AMS-BP 0.0.2__tar.gz

ams_bp-0.0.2/.github/workflows/lint.yml

@@ -0,0 +1,26 @@
+name: ruff
+on: 
+  push:
+    branches:
+      - "master"
+    paths-ignore:
+      - "docs/**"
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      # Update output format to enable automatic inline annotations.
+      - name: Run Ruff
+        run: |
+          ruff check --fix
+          ruff format
+          ruff format --check --diff

ams_bp-0.0.2/.github/workflows/pages.yml

@@ -0,0 +1,36 @@
+name: pages
+on:
+  push:
+    branches:
+      - master 
+    paths:
+      - 'docs/**'
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install mkdocs and pymdown-extensions
+        run: |
+          python -m pip install --upgrade pip
+          pip install mkdocs mkdocs-material pymdown-extensions mkdocstrings-python
+
+      - run: python -m pip install -e .
+      - name: Build and deploy
+        run: |
+          mkdocs build
+          mkdocs gh-deploy --force
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

ams_bp-0.0.2/.github/workflows/publish_pypi.yml

@@ -0,0 +1,93 @@
+name: Publish Python 🐍 distribution 📦 to PyPI 
+
+on: push
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
+    - name: Set up Python
+      run: uv python install ${{ matrix.python-version }}
+    - name: Build a binary wheel and a source tarball
+      run: uv build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/AMS_BP  
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

ams_bp-0.0.2/.gitignore

@@ -0,0 +1,168 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

ams_bp-0.0.2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Baljyot Parmar
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ams_bp-0.0.2/PKG-INFO

@@ -0,0 +1,173 @@
+Metadata-Version: 2.4
+Name: AMS_BP
+Version: 0.0.2
+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>
+Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
+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
+Requires-Dist: scipy>=1.7.1
+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 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)
+- [Configuration File](#configuration-file)
+- [Running Experiments](#running-experiments)
+- [Advanced Usage](#advanced-usage)
+
+## Installation
+
+
+### ***Installing the CLI tool using UV***
+
+
+
+
+1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
+2. Run the command:
+```bash
+uv tool install AMS_BP
+```
+3. You will have access to two CLI commands (using the uv interface):
+    - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
+    - `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:
+
+```bash
+# Generate a default configuration file
+run_AMS_BP config [OPTIONS]
+
+# Run a simulation using a configuration file
+run_AMS_BP runsim CONFIG_FILE
+```
+
+### Config Command Options
+
+- `-o, --output_path PATH`: Specify the output directory for the configuration file
+- `-r, --recursive_o`: Create output directory if it doesn't exist
+
+## Configuration 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/).
+### Basic Units
+```toml
+version = "0.1"
+length_unit = "um"        # micrometers
+time_unit = "ms"          # milliseconds
+diffusion_unit = "um^2/s" # diffusion coefficient units
+```
+
+### Key Configuration Sections
+
+1. **Cell Parameters**
+   - Define cell space dimensions
+   - Set cell axial radius
+
+2. **Molecule Parameters**
+   - Number of molecules per type
+   - Tracking types (constant/fbm)
+   - Diffusion coefficients
+   - State transition probabilities
+
+3. **Global Parameters**
+   - Sample plane dimensions
+   - Cycle count -> Exposure time + Interval time
+   - Exposure and interval times
+
+4. **Fluorophore Configuration**
+   - Any number of fluorophores
+   - Any number of States per fluorophore
+   - Fluorophore StateType: (bright, dark, bleached) -> All States must be one of these.
+   - Transition parameters
+   - Spectral properties
+
+5. **Optical Configuration**
+   - PSF parameters
+   - Laser settings
+   - Channel configuration
+   - Camera settings
+
+## Running Experiments
+
+AMS-BP supports two types of experiments:
+
+### 1. Time Series
+```toml
+[experiment]
+experiment_type = "time-series"
+z_position = 0.0
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+### 2. Z-Stack
+```toml
+[experiment]
+experiment_type = "z-stack"
+z_position = [-0.5, -0.4, -0.3, -0.2, -0.1, 0, 0.1, 0.2, 0.3, 0.4, 0.5]
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+## Advanced Usage
+
+### Using AMS-BP as a Library
+
+For programmatic control, you can import and use AMS-BP as a Python library:
+
+```python
+from AMS_BP.configio.convertconfig import ConfigLoader
+
+# Configuration loader intialization
+config_loader = ConfigLoader(config_path="path/to/config.toml")
+
+# Setup microscope
+setup_config = config_loader.setup_microscope()
+microscope = setup_config["microscope"]
+config_exp = setup_config["experiment_config"]
+function_exp = setup_config["experiment_func"]
+
+# Run simulation
+frames, metadata = function_exp(microscope=microscope, config=config_exp)
+
+# Save results
+from AMS_BP.configio.saving import save_config_frames
+save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
+```

