "MovieSettings")["frametomin"])
+		self.len_movie = float(config_section_to_dict(self.config, "MovieSettings")["len_movie"])
+		self.shape_x = int(config_section_to_dict(self.config, "MovieSettings")["shape_x"])
+		self.shape_y = int(config_section_to_dict(self.config, "MovieSettings")["shape_y"])
 
 		self.channel_names, self.channel_indices = extract_experiment_channels(self.exp_dir)
 		self.nbr_channels = len(self.channel_names)
@@ -240,7 +244,9 @@ class TrackingProcess(Process):
 
 		print('Features successfully measured...')
 
-		df = pd.concat(self.timestep_dataframes)	
+		df = pd.concat(self.timestep_dataframes)
+		df = df.replace([np.inf, -np.inf], np.nan)
+
 		df.reset_index(inplace=True, drop=True)
 		df = _mask_intensity_measurements(df, self.mask_channels)
 
@@ -274,8 +280,7 @@ class TrackingProcess(Process):
 		trajectories.to_csv(self.pos+os.sep.join(['output', 'tables', self.table_name]), index=False)
 		print(f"Trajectory table successfully exported in {os.sep.join(['output', 'tables'])}...")
 
-		if os.path.exists(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')])):
-			os.remove(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')]))
+		remove_file_if_exists(self.pos+os.sep.join(['output', 'tables', self.table_name.replace('.csv','.pkl')]))
 
 		del trajectories; del napari_data;
 		gc.collect()		

celldetective/gui/seg_model_loader.py

@@ -1,8 +1,8 @@
-from PyQt5.QtWidgets import QWidget, QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
+from PyQt5.QtWidgets import QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window
+from celldetective.gui.gui_utils import center_window, generic_message
 from celldetective.gui.layouts import ChannelNormGenerator
-from celldetective.gui import ThresholdConfigWizard
+from celldetective.gui import ThresholdConfigWizard, CelldetectiveWidget
 from PyQt5.QtGui import QDoubleValidator
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
@@ -16,7 +16,7 @@ import gc
 from cellpose.models import CellposeModel
 
 
-class SegmentationModelLoader(QWidget, Styles):
+class SegmentationModelLoader(CelldetectiveWidget):
 	
 	"""
 	Upload a segmentation model or define a Threshold pipeline.
@@ -27,15 +27,10 @@ class SegmentationModelLoader(QWidget, Styles):
 		super().__init__()
 		self.parent_window = parent_window
 		self.mode = self.parent_window.mode
-		if self.mode=="targets":
-			self.target_folder = "segmentation_targets"
-		elif self.mode=="effectors":
-			self.target_folder = "segmentation_effectors"
+		self.target_folder = f"segmentation_{self.mode}"
 		self.setWindowTitle('Upload model')
 		self.generate_content()
-		self.setWindowIcon(self.celldetective_icon)
 		center_window(self)
-		self.setAttribute(Qt.WA_DeleteOnClose)
 
 	def generate_content(self):
 
@@ -230,14 +225,9 @@ class SegmentationModelLoader(QWidget, Styles):
 						self.destination = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
 						self.folder_dest = self.destination
 					else:
-						msgBox = QMessageBox()
-						msgBox.setIcon(QMessageBox.Warning)
-						msgBox.setText("StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
-						msgBox.setWindowTitle("Warning")
-						msgBox.setStandardButtons(QMessageBox.Ok)
-						returnValue = msgBox.exec()
-						if returnValue == QMessageBox.Ok:
-							return None					
+						generic_message(
+							"StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
+						return None
 				
 				if self.seg_mode=="cellpose":
 					self.file_label.setText(self.filename.split("/")[-1])
@@ -264,15 +254,8 @@ class SegmentationModelLoader(QWidget, Styles):
 					self.merge_lbl.hide()
 					self.file_label.setText(self.filename[0].split("/")[-1])
 				else:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						pass
-
+					generic_message(
+						"You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
 					self.merge_cb.show()
 					self.merge_lbl.show()
 					self.file_label.setText(f"{n_files} configs loaded...")
@@ -327,14 +310,8 @@ class SegmentationModelLoader(QWidget, Styles):
 			channels.append(self.channel_layout.channel_cbs[i].currentText())
 
 		if self.file_label.text()=='No file chosen':
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please select a model first.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
+			generic_message('Please select a model first...')
+			return None
 
 		if not self.threshold_button.isChecked():
 			
@@ -343,14 +320,8 @@ class SegmentationModelLoader(QWidget, Styles):
 				try:
 					shutil.copytree(self.filename, self.destination)
 				except FileExistsError:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						return None
+					generic_message("A model with the same name already exists in the models folder. Please rename it.")
+					return None
 
 			elif self.cellpose_button.isChecked():
 
