komamripy 0.0.2__tar.gz

komamripy-0.0.2/.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  # Keep GitHub Actions versions (checkout, setup-uv, cache, etc.) up to date.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      # Bundle all action bumps into one PR instead of one PR per action.
+      actions:
+        patterns:
+          - "*"

komamripy-0.0.2/.github/workflows/ci.yml

@@ -0,0 +1,76 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+      - name: Ruff lint
+        run: uv run --group lint ruff check .
+      - name: Ruff format check
+        run: uv run --group lint ruff format --check .
+
+  test:
+    name: Test (Python ${{ matrix.python-version }} - ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      # Python coverage (floor + ceiling) runs on Linux; Windows and macOS each
+      # run once at the ceiling. OS bugs are Python-version-independent and
+      # Python bugs are OS-independent, so this covers both axes without the
+      # full 3x2 cross-product -- and the floor never lands on the OS/old-Python
+      # cells that needed special handling, so one install path works for all.
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.10"
+          - os: ubuntu-latest
+            python-version: "3.14"
+          - os: macos-latest
+            python-version: "3.14"
+          - os: windows-latest
+            python-version: "3.14"
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/setup-python@v6
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+          check-latest: true
+
+      # Install a known-good Julia and force juliacall to use it (see
+      # PYTHON_JULIAPKG_EXE below), so it doesn't pick a runner Julia with
+      # broken embed paths.
+      - uses: julia-actions/setup-julia@v3
+        id: setup-julia
+        with:
+          version: "1.11"
+
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Cache Julia depot
+        uses: actions/cache@v6
+        with:
+          path: ~/.julia
+          key: julia-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('komamripy/juliapkg.json') }}
+
+      - name: Install package and test tools
+        run: uv sync --group test --python "${{ steps.setup-python.outputs.python-path }}"
+
+      - name: Run tests
+        env:
+          # Point juliapkg at the Julia installed above (full exe path, so
+          # juliacall can derive its bindir), instead of selecting a runner one.
+          PYTHON_JULIAPKG_EXE: ${{ steps.setup-julia.outputs.julia-bindir }}${{ runner.os == 'Windows' && '\julia.exe' || '/julia' }}
+        run: uv run --group test pytest -v -s

komamripy-0.0.2/.github/workflows/publish.yml

@@ -0,0 +1,38 @@
+name: Publish
+
+# Does not pin updated dependencies, full manual release
+# Manual release: triggered by pushing a version tag
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  pypi:
+    name: Publish package to PyPI
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      contents: read
+      id-token: write   # required for Trusted Publishing
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v7
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Build package
+        run: uv build
+
+      - name: Check package metadata
+        run: uv run --with twine python -m twine check dist/*
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

komamripy-0.0.2/.gitignore

@@ -0,0 +1,218 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

komamripy-0.0.2/.mailmap

@@ -0,0 +1 @@
+anvika-singhal <anvikasinghal@outlook.com> anvikasinghal <asinghal@caltech.edu>

komamripy-0.0.2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Carlos Castillo Passi
+
+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.

