AMS-BP 0.0.21__tar.gz → 0.0.24__tar.gz

{ams_bp-0.0.21 → ams_bp-0.0.24}/.github/workflows/lint.yml

@@ -21,6 +21,5 @@ jobs:
       # Update output format to enable automatic inline annotations.
       - name: Run Ruff
         run: |
-          ruff check --fix
           ruff format
           ruff format --check --diff

{ams_bp-0.0.21 → ams_bp-0.0.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.21
+Version: 0.0.24
 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
@@ -10,7 +10,6 @@ License-File: LICENSE
 Keywords: SMS
 Requires-Python: >=3.10
 Requires-Dist: jsonschema>=4.23.0
-Requires-Dist: matplotlib>=3.6.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
 Requires-Dist: scikit-image>=0.18.3
@@ -172,3 +171,5 @@ frames, metadata = function_exp(microscope=microscope, config=config_exp)
 from AMS_BP.configio.saving import save_config_frames
 save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
 ```
+
+> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb)

{ams_bp-0.0.21 → ams_bp-0.0.24}/README.md

@@ -151,3 +151,5 @@ frames, metadata = function_exp(microscope=microscope, config=config_exp)
 from AMS_BP.configio.saving import save_config_frames
 save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
 ```
+
+> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb)

{ams_bp-0.0.21 → ams_bp-0.0.24}/docs/API_Documentation/configio/configmodels.md

@@ -41,18 +41,10 @@ class MoleculeParameters(BaseModel)
   - Description: Diffusion coefficients in μm²/s
   - 2D array automatically converted to numpy array
 
-- `diffusion_track_amount: List[List[float]]`
-  - Description: Amount of diffusive tracking for each state
-  - 2D array automatically converted to numpy array
-
 - `hurst_exponent: List[List[float]]`
   - Description: Hurst exponents for fractional Brownian motion
   - 2D array automatically converted to numpy array
 
-- `hurst_track_amount: List[List[float]]`
-  - Description: Amount of Hurst tracking for each state
-  - 2D array automatically converted to numpy array
-
 - `allow_transition_probability: List[bool]`
   - Description: Whether to allow state transitions
 

{ams_bp-0.0.21 → ams_bp-0.0.24}/docs/API_Documentation/optics/psf/psf_engine.md

@@ -12,14 +12,35 @@ This module provides functionality for generating Point Spread Functions (PSFs)
   - [_calculate_sigma_z](#_calculate_sigma_z)
   - [_generate_grid](#_generate_grid)
   - [calculate_psf_size](#calculate_psf_size)
+  - [_generate_pinhole_mask](#_generate_pinhole_mask)
 
 ---
 
 ## Classes
 
 ### `PSFParameters`
-
-
+#### Description
+This is a frozen dataclass (enum-ish?) with the following parameters / cached properties
+```python
+emission_wavelength: float
+numerical_aperture: float
+pixel_size: float
+z_step: float
+refractive_index: float = 1.0
+pinhole_diameter: Optional[float] = None  # um
+
+@cached_property
+def wavelength_um(self) -> float:
+    """Emission wavelength in micrometers."""
+    return self.emission_wavelength / 1000.0
+@cached_property
+def pinhole_radius(self) -> Optional[float]:
+  """Pinhole radius in micrometers."""
+  return (
+    self.pinhole_diameter / 2.0 if self.pinhole_diameter is not None else None
+  )
+```
+### `PSFEngine`
 #### Methods
 
 - **`__init__`**: Initializes the PSF engine with the given parameters.
@@ -29,6 +50,7 @@ This module provides functionality for generating Point Spread Functions (PSFs)
 - **`_3d_normalization_A`**: Computes the normalization factor for a 3D Gaussian PSF.
 - **`_2d_normalization_A`**: Computes the normalization factor for a 2D Gaussian PSF.
 - **`normalize_psf`**: Normalizes the PSF using different schemes.
+- **`_generate_pinhole_mask`**: Generate a binary mask representing the pinhole's spatial filtering.
 
 ---
 
@@ -105,4 +127,21 @@ Calculates the appropriate PSF size based on physical parameters.
 
 #### Returns
 
-- **`Tuple[int, ...]`**: Tuple of dimensions (z, y, x) or (y, x) for the PSF calculation.
+- **`Tuple[int, ...]`**: Tuple of dimensions (z, y, x) or (y, x) for the PSF calculation.
+
+---
+
+### `_generate_pinhole_mask`
+
+
+#### Description
+
+Generate a binary mask representing the pinhole's spatial filtering.
+
+The pinhole blocks emission light based on position in the image plane,
+affecting what portion of the diffracted light reaches the detector.
+
+#### Parameters
+#### Returns
+
+- **`NDArray[np.float64]`**: Same dimensions as the psf generated but with binary values (0,1) indicating the transmittance of the psf due to the pinhole. Note, if the pinhole size is smaller than 1*airy disk diameter, then diffraction due to the pinhole is NOT non negligiable and diffraction effects will be introduced. A ValueError is thrown if this is the case.   

{ams_bp-0.0.21 → ams_bp-0.0.24}/docs/API_Documentation/sim_config.md

@@ -224,6 +224,7 @@ Each fluorophore has transitions defined with the following parameters:
 - **Properties**:
   - **`numerical_aperture`**: The numerical aperture (typical range: 0.1 - 1.5).
   - **`refractive_index`**: The refractive index (default is air: 1.0).
+  - **`pinhole_diameter`**: None or float. In units of um. None = no pinhole before the detector.
 
 ---