@@ -359,15 +330,8 @@ class SegmentationModelLoader(QWidget, Styles):
 						os.mkdir(self.folder_dest)
 					shutil.copy(self.filename, self.destination)
 				except FileExistsError:
-					msgBox = QMessageBox()
-					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("A model with the same name already exists in the models folder. Please rename it.")
-					msgBox.setWindowTitle("Warning")
-					msgBox.setStandardButtons(QMessageBox.Ok)
-					returnValue = msgBox.exec()
-					if returnValue == QMessageBox.Ok:
-						return None
-				
+					generic_message("A model with the same name already exists in the models folder. Please rename it.")
+					return None
 				try:
 					model = CellposeModel(pretrained_model=self.destination, model_type=None, nchan=len(channels))
 					self.scale_model = model.diam_mean
@@ -392,16 +356,11 @@ class SegmentationModelLoader(QWidget, Styles):
 			if not isinstance(self.filename, list):
 				if not self.filename is None:
 					self.filename = [self.filename]
-			if self.mode=="targets":
-				self.parent_window.threshold_config_targets = self.filename
-				self.parent_window.seg_model_list.setCurrentText('Threshold')
-				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
-				self.close()
-			elif self.mode=="effectors":
-				self.parent_window.threshold_config_effectors = self.filename
-				self.parent_window.seg_model_list.setCurrentText('Threshold')
-				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
-				self.close()
+
+			idx = self.parent_window.parent_window.populations.index(self.mode)
+			self.parent_window.threshold_configs[idx] = self.filename
+			self.parent_window.seg_model_list.setCurrentText('Threshold')
+			self.close()
 
 	def generate_input_config(self):
 

celldetective/gui/settings/__init__.py

@@ -0,0 +1,7 @@
+from ._settings_measurements import SettingsMeasurements
+from ._settings_segmentation import SettingsSegmentation
+from ._settings_tracking import SettingsTracking
+from ._settings_segmentation_model_training import SettingsSegmentationModelTraining
+from ._settings_event_model_training import SettingsEventDetectionModelTraining
+from ._settings_signal_annotator import SettingsSignalAnnotator
+from ._settings_neighborhood import SettingsNeighborhood

celldetective/gui/settings/_settings_base.py

@@ -0,0 +1,70 @@
+from abc import abstractmethod
+from PyQt5.QtWidgets import QApplication, QScrollArea, QSizePolicy, QVBoxLayout, QPushButton
+from PyQt5.QtCore import Qt
+from celldetective.utils import get_software_location
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
+
+class CelldetectiveSettingsPanel(CelldetectiveMainWindow):
+	
+	def __init__(self, title=""):
+		
+		super().__init__()
+		self.setWindowTitle(title)
+		
+		self._get_screen_height()
+		#self.setMinimumWidth(500)
+		self.setMaximumHeight(int(0.8 * self._screen_height))
+		self._scroll_area = QScrollArea(self)
+		self._floatValidator = QDoubleValidator()
+		self._intValidator = QIntValidator()
+		self._software_path = get_software_location()
+
+		self._create_widgets()
+		self._build_layouts()
+		self.center_window()
+	
+	def _create_widgets(self):
+		self.submit_btn: QPushButton = QPushButton("Save")
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
+		self.submit_btn.clicked.connect(self._write_instructions)
+	
+	def center_window(self):
+		return center_window(self)
+	
+	def _get_screen_height(self):
+		app = QApplication.instance()
+		screen = app.primaryScreen()
+		geometry = screen.availableGeometry()
+		self._screen_width, self._screen_height = geometry.getRect()[-2:]
+	
+	def _adjustSize(self):
+		self._widget.adjustSize()
+		self._scroll_area.adjustSize()
+		self.adjustSize()
+	
+	def _build_layouts(self):
+		
+		self._layout: QVBoxLayout = QVBoxLayout()
+		self._widget: CelldetectiveWidget = CelldetectiveWidget()
+		self._widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+		
+		# Create button widget and layout
+		self._widget.setLayout(self._layout)
+		self._layout.setContentsMargins(30, 30, 30, 30)
+		
+		self._scroll_area.setAlignment(Qt.AlignCenter)
+		self._scroll_area.setWidget(self._widget)
+		self._scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self._scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+		self._scroll_area.setWidgetResizable(True)
+		self.setCentralWidget(self._scroll_area)
+		
+		QApplication.processEvents()
+	
+	@abstractmethod
+	def _load_previous_instructions(self): pass
+	
+	@abstractmethod
+	def _write_instructions(self): pass