AMS-BP 0.0.11__tar.gz → 0.0.22__tar.gz

{ams_bp-0.0.11 → ams_bp-0.0.22}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.11
-Summary: Advanced Molecule Simulations and Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
+Version: 0.0.22
+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
 Author-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
@@ -19,11 +19,17 @@ Requires-Dist: tomli>=2.0.2
 Requires-Dist: typer>=0.12.5
 Description-Content-Type: text/markdown
 
-# AMS-BP User Guide
-## Advanced Molecule Simulation Tool
+# AMS-BP
+<p>
+<img src="./docs/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.
 
+> **_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.
+
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -49,6 +55,14 @@ uv tool install AMS_BP
     - `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)
     - 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. Run:
+```bash
+pip install AMS_BP
+```
+
 ## Command Line Interface
 
 AMS-BP provides a command-line interface with two main commands:
@@ -70,7 +84,7 @@ run_AMS_BP runsim CONFIG_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"
@@ -158,40 +172,3 @@ 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)
 ```
-
-### 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
-
-### Custom Experiment Types
-
-When using AMS-BP as a library, you can create custom experiment types by:
-
-1. Extending the base experiment class
-2. Implementing custom scanning patterns
-3. Defining new molecule behaviors
-4. Creating specialized analysis routines
-
-## Tips and Best Practices
-
-1. **Configuration Management**
-   - Keep separate config files for different experiment types
-   - Version control your configurations
-   - Document any custom modifications
-
-2. **Resource Usage**
-   - Monitor memory usage for large simulations
-   - Use appropriate sampling rates
-
-3. **Data Output**
-   - Set appropriate output paths
-   - Use meaningful naming conventions
-   - Consider data format requirements for analysis
-
-## Troubleshooting
-
-Common issues and their solutions:
-TODO

{ams_bp-0.0.11 → ams_bp-0.0.22}/README.md

@@ -1,8 +1,14 @@
-# AMS-BP User Guide
-## Advanced Molecule Simulation Tool
+# AMS-BP
+<p>
+<img src="./docs/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.
 
+> **_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.
+
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -28,6 +34,14 @@ uv tool install AMS_BP
     - `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)
     - 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. Run:
+```bash
+pip install AMS_BP
+```
+
 ## Command Line Interface
 
 AMS-BP provides a command-line interface with two main commands:
@@ -49,7 +63,7 @@ run_AMS_BP runsim CONFIG_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"
@@ -137,40 +151,3 @@ 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)
 ```
-
-### 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
-
-### Custom Experiment Types
-
-When using AMS-BP as a library, you can create custom experiment types by:
-
-1. Extending the base experiment class
-2. Implementing custom scanning patterns
-3. Defining new molecule behaviors
-4. Creating specialized analysis routines
-
-## Tips and Best Practices
-
-1. **Configuration Management**
-   - Keep separate config files for different experiment types
-   - Version control your configurations
-   - Document any custom modifications
-
-2. **Resource Usage**
-   - Monitor memory usage for large simulations
-   - Use appropriate sampling rates
-
-3. **Data Output**
-   - Set appropriate output paths
-   - Use meaningful naming conventions
-   - Consider data format requirements for analysis
-
-## Troubleshooting
-
-Common issues and their solutions:
-TODO

{ams_bp-0.0.11 → ams_bp-0.0.22}/docs/API_Documentation/configio/configmodels.md

@@ -107,23 +107,24 @@ class CondensateParameters(BaseModel)
 ```
 
 #### Fields
-- `initial_centers: List[List[float]]`
+First dimension represents the types of molecules. (similar to the MoleculeParameters)
+- `initial_centers: List[List[List[float]]]`
   - Description: Initial centers in micrometers
   - 2D array automatically converted to numpy array
 
-- `initial_scale: List[float]`
+- `initial_scale: List[List[float]]`
   - Description: Initial scale in micrometers
   - Automatically converted to numpy array
 
-- `diffusion_coefficient: List[float]`
+- `diffusion_coefficient: List[List[float]]`
   - Description: Diffusion coefficients in μm²/s
   - Automatically converted to numpy array
 
-- `hurst_exponent: List[float]`
+- `hurst_exponent: List[List[float]]`
   - Description: Hurst exponents for motion
   - Automatically converted to numpy array
 
-- `density_dif: int`
+- `density_dif: List[int]`
   - Description: Density difference parameter
 
 ### OutputParameters
@@ -190,11 +191,11 @@ config = ConfigList(
         oversample_motion_time=10
     ),
     CondensateParameters=CondensateParameters(
-        initial_centers=[[5.0, 5.0]],
-        initial_scale=[2.0],
-        diffusion_coefficient=[0.1],
-        hurst_exponent=[0.7],
-        density_dif=2
+        initial_centers=[[[5.0, 5.0]]],
+        initial_scale=[[2.0]],
+        diffusion_coefficient=[[0.1]],
+        hurst_exponent=[[0.7]],
+        density_dif=[2]
     ),
     OutputParameters=OutputParameters(
         output_path="./output",
@@ -208,4 +209,4 @@ config = ConfigList(
 ## Dependencies
 - `pydantic`: For data validation and settings management
 - `numpy`: For array operations
-- `typing`: For type hints
+- `typing`: For type hints

{ams_bp-0.0.11 → ams_bp-0.0.22}/docs/API_Documentation/configio/convertconfig.md

@@ -108,13 +108,13 @@ Creates sample plane from parameters.
 
 ### `make_condensatedict`
 ```python
-def make_condensatedict(condensate_params, cell) -> dict
+def make_condensatedict(condensate_params, cell) -> List[dict]
 ```
-Creates condensate dictionary from parameters.
+Creates condensate dictionaries from parameters.
 - **Parameters:**
   - `condensate_params`: Condensate parameters
   - `cell`: Cell instance
-- **Returns:** Condensate dictionary
+- **Returns:** Condensate dictionaries
 
 ### `get_tracks`
 ```python

