celldetective 1.2.1__py3-none-any.whl → 1.2.2__py3-none-any.whl

celldetective/gui/configure_new_exp.py

@@ -1,15 +1,16 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QDialog, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QSlider, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
+from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
 from PyQt5.QtGui import QIntValidator, QDoubleValidator
-from celldetective.gui.gui_utils import center_window
+from celldetective.gui.gui_utils import center_window, help_generic
 from celldetective.gui.styles import Styles
+from celldetective.utils import get_software_location
+import json
+
 from superqt import QLabeledSlider
 from PyQt5.QtCore import Qt, QSize
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from configparser import ConfigParser
 import os
-from shutil import copyfile
-import time
 from functools import partial
 import numpy as np
 from celldetective.gui import Styles
@@ -119,6 +120,15 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.number_of_wells = QLabel("Number of wells:")
 		self.ms_grid.addWidget(self.number_of_wells, 1, 0, 1, 3)
 
+		self.help_btn = QPushButton()
+		self.help_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_btn.setIconSize(QSize(20, 20))
+		self.help_btn.clicked.connect(self.help_structure)
+		self.help_btn.setStyleSheet(self.button_select_all)
+		self.help_btn.setToolTip("Help.")
+		self.ms_grid.addWidget(self.help_btn, 1, 0, 1, 3, alignment=Qt.AlignRight)
+
+
 		self.SliderWells = QLabeledSlider(Qt.Horizontal, self)
 		self.SliderWells.setMinimum(1)
 		self.SliderWells.setMaximum(32)
@@ -189,6 +199,29 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.shape_y_field.setText("2048")
 		self.ms_grid.addWidget(self.shape_y_field, 16, 0, 1, 3)
 
+	def help_structure(self):
+
+		"""
+		Helper to choose an experiment structure.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','exp-structure.json'])
+
+		with open(dict_path) as f:
+			d = json.load(f)
+
+		suggestion = help_generic(d)
+		if isinstance(suggestion, str):
+			print(f"{suggestion=}")
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Information)
+			msgBox.setTextFormat(Qt.RichText)
+			msgBox.setText(suggestion+"\nSee <a href='https://celldetective.readthedocs.io/en/latest/get-started.html#data-organization'>the docs</a> for more information.")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None		
 
 	def generate_channel_params_box(self):
 

celldetective/gui/control_panel.py

@@ -1,10 +1,10 @@
 from PyQt5.QtWidgets import QMainWindow, QComboBox, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
 	QTabWidget, QVBoxLayout, QMessageBox, QScrollArea, QDesktopWidget
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIcon
 from celldetective.gui.gui_utils import center_window, QHSeperationLine
 from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
+from celldetective.io import get_experiment_wells, get_config, get_spatial_calibration, get_temporal_calibration, get_experiment_concentrations, get_experiment_cell_types, get_experiment_antibodies, get_experiment_pharmaceutical_agents
 from natsort import natsorted
 from glob import glob
 import os
@@ -28,7 +28,7 @@ class ControlPanel(QMainWindow, Styles):
 		if not self.exp_dir.endswith(os.sep):
 			self.exp_dir = self.exp_dir+os.sep
 		self.setWindowTitle("celldetective")
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','logo.png'])))
+		self.setWindowIcon(self.celldetective_icon)
 		self.parent_window = parent_window
 		center_window(self)
 
@@ -98,7 +98,7 @@ class ControlPanel(QMainWindow, Styles):
 		Detect the wells in the experiment folder and the associated positions.
 		"""
 		
-		self.wells = natsorted(glob(self.exp_dir + "W*" + os.sep))
+		self.wells = get_experiment_wells(self.exp_dir) #natsorted(glob(self.exp_dir + "W*" + os.sep))
 		self.positions = []
 		for w in self.wells:
 			w = os.path.split(w[:-1])
@@ -247,9 +247,12 @@ class ControlPanel(QMainWindow, Styles):
 		This methods load the configuration read in the config.ini file of the experiment.
 		'''
 
-		self.exp_config = self.exp_dir + "config.ini"
-		self.PxToUm = float(ConfigSectionMap(self.exp_config,"MovieSettings")["pxtoum"])
-		self.FrameToMin = float(ConfigSectionMap(self.exp_config,"MovieSettings")["frametomin"])
+		print('Reading experiment configuration...')
+		self.exp_config = get_config(self.exp_dir)
+
+		self.PxToUm = get_spatial_calibration(self.exp_dir)
+		self.FrameToMin = get_temporal_calibration(self.exp_dir)
+
 		self.len_movie = int(ConfigSectionMap(self.exp_config,"MovieSettings")["len_movie"])
 		self.shape_x = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_x"])
 		self.shape_y = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_y"])
@@ -262,31 +265,12 @@ class ControlPanel(QMainWindow, Styles):
 		number_of_wells = len(self.wells)
 		self.well_labels = _extract_labels_from_config(self.exp_config,number_of_wells)
 
-		self.concentrations = ConfigSectionMap(self.exp_config,"Labels")["concentrations"].split(",")
-		if number_of_wells != len(self.concentrations):
-			self.concentrations = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]		
-
-		#self.antibodies = extract_labels_from_config(config, number_of_wells)
+		self.concentrations = get_experiment_concentrations(self.exp_dir)
+		self.cell_types = get_experiment_cell_types(self.exp_dir)
+		self.antibodies = get_experiment_antibodies(self.exp_dir)
+		self.pharmaceutical_agents = get_experiment_pharmaceutical_agents(self.exp_dir)
 
-		self.cell_types = ConfigSectionMap(self.exp_config,"Labels")["cell_types"].split(",")
-		if number_of_wells != len(self.cell_types):
-			self.cell_types = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]		
-
-		try:
-			self.antibodies = ConfigSectionMap(self.exp_config,"Labels")["antibodies"].split(",")
-			if number_of_wells != len(self.antibodies):
-				self.antibodies = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
-		except:
-			print("Warning... antibodies not found...")
-			self.antibodies = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
-
-		try:
-			self.pharmaceutical_agents = ConfigSectionMap(self.exp_config,"Labels")["pharmaceutical_agents"].split(",")
-			if number_of_wells != len(self.pharmaceutical_agents):
-				self.pharmaceutical_agents = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
-		except:
-			print("Warning... pharmaceutical agents not found...")
-			self.pharmaceutical_agents = [str(s) for s in np.linspace(0,number_of_wells-1,number_of_wells)]
+		print('Experiment configuration successfully read...')
 
 	def closeEvent(self, event):