unimri 0.0.1a1__tar.gz

unimri-0.0.1a1/.gitignore

@@ -0,0 +1,66 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Distribution / packaging
+.Python
+build/
+dist/
+downloads/
+*.egg-info/
+.installed.cfg
+*.egg
+pip-wheel-metadata/
+
+# Virtual environments
+.venv/
+venv/
+env/
+ENV/
+
+# Test / coverage
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+.tox/
+.nox/
+.mypy_cache/
+.ruff_cache/
+.hypothesis/
+
+# Docs
+site/
+
+# Editors / OS
+.vscode/
+.idea/
+*.swp
+.DS_Store
+Thumbs.db
+
+# MRI data (do not commit patient / raw data)
+*.dat
+*.h5
+*.hdf5
+*.mrd
+*.ismrmrd
+*.mat
+*.npy
+*.npz
+*.7
+*.nii
+*.nii.gz
+*.cfl
+*.cfl.hdr
+# Anchored to repo root: unimri's own src/unimri/data/ package must not match.
+/data/
+/scratch/
+
+# Output images/arrays written by running the examples from the repo root
+# (tracked images belong in assets/, not the root)
+/*.png
+/*.npy
+/coverage.xml

unimri-0.0.1a1/CHANGELOG.md

@@ -0,0 +1,76 @@
+# Changelog
+
+All notable changes to this project are documented here. The format is based on
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project
+adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.0.1a1] - 2026-09-14
+
+First alpha release.
+
+### Added
+- Initial project scaffold: packaging, CI, documentation skeleton.
+- Design specification (`docs/architecture.md`, `docs/data-model.md`).
+- Public interfaces: `MRIData` and its components, `Reader` + reader registry,
+  `LinearOperator` with `IdentityOperator` / `ScaledOperator` /
+  `CompositeOperator` and an adjoint dot-test.
+- Contract test suite for the data model, operator algebra, and reader registry.
+- `unimri.testing`: analytic phantoms, trajectory generators (2D/3D radial,
+  stack-of-stars, Cartesian), a brute-force reference NDFT, and
+  `synthetic_dataset(pattern)` returning one valid `MRIData` per
+  `SamplingPattern` with known ground truth.
+- `examples/` — six runnable examples (data model, synthetic datasets, operator
+  algebra, reference radial reconstruction, custom reader, multinuclear) plus
+  the aspirational end-to-end API; `test_examples.py` runs them in CI.
+- `docs/acknowledgments.md` — credit for every library, standard, and method
+  UniMRI uses or is built to use, with licenses.
+- Project logo, architecture diagram, and README status badges.
+- API reference pages (`docs/reference/`, mkdocstrings) in the docs nav.
+- `SECURITY.md`, `RELEASING.md`, `.editorconfig`, `.github/dependabot.yml`,
+  `.github/ISSUE_TEMPLATE/config.yml`.
+- Version single-sourced from `src/unimri/__init__.py` via `hatch.version`;
+  a test keeps `CITATION.cff` in sync.
+- CI now runs on Linux/Windows/macOS, builds and `twine check`s the wheel, and
+  installs it in a clean env; a coverage floor of 80% is enforced.
+- Workflows: `docs.yml` deploys the MkDocs site to GitHub Pages; `release.yml`
+  publishes to PyPI via Trusted Publishing on a `v*` tag.
+- `NUFFTOperator` — FINUFFT-backed non-uniform FFT (2-D and 3-D), passes the
+  adjoint dot-test and matches the reference NDFT. Optional `nufft` extra.
+- `unimri.reconstruct(data, method="adjoint")` — centered inverse FFT for
+  Cartesian data, density-compensated NUFFT gridding for non-Cartesian, with
+  RSS / sum / no coil combination.
+- `examples/sodium_radial.py` — end-to-end reconstruction of real 3-D
+  density-adapted radial ²³Na data; `04` now uses `unimri.reconstruct`.
+- Trajectory axis convention pinned: `coords` row `d` pairs with image axis `d`
+  (`(kz, ky, kx)` for 3-D). `unimri.testing` trajectories and the docs updated.
+- `viz` extra (matplotlib) for the plotting examples.
+- `FourierOperator` (Cartesian, unnormalized/exact-adjoint convention matching
+  `NUFFTOperator` and the reference NDFT) and `SensitivityOperator` (coils),
+  both composable via `@`; `UncheckedOperator`/`unchecked()` for batched
+  (multi-coil) use through operators declared for a single instance.
+- `unimri.calibration.estimate_sensitivity(method="rss")` — RSS-normalized
+  coil sensitivity baseline.
+- `unimri.optimization.conjugate_gradient` — CG for `(AᴴA + l2·I)x = Aᴴy`.
+- `unimri.reconstruct(data, method="cg")` — CG-SENSE, trajectory-agnostic;
+  beats `"adjoint"` on undersampled/noisy radial data.
+- `examples/07_cg_sense.py`; `99_aspirational_api.py` trimmed to just the
+  still-missing reader half.
+- Fixed: `FourierOperator` previously used a unitary ("ortho") FFT convention
+  inconsistent with `NUFFTOperator`/`ndft`'s unnormalized convention -- caught
+  while wiring `reconstruct(method="cg")` to swap between them transparently.
+- Fixed: an unanchored `data/` pattern in `.gitignore` matched `src/unimri/data/`
+  (the `MRIData` data model) as well as the intended top-level scratch
+  directory, so it had never actually been committed -- every CI job and a
+  real wheel install failed on import. Anchored the pattern to the repo root.
+
+### Not yet implemented
+- All vendor readers (`ismrmrd`, `twix`, `hdf5`) — interfaces only.
+- All operators beyond the algebraic base (`fourier`, `nufft`, `sampling`,
+  `coil`) — docstring stubs only.
+- All reconstruction, calibration, preprocessing, optimization, pipeline stages.
+
+## [0.0.0]
+
+- Reserved for the first tagged scaffold commit.

