AMS-BP 0.4.41__tar.gz → 0.4.42__tar.gz

{ams_bp-0.4.41 → ams_bp-0.4.42}/.github/workflows/publish_pypi.yml

@@ -54,12 +54,12 @@ jobs:
       Sign the Python 🐍 distribution 📦 with Sigstore
       and upload them to GitHub Release
     needs:
-    - publish-to-pypi
+      - publish-to-pypi
     runs-on: ubuntu-latest
 
     permissions:
-      contents: write  # IMPORTANT: mandatory for making GitHub Releases
-      id-token: write  # IMPORTANT: mandatory for sigstore
+      contents: write  # mandatory for making GitHub Releases
+      id-token: write  # mandatory for sigstore
 
     steps:
     - name: Download all the dists
@@ -67,26 +67,42 @@ jobs:
       with:
         name: python-package-distributions
         path: dist/
+
     - name: Sign the dists with Sigstore
       uses: sigstore/gh-action-sigstore-python@v3.0.0
       with:
         inputs: >-
           ./dist/*.tar.gz
           ./dist/*.whl
+
+    - name: Generate Changelog
+      id: changelog
+      run: |
+        git fetch --tags
+        PREV_TAG=$(git describe --tags --abbrev=0 HEAD^)
+        CURRENT_TAG=$(git describe --tags --abbrev=0 HEAD)
+        echo "Previous tag: $PREV_TAG"
+        echo "Current tag: $CURRENT_TAG"
+        echo "## Changes" > changelog.txt
+        echo "" >> changelog.txt
+        git log $PREV_TAG..$CURRENT_TAG --pretty=format:"- %s (%h)" >> changelog.txt
+        echo 'changelog<<EOF' >> $GITHUB_ENV
+        cat changelog.txt >> $GITHUB_ENV
+        echo 'EOF' >> $GITHUB_ENV
+
     - name: Create GitHub Release
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        changelog: ${{ env.changelog }}
       run: >-
         gh release create
         '${{ github.ref_name }}'
         --repo '${{ github.repository }}'
-        --notes ""
+        --notes "${changelog}"
+
     - name: Upload artifact signatures to GitHub Release
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
       run: >-
         gh release upload
         '${{ github.ref_name }}' dist/**

{ams_bp-0.4.41 → ams_bp-0.4.42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.4.41
+Version: 0.4.42
 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

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.41"
+__version__ = "0.4.42"

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/core/configio/convertconfig.py

@@ -6,6 +6,9 @@ import numpy as np
 import tomli
 from pydantic import BaseModel
 
+from ...core.optics.collection_efficiency import (
+    collection_efficiency_isotropic_emission,
+)
 from ..cells import BaseCell, create_cell
 from ..motion import Track_generator, create_condensate_dict
 from ..motion.track_gen import (
@@ -274,11 +277,19 @@ def create_psf_from_config(config: Dict[str, Any]) -> Tuple[Callable, Dict[str,
     additional_config = {
         "type": psf_config.get("type", "gaussian"),
         "custom_path": psf_config.get("custom_path", ""),
+        "psf_config": psf_config,
     }
 
     return Partial_PSFengine, additional_config
 
 
+def create_collection_efficiency(config: Dict[str, Any]) -> float:
+    na = config.get("psf").get("parameters").get("numerical_aperture")
+    n = config.get("psf").get("parameters").get("refractive_index")
+    col_eff = collection_efficiency_isotropic_emission(na=na, n=n)
+    return col_eff
+
+
 # Helper function to find pixel size
 def find_pixel_size(magnification: float, pixel_detector_size: float) -> float:
     return pixel_detector_size / magnification
@@ -728,6 +739,7 @@ def setup_microscope(config: Dict[str, Any]) -> dict:
     fluorophores = create_fluorophores_from_config(config)
     # psf config
     psf, psf_config = create_psf_from_config(config)
+    collection_efficiency = create_collection_efficiency(config)
     # lasers config
     lasers = create_lasers_from_config(config)
     # channels config
@@ -776,6 +788,7 @@ def setup_microscope(config: Dict[str, Any]) -> dict:
         channels=channels,
         psf=psf,
         config=base_config,
+        collection_efficiency=collection_efficiency,
     )
 
