AMS-BP 0.4.22__py3-none-any.whl → 0.4.31__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.22"
+__version__ = "0.4.31"

AMS_BP/gui/configuration_window.py

@@ -2,14 +2,16 @@ from pathlib import Path
 
 import tomli
 import tomlkit
+from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
-    QComboBox,
     QDialog,
     QFileDialog,
     QHBoxLayout,
     QLabel,
+    QListWidget,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QStackedWidget,
     QTextEdit,
     QVBoxLayout,
@@ -36,54 +38,63 @@ class ConfigEditor(QWidget):
         super().__init__()
         self.setWindowTitle("Simulation Configuration Editor")
 
-        # Create the main layout for the window
-        layout = QVBoxLayout()
-
-        # Create a horizontal layout for the dropdown and the tab index label
-        dropdown_layout = QHBoxLayout()
-
-        # Add a QLabel for the instruction/title about the dropdown
-        dropdown_title = QLabel(
-            "Use the dropdown below to set the parameters for each tab:"
-        )
-        dropdown_layout.addWidget(dropdown_title)
-
-        # Create a QComboBox (dropdown menu) for selecting tabs
-        self.dropdown = QComboBox()
-        self.dropdown.addItems(
-            [
-                "General",
-                "Global Parameters",
-                "Cell Parameters",
-                "Molecule Parameters",
-                "Condensate Parameters",
-                "Define fluorophores",
-                "Camera Parameters",
-                "PSF Parameters",
-                "Laser Parameters",
-                "Channels Parameters",
-                "Saving Instructions",
-                "Experiment Builder",
-            ]
+        # === Main horizontal layout: [Side Navigation | Content Area] ===
+        main_layout = QHBoxLayout(self)
+
+        # === Sidebar: Section Navigation ===
+        self.nav_list = QListWidget()
+        self.sections = [
+            "General",
+            "Global Parameters",
+            "Cell Parameters",
+            "Molecule Parameters",
+            "Condensate Parameters",
+            "Define fluorophores",
+            "Camera Parameters",
+            "PSF Parameters",
+            "Laser Parameters",
+            "Channels Parameters",
+            "Saving Instructions",
+            "Experiment Builder",
+        ]
+        self.nav_list.addItems(self.sections)
+        self.nav_list.setFixedWidth(220)
+        self.nav_list.setSpacing(4)
+        self.nav_list.setCurrentRow(0)
+        self.nav_list.currentRowChanged.connect(self.on_tab_selected)
+        main_layout.addWidget(self.nav_list)
+
+        # === Right panel layout ===
+        right_panel = QVBoxLayout()
+
+        # Step/breadcrumb label
+        self.step_label = QLabel()
+        self.step_label.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        right_panel.addWidget(self.step_label)
+
+        # === Stack of config widgets ===
+        self.stacked_widget = QStackedWidget()
+        self.stacked_widget.setSizePolicy(
+            QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding
         )
-        self.dropdown.currentIndexChanged.connect(
-            self.on_dropdown_change
-        )  # Connect to the change event
+        right_panel.addWidget(self.stacked_widget)
 
-        # Create a QLabel for displaying the current tab index
-        self.tab_index_label = QLabel("1/10")
+        # === Buttons at the bottom ===
+        self.save_button = QPushButton("Ready to save configuration?")
+        self.save_button.clicked.connect(self.save_config)
+        right_panel.addWidget(self.save_button)
 
-        # Add the dropdown and label to the layout
-        dropdown_layout.addWidget(self.dropdown)
-        dropdown_layout.addWidget(self.tab_index_label)
+        self.preview_button = QPushButton("Preview Configuration TOML")
+        self.preview_button.clicked.connect(self.preview_config)
+        right_panel.addWidget(self.preview_button)
 
-        # Add the dropdown layout to the main layout
-        layout.addLayout(dropdown_layout)
+        self.help_button = QPushButton("Get Help on this section")
+        self.help_button.clicked.connect(self.show_help)
+        right_panel.addWidget(self.help_button)
 
-        # Create a QStackedWidget to hold the content for each "tab"
-        self.stacked_widget = QStackedWidget()
+        main_layout.addLayout(right_panel)
 
-        # Initialize the widgets for each "tab"
+        # === Create tab content widgets ===
         self.general_tab = GeneralConfigWidget()
         self.global_tab = GlobalConfigWidget()
         self.cell_tab = CellConfigWidget()
@@ -97,36 +108,35 @@ class ConfigEditor(QWidget):
         self.detector_tab = CameraConfigWidget()
         self.experiment_tab = ExperimentConfigWidget()
 