unimri-0.0.1a1/CITATION.cff

@@ -0,0 +1,26 @@
+cff-version: 1.2.0
+title: "UniMRI: A Unified Python Framework for MRI Raw Data Processing and Reconstruction"
+message: "If you use this software, please cite it using these metadata."
+type: software
+authors:
+  - given-names: Istiyak Amin
+    family-names: Santo
+    alias: istiyakamin
+repository-code: "https://github.com/istiyakamin/UniMRI"
+url: "https://github.com/istiyakamin/UniMRI"
+abstract: >-
+  UniMRI is an open-source Python framework that provides a common data model and
+  computational abstraction layer for MRI raw data acquired from different
+  scanners, vendors, and acquisition strategies (Cartesian and non-Cartesian),
+  enabling reconstruction algorithms to operate independently of the original
+  vendor format.
+keywords:
+  - MRI
+  - image reconstruction
+  - k-space
+  - ISMRMRD
+  - non-Cartesian
+  - NUFFT
+license: MIT
+version: 0.0.1a1
+date-released: "2026-09-14"

unimri-0.0.1a1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Istiyak Amin Santo
+
+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.

unimri-0.0.1a1/PKG-INFO

@@ -0,0 +1,187 @@
+Metadata-Version: 2.5
+Name: unimri
+Version: 0.0.1a1
+Summary: A unified Python framework for MRI raw-data processing and reconstruction
+Project-URL: Homepage, https://github.com/istiyakamin/UniMRI
+Project-URL: Repository, https://github.com/istiyakamin/UniMRI
+Project-URL: Documentation, https://istiyakamin.github.io/UniMRI/
+Project-URL: Changelog, https://github.com/istiyakamin/UniMRI/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/istiyakamin/UniMRI/issues
+Author: Istiyak Amin Santo
+License: MIT License
+        
+        Copyright (c) 2026 Istiyak Amin Santo
+        
+        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.
+License-File: LICENSE
+Keywords: ismrmrd,k-space,mri,non-cartesian,nufft,reconstruction,twix
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: h5py>=3.8
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == 'dev'
+Requires-Dist: finufft>=2.2; extra == 'dev'
+Requires-Dist: matplotlib>=3.7; extra == 'dev'
+Requires-Dist: mypy>=1.11; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: tomli>=2.0; (python_version < '3.11') and extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.26; extra == 'docs'
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda12x>=13.0; extra == 'gpu'
+Provides-Extra: ismrmrd
+Requires-Dist: ismrmrd>=1.14; extra == 'ismrmrd'
+Provides-Extra: nufft
+Requires-Dist: finufft>=2.2; extra == 'nufft'
+Provides-Extra: torch
+Requires-Dist: torch>=2.1; extra == 'torch'
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == 'viz'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="assets/logo.png" alt="UniMRI — one interface for MRI raw data" width="380">
+</p>
+
+<h1 align="center">UniMRI</h1>
+
+<p align="center"><strong>One interface for MRI raw data.</strong></p>
+
+<p align="center">
+  <a href="https://github.com/istiyakamin/UniMRI/actions/workflows/ci.yml"><img src="https://github.com/istiyakamin/UniMRI/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <img src="https://img.shields.io/badge/status-pre--alpha-orange.svg" alt="Status: pre-alpha">
+  <img src="https://img.shields.io/badge/python-3.10%2B-blue.svg" alt="Python 3.10+">
+  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-blue.svg" alt="License: MIT"></a>
+  <a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff"></a>
+  <img src="https://img.shields.io/badge/types-typed-brightgreen.svg" alt="Typed">
+  <a href="https://istiyakamin.github.io/UniMRI/"><img src="https://img.shields.io/badge/docs-mkdocs-blue.svg" alt="Docs"></a>
+</p>
+
+<!-- Enable once the package is actually on PyPI (after the first `v0.0.1a1` tag publishes):
+  <a href="https://pypi.org/project/unimri/"><img src="https://img.shields.io/pypi/v/unimri.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/unimri/"><img src="https://img.shields.io/pypi/dm/unimri.svg?label=PyPI%20downloads" alt="PyPI downloads"></a>
+  <a href="https://doi.org/PLACEHOLDER"><img src="https://img.shields.io/badge/DOI-PLACEHOLDER-blue.svg" alt="DOI"></a>
