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

celldetective/gui/classifier_widget.py

@@ -10,6 +10,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 import json
 
+from celldetective.exceptions import EmptyQueryError, MissingColumnsError, QueryError
 from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic
 from celldetective.gui.base_components import CelldetectiveWidget
 from celldetective.utils import get_software_location
@@ -351,26 +352,30 @@ class ClassifierWidget(CelldetectiveWidget):
 			self.propscanvas.canvas.draw_idle()
 		
 		except Exception as e:
-			pass
+			print("Exception L355 ", e)
+	
+	def show_warning(self, message: str):
+		msgBox = QMessageBox()
+		msgBox.setIcon(QMessageBox.Warning)
+		link = "https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html"
+		msgBox.setText(f"{message}<br><br>See <a href='{link}'>documentation</a>.")
+		msgBox.setWindowTitle("Warning")
+		msgBox.setStandardButtons(QMessageBox.Ok)
+		msgBox.exec()
 
 	def apply_property_query(self):
 		
 		query = self.property_query_le.text()
-		
 		try:
 			self.df = classify_cells_from_query(self.df, self.name_le.text(), query)
+		except EmptyQueryError as e:
+			self.show_warning(str(e))
+		except MissingColumnsError as e:
+			self.show_warning(f"{e}. Please check your column names.")
+		except QueryError as e:
+			self.show_warning(f"{e}. Wrap features in backticks if needed.")
 		except Exception as e:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			link = "https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html"
-			msg = "The query could not be understood. Please write a valid query following <a href='%s'>the documentation</a>. Wrap features in backticks (e.g. `feature` > 1) to facilitate query interpretation. " % link
-			msgBox.setText(msg)
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				self.auto_close = False
-				return None
+			self.show_warning(f"Unexpected error: {e}")
 
 		self.class_name = "status_"+self.name_le.text()
 		if self.df is None:

celldetective/gui/configure_new_exp.py

@@ -1,4 +1,4 @@
-from PyQt5.QtWidgets import QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton
+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.utils import get_software_location
@@ -169,7 +169,7 @@ class ConfigNewExperiment(CelldetectiveMainWindow):
 		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.setMinimum(1)
 		#self.MovieLengthSlider.setMaximum(128)
 		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
 
@@ -566,30 +566,69 @@ class SetupConditionLabels(CelldetectiveWidget):
 		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')
@@ -602,27 +641,9 @@ class SetupConditionLabels(CelldetectiveWidget):
 			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):
 		

celldetective/gui/control_panel.py

@@ -4,7 +4,7 @@ from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
 from PyQt5.QtCore import Qt, QSize
 from celldetective.gui.gui_utils import center_window, QHSeperationLine, QCheckableComboBox, generic_message
-from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_identity_col
+from celldetective.utils import _extract_labels_from_config, config_section_to_dict, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
 from celldetective.io import extract_position_name, 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, get_experiment_populations, extract_well_name_and_number
 from natsort import natsorted
@@ -318,10 +318,10 @@ class ControlPanel(CelldetectiveMainWindow):
 		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"])
-		self.movie_prefix = ConfigSectionMap(self.exp_config,"MovieSettings")["movie_prefix"]
+		self.len_movie = int(config_section_to_dict(self.exp_config, "MovieSettings")["len_movie"])
+		self.shape_x = int(config_section_to_dict(self.exp_config, "MovieSettings")["shape_x"])
+		self.shape_y = int(config_section_to_dict(self.exp_config, "MovieSettings")["shape_y"])
+		self.movie_prefix = config_section_to_dict(self.exp_config, "MovieSettings")["movie_prefix"]
 
 		# Read channels
 		self.exp_channels, channel_indices = extract_experiment_channels(self.exp_dir)
@@ -335,7 +335,7 @@ class ControlPanel(CelldetectiveMainWindow):
 		self.antibodies = get_experiment_antibodies(self.exp_dir)
 		self.pharmaceutical_agents = get_experiment_pharmaceutical_agents(self.exp_dir)
 
-		self.metadata = ConfigSectionMap(self.exp_config,"Metadata")
+		self.metadata = config_section_to_dict(self.exp_config, "Metadata")
 		print('Experiment configuration successfully read...')
 
 	def closeEvent(self, event):
@@ -505,7 +505,10 @@ class ControlPanel(CelldetectiveMainWindow):
 				for i,p in enumerate(self.ProcessPopulations):
 					p.check_seg_btn.setEnabled(True)
 					if os.path.exists(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv'])):
-						df = pd.read_csv(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv']), nrows=1)
+						try:
+							df = pd.read_csv(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv']), nrows=1)
+						except Exception as e:
+							continue
 						id_col = extract_identity_col(df)
 						p.check_measurements_btn.setEnabled(True)