AMS-BP 0.0.251__tar.gz → 0.3.0__tar.gz

{ams_bp-0.0.251 → ams_bp-0.3.0}/.github/workflows/pages.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10.13"]
+        python-version: ["3.12"]
 
     steps:
       - uses: actions/checkout@v4

{ams_bp-0.0.251 → ams_bp-0.3.0}/.github/workflows/publish_pypi.yml

@@ -68,7 +68,7 @@ jobs:
         name: python-package-distributions
         path: dist/
     - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
       with:
         inputs: >-
           ./dist/*.tar.gz

{ams_bp-0.0.251 → ams_bp-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.251
+Version: 0.3.0
 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
@@ -8,10 +8,12 @@ Author-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
 Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
 License-File: LICENSE
 Keywords: SMS
-Requires-Python: >=3.10
+Requires-Python: >=3.12
+Requires-Dist: boundedfbm>=0.4.0
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
+Requires-Dist: pyvista>=0.44.2
 Requires-Dist: scikit-image>=0.18.3
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: tomli>=2.0.2
@@ -79,6 +81,14 @@ run_AMS_BP runsim CONFIG_FILE
 - `-o, --output_path PATH`: Specify the output directory for the configuration file
 - `-r, --recursive_o`: Create output directory if it doesn't exist
 
+## Overview of Simulation Workflow
+![Overview Schematic](./docs/assets/figures/Fig1_Schema.svg)
+*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+
+
+
+
+
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:
@@ -96,7 +106,6 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 1. **Cell Parameters**
    - Define cell space dimensions
-   - Set cell axial radius
 
 2. **Molecule Parameters**
    - Number of molecules per type
@@ -124,7 +133,8 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 ## Running Experiments
 
-AMS-BP supports two types of experiments:
+AMS-BP's CLI currently supports two types of experiments:
+> (however this can be extended when used as a library) 
 
 ### 1. Time Series
 ```toml
@@ -145,7 +155,17 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
+```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 ## Advanced Usage
 
 ### Using AMS-BP as a Library
@@ -172,4 +192,13 @@ from AMS_BP.configio.saving import save_config_frames
 save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
 ```
 
+## API Reference and Docs
+Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
 > 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.
+
+## High Priority Features
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
+2. Stimulated Emission models
+3. STORM workflow examples
+4. CTRW motion models
+5. Simpler configurations

{ams_bp-0.0.251 → ams_bp-0.3.0}/README.md

@@ -59,6 +59,14 @@ run_AMS_BP runsim CONFIG_FILE
 - `-o, --output_path PATH`: Specify the output directory for the configuration file
 - `-r, --recursive_o`: Create output directory if it doesn't exist
 
+## Overview of Simulation Workflow
+![Overview Schematic](./docs/assets/figures/Fig1_Schema.svg)
+*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+
+
+
+
+
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:
@@ -76,7 +84,6 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 1. **Cell Parameters**
    - Define cell space dimensions
-   - Set cell axial radius
 
 2. **Molecule Parameters**
    - Number of molecules per type
@@ -104,7 +111,8 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 ## Running Experiments
 
-AMS-BP supports two types of experiments:
+AMS-BP's CLI currently supports two types of experiments:
+> (however this can be extended when used as a library) 
 
 ### 1. Time Series
 ```toml
@@ -125,7 +133,17 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
+```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 ## Advanced Usage
 
 ### Using AMS-BP as a Library
@@ -152,4 +170,13 @@ from AMS_BP.configio.saving import save_config_frames
 save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
 ```
 
+## API Reference and Docs
+Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
 > 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.
+
+## High Priority Features
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
+2. Stimulated Emission models
+3. STORM workflow examples
+4. CTRW motion models
+5. Simpler configurations

{ams_bp-0.0.251 → ams_bp-0.3.0}/docs/API_Documentation/configio/configmodels.md

@@ -5,6 +5,7 @@ The configuration models module defines Pydantic BaseModel classes for validatin
 
 ## Models
 
+
 ### CellParameters
 Defines the physical parameters of the cell being simulated.
 
