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

celldetective/gui/configure_new_exp.py

@@ -1,7 +1,6 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
+from PyQt5.QtWidgets import QApplication,QWidget, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton
 from PyQt5.QtGui import QIntValidator, QDoubleValidator
 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
 
@@ -13,9 +12,10 @@ from configparser import ConfigParser
 import os
 from functools import partial
 import numpy as np
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
-class ConfigNewExperiment(QMainWindow, Styles):
+
+class ConfigNewExperiment(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None):
 		
@@ -34,11 +34,11 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		button_widget = QWidget()
+		button_widget = CelldetectiveWidget()
 		self.grid = QGridLayout()
 		button_widget.setLayout(self.grid)
 
-		self.grid.setContentsMargins(30,30,30,30)
+		self.grid.setContentsMargins(30, 30, 30, 30)
 		self.grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
 		self.supFolder = QLineEdit()
 		self.supFolder.setAlignment(Qt.AlignLeft)	
@@ -64,17 +64,20 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.grid.addWidget(self.expName, 3, 0, 1, 3)
 
 		self.generate_movie_settings()
-		self.grid.addLayout(self.ms_grid,29,0,1,3)
+		self.grid.addLayout(self.ms_grid, 29, 0, 1, 3)
 
 		self.generate_channel_params_box()
-		self.grid.addLayout(self.channel_grid,30,0,1,3)
+		self.grid.addLayout(self.channel_grid, 30, 0, 1, 3)
+
+		self.generate_population_params_box()
+		self.grid.addLayout(self.population_grid, 31, 0, 1, 3)
 
 		self.validate_button = QPushButton("Submit")
 		self.validate_button.clicked.connect(self.create_config)
 		self.validate_button.setStyleSheet(self.button_style_sheet)
 		#self.validate_button.setIcon(QIcon_from_svg(abs_path+f"/icons/process.svg", color='white'))
 
-		self.grid.addWidget(self.validate_button, 31, 0, 1, 3, alignment = Qt.AlignBottom)		
+		self.grid.addWidget(self.validate_button, 32, 0, 1, 3, alignment = Qt.AlignBottom)		
 		button_widget.adjustSize()
 
 		self.scroll_area.setAlignment(Qt.AlignCenter)
@@ -128,10 +131,9 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		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)
+		self.SliderWells.setMaximum(512)
 		self.ms_grid.addWidget(self.SliderWells, 2, 0, 1, 3, alignment=Qt.AlignTop)
 
 		self.number_of_positions = QLabel("Number of positions per well:")
@@ -139,7 +141,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 		self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
 		self.SliderPos.setMinimum(1)
-		self.SliderPos.setMaximum(50)
+		self.SliderPos.setMaximum(512)
 
 		self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
 
@@ -167,8 +169,8 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.movie_length.setToolTip('Optional: depending on how the movies are encoded, the automatic extraction of the number of frames can be difficult.\nThe software will then rely on this value.')
 		self.ms_grid.addWidget(self.movie_length,9, 0, 1, 3)
 		self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
-		self.MovieLengthSlider.setMinimum(2)
-		self.MovieLengthSlider.setMaximum(128)
+		self.MovieLengthSlider.setMinimum(1)
+		#self.MovieLengthSlider.setMaximum(128)
 		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
 
 		self.prefix_lbl = QLabel("Prefix for the movies:")
@@ -181,7 +183,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.movie_prefix_field.setText("")
 		self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("X shape in pixels:"), 13, 0, 1, 3)
+		self.ms_grid.addWidget(QLabel("Image width:"), 13, 0, 1, 3)
 		self.shape_x_field = QLineEdit()
 		self.shape_x_field.setValidator(onlyInt)
 		self.shape_x_field.setAlignment(Qt.AlignLeft)	
@@ -190,7 +192,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.shape_x_field.setText("2048")
 		self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("Y shape in pixels:"), 15, 0, 1, 3)
+		self.ms_grid.addWidget(QLabel("Image height:"), 15, 0, 1, 3)
 		self.shape_y_field = QLineEdit()
 		self.shape_y_field.setValidator(onlyInt)
 		self.shape_y_field.setAlignment(Qt.AlignLeft)	
@@ -271,7 +273,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 	def add_custom_channel(self):
 
-		self.CustomChannelWidget = QWidget()
+		self.CustomChannelWidget = CelldetectiveWidget()
 		self.CustomChannelWidget.setWindowTitle("Custom channel")
 		layout = QVBoxLayout()
 		self.CustomChannelWidget.setLayout(layout)
@@ -323,6 +325,83 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		else:
 			self.sliders[index].setEnabled(False)
 
