AMS-BP 0.4.22__py3-none-any.whl → 0.4.40__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.22"
+__version__ = "0.4.40"

AMS_BP/{configio → core/configio}/experiments.py

@@ -20,6 +20,7 @@ class TimeSeriesExpConfig(BaseExpConfig):
     laser_powers_active: List[float]
     laser_positions_active: List
     xyoffset: Tuple[float, float]
+    scanning: bool = False
 
     exposure_time: Optional[int] = None
     interval_time: Optional[int] = None
@@ -61,6 +62,8 @@ class zStackExpConfig(BaseExpConfig):
     exposure_time: int
     interval_time: int
 
+    scanning: bool = False
+
     def __post_init__(self):
         len_ln = len(self.laser_names_active)
         len_lpow = len(self.laser_powers_active)
@@ -94,6 +97,7 @@ def timeseriesEXP(
         duration_total=config.duration_time,
         exposure_time=config.exposure_time,
         interval_time=config.interval_time,
+        scanning=config.scanning,
     )
     return np.array([frames]), metadata
 
@@ -112,6 +116,7 @@ def zseriesEXP(
             duration_total=config.exposure_time + config.interval_time,
             exposure_time=config.exposure_time,
             interval_time=config.interval_time,
+            scanning=config.scanning,
         )
         frames.append(f)
     # m.Channel = {"name": microscope.channels.names}

AMS_BP/{motion → core/motion}/condensate_movement.py

@@ -25,8 +25,8 @@ from typing import Optional
 
 import numpy as np
 
+from ...utils.decorators import cache
 from ..cells import BaseCell
-from ..utils.decorators import cache
 from .track_gen import Track_generator
 
 

AMS_BP/{motion → core/motion}/movement/boundary_conditions.py

@@ -5,7 +5,7 @@ Removal Time: NDY (not determined yet)
 
 import numpy as np
 
-from ...utils.decorators import _catch_recursion_error, deprecated
+from ....utils.decorators import _catch_recursion_error, deprecated
 
 # Reflecting boundary condition which is a recursive function so that even if the first candidate
 # is out of the space limit, the function will keep calling itself until the candidate is within the space limit

AMS_BP/{photophysics → core/photophysics}/photon_physics.py

@@ -3,6 +3,7 @@ from typing import Callable, List, Optional, Tuple
 
 import numpy as np
 
+from ...utils.constants import H_C_COM
 from ..optics.camera.detectors import photon_noise
 from ..optics.camera.quantum_eff import QuantumEfficiency
 from ..optics.filters.filters import FilterSpectrum
@@ -11,7 +12,6 @@ from ..sample.flurophores.flurophore_schema import (
     SpectralData,
     WavelengthDependentProperty,
 )
-from ..utils.constants import H_C_COM
 
 
 @dataclass

AMS_BP/{sample → core/sample}/flurophores/flurophore_schema.py

@@ -4,7 +4,7 @@ from typing import Any, Callable, Dict, List, Optional, TypeVar
 import numpy as np
 from pydantic import BaseModel, Field, field_validator
 
-from ...utils.constants import H_C_COM, N_A
+from ....utils.constants import H_C_COM, N_A
 
 NumericType = TypeVar("NumericType", float, np.ndarray, List[float])
 

AMS_BP/{sim_microscopy.py → core/sim_microscopy.py}

@@ -3,6 +3,7 @@ from typing import Callable, Dict, List, Literal, Optional, Tuple, Union
 
 import numpy as np
 
+from ..utils.util_functions import ms_to_seconds
 from .configio.configmodels import ConfigList
 from .metadata.metadata import MetaData
 from .optics.camera.detectors import Detector
@@ -18,7 +19,6 @@ from .photophysics.photon_physics import (
 from .photophysics.state_kinetics import StateTransitionCalculator
 from .sample.flurophores.flurophore_schema import StateType, WavelengthDependentProperty
 from .sample.sim_sampleplane import EMPTY_STATE_HISTORY_DICT, SamplePlane
-from .utils.util_functions import ms_to_seconds
 
 
 class VirtualMicroscope:

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,
@@ -17,11 +18,12 @@ from PyQt6.QtWidgets import (
     QWidget,
 )
 
-from ..logging.logutil import LoggerManager
-from ..logging.setup_run_directory import setup_run_directory
-from .logging_window import LogWindow
+from ..tools.logging.logutil import LoggerManager
+from ..tools.logging.setup_run_directory import setup_run_directory
 from .sim_worker import SimulationWorker
-from .template_window_selection import TemplateSelectionWindow
+from .widgets.utility_widgets.toggleswitch_widget import ToggleSwitch
+from .windows.logging_window import LogWindow
+from .windows.template_window_selection import TemplateSelectionWindow
 
 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/sim_worker.py

@@ -2,7 +2,9 @@ from pathlib import Path
 
 from PyQt6.QtCore import QObject, pyqtSignal
 
-from ..logging.logutil import LogEmitter
+from ..core.configio.convertconfig import load_config, setup_microscope
+from ..core.configio.saving import save_config_frames
+from ..tools.logging.logutil import LogEmitter
 
 
 class SimulationWorker(QObject):
@@ -20,9 +22,6 @@ class SimulationWorker(QObject):
         try:
             self.emitter.message.emit(f"Starting simulation for {self.config_path}")
 
-            from ..configio.convertconfig import load_config, setup_microscope
-            from ..configio.saving import save_config_frames
-
             loadedconfig = load_config(self.config_path)
 
             if "version" in loadedconfig:

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

@@ -8,23 +8,30 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QVBoxLayout,
     QWidget,
 )
 
+from ...core.configio.convertconfig import create_quantum_efficiency_from_config
+from ...core.optics.camera.detectors import (
+    CMOSDetector,
+)
 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 +96,10 @@ 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:
@@ -115,11 +126,6 @@ class CameraConfigWidget(QWidget):
             # You can now use this data wherever needed, e.g., saving or validation
 
     def validate(self) -> bool:
-        from ...configio.convertconfig import create_quantum_efficiency_from_config
-        from ...optics.camera.detectors import (
-            CMOSDetector,
-        )
-
         try:
             data = self.get_data()
 

AMS_BP/gui/widgets/cell_config_widget.py

@@ -8,21 +8,26 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QStackedWidget,
     QVBoxLayout,
     QWidget,
 )
 
+from ...core.cells import create_cell
+from ...core.configio.configmodels import CellParameters
+
 
 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(
@@ -46,10 +51,11 @@ class CellConfigWidget(QWidget):
         layout.addWidget(self.param_stack)
         self.setLayout(layout)
 
-    def validate(self) -> bool:
-        from ...cells import create_cell
-        from ...configio.configmodels import CellParameters
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
 
+    def validate(self) -> bool:
         try:
             data = self.get_data()
 

AMS_BP/gui/widgets/channel_config_widget.py

@@ -8,12 +8,15 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
     QWidget,
 )
 
+from ...core.configio.convertconfig import create_channels
+
 
 class ChannelConfigWidget(QWidget):
     def __init__(self):
@@ -21,11 +24,12 @@ 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)
@@ -40,10 +44,12 @@ 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
-
             data = self.get_data()
 
             # Full simulation-level validation

AMS_BP/gui/widgets/condensate_config_widget.py

@@ -11,12 +11,17 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
     QWidget,
 )
 
+from ...core.cells import create_cell
+from ...core.configio.configmodels import CondensateParameters
+from ...core.motion import create_condensate_dict
+
 
 class CondensateConfigWidget(QWidget):
     # Signal to notify when molecule count changes
@@ -31,6 +36,10 @@ 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 +122,18 @@ 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 +147,16 @@ 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 +254,7 @@ 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]
@@ -291,10 +304,6 @@ class CondensateConfigWidget(QWidget):
         }
 
     def validate(self) -> bool:
-        from ...cells import create_cell
-        from ...configio.configmodels import CondensateParameters
-        from ...motion import create_condensate_dict
-
         try:
             data = self.get_data()