     return {

ams_bp-0.4.42/src/AMS_BP/core/optics/collection_efficiency.py

@@ -0,0 +1,24 @@
+import warnings
+from functools import lru_cache
+
+import numpy as np
+
+
+@lru_cache(maxsize=None)
+def collection_efficiency_isotropic_emission(na: float, n: float) -> float:
+    ratio = na / n
+
+    if ratio > 1.0:
+        warnings.warn(
+            f"NA ({na}) exceeds refractive index n ({n}), which is unphysical. "
+            f"Clipping NA/n to 1.0 for collection efficiency calculation."
+        )
+        ratio = 1.0
+    elif ratio < 0.0:
+        warnings.warn(
+            f"NA ({na}) is negative, which is unphysical. " f"Clipping NA/n to 0.0."
+        )
+        ratio = 0.0
+
+    # Use identity: cos(arcsin(x)) = sqrt(1 - x^2)
+    return 0.5 * (1 - np.sqrt(1 - ratio**2))

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/core/photophysics/photon_physics.py

@@ -157,7 +157,9 @@ class incident_photons:
             else:
                 self.generator.append(0)
 
-    def incident_photons_calc(self, dt: float) -> Tuple[float, List]:
+    def incident_photons_calc(
+        self, dt: float, collection_efficiency: float = 1
+    ) -> Tuple[float, List]:
         photons = 0
         psf_hold = []
         for i in range(len(self.transmission_photon_rate.wavelengths)):
@@ -165,7 +167,9 @@ class incident_photons:
                 qe_lam = self.quantumEff.get_qe(
                     self.transmission_photon_rate.wavelengths[i]
                 )
-                photons_n = self.transmission_photon_rate.values[i] * dt
+                photons_n = (
+                    self.transmission_photon_rate.values[i] * dt * collection_efficiency
+                )
                 photons += photons_n
                 psf_gen = (
                     self.generator[i].psf_z(

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/core/sim_microscopy.py

@@ -30,6 +30,7 @@ class VirtualMicroscope:
         channels: Channels,
         psf: Callable[[float | int, Optional[float | int]], PSFEngine],
         config: ConfigList,
+        collection_efficiency: float = 1,
         start_time: int = 0,
     ):
         # Core components
@@ -41,6 +42,7 @@ class VirtualMicroscope:
         self.psf = psf
         self._time = start_time  # ms
         self.config = config
+        self.collection_efficiency = collection_efficiency
 
         # Cached initial configuration
         self._cached_initial_config()
@@ -271,7 +273,9 @@ class VirtualMicroscope:
                                 self.psf,
                                 florPos,
                             )
-                            _, psfs = inc.incident_photons_calc(deltaTime)
+                            _, psfs = inc.incident_photons_calc(
+                                deltaTime, self.collection_efficiency
+                            )
                             for ipsf in psfs:
                                 mapSC[self.channels.names[channel_num]].add_psf_frame(
                                     ipsf, florPos[:2], frame_list[time_index]

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/main.py

@@ -36,12 +36,10 @@ class MainWindow(QMainWindow):
         # Set up the main layout
         layout = QVBoxLayout()
 
-        # Add logo as a placeholder (SVG format)
         self.logo_label = QLabel()  # Label to hold the logo
         self.set_svg_logo(LOGO_PATH)  # Set the SVG logo
         layout.addWidget(self.logo_label, alignment=Qt.AlignmentFlag.AlignCenter)
 
-        # Add the maintainer's name under the image
         self.maintainer_label = QLabel(
             "Maintainer: Baljyot Parmar \n baljyotparmar@hotmail.com"
         )
@@ -96,7 +94,6 @@ class MainWindow(QMainWindow):
     def package_logs(self):
         log_dir = Path.home() / "AMS_runs"
 