komamripy-0.0.2/PKG-INFO

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: komamripy
+Version: 0.0.2
+Summary: Pulseq-compatible, high-performance MRI simulation in Python, powered by KomaMRI.jl.
+Project-URL: Homepage, https://github.com/JuliaHealth/komamripy
+Project-URL: Repository, https://github.com/JuliaHealth/komamripy
+Project-URL: Issues, https://github.com/JuliaHealth/komamripy/issues
+Author: Anvika Singhal
+Author-email: Carlos Castillo Passi <cacp@stanford.edu>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: Julia,KomaMRI,MRI,Pulseq,medical-imaging,simulation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: juliacall>=0.9.20
+Description-Content-Type: text/markdown
+
+# komamripy
+
+[![CI](https://github.com/JuliaHealth/komamripy/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/JuliaHealth/komamripy/actions/workflows/ci.yml)
+
+**Pulseq-compatible, high-performance MRI simulation in Python.**
+
+`komamripy` is a thin Python interface to
+[KomaMRI.jl](https://github.com/JuliaHealth/KomaMRI.jl), a high-performance
+Julia framework for MRI simulation. It exposes KomaMRI to Python through
+[juliacall](https://juliapy.github.io/PythonCall.jl/stable/juliacall/), so
+Python users can run fast CPU/GPU MRI simulations without writing any Julia.
+
+## Installation
+
+Install by using [uv](https://docs.astral.sh/uv/) (recommended) or pip (remove uv):
+
+```bash
+uv pip install git+https://github.com/JuliaHealth/komamripy
+```
+
+You do **not** need to install Julia yourself: `juliacall` provisions a suitable
+Julia automatically, and KomaMRI is installed on first import.
+
+## Quick start
+
+The first import downloads Julia and precompiles KomaMRI, which can take a few
+minutes. Subsequent runs are fast.
+
+```python
+import komamripy as km
+import numpy as np
+
+sys = km.Scanner()                       # scanner hardware
+obj = km.brain_phantom2D()               # 2D brain phantom
+seq = km.PulseDesigner.EPI_example()     # example EPI sequence
+
+sim_params = km.KomaMRICore.default_sim_params()
+sim_params["return_type"] = "mat"        # return the raw signal matrix
+
+raw = km.simulate(obj, seq, sys, sim_params=sim_params)
+signal = np.asarray(raw)
+
+print(signal.shape)
+```
+
+A runnable version lives in [`examples/`](examples/).
+
+## How it works
+
+`komamripy` mirrors the KomaMRI Julia namespace: any function or type that
+KomaMRI exposes is available as an attribute of `komamripy`. Julia code
+therefore translates to Python almost line for line.
+
+Simulation results are returned as Julia objects; convert array-like results to
+NumPy with `numpy.asarray`.
+
+## Status
+
+`komamripy` is under active development as a Google Summer of Code project.
+
+Currently supported: the core simulation pipeline and reading Pulseq files.
+
+Planned: PyPI releases, GPU backend selection, tighter pypulseq integration,
+and differentiable workflows.

komamripy-0.0.2/README.md

@@ -0,0 +1,64 @@
+# komamripy
+
+[![CI](https://github.com/JuliaHealth/komamripy/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/JuliaHealth/komamripy/actions/workflows/ci.yml)
+
+**Pulseq-compatible, high-performance MRI simulation in Python.**
+
+`komamripy` is a thin Python interface to
+[KomaMRI.jl](https://github.com/JuliaHealth/KomaMRI.jl), a high-performance
+Julia framework for MRI simulation. It exposes KomaMRI to Python through
+[juliacall](https://juliapy.github.io/PythonCall.jl/stable/juliacall/), so
+Python users can run fast CPU/GPU MRI simulations without writing any Julia.
+
+## Installation
+
+Install by using [uv](https://docs.astral.sh/uv/) (recommended) or pip (remove uv):
+
+```bash
+uv pip install git+https://github.com/JuliaHealth/komamripy
+```
+
+You do **not** need to install Julia yourself: `juliacall` provisions a suitable
+Julia automatically, and KomaMRI is installed on first import.
+
+## Quick start
+
+The first import downloads Julia and precompiles KomaMRI, which can take a few
+minutes. Subsequent runs are fast.
+
+```python
+import komamripy as km
+import numpy as np
+
+sys = km.Scanner()                       # scanner hardware
+obj = km.brain_phantom2D()               # 2D brain phantom
+seq = km.PulseDesigner.EPI_example()     # example EPI sequence
+
+sim_params = km.KomaMRICore.default_sim_params()
+sim_params["return_type"] = "mat"        # return the raw signal matrix
+
+raw = km.simulate(obj, seq, sys, sim_params=sim_params)
+signal = np.asarray(raw)
+
+print(signal.shape)
+```
+
+A runnable version lives in [`examples/`](examples/).
+
+## How it works
+
+`komamripy` mirrors the KomaMRI Julia namespace: any function or type that
+KomaMRI exposes is available as an attribute of `komamripy`. Julia code
+therefore translates to Python almost line for line.
+
+Simulation results are returned as Julia objects; convert array-like results to
+NumPy with `numpy.asarray`.
+
+## Status
+
+`komamripy` is under active development as a Google Summer of Code project.
+
+Currently supported: the core simulation pipeline and reading Pulseq files.
+
+Planned: PyPI releases, GPU backend selection, tighter pypulseq integration,
+and differentiable workflows.

