AMS-BP 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl

AMS_BP/gui/README.md

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+# AMS-BP GUI
+
+The AMS-BP GUI provides a user-friendly interface for constructing and validating configuration files for the AMS-BP fluorescence microscopy simulation framework. It integrates simulation execution, configuration design, log packaging, and data visualization in one cohesive window.
+
+## Overview
+
+This GUI supports:
+
+A template-based configuration builder for quick setup.
+A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
+Interactive help sections for each tab.
+Simulation execution using prebuilt configs.
+Napari integration for visualization of resulting microscopy data.
+Packaging of simulation logs for easy sharing.
+
+## Launching the GUI
+
+```bash
+run_AMS_BP gui
+```
+## GUI Structure
+
+### Main Window
+The main window (MainWindow) acts as the launchpad for:
+
+Configuration Builder — Launches a template selector and opens a full editor.
+Run Simulation from Config — Lets you pick a .toml file and start the simulation.
+Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
+Package Logs for Sharing — Archives a run_* folder into a .zip.
+#### Configuration Editor
+Once a template is selected, the ConfigEditor is launched. It contains:
+
+A dropdown navigation system replacing traditional tabs.
+A floating tab counter and preview/save buttons.
+A help button per section (reads *.md files from help_docs/).
+Live validation using internal config models (convertconfig.py).
+##### Tabs & Widgets
+Each configuration section is implemented as a modular PyQt widget, including:
+
+GlobalConfigWidget
+CellConfigWidget
+MoleculeConfigWidget
+FluorophoreConfigWidget
+CondensateConfigWidget
+LaserConfigWidget
+ExperimentConfigWidget
+...and more
+Each widget supports:
+
+get_data() → Extract validated dictionary data
+set_data(data: dict) → Load existing config into the UI
+validate() → Validate using backend logic
+get_help_path() → Load the corresponding markdown help page
+
+####  Running a Simulation
+
+Once you've completed the config file setup via the GUI:
+
+Click "Preview Configuration TOML" to confirm contents.
+Click "Ready to Save Configuration" and choose a .toml path.
+Return to the main window, click "Run Simulation from Config".
+Simulation will launch in a background thread and print logs to a live window.
+Once done, results will be saved in a run_*/ folder.
+
+#### Viewing Results
+
+Click "Visualize Microscopy Data (Napari)"
+Select any .tif, .tiff, .nd2, or .zarr file
+The data will be loaded into a new Napari viewer session
+
+#### Packaging Logs
+
+To share or archive a completed simulation:
+
+Click "Package Logs for Sharing".
+Select the run_* folder you want.
+Choose a destination for the .zip file.

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AMS_BP/gui/configuration_window.py