-        # Step 1: Open dialog to select folders
         folder_paths = QFileDialog.getExistingDirectory(
             self,
             "Select Folder Containing Run Logs",
@@ -107,7 +104,6 @@ class MainWindow(QMainWindow):
         if not folder_paths:
             return
 
-        # QFileDialog.getExistingDirectory() returns a single path.
         # For now, let's treat this as a single run_* folder being selected.
 
         run_dir = Path(folder_paths)
@@ -117,7 +113,6 @@ class MainWindow(QMainWindow):
             )
             return
 
-        # Step 2: Ask for destination .zip archive
         zip_path_str, _ = QFileDialog.getSaveFileName(
             self,
             "Save Zipped Folder As",
@@ -220,7 +215,6 @@ class MainWindow(QMainWindow):
 
         if file_path:
             try:
-                # Load the image (expand here if you want ND2 or Zarr support)
                 image = tifffile.imread(file_path)
 
                 # Open Napari viewer and display the image
@@ -233,7 +227,6 @@ class MainWindow(QMainWindow):
 
     def set_svg_logo(self, svg_path):
         """Set an SVG logo to the QLabel, maintaining the aspect ratio."""
-        # Create a QSvgRenderer to render the SVG
         renderer = QSvgRenderer(svg_path)
         if renderer.isValid():
             # Get the size of the SVG image

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/widgets/camera_config_widget.py

@@ -123,7 +123,6 @@ class CameraConfigWidget(QWidget):
                 "wavelengths": dialog.wavelengths,
                 "quantum_efficiency": dialog.intensities,
             }
-            # You can now use this data wherever needed, e.g., saving or validation
 
     def validate(self) -> bool:
         try:
@@ -132,7 +131,6 @@ class CameraConfigWidget(QWidget):
             # Convert QE before passing
             qe = create_quantum_efficiency_from_config(data["quantum_efficiency"])
 
-            # Prepare CMOS-specific parameters only (drop "type" and "quantum_efficiency")
             camera_data = {
                 k: v for k, v in data.items() if k not in {"type", "quantum_efficiency"}
             }
@@ -168,9 +166,7 @@ class CameraConfigWidget(QWidget):
             "sensitivity": self.sensitivity.value(),
             "base_adu": self.base_adu.value(),
             "binning_size": self.binning_size.value(),
-            "quantum_efficiency": convert_dict_to_2_list(
-                self.quantum_efficiency_data
-            ),  # Use edited data here
+            "quantum_efficiency": convert_dict_to_2_list(self.quantum_efficiency_data),
         }
         return camera_data
 

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/widgets/channel_config_widget.py

@@ -55,7 +55,6 @@ class ChannelConfigWidget(QWidget):
             # Full simulation-level validation
             channels = create_channels({"channels": data})
 
-            # Optional: Validate shape consistency
             if len(channels.names) != channels.num_channels:
                 raise ValueError("Channel count does not match number of names.")
 

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/widgets/condensate_config_widget.py

@@ -122,7 +122,6 @@ 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:"))
 
@@ -133,7 +132,6 @@ class CondensateConfigWidget(QWidget):
         density_layout.addWidget(density_spin)
         layout.addLayout(density_layout)
 
-        # === Condensate containers BELOW this point ===
         condensate_container = QVBoxLayout()
         layout.addLayout(condensate_container)
 
@@ -307,10 +305,8 @@ class CondensateConfigWidget(QWidget):
         try:
             data = self.get_data()
 
-            # Step 1: Validate with Pydantic
             validated = CondensateParameters(**data)
 
-            # Step 2: Validate simulation compatibility for each condensate
             # Create a dummy cell just for validation context
             dummy_cell = create_cell(
                 "SphericalCell", {"center": [0, 0, 0], "radius": 5.0}

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/widgets/utility_widgets/toggleswitch_widget.py

@@ -41,13 +41,11 @@ class ToggleSwitch(QWidget):
         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)
 

{ams_bp-0.4.41 → ams_bp-0.4.42}/src/AMS_BP/gui/windows/configuration_window.py

@@ -198,23 +198,19 @@ class ConfigEditor(QWidget):
     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)