-        # connections
-        # PSF -> confocal -> lasers
+        # === Widget interconnections ===
         self.psf_tab.confocal_mode_changed.connect(self.laser_tab.set_confocal_mode)
-        # === Molecule -> Fluorophore & Condensate ===
+
         self.molecule_tab.molecule_count_changed.connect(
             self.fluorophore_tab.set_mfluorophore_count
         )
         self.molecule_tab.molecule_count_changed.connect(
             self.condensate_tab.set_molecule_count
         )
-        # === Fluorophore -> Molecule & Condensate ===
+
         self.fluorophore_tab.mfluorophore_count_changed.connect(
             self.molecule_tab.set_molecule_count
         )
         self.fluorophore_tab.mfluorophore_count_changed.connect(
             self.condensate_tab.set_molecule_count
         )
-        # === Condensate -> Molecule & Fluorophore ===
+
         self.condensate_tab.molecule_count_changed.connect(
             self.molecule_tab.set_molecule_count
         )
         self.condensate_tab.molecule_count_changed.connect(
             self.fluorophore_tab.set_mfluorophore_count
         )
-        # === Laser -> Experiment
+
         self.laser_tab.laser_names_updated.connect(
             self.experiment_tab.set_active_lasers
         )
 
-        # Add each tab's widget to the stacked widget
+        # === Add tab widgets to the stack ===
         self.stacked_widget.addWidget(self.general_tab)
         self.stacked_widget.addWidget(self.global_tab)
         self.stacked_widget.addWidget(self.cell_tab)
@@ -140,27 +150,13 @@ class ConfigEditor(QWidget):
         self.stacked_widget.addWidget(self.output_tab)
         self.stacked_widget.addWidget(self.experiment_tab)
 
-        # Set the stacked widget as the central widget
-        layout.addWidget(self.stacked_widget)
-
-        # Create and add the save and help buttons at the bottom
-        self.save_button = QPushButton("Ready to save configuration?")
-        self.save_button.clicked.connect(self.save_config)
-        layout.addWidget(self.save_button)
-
-        self.preview_button = QPushButton("Preview Configuration TOML")
-        self.preview_button.clicked.connect(self.preview_config)
-        layout.addWidget(self.preview_button)
-
-        self.help_button = QPushButton("Get Help on this section")
-        self.help_button.clicked.connect(self.show_help)
-        layout.addWidget(self.help_button)
-
-        # Set the layout for the main window
-        self.setLayout(layout)
+        # Final layout and window size
+        self.setLayout(main_layout)
+        self.setMinimumSize(1100, 750)
+        self.resize(1250, 850)
 
-        # Set initial display
-        self.on_dropdown_change(0)  # Show the first tab (index 0)
+        # Initial tab display
+        self.on_tab_selected(0)
 
     def set_data(self, config: dict):
         if "Cell_Parameters" in config:
@@ -236,14 +232,12 @@ class ConfigEditor(QWidget):
             doc[key] = val
         return doc
 
-    def on_dropdown_change(self, index):
-        """Change the displayed widget based on the dropdown selection."""
+    def on_tab_selected(self, index: int):
+        """Change the displayed widget and update breadcrumb/step label."""
         self.stacked_widget.setCurrentIndex(index)
-        # Update the tab index label (1-based index)
-        total_tabs = (
-            self.dropdown.count()
-        )  # Corrected way to get the total number of items
-        self.tab_index_label.setText(f"{index + 1}/{total_tabs}")
+        total = self.nav_list.count()
+        current = self.nav_list.item(index).text()
+        self.step_label.setText(f"Step {index + 1}/{total} — {current}")
 
     def validate_all_tabs(self) -> bool:
         return all(

AMS_BP/gui/main.py

@@ -4,10 +4,11 @@ from zipfile import ZipFile
 
 import napari
 import tifffile
-from PyQt6.QtCore import Qt, QThread
+from PyQt6.QtCore import QSettings, Qt, QThread
 from PyQt6.QtGui import QPainter, QPixmap
 from PyQt6.QtSvg import QSvgRenderer
 from PyQt6.QtWidgets import (
+    QApplication,
     QFileDialog,
     QLabel,
     QMainWindow,
@@ -22,6 +23,7 @@ from ..logging.setup_run_directory import setup_run_directory
 from .logging_window import LogWindow
 from .sim_worker import SimulationWorker
 from .template_window_selection import TemplateSelectionWindow
+from .widgets.utility_widgets.toggleswitch_widget import ToggleSwitch
 
 LOGO_PATH = str(Path(__file__).parent / "assets" / "drawing.svg")
 