@@ -0,0 +1,333 @@
+from pathlib import Path
+
+import tomli
+import tomlkit
+from PyQt6.QtWidgets import (
+    QComboBox,
+    QDialog,
+    QFileDialog,
+    QHBoxLayout,
+    QLabel,
+    QMessageBox,
+    QPushButton,
+    QStackedWidget,
+    QTextEdit,
+    QVBoxLayout,
+    QWidget,
+)
+
+from .help_window import HelpWindow
+from .widgets.camera_config_widget import CameraConfigWidget
+from .widgets.cell_config_widget import CellConfigWidget
+from .widgets.channel_config_widget import ChannelConfigWidget
+from .widgets.condensate_config_widget import CondensateConfigWidget
+from .widgets.experiment_config_widget import ExperimentConfigWidget
+from .widgets.flurophore_config_widget import FluorophoreConfigWidget
+from .widgets.general_config_widget import GeneralConfigWidget
+from .widgets.global_config_widget import GlobalConfigWidget
+from .widgets.laser_config_widget import LaserConfigWidget
+from .widgets.molecule_config_widget import MoleculeConfigWidget
+from .widgets.output_config_widget import OutputConfigWidget
+from .widgets.psf_config_widget import PSFConfigWidget
+
+
+class ConfigEditor(QWidget):
+    def __init__(self):
+        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",
+            ]
+        )
+        self.dropdown.currentIndexChanged.connect(
+            self.on_dropdown_change
+        )  # Connect to the change event
+
+        # Create a QLabel for displaying the current tab index
+        self.tab_index_label = QLabel("1/10")
+
+        # Add the dropdown and label to the layout
+        dropdown_layout.addWidget(self.dropdown)
+        dropdown_layout.addWidget(self.tab_index_label)
+
+        # Add the dropdown layout to the main layout
+        layout.addLayout(dropdown_layout)
+
+        # Create a QStackedWidget to hold the content for each "tab"
+        self.stacked_widget = QStackedWidget()
+
+        # Initialize the widgets for each "tab"
+        self.general_tab = GeneralConfigWidget()
+        self.global_tab = GlobalConfigWidget()
+        self.cell_tab = CellConfigWidget()
+        self.molecule_tab = MoleculeConfigWidget()
+        self.condensate_tab = CondensateConfigWidget()
+        self.output_tab = OutputConfigWidget()
+        self.fluorophore_tab = FluorophoreConfigWidget()
+        self.psf_tab = PSFConfigWidget()
+        self.laser_tab = LaserConfigWidget()
+        self.channel_tab = ChannelConfigWidget()
+        self.detector_tab = CameraConfigWidget()
+        self.experiment_tab = ExperimentConfigWidget()
+
+        # connections
+        # PSF -> confocal -> lasers
+        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
+        self.stacked_widget.addWidget(self.general_tab)
+        self.stacked_widget.addWidget(self.global_tab)
+        self.stacked_widget.addWidget(self.cell_tab)
+        self.stacked_widget.addWidget(self.molecule_tab)
+        self.stacked_widget.addWidget(self.condensate_tab)
+        self.stacked_widget.addWidget(self.fluorophore_tab)
+        self.stacked_widget.addWidget(self.detector_tab)
+        self.stacked_widget.addWidget(self.psf_tab)
+        self.stacked_widget.addWidget(self.laser_tab)
+        self.stacked_widget.addWidget(self.channel_tab)
+        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)
+
+        # Set initial display
+        self.on_dropdown_change(0)  # Show the first tab (index 0)
+
+    def set_data(self, config: dict):
+        if "Cell_Parameters" in config:
+            self.cell_tab.set_data(config["Cell_Parameters"])
+
+        if "Global_Parameters" in config:
+            self.global_tab.set_data(config["Global_Parameters"])
+
+        if "Molecule_Parameters" in config:
+            self.molecule_tab.set_data(config["Molecule_Parameters"])
+
+        if "fluorophores" in config:
+            self.fluorophore_tab.set_data(config["fluorophores"])
+
+        if "Condensate_Parameters" in config:
+            self.condensate_tab.set_data(config["Condensate_Parameters"])
+
+        if "Output_Parameters" in config:
+            self.output_tab.set_data(config["Output_Parameters"])
+
+        if "lasers" in config:
+            self.laser_tab.set_data(config["lasers"])
+
+        if "experiment" in config:
+            self.experiment_tab.set_data(config["experiment"])
+
+        if "channels" in config:
+            self.channel_tab.set_data(config["channels"])
+
+        if "camera" in config:
+            self.detector_tab.set_data(config["camera"])
+
+        if "psf" in config:
+            self.psf_tab.set_data(config["psf"])
+
+    def preview_config(self):
+        """Preview the full TOML config in a dialog before saving."""
+        try:
+            # Step 1: Validate tabs
+            if not self.validate_all_tabs():
+                QMessageBox.warning(
+                    self, "Validation Error", "Fix errors before preview."
+                )
+                return
+
+            # Step 2: Collect config data
+            config = self.collect_all_config()
+
+            # Step 3: Convert to TOML string
+            toml_doc = tomlkit.document()
+            for key, value in config.items():
+                toml_doc[key] = value
+            toml_str = tomlkit.dumps(toml_doc)
+
+            # Step 4: Show preview dialog
+            preview_dialog = QDialog(self)
+            preview_dialog.setWindowTitle("Preview TOML Configuration")
+            layout = QVBoxLayout(preview_dialog)
+            text_edit = QTextEdit()
+            text_edit.setPlainText(toml_str)
+            text_edit.setReadOnly(True)
+            layout.addWidget(text_edit)
+            preview_dialog.resize(800, 600)
+            preview_dialog.exec()
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Preview failed: {str(e)}")
+
+    def build_toml_doc(self, config: dict) -> tomlkit.TOMLDocument:
+        """Build a TOML document from the configuration dictionary."""
+        doc = tomlkit.document()
+        for key, val in config.items():
+            doc[key] = val
+        return doc
+
+    def on_dropdown_change(self, index):
+        """Change the displayed widget based on the dropdown selection."""
+        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}")
+
+    def validate_all_tabs(self) -> bool:
+        return all(
+            [
+                self.global_tab.validate(),
+                self.cell_tab.validate(),
+                self.molecule_tab.validate(),
+                self.condensate_tab.validate(),
+                self.fluorophore_tab.validate(),
+                self.psf_tab.validate(),
+                self.laser_tab.validate(),
+                self.channel_tab.validate(),
+                self.detector_tab.validate(),
+                self.experiment_tab.validate(),
+            ]
+        )
+
+    def collect_all_config(self) -> dict:
+        return {
+            **self.general_tab.get_data(),
+            "Global_Parameters": self.global_tab.get_data(),
+            "Cell_Parameters": self.cell_tab.get_data(),
+            "Molecule_Parameters": self.molecule_tab.get_data(),
+            "Condensate_Parameters": self.condensate_tab.get_data(),
+            "Output_Parameters": self.output_tab.get_data(),
+            "fluorophores": self.fluorophore_tab.get_data(),
+            "psf": self.psf_tab.get_data(),
+            "lasers": self.laser_tab.get_data(),
+            "channels": self.channel_tab.get_data(),
+            "camera": self.detector_tab.get_data(),
+            "experiment": self.experiment_tab.get_data(),
+        }
+
+    def show_help(self):
+        current_widget = self.stacked_widget.currentWidget()
+        if hasattr(current_widget, "get_help_path"):
+            help_path = current_widget.get_help_path()
+            if help_path.exists():
+                help_window = HelpWindow(help_path, self)
+                help_window.exec()
+                return
+
+        QMessageBox.warning(self, "Help", "Help content not found for this section.")
+
+    def save_config(self):
+        """Collect data from all tabs and save the configuration."""
+        try:
+            # Validate all required tabs
+
+            if self.validate_all_tabs:
+                config = self.collect_all_config()
+                toml_doc = self.build_toml_doc(config)
+
+                # Ask user where to save
+                file_path, _ = QFileDialog.getSaveFileName(
+                    self, "Save Configuration", "", "TOML Files (*.toml);;All Files (*)"
+                )
+
+                if file_path:
+                    if not file_path.endswith(".toml"):
+                        file_path += ".toml"
+
+                    with open(file_path, "w") as f:
+                        tomlkit.dump(toml_doc, f)
+
+                    QMessageBox.information(
+                        self, "Success", "Configuration has been saved successfully."
+                    )
+                else:
+                    QMessageBox.warning(
+                        self, "Save Cancelled", "No file selected. Save was aborted."
+                    )
+            else:
+                QMessageBox.warning(
+                    self,
+                    "Validation Error",
+                    "Please correct the errors in all tabs before saving.",
+                )
+        except Exception as e:
+            QMessageBox.critical(
+                self, "Error", f"An error occurred while saving: {str(e)}"
+            )
+
+    def load_config_from_toml(self, path: Path):
+        with open(path, "rb") as f:
+            config = tomli.load(f)
+        self.set_data(config)