@@ -13,14 +14,51 @@ class CellParameters(BaseModel)
 ```
 
 #### Fields
-- `cell_space: List[List[float]]`
-  - Description: Cell space dimensions in micrometers
-  - Format: 2D array defining spatial boundaries
-  - Automatically converted to numpy array
+- `cell_type: Union[str, CellType]`
+  - Type of cell. 
+  - Supported: RectangularCell, SphericalCell, OvoidCell, RodCell, BuddingCell
+
+- `params: Dict[str, Any]`
+  - Key value pairs of the parameters of the specified cell.
 
-- `cell_axial_radius: float`
-  - Description: Axial radius in micrometers
-  - Defines the cell's axial dimension
+```python
+# SphericalCell
+params = {
+    "center": [0, 0, 0],   # 3D center coordinates
+    "radius": 10.0         # Radius of sphere
+}
+```
+
+
+```python
+# RodCell
+params = {
+    "center": [0, 0, 0],       # 3D center coordinates
+    "direction": [0, 0, 1],    # Direction vector (will be normalized)
+    "height": 20.0,            # Length of the rod
+    "radius": 5.0              # Radius of the rod
+}
+```
+
+
+```python
+# RectangularCell
+params = {
+    "bounds": [-10, 10, -10, 10, -10, 10]  # [xmin, xmax, ymin, ymax, zmin, zmax]
+}
+```
+
+
+```python
+# OvoidCell
+params = {
+    "center": [0, 0, 0],       # 3D center coordinates
+    "direction": [0, 0, 1],    # Direction vector (will be normalized)
+    "xradius": 10.0,           # Radius in x-direction
+    "yradius": 15.0,           # Radius in y-direction
+    "zradius": 20.0            # Radius in z-direction
+}
+```
 
 ### MoleculeParameters
 Defines parameters for molecular motion and behavior simulation.

{ams_bp-0.0.251 → ams_bp-0.3.0}/docs/API_Documentation/configio/convertconfig.md

@@ -98,12 +98,12 @@ Creates cell instance from parameters.
 
 ### `make_sample`
 ```python
-def make_sample(global_params, cell_params) -> SamplePlane
+def make_sample(global_params, cell) -> SamplePlane
 ```
 Creates sample plane from parameters.
 - **Parameters:**
   - `global_params`: Global parameters
-  - `cell_params`: Cell parameters
+  - `cell`: Instance of BaseCell
 - **Returns:** SamplePlane instance
 
 ### `make_condensatedict`

ams_bp-0.3.0/docs/API_Documentation/groundtruth_generators/nuclearporecomplexes.md

@@ -0,0 +1 @@
+::: AMS_BP.groundtruth_generators.nuclearporecomplexes

{ams_bp-0.0.251 → ams_bp-0.3.0}/docs/API_Documentation/sim_config.md

@@ -30,14 +30,54 @@ This document provides a detailed explanation of the TOML configuration file use
 
 ## 2. **Cell Parameters**
 
-### `cell_space`
-- **Type**: Array of Arrays of Numbers
-- **Shape**: `[[x_min, x_max], [y_min, y_max]]`
-- **Description**: Defines the spatial boundaries of the cell in micrometers (`um`).
+### `cell_type`
+- **Type**: Union[str, CellType]
+- **Description**: Defines the type of the cell to simulate.
+  - Supported: RectangularCell, SphericalCell, OvoidCell, RodCell, BuddingCell
+
+### `params`
+- **Type**: dictionary of parameter names (String) and values (Any)
+- **Description**: Values for the cell_type specified above. The following the general structure:
+
+```python
+# SphericalCell
+params = {
+    "center": [0, 0, 0],   # 3D center coordinates
+    "radius": 10.0         # Radius of sphere
+}
+```
+
+
+```python
+# RodCell
+params = {
+    "center": [0, 0, 0],       # 3D center coordinates
+    "direction": [0, 0, 1],    # Direction vector (will be normalized)
+    "height": 20.0,            # Length of the rod
+    "radius": 5.0              # Radius of the rod
+}
+```
+
+
+```python
+# RectangularCell
+params = {
+    "bounds": [-10, 10, -10, 10, -10, 10]  # [xmin, xmax, ymin, ymax, zmin, zmax]
+}
+```
+
+
+```python
+# OvoidCell
+params = {
+    "center": [0, 0, 0],       # 3D center coordinates
+    "direction": [0, 0, 1],    # Direction vector (will be normalized)
+    "xradius": 10.0,           # Radius in x-direction
+    "yradius": 15.0,           # Radius in y-direction
+    "zradius": 20.0            # Radius in z-direction
+}
+```
 
-### `cell_axial_radius`
-- **Type**: Number
-- **Description**: The axial radius of the cell in either direction from 0 (focal plane) in micrometers (`um`). The total z-range is `2 * cell_axial_radius`.
 
 ---
 

{ams_bp-0.0.251 → ams_bp-0.3.0}/docs/API_Documentation/sim_microscopy.md

@@ -54,7 +54,7 @@ Sets the power of the lasers. Raises a `ValueError` if the provided power exceed
 
 Sets the positions of the lasers.
 
-#### `run_sim(self, z_val: float, laser_power: Dict[str, float], xyoffset: Tuple[float, float], laser_position: Dict[str, Tuple[float, float, float]] | None, duration_total: Optional[int] = None, exposure_time: Optional[int] = None, interval_time: Optional[int] = None) -> Tuple[np.ndarray, MetaData]`
+#### `run_sim(self, z_val: float, laser_power:Dict[str, Union[float, Callable[[float], float]], xyoffset: Tuple[float, float], laser_position: Optional[Dict[str, Union[Tuple[float, float, float], Callable[[float], Tuple[float, float, float]]]]] = None, duration_total: Optional[int] = None, exposure_time: Optional[int] = None, interval_time: Optional[int] = None, scanning: Optional[bool] = False) -> Tuple[np.ndarray, MetaData]`
 
 Runs the simulation for the given parameters and returns the resulting image stack and metadata.