espirit 0.1.0__tar.gz

espirit-0.1.0/.github/workflows/python-publish.yml

@@ -0,0 +1,70 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

espirit-0.1.0/LICENSE

@@ -0,0 +1,60 @@
+MIT License
+
+Copyright (c) 2026 Oscar van der Heide
+
+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.
+
+---
+
+### Third-Party Software Attribution
+
+This package contains a PyTorch translation of the ESPIRiT implementation from the
+BART (Berkeley Advanced Reconstruction Toolbox):
+https://codeberg.org/mrirecon/bart
+
+Portions of this code are:
+Copyright (c) 2013-2026. The Regents of the University of California.
+Copyright (c) 2013-2026. BART Developer Team and Contributors.
+
+BART is licensed under the BSD 3-Clause License:
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

espirit-0.1.0/PKG-INFO

@@ -0,0 +1,80 @@
+Metadata-Version: 2.4
+Name: espirit
+Version: 0.1.0
+Summary: PyTorch-based ESPIRiT coil sensitivity calibration for MRI
+Project-URL: Repository, https://github.com/oscarvanderheide/espirit
+Author: Oscar van der Heide
+License: MIT
+License-File: LICENSE
+Keywords: coil-sensitivity,csm,espirit,medical-imaging,mri,pytorch
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Requires-Dist: numpy>=2.0
+Requires-Dist: torch>=2.0
+Description-Content-Type: text/markdown
+
+# ESPIRiT
+
+PyTorch-based ESPIRiT coil sensitivity calibration for MRI.
+
+Single codebase that runs on **CPU**, **CUDA GPU**, and **Apple Silicon (MPS)** — no separate code paths needed.
+
+## Notice
+
+This package contains a PyTorch translation of the ESPIRiT implementation from the BART (Berkeley Advanced Reconstruction Toolbox), © 2013–2026 The Regents of the University of California and BART Developer Team. BART is licensed under the BSD 3-Clause License. See https://codeberg.org/mrirecon/bart.
+
+## Installation
+
+```bash
+uv add espirit
+```
+
+## Usage
+
+### Command Line
+```bash
+uvx espirit kspace.npy
+```
+
+### Python API
+```python
+import numpy as np
+import torch
+from espirit import espirit
+
+# NumPy
+kspace_np = np.load("kspace.npy")
+csm_np = espirit(kspace_np)
+
+# PyTorch 
+kspace_torch = torch.randn(8, 24, 24, 24, dtype=torch.complex64)
+csm_torch = espirit(kspace_torch)
+```
+
+### Advanced
+All arguments for the `espirit()` function:
+```python
+csm = espirit(
+    kspace,             # (n_coils, *spatial_dims)
+    calib_size=24,      # size of calibration region
+    kernel_size=6,      # sliding-window kernel size
+    threshold=0.01,     # relative singular-value threshold
+    mask_threshold=0.8, # eigenvalue mask threshold
+    normalize=True,     # RSS=1 normalization
+    rotphase=True,      # remove global phase ambiguity
+    device=None         # auto-detect (cuda, mps, cpu)
+)
+```
+
+## Device support
+
+| Device | Backend | Notes |
+|--------|---------|-------|
+| `cpu`  | NumPy/MKL | Always available |
+| `cuda` | NVIDIA GPU | Requires CUDA toolkit |
+| `mps`  | Apple Metal | macOS with Apple Silicon |
+
+The same code runs on all devices — PyTorch handles dispatch automatically.

