AMS-BP 0.0.3__tar.gz → 0.0.11__tar.gz

{ams_bp-0.0.3 → ams_bp-0.0.11}/.github/workflows/lint.yml

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

{ams_bp-0.0.3 → ams_bp-0.0.11}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.3
-Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
+Version: 0.0.11
+Summary: Advanced Molecule Simulations and 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>
@@ -10,6 +10,7 @@ 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
@@ -18,17 +19,11 @@ Requires-Dist: tomli>=2.0.2
 Requires-Dist: typer>=0.12.5
 Description-Content-Type: text/markdown
 
-# 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 User Guide
+## Advanced Molecule 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)
@@ -54,14 +49,6 @@ 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:
@@ -83,7 +70,7 @@ 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](https://joemans3.github.io/AMS_BP/API_Documentation/sim_config/).
+#### For a detailed description of the configuration file, refer to the [Configuration File Reference](./API_Documentation/sim_config.md).
 ### Basic Units
 ```toml
 version = "0.1"
@@ -172,4 +159,39 @@ 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). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
+### 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-0.0.3 → ams_bp-0.0.11}/README.md

@@ -1,14 +1,8 @@
-# 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 User Guide
+## Advanced Molecule 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)
@@ -34,14 +28,6 @@ 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:
@@ -63,7 +49,7 @@ 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](https://joemans3.github.io/AMS_BP/API_Documentation/sim_config/).
+#### For a detailed description of the configuration file, refer to the [Configuration File Reference](./API_Documentation/sim_config.md).
 ### Basic Units
 ```toml
 version = "0.1"
@@ -152,4 +138,39 @@ 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). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
+### 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-0.0.3 → ams_bp-0.0.11}/docs/API_Documentation/configio/configmodels.md