@@ -77,6 +79,20 @@ class MainWindow(QMainWindow):
         self.package_logs_button.clicked.connect(self.package_logs)
         layout.addWidget(self.package_logs_button)
 
+        # Load theme preference
+        self.settings = QSettings("AMS", "AMSConfig")
+        theme_pref = self.settings.value("theme", "light")
+
+        # Add toggle switch with label
+        self.theme_toggle = ToggleSwitch(checked=(theme_pref == "dark"))
+        self.theme_toggle.toggled.connect(self.toggle_theme)
+        self.theme_label = QLabel("Dark Mode" if theme_pref == "dark" else "Light Mode")
+        layout.addWidget(self.theme_label)
+        layout.addWidget(self.theme_toggle, alignment=Qt.AlignmentFlag.AlignCenter)
+
+        # Apply initial theme
+        self.apply_theme(theme_pref)
+
     def package_logs(self):
         log_dir = Path.home() / "AMS_runs"
 
@@ -245,6 +261,21 @@ class MainWindow(QMainWindow):
         else:
             print("Failed to load SVG file.")
 
+    def toggle_theme(self, is_dark: bool):
+        theme = "dark" if is_dark else "light"
+        self.settings.setValue("theme", theme)
+        self.apply_theme(theme)
+        self.theme_label.setText("Dark Mode" if is_dark else "Light Mode")
+
+    def apply_theme(self, theme: str):
+        theme_file = Path(__file__).parent / "themes" / f"{theme}_theme.qss"
+        try:
+            with open(theme_file, "r") as f:
+                stylesheet = f.read()
+                QApplication.instance().setStyleSheet(stylesheet)
+        except Exception as e:
+            QMessageBox.warning(self, "Theme Error", f"Failed to load theme:\n{e}")
+
     def open_config_editor(self):
         """Launch template selection first, then open ConfigEditor."""
         self.template_window = TemplateSelectionWindow()

AMS_BP/gui/themes/dark_theme.qss

@@ -0,0 +1,86 @@
+/* Dark Theme */
+* {
+    font-family: "Segoe UI", "Arial", sans-serif;
+    font-size: 14px;
+    color: #e0e0e0;
+}
+
+QWidget {
+    background-color: #2b2b2b;
+}
+
+QLabel {
+    color: #dddddd;
+}
+
+QPushButton {
+    background-color: #3daee9;
+    color: #ffffff;
+    border-radius: 6px;
+    padding: 6px 12px;
+}
+QPushButton:hover {
+    background-color: #5dbff0;
+}
+QPushButton:pressed {
+    background-color: #2a97cc;
+}
+
+QLineEdit, QComboBox, QSpinBox, QDoubleSpinBox, QTextEdit {
+    background-color: #3c3f41;
+    border: 1px solid #555;
+    border-radius: 4px;
+    padding: 4px;
+    color: #eeeeee;
+}
+
+QGroupBox {
+    border: 1px solid #444;
+    border-radius: 6px;
+    margin-top: 10px;
+}
+QGroupBox:title {
+    subcontrol-origin: margin;
+    subcontrol-position: top left;
+    padding: 0 6px;
+    font-weight: bold;
+    color: #aaaaaa;
+}
+
+QTabWidget::pane {
+    border: 1px solid #444;
+    background: #3c3f41;
+    border-radius: 6px;
+}
+
+QTabBar::tab {
+    background: #444;
+    border: 1px solid #555;
+    padding: 6px 12px;
+    border-top-left-radius: 6px;
+    border-top-right-radius: 6px;
+}
+QTabBar::tab:selected {
+    background: #2b2b2b;
+    border-bottom-color: #2b2b2b;
+}
+
+QScrollArea {
+    border: none;
+}
+
+QListWidget {
+    background-color: #2f2f2f;
+    border-right: 1px solid #444;
+}
+
+QListWidget::item {
+    padding: 6px;
+    border-radius: 4px;
+    color: #dddddd;
+}
+
+QListWidget::item:selected {
+    background-color: #3daee9;
+    color: #ffffff;
+}