espirit-0.1.0/README.md

@@ -0,0 +1,62 @@
+# ESPIRiT
+
+PyTorch-based ESPIRiT coil sensitivity calibration for MRI.
+
+Single codebase that runs on **CPU**, **CUDA GPU**, and **Apple Silicon (MPS)** — no separate code paths needed.
+
+## Notice
+
+This package contains a PyTorch translation of the ESPIRiT implementation from the BART (Berkeley Advanced Reconstruction Toolbox), © 2013–2026 The Regents of the University of California and BART Developer Team. BART is licensed under the BSD 3-Clause License. See https://codeberg.org/mrirecon/bart.
+
+## Installation
+
+```bash
+uv add espirit
+```
+
+## Usage
+
+### Command Line
+```bash
+uvx espirit kspace.npy
+```
+
+### Python API
+```python
+import numpy as np
+import torch
+from espirit import espirit
+
+# NumPy
+kspace_np = np.load("kspace.npy")
+csm_np = espirit(kspace_np)
+
+# PyTorch 
+kspace_torch = torch.randn(8, 24, 24, 24, dtype=torch.complex64)
+csm_torch = espirit(kspace_torch)
+```
+
+### Advanced
+All arguments for the `espirit()` function:
+```python
+csm = espirit(
+    kspace,             # (n_coils, *spatial_dims)
+    calib_size=24,      # size of calibration region
+    kernel_size=6,      # sliding-window kernel size
+    threshold=0.01,     # relative singular-value threshold
+    mask_threshold=0.8, # eigenvalue mask threshold
+    normalize=True,     # RSS=1 normalization
+    rotphase=True,      # remove global phase ambiguity
+    device=None         # auto-detect (cuda, mps, cpu)
+)
+```
+
+## Device support
+
+| Device | Backend | Notes |
+|--------|---------|-------|
+| `cpu`  | NumPy/MKL | Always available |
+| `cuda` | NVIDIA GPU | Requires CUDA toolkit |
+| `mps`  | Apple Metal | macOS with Apple Silicon |
+
+The same code runs on all devices — PyTorch handles dispatch automatically.

espirit-0.1.0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "espirit"
+version = "0.1.0"
+description = "PyTorch-based ESPIRiT coil sensitivity calibration for MRI"
+readme = "README.md"
+requires-python = ">=3.12"
+authors = [
+    { name = "Oscar van der Heide" }
+]
+license = { text = "MIT" }
+keywords = ["espirit", "csm", "coil-sensitivity", "mri", "medical-imaging", "pytorch"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+]
+
+dependencies = [
+    "torch>=2.0",
+    "numpy>=2.0",
+]
+
+[project.scripts]
+espirit = "espirit.espirit:main"
+
+[project.urls]
+Repository = "https://github.com/oscarvanderheide/espirit"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/espirit"]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.0",
+]

espirit-0.1.0/src/espirit/__init__.py

@@ -0,0 +1,17 @@
+"""ESPIRiT — PyTorch-based coil sensitivity calibration for MRI."""
+
+from .device import available_devices, select_device
+from .espirit import espirit
+from .fft import fft2c, fft3c, ifft2c, ifft3c
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "espirit",
+    "select_device",
+    "available_devices",
+    "fft2c",
+    "fft3c",
+    "ifft2c",
+    "ifft3c",
+]

espirit-0.1.0/src/espirit/device.py

@@ -0,0 +1,39 @@
+"""Device selection utilities for ESPIRiT."""
+
+import torch
+
+
+def select_device(preference: str | None = None) -> torch.device:
+    """
+    Select the best available torch device.
+
+    Priority: cuda > mps > cpu (unless overridden by *preference*).
+
+    Parameters
+    ----------
+    preference : str, optional
+        Force a specific device ("cpu", "cuda", "mps").
+        When None, auto-detects the best available.
+
+    Returns
+    -------
+    torch.device
+    """
+    if preference is not None:
+        return torch.device(preference)
+
+    if torch.cuda.is_available():
+        return torch.device("cuda")
+    if torch.backends.mps.is_available():
+        return torch.device("mps")
+    return torch.device("cpu")
+
+
+def available_devices() -> list[torch.device]:
+    """Return a list of all available torch devices (for testing)."""
+    devices = [torch.device("cpu")]
+    if torch.cuda.is_available():
+        devices.append(torch.device("cuda"))
+    if torch.backends.mps.is_available():
+        devices.append(torch.device("mps"))
+    return devices