komamripy-0.0.2/examples/basic_simulation.py

@@ -0,0 +1,29 @@
+"""Minimal end-to-end example: simulate an EPI acquisition and read the signal.
+
+Run from the repository root after installing the package (see the README)::
+
+    python examples/basic_simulation.py
+"""
+
+import numpy as np
+
+import komamripy as km
+
+# Build the simulation inputs. These mirror KomaMRI's Julia API directly.
+sys = km.Scanner()
+obj = km.brain_phantom2D()
+seq = km.PulseDesigner.EPI_example()
+
+# Request the plain signal matrix.
+sim_params = km.KomaMRICore.default_sim_params()
+sim_params["return_type"] = "mat"
+
+# The first call compiles Julia code and may take a little while.
+raw = km.simulate(obj, seq, sys, sim_params=sim_params)
+
+# `raw` already behaves like an array: NumPy functions such as np.abs or np.sum
+# accept it directly. Use np.asarray only when you want a native NumPy array.
+signal = np.asarray(raw)
+
+print("signal shape:", signal.shape)
+print("first sample magnitudes:", np.abs(signal[:5]).ravel())

komamripy-0.0.2/komamripy/__init__.py

@@ -0,0 +1,56 @@
+"""komamripy — a Python interface to KomaMRI.jl, the Julia MRI simulator.
+
+komamripy mirrors the KomaMRI Julia namespace through juliacall: any name that
+KomaMRI exposes is available as an attribute of ``komamripy``. As a result,
+Julia code translates to Python almost line for line.
+
+Julia::
+
+    using KomaMRI
+    sys = Scanner()
+    obj = brain_phantom2D()
+    seq = PulseDesigner.EPI_example()
+    sim_params = KomaMRICore.default_sim_params()
+    raw = simulate(obj, seq, sys; sim_params)
+
+Python::
+
+    import komamripy as km
+    import numpy as np
+
+    sys = km.Scanner()
+    obj = km.brain_phantom2D()
+    seq = km.PulseDesigner.EPI_example()
+    sim_params = km.KomaMRICore.default_sim_params()
+    raw = km.simulate(obj, seq, sys, sim_params=sim_params)
+
+Simulation results are returned as Julia objects; use ``numpy.asarray`` to
+convert array-like results (such as a ``"mat"`` signal) into NumPy arrays.
+"""
+
+from ._session import get_julia
+
+
+def __getattr__(name):
+    """Resolve attribute access against the Julia session (the KomaMRI mirror).
+
+    Python invokes this only when normal module lookup fails, so anything
+    defined or imported in this module takes precedence, and the Julia session
+    starts lazily on the first real attribute access.
+
+    Note: any Python-side helper submodule added in future must be imported
+    explicitly in this file, otherwise the mirror would shadow it whenever its
+    name also exists in Julia (Julia's Base exports ``diff``, for instance).
+    """
+    # Avoid starting Julia just to answer dunder probes from the import system.
+    if name.startswith("__") and name.endswith("__"):
+        raise AttributeError(name)
+
+    jl = get_julia()
+
+    try:
+        return getattr(jl, name)
+    except AttributeError as exc:
+        raise AttributeError(
+            f"module 'komamripy' has no attribute '{name}'; KomaMRI does not expose it"
+        ) from exc