AMS_BP/gui/themes/light_theme.qss

@@ -0,0 +1,85 @@
+/* Light Theme */
+* {
+    font-family: "Segoe UI", "Arial", sans-serif;
+    font-size: 14px;
+    color: #2b2b2b;
+}
+
+QWidget {
+    background-color: #f5f7fa;
+}
+
+QLabel {
+    color: #333;
+}
+
+QPushButton {
+    background-color: #007acc;
+    color: white;
+    border-radius: 6px;
+    padding: 6px 12px;
+}
+QPushButton:hover {
+    background-color: #005f9e;
+}
+QPushButton:pressed {
+    background-color: #004d80;
+}
+
+QLineEdit, QComboBox, QSpinBox, QDoubleSpinBox, QTextEdit {
+    background-color: white;
+    border: 1px solid #ccc;
+    border-radius: 4px;
+    padding: 4px;
+}
+
+QGroupBox {
+    border: 1px solid #d6d9dc;
+    border-radius: 6px;
+    margin-top: 10px;
+}
+QGroupBox:title {
+    subcontrol-origin: margin;
+    subcontrol-position: top left;
+    padding: 0 6px;
+    font-weight: bold;
+    color: #555;
+}
+
+QTabWidget::pane {
+    border: 1px solid #d1dbe3;
+    background: #ffffff;
+    border-radius: 6px;
+}
+
+QTabBar::tab {
+    background: #e6ebf1;
+    border: 1px solid #cfd7df;
+    padding: 6px 12px;
+    border-top-left-radius: 6px;
+    border-top-right-radius: 6px;
+}
+QTabBar::tab:selected {
+    background: #ffffff;
+    border-bottom-color: #ffffff;
+}
+
+QScrollArea {
+    border: none;
+}
+
+QListWidget {
+    background-color: #f0f0f0;
+    border-right: 1px solid #ccc;
+}
+
+QListWidget::item {
+    padding: 6px;
+    border-radius: 4px;
+}
+
+QListWidget::item:selected {
+    background-color: #007acc;
+    color: white;
+}
+

AMS_BP/gui/widgets/camera_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QVBoxLayout,
     QWidget,
@@ -19,12 +20,14 @@ from .utility_widgets.spectrum_widget import SpectrumEditorDialog
 class CameraConfigWidget(QWidget):
     def __init__(self):
         super().__init__()
+
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         # Camera type (Only "CMOS" is available)
         self.camera_type = QComboBox()
@@ -89,6 +92,10 @@ class CameraConfigWidget(QWidget):
         layout.addLayout(form)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def _hbox(self, widgets):
         box = QHBoxLayout()
         for w in widgets:

AMS_BP/gui/widgets/cell_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QStackedWidget,
     QVBoxLayout,
     QWidget,
@@ -18,11 +19,12 @@ class CellConfigWidget(QWidget):
     def __init__(self):
         super().__init__()
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.cell_type = QComboBox()
         self.cell_type.addItems(
@@ -46,6 +48,10 @@ class CellConfigWidget(QWidget):
         layout.addWidget(self.param_stack)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def validate(self) -> bool:
         from ...cells import create_cell
         from ...configio.configmodels import CellParameters

AMS_BP/gui/widgets/channel_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -21,11 +22,12 @@ class ChannelConfigWidget(QWidget):
         self.channel_widgets = []
 
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.num_channels = QSpinBox()
         self.num_channels.setRange(1, 10)
@@ -40,6 +42,10 @@ class ChannelConfigWidget(QWidget):
         layout.addWidget(self.channel_tabs)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def validate(self) -> bool:
         try:
             from ...configio.convertconfig import create_channels

AMS_BP/gui/widgets/condensate_config_widget.py

@@ -11,6 +11,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -31,6 +32,10 @@ class CondensateConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
         # Instructions label
         instructions = QLabel(
@@ -113,6 +118,18 @@ class CondensateConfigWidget(QWidget):
         condensate_controls.addWidget(condensate_count)
         layout.addLayout(condensate_controls)
 
+        # === Density Difference field RIGHT AFTER the condensate count ===
+        density_layout = QHBoxLayout()
+        density_layout.addWidget(QLabel("Density Difference:"))
+
+        density_spin = QDoubleSpinBox()
+        density_spin.setRange(0, 100)
+        density_spin.setValue(1.0)
+        density_spin.setDecimals(3)
+        density_layout.addWidget(density_spin)
+        layout.addLayout(density_layout)
+
+        # === Condensate containers BELOW this point ===
         condensate_container = QVBoxLayout()
         layout.addLayout(condensate_container)
 
@@ -126,25 +143,16 @@ class CondensateConfigWidget(QWidget):
             )
         )
 
