| Name | uq-physicell JSON |
| Version |
1.1.0
JSON |
| download |
| home_page | None |
| Summary | Project to perform uncertainty quantification of PhysiCell models |
| upload_time | 2025-01-09 21:39:17 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
physicell
uncertainty quantification
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Installation
Install the package using pip:
```
pip install uq_physicell
```
## External Modules
These modules must be installed separately. Install them using `pip`:
```bash
pip install pandas numpy pcdl
```
[pcdl](https://github.com/elmbeech/physicelldataloader) is a Python package designed to load [PhysiCell](https://physicell.org) simulations in a Pythonic way.
# Examples
Here are some examples to help you get started with the package:
## Example 1: Basic Usage
- Description: Print information about two model structures, [physicell_model_1](examples/SampleModel.ini#l1) and [physicell_model_2](examples/SampleModel.ini#l18), as defined in the config file [examples/SampleModel.ini](examples/SampleModel.ini#l20). This operation does not run a PhysiCell simulation. See [example 1](examples/ex1_print.py).
```bash
python examples/ex1_print.py
```
## Example 2: Running PhysiCell Simulations
- Requirements: A PhysiCell folder is required.
- Description: Run three PhysiCell simulations associated with the key [physicell_model_2](examples/SampleModel.ini#l18) in the config file [SampleModel.ini](examples/SampleModel.ini). This corresponds to the `virus_macrophage` example in `PhysiCell's sample projects`. See [example 2](examples/ex2_runModel.py).
- **First simulation:** Demonstrates running a simulation with a predefined summary function that summarizes the final population of live and dead cells, storing results in a new folder `output2`.
- **Second simulation:** Runs the simulation while preserving the config files and retaining the complete PhysiCell output without summarization.
- **Third simulation:** Configures the execution to summarize the output and returns a DataFrame with the summary.
Run script:
```bash
python examples/ex2_runModel.py
```
Alternatively, download the lastest PhysiCell version with:
```bash
bash examples/PhysiCell.sh
```
This will create a folder named `PhysiCell-master` inside `examples`. Populate and compile the project (Step 1 below) without modifying [SampleModel.ini](examples/SampleModel.ini).
- Step 1: Compile the `virus-macrophage` example in the PhysiCell folder:
```bash
make reset && make virus-macrophage-sample && make
```
- Step 2: Update the `executable` and `configFile_ref` paths in the [physicell_model_2](examples/SampleModel.ini#l20) model in the [examples/SampleModel.ini](examples/SampleModel.ini) section of [SampleModel.ini](examples/SampleModel.ini).
```ini
executable = [new path]
configFile_ref = [new path]
```
- Step 3: Execute the script:
```bash
python examples/ex2_runModel.py
```
## Example 3: Customizable Summary Function
- Requirements: A PhysiCell folder is required.
- Description: Run two simulations of [physicell_model_2](examples/SampleModel.ini#l18) using a customizable summary function to generate population time series. See [example 3](examples/ex3_runModelCust.py).
- **First simulation:** Runs the simulation while preserving the config files definitions and using a custom summary function.
- **Second simulation:** Similar to the first, but adjust the model for 4 OpenMP threads and returns a DataFrame instead of a summary file.
- Run script:
```bash
python examples/ex3_runModelCust.py
```
## Example 4: Sensitivity Analysis (Single Task)
- Requirements: A PhysiCell folder and the ``SALib`` Python package.
- Description: Perform sensitivity analysis using the Sobol method. See [example 4](examples/ex4_runSA_singletask.py).
- Run script:
```bash
python examples/ex4_runSA_singleTask.py
```
## Example 5: Sensitivity Analysis (Parallel Tasks with MPI)
- Requirements: A PhysiCell folder, and the `SALib` and `mpi4py` Python packages.
- Description: Perform sensitivity analysis using the Sobol method with MPI. See [example 5](examples/ex5_runSA_MPI.py).
- Run script:
```bash
mpiexec -n 2 python -m mpi4py examples/ex5_runSA_MPI.py
```
## Example 6: Sensitivity Analysis with Constrained Parameters (MPI).
- Requirements: A PhysiCell folder (SampleModel.ini assumes it is located in the examples folder) and the `SALib` and `mpi4py` Python packages. Compile the asymmetric_division example:
```bash
make reset && make asymmetric-division-sample && make
```
- Description: Perform sensitivity analysis (Sobol method) with MPI, handling constrained parameters. This example uses the `asymmetric_division` model from `PhysiCell's sample_projects` and includes analyzing `parameters of rules`. See [example 6](examples/ex6_runSA_AsymDiv.py).
- Run script:
```bash
mpiexec -n 2 python -m mpi4py examples/ex6_runSA_AsymDiv.py
```
Feel free to explore these examples to understand the package's capabilities and how to use it.