komamripy-0.0.2/komamripy/_session.py

@@ -0,0 +1,30 @@
+"""Management of the Julia session that backs komamripy.
+
+The Julia runtime and KomaMRI are loaded lazily on first use, so importing
+komamripy stays inexpensive until a Julia-backed feature is actually called.
+All access to Julia flows through :func:`get_julia`.
+"""
+
+from __future__ import annotations
+
+_session = None  # cached juliacall ``Main`` module, created on first use
+
+
+def get_julia():
+    """Return the initialized Julia ``Main`` module, starting it if needed.
+
+    On the first call this imports juliacall (which provisions a private Julia
+    if one is not already available), loads KomaMRI, and caches the resulting
+    ``Main`` module for reuse.
+
+    ``using KomaMRI`` is evaluated as source because ``using`` is Julia syntax
+    rather than a callable; every other interaction with KomaMRI uses ordinary
+    attribute access on the returned module.
+    """
+    global _session
+    if _session is None:
+        from juliacall import Main as jl
+
+        jl.seval("using KomaMRI")
+        _session = jl
+    return _session

komamripy-0.0.2/komamripy/juliapkg.json

@@ -0,0 +1,24 @@
+{
+  "packages": {
+    "KomaMRI": {
+      "uuid": "6a340f8b-2cdf-4c04-99be-4953d9b66d0a",
+      "version": "=0.10.4"
+    },
+    "KomaMRIBase": {
+      "uuid": "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c",
+      "version": "=0.11.3"
+    },
+    "KomaMRICore": {
+      "uuid": "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e",
+      "version": "=0.11.3"
+    },
+    "KomaMRIFiles": {
+      "uuid": "fcf631a6-1c7e-4e88-9e64-b8888386d9dc",
+      "version": "=0.10.4"
+    },
+    "KomaMRIPlots": {
+      "uuid": "76db0263-63f3-4d26-bb9a-5dba378db904",
+      "version": "=0.11.0"
+    }
+  }
+}

komamripy-0.0.2/pyproject.toml

@@ -0,0 +1,47 @@
+[project]
+name = "komamripy"
+version = "0.0.2"
+
+description = "Pulseq-compatible, high-performance MRI simulation in Python, powered by KomaMRI.jl."
+readme = "README.md"
+requires-python = ">=3.10"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Carlos Castillo Passi", email = "cacp@stanford.edu" },
+    { name = "Anvika Singhal" },
+]
+keywords = ["MRI", "simulation", "Pulseq", "KomaMRI", "Julia", "medical-imaging"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "juliacall >=0.9.20",
+]
+
+[project.urls]
+Homepage = "https://github.com/JuliaHealth/komamripy"
+Repository = "https://github.com/JuliaHealth/komamripy"
+Issues = "https://github.com/JuliaHealth/komamripy/issues"
+
+[dependency-groups]
+test = ["pytest", "numpy"]
+lint = ["ruff"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["komamripy"]
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "W", "B", "UP"]
+
+[tool.hatch.version]
+path = "komamripy/__init__.py"

komamripy-0.0.2/tests/test_integration.py

@@ -0,0 +1,21 @@
+"""Integration tests that exercise the Julia/KomaMRI backend end to end.
+Thorough tests to check functionality.
+"""
+
+import numpy as np
+
+import komamripy as km
+
+
+def test_epi_simulation_returns_signal():
+    sys = km.Scanner()
+    obj = km.brain_phantom2D()
+    seq = km.PulseDesigner.EPI_example()
+
+    sim_params = km.KomaMRICore.default_sim_params()
+    sim_params["return_type"] = "mat"
+
+    signal = np.asarray(km.simulate(obj, seq, sys, sim_params=sim_params))
+
+    assert np.iscomplexobj(signal)
+    assert signal.shape[0] == 10201