-        # Density Difference per molecule type
-        density_layout = QHBoxLayout()
-        density_layout.addWidget(QLabel("Density Difference:"))
-
-        density_spin = QDoubleSpinBox()
-        density_spin.setRange(0, 100)
-        density_spin.setValue(1.0)
-        density_spin.setDecimals(3)
-        density_layout.addWidget(density_spin)
-        layout.addLayout(density_layout)
         self.condensate_widgets.append(
             {
                 "condensates": condensate_widgets,
                 "density_widget": density_spin,
+                "condensate_count_spinner": condensate_count,
             }
         )
+
         molecule_widget.setLayout(layout)
         scroll_area.setWidget(molecule_widget)
-
         self.tab_widget.addTab(scroll_area, f"Molecule Type {index + 1}")
 
     def add_condensate_group(self, index, condensate_widgets, condensate_container):
@@ -242,6 +250,7 @@ class CondensateConfigWidget(QWidget):
                 molecule_group["condensates"],
                 molecule_group_layout,
             )
+            molecule_group["condensate_count_spinner"].setValue(num_condensates)
 
             for j in range(num_condensates):
                 condensate = molecule_group["condensates"][j]

AMS_BP/gui/widgets/experiment_config_widget.py

@@ -10,6 +10,8 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -25,6 +27,10 @@ class ExperimentConfigWidget(QWidget):
         self.laser_position_widgets = {}
 
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
         form = QFormLayout()
 
         # Experiment Info
@@ -38,13 +44,20 @@ class ExperimentConfigWidget(QWidget):
         self.type_field.addItems(["time-series", "z-stack"])
         form.addRow("Experiment Type:", self.type_field)
 
-        # Z Position (just one for time-series)
+        # Z Position inputs
         self.z_position_inputs: List[QDoubleSpinBox] = []
 
+        # Scrollable container for z-position inputs
+        self.z_scroll_area = QScrollArea()
+        self.z_scroll_area.setWidgetResizable(True)
+        self.z_scroll_area.setFixedHeight(150)  # Adjust height as needed
+
         self.z_position_container = QWidget()
-        self.z_position_layout = QVBoxLayout()
+        self.z_position_layout = QVBoxLayout(self.z_position_container)
         self.z_position_container.setLayout(self.z_position_layout)
-        form.addRow("Z Position(s):", self.z_position_container)
+
+        self.z_scroll_area.setWidget(self.z_position_container)
+        form.addRow("Z Position(s):", self.z_scroll_area)
 
         self.add_z_button = QPushButton("Add Z-Position")
         self.remove_z_button = QPushButton("Remove Z-Position")
@@ -83,13 +96,13 @@ class ExperimentConfigWidget(QWidget):
         layout.addWidget(QLabel("Active Laser Parameters:"))
         layout.addWidget(self.laser_tabs)
 
+        self.setLayout(layout)
+
         # Validate Button
-        self.validate_button = QPushButton("Validate")
+        self.validate_button = QPushButton("Validate Parameters")
         self.validate_button.clicked.connect(self.validate)
         layout.addWidget(self.validate_button)
 
-        self.setLayout(layout)
-
     def update_z_position_mode(self, mode: str):
         # Clear existing
         for i in reversed(range(self.z_position_layout.count())):

AMS_BP/gui/widgets/flurophore_config_widget.py

@@ -11,6 +11,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -33,6 +34,10 @@ class FluorophoreConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
         instructions = QLabel(
             "Configure fluorophores and their respective states and transitions."

AMS_BP/gui/widgets/global_config_widget.py

@@ -5,6 +5,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QVBoxLayout,
     QWidget,
@@ -18,11 +19,12 @@ class GlobalConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
+
         form = QFormLayout()
-        # Validation button
-        self.validate_button = QPushButton("Validate Parameters")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
 
         # Sample plane dimensions
         self.sample_plane_width = QSpinBox()
@@ -71,6 +73,11 @@ class GlobalConfigWidget(QWidget):
 
         self.setLayout(layout)
 
+        # Validation button
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def set_defaults(self):
         """Set default values for the form fields"""
         self.sample_plane_width.setValue(50)  # 1000 μm

AMS_BP/gui/widgets/laser_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -22,11 +23,12 @@ class LaserConfigWidget(QWidget):
         super().__init__()
         self.laser_name_widgets = []
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.num_lasers = QSpinBox()
         self.num_lasers.setRange(1, 10)
@@ -44,6 +46,10 @@ class LaserConfigWidget(QWidget):
         layout.addWidget(self.laser_tabs)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def set_confocal_mode(self, enabled: bool):
         for i in range(self.laser_tabs.count()):
             tab = self.laser_tabs.widget(i)

AMS_BP/gui/widgets/molecule_config_widget.py

@@ -13,6 +13,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -28,6 +29,11 @@ class MoleculeConfigWidget(QWidget):
         super().__init__()
 
         self.main_layout = QVBoxLayout()
+        self.main_layout.setContentsMargins(10, 10, 10, 10)
+        self.main_layout.setSpacing(10)
+        self.setLayout(self.main_layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
+
         self.setLayout(self.main_layout)
 