ams_bp-0.0.2/README.md

@@ -0,0 +1,152 @@
+# 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)
+- [Configuration File](#configuration-file)
+- [Running Experiments](#running-experiments)
+- [Advanced Usage](#advanced-usage)
+
+## Installation
+
+
+### ***Installing the CLI tool using UV***
+
+
+
+
+1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
+2. Run the command:
+```bash
+uv tool install AMS_BP
+```
+3. You will have access to two CLI commands (using the uv interface):
+    - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
+    - `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:
+
+```bash
+# Generate a default configuration file
+run_AMS_BP config [OPTIONS]
+
+# Run a simulation using a configuration file
+run_AMS_BP runsim CONFIG_FILE
+```
+
+### Config Command Options
+
+- `-o, --output_path PATH`: Specify the output directory for the configuration file
+- `-r, --recursive_o`: Create output directory if it doesn't exist
+
+## Configuration 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/).
+### Basic Units
+```toml
+version = "0.1"
+length_unit = "um"        # micrometers
+time_unit = "ms"          # milliseconds
+diffusion_unit = "um^2/s" # diffusion coefficient units
+```
+
+### Key Configuration Sections
+
+1. **Cell Parameters**
+   - Define cell space dimensions
+   - Set cell axial radius
+
+2. **Molecule Parameters**
+   - Number of molecules per type
+   - Tracking types (constant/fbm)
+   - Diffusion coefficients
+   - State transition probabilities
+
+3. **Global Parameters**
+   - Sample plane dimensions
+   - Cycle count -> Exposure time + Interval time
+   - Exposure and interval times
+
+4. **Fluorophore Configuration**
+   - Any number of fluorophores
+   - Any number of States per fluorophore
+   - Fluorophore StateType: (bright, dark, bleached) -> All States must be one of these.
+   - Transition parameters
+   - Spectral properties
+
+5. **Optical Configuration**
+   - PSF parameters
+   - Laser settings
+   - Channel configuration
+   - Camera settings
+
+## Running Experiments
+
+AMS-BP supports two types of experiments:
+
+### 1. Time Series
+```toml
+[experiment]
+experiment_type = "time-series"
+z_position = 0.0
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+### 2. Z-Stack
+```toml
+[experiment]
+experiment_type = "z-stack"
+z_position = [-0.5, -0.4, -0.3, -0.2, -0.1, 0, 0.1, 0.2, 0.3, 0.4, 0.5]
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+## Advanced Usage
+
+### Using AMS-BP as a Library
+
+For programmatic control, you can import and use AMS-BP as a Python library:
+
+```python
+from AMS_BP.configio.convertconfig import ConfigLoader
+
+# Configuration loader intialization
+config_loader = ConfigLoader(config_path="path/to/config.toml")
+
+# Setup microscope
+setup_config = config_loader.setup_microscope()
+microscope = setup_config["microscope"]
+config_exp = setup_config["experiment_config"]
+function_exp = setup_config["experiment_func"]
+
+# Run simulation
+frames, metadata = function_exp(microscope=microscope, config=config_exp)
+
+# Save results
+from AMS_BP.configio.saving import save_config_frames
+save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
+```