@@ -41,10 +41,18 @@ 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
 
@@ -99,24 +107,23 @@ class CondensateParameters(BaseModel)
 ```
 
 #### Fields
-First dimension represents the types of molecules. (similar to the MoleculeParameters)
-- `initial_centers: List[List[List[float]]]`
+- `initial_centers: List[List[float]]`
   - Description: Initial centers in micrometers
   - 2D array automatically converted to numpy array
 
-- `initial_scale: List[List[float]]`
+- `initial_scale: List[float]`
   - Description: Initial scale in micrometers
   - Automatically converted to numpy array
 
-- `diffusion_coefficient: List[List[float]]`
+- `diffusion_coefficient: List[float]`
   - Description: Diffusion coefficients in μm²/s
   - Automatically converted to numpy array
 
-- `hurst_exponent: List[List[float]]`
+- `hurst_exponent: List[float]`
   - Description: Hurst exponents for motion
   - Automatically converted to numpy array
 
-- `density_dif: List[int]`
+- `density_dif: int`
   - Description: Density difference parameter
 
 ### OutputParameters
@@ -183,11 +190,11 @@ 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",
@@ -201,4 +208,4 @@ config = ConfigList(
 ## Dependencies
 - `pydantic`: For data validation and settings management
 - `numpy`: For array operations
-- `typing`: For type hints
+- `typing`: For type hints

{ams_bp-0.0.3 → ams_bp-0.0.11}/docs/API_Documentation/configio/convertconfig.md

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

{ams_bp-0.0.3 → ams_bp-0.0.11}/docs/API_Documentation/optics/psf/psf_engine.md

@@ -12,35 +12,14 @@ 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.
@@ -50,7 +29,6 @@ def pinhole_radius(self) -> Optional[float]:
 - **`_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.
 
 ---
 
@@ -127,21 +105,4 @@ 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.
-
----
-
-### `_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.   
+- **`Tuple[int, ...]`**: Tuple of dimensions (z, y, x) or (y, x) for the PSF calculation.

{ams_bp-0.0.3 → ams_bp-0.0.11}/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 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.
+- **Type**: Array of Arrays of Numbers
+- **Shape**: `[[x, y, z], ...]`
+- **Description**: The initial centers of condensates in micrometers (`um`).
 
 ### `initial_scale`
-- **Type**: Array of Array of Numbers
+- **Type**: Array of Numbers
 - **Description**: The initial scale of condensates in micrometers (`um`).
 
 ### `diffusion_coefficient`
-- **Type**: Array of Array of Numbers
+- **Type**: Array of Numbers
 - **Description**: The diffusion coefficients of condensates in `um^2/s`.
 
 ### `hurst_exponent`
-- **Type**: Array of Array of Numbers
+- **Type**: Array of Numbers
 - **Description**: The Hurst exponents of condensates.
 
 ### `density_dif`
-- **Type**: Array of Number
+- **Type**: Number
 - **Description**: The density difference between the condensate and the background.
 
 ---
@@ -224,7 +224,6 @@ 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.
 
 ---
 

{ams_bp-0.0.3 → ams_bp-0.0.11}/docs/index.md

@@ -1,8 +1,5 @@
 # AMS-BP User Guide
-<p>
-<img src="assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
-</p>
-## Advanced Fluorescence Microscopy Simulation Tool
+## Advanced Molecule 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-0.0.3 → ams_bp-0.0.11}/mkdocs.yml

@@ -3,7 +3,6 @@ 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-0.0.3 → ams_bp-0.0.11}/pyproject.toml

@@ -3,7 +3,7 @@ name = "AMS_BP"
 
 dynamic = ["version"]
 
-description = "Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar"
+description = "Advanced Molecule Simulations and Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar"
 
 readme = "README.md"
 
@@ -22,6 +22,7 @@ maintainers = [
 
 dependencies = [
   "numpy>=1.21.2",
+  "matplotlib>=3.6.0",
   "scipy>=1.7.1",
   "scikit-image>=0.18.3",
   "typer>=0.12.5",
@@ -40,10 +41,8 @@ venv = ".venv"
 
 [tool.uv]
 dev-dependencies = [
-  "matplotlib>=3.10.0",
   "mkdocs-material==9.5.40",
   "mkdocstrings-python>=1.12.2",
-  "notebook>=7.3.2",
   "pymdown-extensions>=10.11",
   "pyright>=1.1.384",
   "pytest>=8.3.3",

{ams_bp-0.0.3 → ams_bp-0.0.11}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.3"
+__version__ = "0.0.11"

{ams_bp-0.0.3 → ams_bp-0.0.11}/src/AMS_BP/configio/configmodels.py

@@ -21,7 +21,9 @@ class MoleculeParameters(BaseModel):
     diffusion_coefficient: List[List[float]] = Field(
         description="Diffusion coefficients in um^2/s"
     )
+    diffusion_track_amount: List[List[float]]
     hurst_exponent: List[List[float]]
+    hurst_track_amount: List[List[float]]
     allow_transition_probability: List[bool]
     transition_matrix_time_step: List[int] = Field(description="Time step in ms")
     diffusion_transition_matrix: List[List[List[float]]]
@@ -31,7 +33,9 @@ class MoleculeParameters(BaseModel):
 
     @field_validator(
         "diffusion_coefficient",
+        "diffusion_track_amount",
         "hurst_exponent",
+        "hurst_track_amount",
         "state_probability_diffusion",
         "state_probability_hurst",
     )
@@ -56,22 +60,19 @@ class GlobalParameters(BaseModel):
 
 
 class CondensateParameters(BaseModel):
-    initial_centers: List[List[List[float]]] = Field(
-        description="Initial centers in um"
-    )
-    initial_scale: List[List[float]] = Field(description="Initial scale in um")
-    diffusion_coefficient: List[List[float]] = Field(
+    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"
     )
-    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)
-    #
+    hurst_exponent: List[float]
+    density_dif: int
+
+    @field_validator(
+        "initial_centers", "initial_scale", "diffusion_coefficient", "hurst_exponent"
+    )
+    def convert_to_array(cls, v):
+        return np.array(v)
 
 
 class OutputParameters(BaseModel):

{ams_bp-0.0.3 → ams_bp-0.0.11}/src/AMS_BP/configio/convertconfig.py

@@ -324,12 +324,11 @@ class ConfigLoader:
         ):
             # Create PSFParameters instance
             parameters = PSFParameters(
-                emission_wavelength=wavelength,
+                wavelength=wavelength,
                 numerical_aperture=float(params_config["numerical_aperture"]),
                 pixel_size=pixel_size,
                 z_step=float(params_config["z_step"]) if z_step is None else z_step,
                 refractive_index=float(params_config.get("refractive_index", 1.0)),