AMS_BP/gui/help_docs/cell_help.md

@@ -0,0 +1,45 @@
+# Cell Configuration Help
+
+This section defines the geometric model of the cell used in the simulation. Each cell type has specific parameters that describe its spatial extent and shape.
+
+## Fields
+
+### `cell_type`
+- **Type**: `String`
+- **Options**: `"RectangularCell"`, `"SphericalCell"`, `"OvoidCell"`, `"RodCell"`, `"BuddingCell"`
+- **Description**: Specifies the type of cell geometry to simulate.
+
+---
+
+## Parameters by Cell Type
+
+### **SphericalCell**
+- `center`: `[x, y, z]` — 3D coordinates of the center of the sphere.
+- `radius`: `float` — Radius of the sphere in micrometers.
+
+### **RodCell**
+- `center`: `[x, y, z]` — 3D center of the rod.
+- `direction`: `[dx, dy, dz]` — Direction vector of the rod’s long axis (will be normalized).
+- `height`: `float` — Length of the rod in micrometers.
+- `radius`: `float` — Radius of the rod in micrometers.
+
+### **RectangularCell**
+- `bounds`: `[xmin, xmax, ymin, ymax, zmin, zmax]` — Bounds of the cell volume in micrometers. Useful for simulating flat, box-like geometries.
+
+### **OvoidCell**
+- `center`: `[x, y, z]` — 3D center of the ovoid.
+- `xradius`: `float` — Radius along the x-axis.
+- `yradius`: `float` — Radius along the y-axis.
+- `zradius`: `float` — Radius along the z-axis.
+
+### **BuddingCell**
+- *Not currently implemented in the UI.*
+
+---
+
+## Notes
+- The selected `cell_type` determines which fields are editable.
+- All units are in micrometers (`μm`).
+- The coordinate system is 3D and consistent with the z-position defined in the experiment setup.
+- These values define the spatial domain for molecule simulation, diffusion, and tracking.
+