+  <a href="https://securityscorecards.dev/viewer/?uri=github.com/istiyakamin/UniMRI"><img src="https://api.securityscorecards.dev/projects/github.com/istiyakamin/UniMRI/badge" alt="OpenSSF Scorecard"></a>
+-->
+
+UniMRI is an open-source Python framework that provides a common computational
+interface for MRI raw data across scanners, vendors, and acquisition strategies —
+Cartesian, radial, spiral, and other non-Cartesian trajectories — so that
+reconstruction algorithms can be written once and run on data from anywhere.
+
+> **Status: pre-alpha (v0.0.1a1).** The data model (`MRIData`), the operator
+> algebra, `FourierOperator`/`NUFFTOperator`/`SensitivityOperator`, and
+> `reconstruct(method="adjoint"|"cg")` — single-pass gridding and CG-SENSE, the
+> same code for Cartesian and non-Cartesian data — all work, validated on real
+> 3-D radial ²³Na data. The vendor readers (`unimri.read`) are still stubs. See
+> the [roadmap](docs/roadmap.md).
+
+> **Name caveat:** `UniMRI` / `unimri` is a provisional working name. A full
+> PyPI / GitHub / trademark clearance is still pending before any public release
+> or PyPI upload.
+
+## The idea
+
+The core problem is fragmentation: every vendor format has its own loader, and
+every reconstruction toolbox has its own data model. UniMRI normalizes vendor
+raw data into one representation, then reconstructs from that.
+
+<p align="center">
+  <img src="assets/idea.png" alt="UniMRI pipeline: raw data from any vendor (Siemens TWIX, GE P-file, Philips RAW, ISMRMRD, HDF5) flows through the I/O layer (format detection + reader registry), into the unified MRIData model (k-space, trajectory, encoding, coils, metadata, provenance), through the operator layer (reconstruction as an inverse problem, y = P F S x), through reconstruction (FFT, SENSE, GRAPPA, CG-SENSE, compressed sensing), to an MRI image — vendor- and trajectory-independent." width="560">
+</p>
+
+## Aspirational API
+
+```python
+import unimri
+
+raw = unimri.read("measurement.dat")  # vendor-agnostic -- NOT YET (docs/roadmap.md, M2)
+image = unimri.reconstruct(raw, method="cg")  # trajectory-agnostic -- WORKS TODAY
+```
+
+```python
+# advanced: reconstruction as an inverse problem -- WORKS TODAY (see examples/07_cg_sense.py)
+from unimri.calibration import estimate_sensitivity
+from unimri.operators import FourierOperator, NUFFTOperator, SensitivityOperator, unchecked
+from unimri.optimization import conjugate_gradient
+
+maps = estimate_sensitivity(raw)
+F = (
+    NUFFTOperator(raw.trajectory, image_shape)
+    if not raw.is_cartesian
+    else FourierOperator(image_shape)
+)
+A = unchecked(F @ SensitivityOperator(maps))
+image = conjugate_gradient(A, raw.kspace, n_iter=30)
+```
+
+The reconstruction half works today (see `examples/`); `unimri.read` for vendor
+formats does not yet.
+
+## Installation (development)
+
+```bash
+git clone https://github.com/istiyakamin/UniMRI
+cd UniMRI
+python -m venv .venv && source .venv/bin/activate   # Windows: .venv\Scripts\activate
+pip install -e ".[dev]"
+pytest
+```
+
+GPU and vendor-specific support are optional extras: `pip install -e ".[gpu]"`,
+`".[torch]"`, `".[ismrmrd]"`.
+
+## Documentation
+
+- [Architecture](docs/architecture.md) — the layered design and the operator model
+- [Data model](docs/data-model.md) — `MRIData` schema and unit conventions
+- [I/O & format support](docs/io-format-support.md)
+- [Roadmap](docs/roadmap.md)
+- [Prior art](docs/prior-art.md) — how UniMRI relates to `mrpro`, `mri-nufft`,
+  `sigpy`, BART, ISMRMRD/Gadgetron, and others
+- [Acknowledgments](docs/acknowledgments.md) — every library, standard, and
+  method UniMRI uses, with credit
+
+## Contributing
+
+UniMRI is meant to grow as a community project. See
+[CONTRIBUTING.md](CONTRIBUTING.md) and the
+[good first issues](https://github.com/istiyakamin/UniMRI/labels/good%20first%20issue).
+
+## Acknowledgments
+
+UniMRI builds on the open-source scientific Python ecosystem — NumPy, SciPy,
+h5py, and (as it grows) ISMRMRD, MRI-NUFFT, SigPy, BART, twixtools, PyTorch, and
+others, plus published reconstruction methods credited to their originators. The
+full list with licenses is in [docs/acknowledgments.md](docs/acknowledgments.md).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