         # Number of molecule types spinner
@@ -41,11 +47,6 @@ class MoleculeConfigWidget(QWidget):
         self.num_types_layout.addWidget(self.num_types_spinner)
         self.num_types_layout.addStretch()
 
-        # Validate button
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        self.num_types_layout.addWidget(self.validate_button)
-
         self.main_layout.addLayout(self.num_types_layout)
 
         # Create tab widget to hold molecule type configs
@@ -56,6 +57,11 @@ class MoleculeConfigWidget(QWidget):
         self.molecule_type_widgets = []
         self.update_molecule_types(1)
 
+        # Add the validate button at the bottom
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        self.main_layout.addWidget(self.validate_button)
+
     def _on_molecule_count_changed(self, count):
         self.update_molecule_types(count)
         self.molecule_count_changed.emit(count)

AMS_BP/gui/widgets/utility_widgets/toggleswitch_widget.py

@@ -0,0 +1,60 @@
+from PyQt6.QtCore import QPropertyAnimation, QSize, Qt, pyqtSignal
+from PyQt6.QtGui import QBrush, QColor, QPainter
+from PyQt6.QtWidgets import QWidget
+
+
+class ToggleSwitch(QWidget):
+    toggled = pyqtSignal(bool)
+
+    def __init__(self, parent=None, checked=False):
+        super().__init__(parent)
+        self.setFixedSize(50, 28)
+        self._checked = checked
+        self._circle_position = 2 if not checked else 24
+
+        self.animation = QPropertyAnimation(self, b"")
+        self.animation.setDuration(200)
+
+    def sizeHint(self):
+        return QSize(50, 28)
+
+    def mousePressEvent(self, event):
+        self._checked = not self._checked
+        self.animate_toggle()
+        self.toggled.emit(self._checked)
+        self.update()
+
+    def animate_toggle(self):
+        start = self._circle_position
+        end = 24 if self._checked else 2
+        self.animation.stop()
+        self.animation.setStartValue(start)
+        self.animation.setEndValue(end)
+        self.animation.valueChanged.connect(self.set_circle_position)
+        self.animation.start()
+
+    def set_circle_position(self, val):
+        self._circle_position = val
+        self.update()
+
+    def paintEvent(self, event):
+        painter = QPainter(self)
+        painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+
+        # NEW: Background indicates *next* theme
+        bg_color = QColor("#dddddd") if self._checked else QColor("#333333")
+        painter.setBrush(QBrush(bg_color))
+        painter.setPen(Qt.PenStyle.NoPen)
+        painter.drawRoundedRect(0, 0, self.width(), self.height(), 14, 14)
+
+        # Handle (always green)
+        painter.setBrush(QBrush(QColor("#008000")))
+        painter.drawEllipse(int(self._circle_position), 2, 24, 24)
+
+    def isChecked(self):
+        return self._checked
+
+    def setChecked(self, checked: bool):
+        self._checked = checked
+        self._circle_position = 24 if checked else 2
+        self.update()

{ams_bp-0.4.22.dist-info → ams_bp-0.4.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.4.22
+Version: 0.4.31
 Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
 Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
 Project-URL: Source code, https://github.com/joemans3/AMS_BP
@@ -46,7 +46,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 > !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
 