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"description": "# Installation\nInstall the package using pip:\n```\npip install uq_physicell\n```\n## External Modules\nThese modules must be installed separately. Install them using `pip`:\n```bash\npip install pandas numpy pcdl\n```\n[pcdl](https://github.com/elmbeech/physicelldataloader) is a Python package designed to load [PhysiCell](https://physicell.org) simulations in a Pythonic way.\n\n# Examples\nHere are some examples to help you get started with the package:\n\n## Example 1: Basic Usage\n - Description: Print information about two model structures, [physicell_model_1](examples/SampleModel.ini#l1) and [physicell_model_2](examples/SampleModel.ini#l18), as defined in the config file [examples/SampleModel.ini](examples/SampleModel.ini#l20). This operation does not run a PhysiCell simulation. See [example 1](examples/ex1_print.py).\n ```bash\n python examples/ex1_print.py\n ```\n\n## Example 2: Running PhysiCell Simulations\n - Requirements: A PhysiCell folder is required.\n - Description: Run three PhysiCell simulations associated with the key [physicell_model_2](examples/SampleModel.ini#l18) in the config file [SampleModel.ini](examples/SampleModel.ini). This corresponds to the `virus_macrophage` example in `PhysiCell's sample projects`. See [example 2](examples/ex2_runModel.py). \n - **First simulation:** Demonstrates running a simulation with a predefined summary function that summarizes the final population of live and dead cells, storing results in a new folder `output2`.\n - **Second simulation:** Runs the simulation while preserving the config files and retaining the complete PhysiCell output without summarization.\n - **Third simulation:** Configures the execution to summarize the output and returns a DataFrame with the summary.\n \n Run script:\n ```bash\n python examples/ex2_runModel.py\n ```\n \n Alternatively, download the lastest PhysiCell version with:\n ```bash\n bash examples/PhysiCell.sh\n ```\n This will create a folder named `PhysiCell-master` inside `examples`. Populate and compile the project (Step 1 below) without modifying [SampleModel.ini](examples/SampleModel.ini).\n - Step 1: Compile the `virus-macrophage` example in the PhysiCell folder:\n ```bash\n make reset && make virus-macrophage-sample && make\n ```\n - Step 2: Update the `executable` and `configFile_ref` paths in the [physicell_model_2](examples/SampleModel.ini#l20) model in the [examples/SampleModel.ini](examples/SampleModel.ini) section of [SampleModel.ini](examples/SampleModel.ini).\n ```ini\n executable = [new path]\n configFile_ref = [new path]\n ```\n - Step 3: Execute the script:\n ```bash\n python examples/ex2_runModel.py\n ``` \n\n## Example 3: Customizable Summary Function\n - Requirements: A PhysiCell folder is required.\n - Description: Run two simulations of [physicell_model_2](examples/SampleModel.ini#l18) using a customizable summary function to generate population time series. See [example 3](examples/ex3_runModelCust.py).\n - **First simulation:** Runs the simulation while preserving the config files definitions and using a custom summary function.\n - **Second simulation:** Similar to the first, but adjust the model for 4 OpenMP threads and returns a DataFrame instead of a summary file.\n - Run script:\n ```bash\n python examples/ex3_runModelCust.py\n ```\n\n## Example 4: Sensitivity Analysis (Single Task)\n - Requirements: A PhysiCell folder and the ``SALib`` Python package.\n - Description: Perform sensitivity analysis using the Sobol method. See [example 4](examples/ex4_runSA_singletask.py).\n - Run script:\n ```bash\n python examples/ex4_runSA_singleTask.py\n ```\n\n## Example 5: Sensitivity Analysis (Parallel Tasks with MPI)\n - Requirements: A PhysiCell folder, and the `SALib` and `mpi4py` Python packages.\n - Description: Perform sensitivity analysis using the Sobol method with MPI. See [example 5](examples/ex5_runSA_MPI.py).\n - Run script:\n ```bash\n mpiexec -n 2 python -m mpi4py examples/ex5_runSA_MPI.py\n ```\n\n## Example 6: Sensitivity Analysis with Constrained Parameters (MPI).\n - Requirements: A PhysiCell folder (SampleModel.ini assumes it is located in the examples folder) and the `SALib` and `mpi4py` Python packages. Compile the asymmetric_division example:\n ```bash\n make reset && make asymmetric-division-sample && make\n ```\n - Description: Perform sensitivity analysis (Sobol method) with MPI, handling constrained parameters. This example uses the `asymmetric_division` model from `PhysiCell's sample_projects` and includes analyzing `parameters of rules`. See [example 6](examples/ex6_runSA_AsymDiv.py).\n - Run script:\n ```bash\n mpiexec -n 2 python -m mpi4py examples/ex6_runSA_AsymDiv.py\n ```\n\nFeel free to explore these examples to understand the package's capabilities and how to use it.",
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