AMS-BP 0.2.0__tar.gz → 0.3.1__tar.gz

{ams_bp-0.2.0 → ams_bp-0.3.1}/.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-0.2.0 → ams_bp-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.2.0
+Version: 0.3.1
 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
@@ -9,7 +9,7 @@ Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
 License-File: LICENSE
 Keywords: SMS
 Requires-Python: >=3.12
-Requires-Dist: boundedfbm>=0.2.0
+Requires-Dist: boundedfbm>=0.4.0
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
@@ -29,8 +29,24 @@ Description-Content-Type: text/markdown
 
 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.
+## Overview of Simulation Workflow
+<img align = "left" src="./docs/assets/figures/Fig1_Schema.svg" width="500"/>
+
+*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**.*
+
+## 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/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
 
+## Examples (Click on the image buttons to be taken to the Jupyter notebooks):
+
+> !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
+
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+
+[<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
+
+[<img align="middle" src="./docs/assets/buttons/ButtonFigure_sptPALM_mmaple.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/sptPALM/motionmodels_sptmmaple.ipynb)
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -81,13 +97,6 @@ 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
 
@@ -155,7 +164,17 @@ 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
@@ -181,13 +200,10 @@ 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)
 ```
-
-## 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.
+> **_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.
 
 ## High Priority Features
-1. Irregular cell shapes with motion models
+~~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

{ams_bp-0.2.0 → ams_bp-0.3.1}/README.md

@@ -7,8 +7,24 @@
 
 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.
+## Overview of Simulation Workflow
+<img align = "left" src="./docs/assets/figures/Fig1_Schema.svg" width="500"/>
+
+*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**.*
+
+## 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/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
 
+## Examples (Click on the image buttons to be taken to the Jupyter notebooks):
+
+> !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
+
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+
+[<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
+
+[<img align="middle" src="./docs/assets/buttons/ButtonFigure_sptPALM_mmaple.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/sptPALM/motionmodels_sptmmaple.ipynb)
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -59,13 +75,6 @@ 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
 
@@ -133,7 +142,17 @@ 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
@@ -159,13 +178,10 @@ 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)
 ```
-
-## 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.
+> **_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.
 
 ## High Priority Features
-1. Irregular cell shapes with motion models
+~~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

{ams_bp-0.2.0 → ams_bp-0.3.1}/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.
 
@@ -203,30 +204,30 @@ All models include automatic validation and conversion:
 ```python
 # Create configuration instance
 config = ConfigList(
-    CellParameters=CellParameters(
+    CellParameter=CellParameters(
         cell_space=[[0, 10], [0, 10]],
         cell_axial_radius=5.0
     ),
-    MoleculeParameters=MoleculeParameters(
+    MoleculeParameter=MoleculeParameters(
         num_molecules=[100],
         track_type=["fbm"],
         # ... other required fields ...
     ),
-    GlobalParameters=GlobalParameters(
+    GlobalParameter=GlobalParameters(
         sample_plane_dim=[20.0, 20.0],
         cycle_count=100,
         exposure_time=100,
         interval_time=100,
         oversample_motion_time=10
     ),
-    CondensateParameters=CondensateParameters(
+    CondensateParameter=CondensateParameters(
         initial_centers=[[[5.0, 5.0]]],
         initial_scale=[[2.0]],
         diffusion_coefficient=[[0.1]],
         hurst_exponent=[[0.7]],
         density_dif=[2]
     ),
-    OutputParameters=OutputParameters(
+    OutputParameter=OutputParameters(
         output_path="./output",
         output_name="simulation",
         subsegment_type="uniform",

{ams_bp-0.2.0 → ams_bp-0.3.1}/docs/API_Documentation/sim_config.md

@@ -71,7 +71,6 @@ params = {
 # 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