-[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
 
 [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 

{ams_bp-0.4.22.dist-info → ams_bp-0.4.31.dist-info}/RECORD

@@ -1,4 +1,4 @@
-AMS_BP/__init__.py,sha256=rV2K-9LYovKnN36znkN8Va6qfaDhXAeytS0ws77n8mU,327
+AMS_BP/__init__.py,sha256=HnVRnFe1LL5sSTGyHrF2PVjE2MvXqg-Uio9i7NfUZfw,327
 AMS_BP/main_cli.py,sha256=DpRzWDsmI0nJvrzJj58F9k1k5ShSj8pCT7N0oH-_8BU,5786
 AMS_BP/run_sim_util.py,sha256=UQr0l9rbtTmzuuWXjkIaTQV-ETO5AqyXRwflF6U2WYs,2415
 AMS_BP/sim_config.toml,sha256=G0wW9qsxciZA1Y0Zm6YgZ00ZDBEBBLw_XXq4gsVRjSY,11778
@@ -15,10 +15,10 @@ AMS_BP/groundtruth_generators/__init__.py,sha256=UPVmhiB81OfyqAes5LoN-n6XgQuBCYC
 AMS_BP/groundtruth_generators/nuclearporecomplexes.py,sha256=1aBcWltsKo0OGd7A9GfuEZ3azQBx5SzpjrSLLMXuYn8,2518
 AMS_BP/gui/README.md,sha256=z2XreAPQeeFmKSXbhsa2kznHbk-YbLD55-VPWikNQp4,2778
 AMS_BP/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/gui/configuration_window.py,sha256=d-eEz099-LWSn0_O8ZKn1425jkMAxoAFW4-BZ3qW90c,12606
+AMS_BP/gui/configuration_window.py,sha256=BNlJvwKKAVPMh7cXxOSl9DGvWVwSc6sPwLlZAGGdGes,12101
 AMS_BP/gui/help_window.py,sha256=Jn844Vez7ULC1VGKb4iGgRvuw3wPTd0pcyRv7VWbeV4,790
 AMS_BP/gui/logging_window.py,sha256=a7HbmfYP3YavLuyT317YRE1xWXJtB4i8EoK9QAstOv8,2938
-AMS_BP/gui/main.py,sha256=VE8jPgWyuGSXTnux-en0BEFWc9D9shrwFDvtzSLcfpI,9311
+AMS_BP/gui/main.py,sha256=O2FPkyIjCcEbn3dPBefowXQx4kfuB1oUkTyIDI5Me8M,10653
 AMS_BP/gui/sim_worker.py,sha256=SYKbHGQNd9laL2YMjPfm755eRTyub434fSTQ5mGS9iM,1989
 AMS_BP/gui/template_window_selection.py,sha256=GgLfApuTa4qNiek0Ksiqy15aqhdOIZyaReFYAS9NDoc,3034
 AMS_BP/gui/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,22 +36,25 @@ AMS_BP/gui/help_docs/laser_help.md,sha256=wzloXV_1WCT6zRTrf1jKC-cMlepntacZV7jbLL
 AMS_BP/gui/help_docs/molecule_help.md,sha256=5wnyNlCTWjCsgwzRFG7XhnlGXao6qXj-2ZL0yfnHQng,2793
 AMS_BP/gui/help_docs/output_help.md,sha256=Rg0dV0N4ClrJvPTt5HaJHuQgHE5nmgKwiQCAHhV0A24,225
 AMS_BP/gui/help_docs/psf_help.md,sha256=onH-suSxocfj9mD6WCE6lG7yxov1yCoGeau82oG-zmo,1854
+AMS_BP/gui/themes/dark_theme.qss,sha256=6MUyaaZnmZCnXTNNJuqi7NN8Om8P8P9pSfAffv4ampA,1462
+AMS_BP/gui/themes/light_theme.qss,sha256=wVEIcnFzGVZN7ohLHrus6zX5ybGnyfTwihAPSvhrDL8,1424
 AMS_BP/gui/widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/gui/widgets/camera_config_widget.py,sha256=hp1fyRH3kVmQK5HVyoli1RAat8dERq8bjnXjRK8qGVA,7559
-AMS_BP/gui/widgets/cell_config_widget.py,sha256=XgSqqnF9j2Gwfk2lOBPrWIEbtRwR-nDdhO7GOVFTvV8,7835
-AMS_BP/gui/widgets/channel_config_widget.py,sha256=WvsoV7iNaY4T9dl3QL-kqCXNKJOWbkWK5w7BqUpVDpM,10780
-AMS_BP/gui/widgets/condensate_config_widget.py,sha256=YI_LZJ_EP73SsFvTdoWjqnE2e0_XLv02Gth1MErc8oM,12128
-AMS_BP/gui/widgets/experiment_config_widget.py,sha256=1FdSIp6lO-Gscd98prGv7MCL-dziklIaN62TwQYNJ6M,9286
-AMS_BP/gui/widgets/flurophore_config_widget.py,sha256=Bri9TttiYM7eBkrcxLVjjvhein5FEsxuz2FYJvcvW1I,19682
+AMS_BP/gui/widgets/camera_config_widget.py,sha256=pYzSSNUBzo2TFzw3qwSW-PuduD6M3q4XqDCGZJpdUWs,7787