+	def generate_population_params_box(self):
+
+		"""
+		Parameters related to the movie channels
+		Rewrite all of it
+
+		"""
+
+		self.population_grid = QGridLayout()
+		self.population_grid.setContentsMargins(21,30,20,30)
+
+		pop_lbl = QLabel("CELL POPULATIONS")
+		pop_lbl.setStyleSheet("""
+			font-weight: bold;
+			""")
+		self.population_grid.addWidget(pop_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
+
+
+		self.populations = ['effectors','targets']
+		self.population_checkboxes = [QCheckBox() for i in range(len(self.populations))]
+
+		for i in range(len(self.populations)):
+
+			self.population_checkboxes[i].setText(self.populations[i])
+			self.population_checkboxes[i].setChecked(True)
+			self.population_grid.addWidget(self.population_checkboxes[i], i+1, 0, 1, 1)
+
+		# Add channel button
+		self.addPopBtn = QPushButton('Add a cell population')
+		self.addPopBtn.setIcon(icon(MDI6.plus,color="white"))
+		self.addPopBtn.setIconSize(QSize(25, 25))
+		self.addPopBtn.setStyleSheet(self.button_style_sheet)
+		self.addPopBtn.clicked.connect(self.add_custom_population)
+		self.population_grid.addWidget(self.addPopBtn, 1000, 0, 1, 1)
+
+
+	def add_custom_population(self):
+		self.CustomPopWidget = CelldetectiveWidget()
+		self.CustomPopWidget.setWindowTitle("Define custom population")
+		layout = QVBoxLayout()
+		self.CustomPopWidget.setLayout(layout)
+
+		self.name_le = QLineEdit()
+		self.name_le.setPlaceholderText('name')
+		self.name_le.textChanged.connect(self.check_population_name)
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('population name: '), 33)
+		hbox.addWidget(self.name_le, 66)
+		layout.addLayout(hbox)
+
+		self.addPopBtn = QPushButton('add')
+		self.addPopBtn.setStyleSheet(self.button_style_sheet)
+		self.addPopBtn.setEnabled(False)
+		self.addPopBtn.clicked.connect(self.write_custom_population)
+		layout.addWidget(self.addPopBtn)
+		center_window(self.CustomPopWidget)
+		self.CustomPopWidget.show()
+
+	def check_population_name(self, text):
+		# define all conditions for valid population name (like no space)
+		if len(text)>0 and ' ' not in text:
+			self.addPopBtn.setEnabled(True)
+		else:
+			self.addPopBtn.setEnabled(False)
+
+	def write_custom_population(self):
+
+		self.new_population_name = self.name_le.text()
+		name_map = self.new_population_name
+
+		self.populations.append(self.new_population_name)
+		self.population_checkboxes.append(QCheckBox())
+		self.CustomPopWidget.close()
+
+		self.population_checkboxes[-1].setText(self.populations[-1])
+		self.population_grid.addWidget(self.population_checkboxes[-1], len(self.populations)+1, 0, 1, 1)
+
 	def browse_experiment_folder(self):
 
 		"""
@@ -362,6 +441,17 @@ class ConfigNewExperiment(QMainWindow, Styles):
 			if returnValue == QMessageBox.Ok:
 				return None
 
+		populations_checked = [self.population_checkboxes[i].isChecked() for i in range(len(self.population_checkboxes))]
+		if not np.any(populations_checked):
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please set at least one cell population before proceeding...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
 		sorted_list = set(channel_indices)
 		expected_list = set(np.arange(max(sorted_list)+1))
 		print(sorted_list, expected_list, sorted_list==expected_list)
@@ -429,8 +519,13 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		Write all user input parameters to a configuration file associated to an experiment.
 		"""
 
+
 		config = ConfigParser(interpolation=None)
 
+		config.add_section('Populations')
+		pops = ','.join([self.populations[i].lower() for i in range(len(self.population_checkboxes)) if self.population_checkboxes[i].isChecked()])
+		config.set('Populations','populations', pops)
+
 		# add a new section and some values
 		config.add_section('MovieSettings')
 		config.set('MovieSettings', 'PxToUm', self.PxToUm_field.text().replace(',','.'))
@@ -456,6 +551,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		config.add_section('Metadata')
 		config.set('Metadata', 'concentration_units', self.concentration_units)
 
+
 		# save to a file
 		with open('config.ini', 'w') as configfile:
 			config.write(configfile)
@@ -464,36 +560,75 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		print(f'New experiment successfully configured in folder {self.directory}...')
 		self.close()
 
