AMS-BP 0.4.22__tar.gz → 0.4.31__tar.gz

{ams_bp-0.4.22 → ams_bp-0.4.31}/PKG-INFO

@@ -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 → ams_bp-0.4.31}/README.md

@@ -20,7 +20,7 @@ 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 → ams_bp-0.4.31}/docs/index.md

@@ -1,15 +1,34 @@
-# AMS-BP User Guide
+# AMS-BP
 <p>
-<img src="assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
+<img src="./assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
 </p>
+
 ## Advanced Fluorescence Microscopy Simulation Tool
 
 AMS-BP is a powerful simulation tool for advanced fluorescence microscopy experiments. This guide covers both command-line usage and library integration.
 
+## Overview of Simulation Workflow
+<img align = "left" src="./assets/figures/Fig1_Schema.svg" width="500"/>
+
+*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+
+## API Reference and Docs
+Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
+> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](../examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](../examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](../examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
+
+## Examples (Click on the image buttons to be taken to the Jupyter notebooks):
+
+> !!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="./assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](../examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](../examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
+
+[<img src="./assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](../examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](../examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 
+[<img align="middle" src="./assets/buttons/ButtonFigure_sptPALM_mmaple.svg" width="300"/>](../examples/QuantitativeExperiments/PALM/sptPALM/motionmodels_sptmmaple.ipynb)
 ## Table of Contents
-- [Installation](#installation) 
+- [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
+- [GUI](#gui)
 - [Configuration File](#configuration-file)
 - [Running Experiments](#running-experiments)
 - [Advanced Usage](#advanced-usage)
@@ -18,23 +37,29 @@ AMS-BP is a powerful simulation tool for advanced fluorescence microscopy experi
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](../src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
+
+### ***PyPi***
+
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
+```bash
+pip install AMS_BP
+```
+
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -42,6 +67,9 @@ run_AMS_BP config [OPTIONS]
 
 # Run a simulation using a configuration file
 run_AMS_BP runsim CONFIG_FILE
+
+#start the GUI
+run_AMS_BP gui
 ```
 
 ### Config Command Options
@@ -49,17 +77,30 @@ run_AMS_BP runsim CONFIG_FILE
 - `-o, --output_path PATH`: Specify the output directory for the configuration file
 - `-r, --recursive_o`: Create output directory if it doesn't exist
 
+## GUI
+In addition to the CLI and programmatic API, AMS-BP comes with a graphical interface to guide users through the configuration, simulation, and analysis pipeline.
 
-## Overview of Simulation Workflow
-![Overview Schematic](./assets/figures/Fig1_Schema.svg)
-*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+### Main GUI Features
+The GUI provides the following tools from a single interface:
+
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
+### Launch the GUI
+To start the GUI, run:
 
+```bash
+
+run_AMS_BP gui
+```
+For detailed walkthrough see the [GUI Documentation](../src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:
 
-#### For a detailed description of the configuration file, refer to the [Configuration File Reference](./API_Documentation/sim_config.md).
+#### For a detailed description of the configuration file, refer to the [Configuration File Reference](https://joemans3.github.io/AMS_BP/API_Documentation/sim_config/).
 ### Basic Units
 ```toml
 version = "0.1"
@@ -99,7 +140,8 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 ## Running Experiments
 
-AMS-BP supports two types of experiments:
+AMS-BP's CLI currently supports two types of experiments:
+> (however this can be extended when used as a library) 
 
 ### 1. Time Series
 ```toml
@@ -120,39 +162,25 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
-## Advanced Usage
-
-### Using AMS-BP as a Library
-
-For programmatic control, you can import and use AMS-BP as a Python library:
-
-```python
-from AMS_BP.configio.convertconfig import ConfigLoader
-
-# Configuration loader intialization
-config_loader = ConfigLoader(config_path="path/to/config.toml")
-
-# Setup microscope
-setup_config = config_loader.setup_microscope()
-microscope = setup_config["microscope"]
-config_exp = setup_config["experiment_config"]
-function_exp = setup_config["experiment_func"]
-
-# Run simulation
-frames, metadata = function_exp(microscope=microscope, config=config_exp)
-
-# Save results
-from AMS_BP.configio.saving import save_config_frames
-save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
 ```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 
-### Key Components When Using as Library
-
-1. **ConfigLoader**: Handles configuration file parsing and validation
-2. **Microscope**: Represents the virtual microscope setup
-3. **Experiment Functions**: Control experiment execution
-4. **Save Functions**: Handle data output
+## High Priority Features
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
+2. Stimulated Emission models
+3. STORM workflow examples
+4. CTRW motion models
+5. Simpler configurations
+> **_NOTE:_** Please note that this application DOES NOT currently model the process of stimulated emission, and as such is not suitable for simulating stimulated emission microscopy ([STED](https://en.wikipedia.org/wiki/STED_microscopy))-type experiments. Work in this area is ongoing.
 
 ### Custom Experiment Types
 
@@ -163,18 +191,6 @@ When using AMS-BP as a library, you can create custom experiment types by:
 3. Defining new molecule behaviors
 4. Creating specialized analysis routines
 
-## API Reference and Docs
-Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
-> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
-
-## High Priority Features
-1. Irregular cell shapes with motion models
-2. Stimulated Emission models
-3. STORM workflow examples
-4. CTRW motion models
-5. Simpler configurations
-
-
 ## Tips and Best Practices
 
 1. **Configuration Management**

{ams_bp-0.4.22 → ams_bp-0.4.31}/src/AMS_BP/__init__.py

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

{ams_bp-0.4.22 → ams_bp-0.4.31}/src/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-0.4.22 → ams_bp-0.4.31}/src/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-0.4.31/src/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;
+}