-                pinhole_diameter=params_config.get("pinhole_diameter", None),
             )
 
             # Create PSF engine
@@ -681,7 +680,7 @@ class ConfigLoader:
         )
 
         # make sampling function
-        sampling_functions = make_samplingfunction(
+        sampling_function = make_samplingfunction(
             condensate_params=base_config.CondensateParameters, cell=cell
         )
 
@@ -690,7 +689,7 @@ class ConfigLoader:
             molecule_params=base_config.MoleculeParameters,
             cell=cell,
             condensate_params=base_config.CondensateParameters,
-            sampling_functions=sampling_functions,
+            sampling_function=sampling_function,
         )
 
         # create the track generator
@@ -777,42 +776,34 @@ def make_sample(global_params, cell_params) -> SamplePlane:
     return sample_plane
 
 
-def make_condensatedict(condensate_params, cell) -> List[dict]:
-    condensates_dict = []
-    for i in range(len(condensate_params.initial_centers)):
-        condensates_dict.append(
-            create_condensate_dict(
-                initial_centers=condensate_params.initial_centers[i],
-                initial_scale=condensate_params.initial_scale[i],
-                diffusion_coefficient=condensate_params.diffusion_coefficient[i],
-                hurst_exponent=condensate_params.hurst_exponent[i],
-                cell=cell,
-            )
-        )
+def make_condensatedict(condensate_params, cell) -> dict:
+    condensates_dict = create_condensate_dict(
+        initial_centers=condensate_params.initial_centers,
+        initial_scale=condensate_params.initial_scale,
+        diffusion_coefficient=condensate_params.diffusion_coefficient,
+        hurst_exponent=condensate_params.hurst_exponent,
+        cell=cell,
+    )
     return condensates_dict
 
 
-def make_samplingfunction(condensate_params, cell) -> List[Callable]:
-    sampling_functions = []
-    for i in range(len(condensate_params.initial_centers)):
-        sampling_functions.append(
-            tp(
-                num_subspace=len(condensate_params.initial_centers[i]),
-                subspace_centers=condensate_params.initial_centers[i],
-                subspace_radius=condensate_params.initial_scale[i],
-                density_dif=condensate_params.density_dif[i],
-                cell=cell,
-            )
-        )
-    return sampling_functions
+def make_samplingfunction(condensate_params, cell) -> Callable:
+    sampling_function = tp(
+        num_subspace=len(condensate_params.initial_centers),
+        subspace_centers=condensate_params.initial_centers,
+        subspace_radius=condensate_params.initial_scale,
+        density_dif=condensate_params.density_dif,
+        cell=cell,
+    )
+    return sampling_function
 
 
-def gen_initial_positions(molecule_params, cell, condensate_params, sampling_functions):
+def gen_initial_positions(molecule_params, cell, condensate_params, sampling_function):
     initials = []
     for i in range(len(molecule_params.num_molecules)):
         num_molecules = molecule_params.num_molecules[i]
         initial_positions = gen_points(
-            pdf=sampling_functions[i],
+            pdf=sampling_function,
             total_points=num_molecules,
             min_x=cell.origin[0],
             max_x=cell.origin[0] + cell.dimensions[0],
@@ -820,7 +811,7 @@ def gen_initial_positions(molecule_params, cell, condensate_params, sampling_fun
             max_y=cell.origin[1] + cell.dimensions[1],
             min_z=-cell.dimensions[2] / 2,
             max_z=cell.dimensions[2] / 2,
-            density_dif=condensate_params.density_dif[i],
+            density_dif=condensate_params.density_dif,
         )
         initials.append(initial_positions)
     return initials

{ams_bp-0.0.3 → ams_bp-0.0.11}/src/AMS_BP/metadata/metadata.py

@@ -1,4 +1,4 @@
-from typing import Dict, Iterator, List, Literal, Union
+from typing import Iterator, List, Literal, Union
 
 from pydantic import BaseModel
 
@@ -77,7 +77,7 @@ class MetaData(BaseModel):
     PhysicalSizeXUnit: Literal["nm", "m"]
     PhysicalSizeY: float
     PhysicalSizeYUnit: Literal["nm", "m"]
-    Channel: Dict[Literal["Name"], List[str]]
+    # Channel: Dict[Literal["Name"], List[str]]
 
     def __post_init__(self):
         if isinstance(self.notes, (list, str)):

{ams_bp-0.0.3 → ams_bp-0.0.11}/src/AMS_BP/motion/condensate_movement.py

@@ -20,6 +20,7 @@ Usage:
         condensate(times, time_unit) -> dict{"Position":np.ndarray, "Scale":float}
 """
 
+import matplotlib.pyplot as plt
 import numpy as np
 
 from ..cells.rectangular_cell import RectangularCell
@@ -309,3 +310,47 @@ class Condensate:
         # make array of length time with the last scale
         scale = np.full(time.shape, last_scale)
         return scale
+
+    def plot_condensate(self, ax, **kwargs):
+        """
+        Plots the condensate
+
+        Parameters:
+        -----------
+        ax: plt.Axes
+            Axes to plot the condensate on.
+        **kwargs:
+            Keyword arguments to pass to the plot function.
+        """
+        # check if the _condensate_positions exists
+        if not hasattr(self, "_condensate_positions"):
+            # if it doesn't then we need to generate the condensate positions
+            self.times = np.array([self.initial_time])
+            self.condensate_positions = np.array([self.initial_position])
+            self.scale = np.array([self.initial_scale])
+
+        # plot the condensate positions
+        ax.plot(
+            self.condensate_positions[:, 0], self.condensate_positions[:, 1], **kwargs
+        )
+
+        # plot a circle at all the positions with the scale as the radius
+        for i in range(len(self.condensate_positions)):
+            ax.add_patch(
+                plt.Circle(
+                    self.condensate_positions[i], self.scale[i], color="r", fill=False
+                )
+            )
+
+        # plot the initial position in a different colour
+        ax.scatter(self.initial_position[0], self.initial_position[1], color="g")
+        # plot the final position in a different colour
+        ax.scatter(
+            self.condensate_positions[-1][0],
+            self.condensate_positions[-1][1],
+            color="b",
+        )
+        if "save_path" in kwargs:
+            plt.savefig(kwargs["save_path"])
+        # plt.show()
+        return ax