-class SetupConditionLabels(QWidget, Styles):
+class SetupConditionLabels(CelldetectiveWidget):
 	def __init__(self, parent_window, n_wells):
 		super().__init__()
 		self.parent_window = parent_window
 		self.n_wells = n_wells
 		self.setWindowTitle("Well conditions")
-		self.layout = QVBoxLayout()
-		self.layout.setContentsMargins(30,30,30,30)
-		self.setLayout(self.layout)
+		
+		# --- Outer layout ---
+		self.outer_layout = QVBoxLayout(self)
+		self.outer_layout.setContentsMargins(10, 10, 10, 10)
+		
+		# --- Scroll area ---
+		self.scroll = QScrollArea(self)
+		self.scroll.setWidgetResizable(True)
+		self.outer_layout.addWidget(self.scroll, stretch=1)  # takes most space
+		
+		# Container inside scroll
+		self.container = QWidget()
+		self.scroll.setWidget(self.container)
+		
+		# Content layout (scrollable part)
+		self.layout = QVBoxLayout(self.container)
+		self.layout.setContentsMargins(30, 30, 30, 30)
+		
 		self.onlyFloat = QDoubleValidator()
 		self.populate()
+		
+		self.concentration_units_le = QLineEdit('pM')
+		self.concentration_units_le.setPlaceholderText('concentration units')
+		
+		concentration_units_layout = QHBoxLayout()
+		concentration_units_layout.addWidget(QLabel('concentration\nunits: '), 5, alignment=Qt.AlignLeft)
+		concentration_units_layout.addWidget(self.concentration_units_le, 10)
+		concentration_units_layout.addWidget(QLabel(''), 85)
+		self.outer_layout.addLayout(concentration_units_layout)
+		
+		# --- Fixed button row (not scrollable) ---
+		btn_hbox = QHBoxLayout()
+		btn_hbox.setContentsMargins(0, 15, 0, 0)
+		
+		self.skip_btn = QPushButton('Skip')
+		self.skip_btn.setStyleSheet(self.button_style_sheet_2)
+		self.skip_btn.clicked.connect(self.set_default_values)
+		btn_hbox.addWidget(self.skip_btn)
+		
+		self.submit_btn = QPushButton('Submit')
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
+		self.submit_btn.clicked.connect(self.set_user_values)
+		btn_hbox.addWidget(self.submit_btn)
+		
+		self.outer_layout.addLayout(btn_hbox)  # outside scroll
+		self.setMinimumWidth(int(0.6 * self.parent_window.parent_window.screen_width))
+		
 		center_window(self)
 
 	def populate(self):
-
 		self.cell_type_cbs = [QLineEdit() for i in range(self.n_wells)]
 		self.antibodies_cbs = [QLineEdit() for i in range(self.n_wells)]
 		self.concentrations_cbs = [QLineEdit() for i in range(self.n_wells)]
 		self.pharmaceutical_agents_cbs = [QLineEdit() for i in range(self.n_wells)]
-		self.concentration_units_le = QLineEdit('pM')
-		self.concentration_units_le.setPlaceholderText('concentration units')
 
 		for i in range(self.n_wells):
 			hbox = QHBoxLayout()
-			hbox.setContentsMargins(15,5,15,5)
+			hbox.setContentsMargins(15, 5, 15, 5)
 			hbox.addWidget(QLabel(f'well {i+1}'), 5, alignment=Qt.AlignLeft)
 			hbox.addWidget(QLabel('cell type: '), 5)
 			hbox.addWidget(self.cell_type_cbs[i], 10)
 			self.cell_type_cbs[i].setPlaceholderText('e.g. T-cell, NK')
-
+			
 			hbox.addWidget(QLabel('antibody: '), 5)
 			hbox.addWidget(self.antibodies_cbs[i], 10)
 			self.antibodies_cbs[i].setPlaceholderText('e.g. anti-CD4')
@@ -506,27 +641,9 @@ class SetupConditionLabels(QWidget, Styles):
 			hbox.addWidget(QLabel('pharmaceutical agents: '), 5)
 			hbox.addWidget(self.pharmaceutical_agents_cbs[i], 10)
 			self.pharmaceutical_agents_cbs[i].setPlaceholderText('e.g. dextran')
-
+			
 			self.layout.addLayout(hbox)
-
-		concentration_units_layout = QHBoxLayout()
-		concentration_units_layout.addWidget(QLabel('concentration\nunits: '),5,alignment=Qt.AlignLeft)
-		concentration_units_layout.addWidget(self.concentration_units_le,10)
-		concentration_units_layout.addWidget(QLabel(''), 85)
-		self.layout.addLayout(concentration_units_layout)
-
-		btn_hbox = QHBoxLayout()
-		btn_hbox.setContentsMargins(0,20,0,0)
-		self.skip_btn = QPushButton('Skip')
-		self.skip_btn.setStyleSheet(self.button_style_sheet_2)
-		self.skip_btn.clicked.connect(self.set_default_values)
-		btn_hbox.addWidget(self.skip_btn)
-
-		self.submit_btn = QPushButton('Submit')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.set_user_values)
-		btn_hbox.addWidget(self.submit_btn)
-		self.layout.addLayout(btn_hbox)
+		
 
 	def set_default_values(self):