+AMS_BP/gui/widgets/cell_config_widget.py,sha256=rNQljIob3oUGa02bKiG9kxHWlE2-o30gEH4oUv43Msg,8062
+AMS_BP/gui/widgets/channel_config_widget.py,sha256=zBfP9xySSqBQWSyXyaGqPViTHJhQKCen6gMcLl9Tgx0,11007
+AMS_BP/gui/widgets/condensate_config_widget.py,sha256=K2sYIHhXbqmpDf6edWaxnYVYEjDYffciucN7XivJc8M,12573
+AMS_BP/gui/widgets/experiment_config_widget.py,sha256=Oa_3XvzOk3TmFdQ0LmOLdq8P8kRb6HVwc-ypw7YFq78,9815
+AMS_BP/gui/widgets/flurophore_config_widget.py,sha256=jOWwo7hmX7b_fNcbaTbHLfaoKTivvdiq8-yHs2b8198,19897
 AMS_BP/gui/widgets/general_config_widget.py,sha256=YbnE11TnWZBgb-xqKWM00p8RdSp-9eTbwTZ9mikPvZc,1321
-AMS_BP/gui/widgets/global_config_widget.py,sha256=6X-NrBz5qc2mfDnH0kBGQKTgBaI3hqaaOAMpegFM7hs,4881
-AMS_BP/gui/widgets/laser_config_widget.py,sha256=gtaZdFsPh8Zai03IoyhSp95hXa6biAoFmhJMaSe38XM,8737
-AMS_BP/gui/widgets/molecule_config_widget.py,sha256=kvN_8JYe-rBJxfNgy0v7yRjT-RuT1KWMs_m0l6-sK1c,27789
+AMS_BP/gui/widgets/global_config_widget.py,sha256=QqkJiPFZfe73a1fbgf6oCmLacbp3Cda7UH4lr0A3rXo,5098
+AMS_BP/gui/widgets/laser_config_widget.py,sha256=oqINXtRUhVzwW4HE9jsHcFWVp3q5n4RBlXumdZZoHjM,8964
+AMS_BP/gui/widgets/molecule_config_widget.py,sha256=Bog31_wjTJ0uyw4qpL_3m8EK7jlc3GNMgn-7EOS-k0g,28063
 AMS_BP/gui/widgets/output_config_widget.py,sha256=pExiAHIHs0-J-dY2lZtfB0ei9oNjZIJKDQtWDSjFZOY,2105
 AMS_BP/gui/widgets/psf_config_widget.py,sha256=75ggeolYI_Sbn5LD_hUGY3S4Z9uRkJGtzZhb79NgsY4,4534
 AMS_BP/gui/widgets/utility_widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/gui/widgets/utility_widgets/scinotation_widget.py,sha256=sLrQqueRJ0wEy4aF1I8UJO0Bolnm7yTsAyfNqrHiAKI,553
 AMS_BP/gui/widgets/utility_widgets/spectrum_widget.py,sha256=QQjYV-aErjyI1HdOZMIPaddHpi0sag6r4V8nBSdgEn8,3659
+AMS_BP/gui/widgets/utility_widgets/toggleswitch_widget.py,sha256=vldANnsLcoqwmM8PNQc6PZAMtPN2h6A-JCCx9etBLKU,1945
 AMS_BP/logging/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/logging/logutil.py,sha256=HkkB0mF8SL68gmJcOngBppNi6InX18Goxro5LJR-inA,2420
 AMS_BP/logging/setup_run_directory.py,sha256=B9sG_N3lOya_gVaJTs7GDVXpTY1Ov3jMPGTj2ttydM0,897
@@ -96,8 +99,8 @@ AMS_BP/utils/decorators.py,sha256=4qFdvzPJne0dhkhD1znPxRln1Rfr5NX8rdcCDcbATRU,62
 AMS_BP/utils/errors.py,sha256=7BOd-L4_YeKmWn3Q4EOdTnNF3Bj_exDa3eg5X0yCZrc,759
 AMS_BP/utils/maskMaker.py,sha256=2ca3n2nc8rFtUh1LurKXOJJsUmhrOpWbRnVX7fjRVvs,335
 AMS_BP/utils/util_functions.py,sha256=9Qlr4kjY04fObktR8TrzB0IgoG1yXtcmxPRX9AN34mM,9671
-ams_bp-0.4.22.dist-info/METADATA,sha256=WQtOOw8Wz5IsbSojZNxRkzVZzCy_cQHFN4HHTxzaezw,9592
-ams_bp-0.4.22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.4.22.dist-info/entry_points.txt,sha256=06NS85P4dz6vosMOKXHfx8l7gK9WXBZxuwjl55XfT2c,65
-ams_bp-0.4.22.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.4.22.dist-info/RECORD,,
+ams_bp-0.4.31.dist-info/METADATA,sha256=ucG63KDguwui6gHxONAZxPfoQOP3PSfPjatmSqjPTkQ,9594
+ams_bp-0.4.31.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.4.31.dist-info/entry_points.txt,sha256=06NS85P4dz6vosMOKXHfx8l7gK9WXBZxuwjl55XfT2c,65
+ams_bp-0.4.31.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.4.31.dist-info/RECORD,,