{ams_bp-0.0.11 → ams_bp-0.0.22}/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-0.0.11 → ams_bp-0.0.22}/docs/API_Documentation/sim_config.md

@@ -122,24 +122,24 @@ This document provides a detailed explanation of the TOML configuration file use
 ## 5. **Condensate Parameters**
 
 ### `initial_centers`
-- **Type**: Array of Arrays of Numbers
-- **Shape**: `[[x, y, z], ...]`
-- **Description**: The initial centers of condensates in micrometers (`um`).
+- **Type**: Array of Array of Arrays of Numbers
+- **Shape**: `[[[x, y, z], ...], ...]`
+- **Description**: The initial centers of condensates in micrometers (`um`). The first dimension is the types of different molecules. Similarr to the `num_molecules` array in the molecule parameters.
 
 ### `initial_scale`
-- **Type**: Array of Numbers
+- **Type**: Array of Array of Numbers
 - **Description**: The initial scale of condensates in micrometers (`um`).
 
 ### `diffusion_coefficient`
-- **Type**: Array of Numbers
+- **Type**: Array of Array of Numbers
 - **Description**: The diffusion coefficients of condensates in `um^2/s`.
 
 ### `hurst_exponent`
-- **Type**: Array of Numbers
+- **Type**: Array of Array of Numbers
 - **Description**: The Hurst exponents of condensates.
 
 ### `density_dif`
-- **Type**: Number
+- **Type**: Array of Number
 - **Description**: The density difference between the condensate and the background.
 
 ---
@@ -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.
 
 ---
 

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+         style="font-style:italic;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:2.18572px;line-height:1.60776px;font-family:sans-serif;-inkscape-font-specification:'sans-serif, Italic';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;text-align:center;text-anchor:middle;fill:#000000;stroke:none;stroke-width:0.290723;stroke-linecap:round;paint-order:fill markers stroke"
+         x="114.30348"
+         y="114.54252"
+         id="text738"
+         transform="scale(1.0494764,0.95285612)"><tspan
+           sodipodi:role="line"
+           id="tspan736"
+           style="font-style:italic;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:2.18572px;font-family:sans-serif;-inkscape-font-specification:'sans-serif, Italic';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke:none;stroke-width:0.290723"
+           x="114.30348"
+           y="114.54252">BP</tspan></text></g></g></svg>

{ams_bp-0.0.11 → ams_bp-0.0.22}/docs/index.md

@@ -1,5 +1,8 @@
 # AMS-BP User Guide
-## Advanced Molecule Simulation Tool
+<p>
+<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.
 

{ams_bp-0.0.11 → ams_bp-0.0.22}/mkdocs.yml

@@ -3,6 +3,7 @@ site_url: https://joemans3.github.io/AMS_BP/
 repo_url: https://github.com/joemans3/AMS_BP
 theme: 
   name: material
+  logo: assets/icons/drawing.png
   icon:
     repo: fontawesome/brands/git-alt
   features:

{ams_bp-0.0.11 → ams_bp-0.0.22}/pyproject.toml

@@ -3,7 +3,7 @@ name = "AMS_BP"
 
 dynamic = ["version"]
 
-description = "Advanced Molecule Simulations and Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar"
+description = "Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar"
 
 readme = "README.md"
 

{ams_bp-0.0.11 → ams_bp-0.0.22}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.11"
+__version__ = "0.0.22"

{ams_bp-0.0.11 → ams_bp-0.0.22}/src/AMS_BP/configio/configmodels.py

@@ -60,19 +60,22 @@ class GlobalParameters(BaseModel):
 
 
 class CondensateParameters(BaseModel):
-    initial_centers: List[List[float]] = Field(description="Initial centers in um")
-    initial_scale: List[float] = Field(description="Initial scale in um")
-    diffusion_coefficient: List[float] = Field(
-        description="Diffusion coefficients in um^2/s"
+    initial_centers: List[List[List[float]]] = Field(
+        description="Initial centers in um"
     )
-    hurst_exponent: List[float]
-    density_dif: int
-
-    @field_validator(
-        "initial_centers", "initial_scale", "diffusion_coefficient", "hurst_exponent"
+    initial_scale: List[List[float]] = Field(description="Initial scale in um")
+    diffusion_coefficient: List[List[float]] = Field(
+        description="Diffusion coefficients in um^2/s"
     )
-    def convert_to_array(cls, v):
-        return np.array(v)
+    hurst_exponent: List[List[float]]
+    density_dif: List[int]
+
+    # @field_validator(
+    #     "initial_centers", "initial_scale", "diffusion_coefficient", "hurst_exponent"
+    # )
+    # def convert_to_array(cls, v):
+    #     return np.array(v)
+    #
 
 
 class OutputParameters(BaseModel):