unimri-0.0.1a1/README.md

@@ -0,0 +1,119 @@
+<p align="center">
+  <img src="assets/logo.png" alt="UniMRI — one interface for MRI raw data" width="380">
+</p>
+
+<h1 align="center">UniMRI</h1>
+
+<p align="center"><strong>One interface for MRI raw data.</strong></p>
+
+<p align="center">
+  <a href="https://github.com/istiyakamin/UniMRI/actions/workflows/ci.yml"><img src="https://github.com/istiyakamin/UniMRI/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <img src="https://img.shields.io/badge/status-pre--alpha-orange.svg" alt="Status: pre-alpha">
+  <img src="https://img.shields.io/badge/python-3.10%2B-blue.svg" alt="Python 3.10+">
+  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-blue.svg" alt="License: MIT"></a>
+  <a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff"></a>
+  <img src="https://img.shields.io/badge/types-typed-brightgreen.svg" alt="Typed">
+  <a href="https://istiyakamin.github.io/UniMRI/"><img src="https://img.shields.io/badge/docs-mkdocs-blue.svg" alt="Docs"></a>
+</p>
+
+<!-- Enable once the package is actually on PyPI (after the first `v0.0.1a1` tag publishes):
+  <a href="https://pypi.org/project/unimri/"><img src="https://img.shields.io/pypi/v/unimri.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/unimri/"><img src="https://img.shields.io/pypi/dm/unimri.svg?label=PyPI%20downloads" alt="PyPI downloads"></a>
+  <a href="https://doi.org/PLACEHOLDER"><img src="https://img.shields.io/badge/DOI-PLACEHOLDER-blue.svg" alt="DOI"></a>
+  <a href="https://securityscorecards.dev/viewer/?uri=github.com/istiyakamin/UniMRI"><img src="https://api.securityscorecards.dev/projects/github.com/istiyakamin/UniMRI/badge" alt="OpenSSF Scorecard"></a>
+-->
+
+UniMRI is an open-source Python framework that provides a common computational
+interface for MRI raw data across scanners, vendors, and acquisition strategies —
+Cartesian, radial, spiral, and other non-Cartesian trajectories — so that
+reconstruction algorithms can be written once and run on data from anywhere.
+
+> **Status: pre-alpha (v0.0.1a1).** The data model (`MRIData`), the operator
+> algebra, `FourierOperator`/`NUFFTOperator`/`SensitivityOperator`, and
+> `reconstruct(method="adjoint"|"cg")` — single-pass gridding and CG-SENSE, the
+> same code for Cartesian and non-Cartesian data — all work, validated on real
+> 3-D radial ²³Na data. The vendor readers (`unimri.read`) are still stubs. See
+> the [roadmap](docs/roadmap.md).
+
+> **Name caveat:** `UniMRI` / `unimri` is a provisional working name. A full
+> PyPI / GitHub / trademark clearance is still pending before any public release
+> or PyPI upload.
+
+## The idea
+
+The core problem is fragmentation: every vendor format has its own loader, and
+every reconstruction toolbox has its own data model. UniMRI normalizes vendor
+raw data into one representation, then reconstructs from that.
+
+<p align="center">
+  <img src="assets/idea.png" alt="UniMRI pipeline: raw data from any vendor (Siemens TWIX, GE P-file, Philips RAW, ISMRMRD, HDF5) flows through the I/O layer (format detection + reader registry), into the unified MRIData model (k-space, trajectory, encoding, coils, metadata, provenance), through the operator layer (reconstruction as an inverse problem, y = P F S x), through reconstruction (FFT, SENSE, GRAPPA, CG-SENSE, compressed sensing), to an MRI image — vendor- and trajectory-independent." width="560">
+</p>
+
+## Aspirational API
+
+```python
+import unimri
+
+raw = unimri.read("measurement.dat")  # vendor-agnostic -- NOT YET (docs/roadmap.md, M2)
+image = unimri.reconstruct(raw, method="cg")  # trajectory-agnostic -- WORKS TODAY
+```
+
+```python
+# advanced: reconstruction as an inverse problem -- WORKS TODAY (see examples/07_cg_sense.py)
+from unimri.calibration import estimate_sensitivity
+from unimri.operators import FourierOperator, NUFFTOperator, SensitivityOperator, unchecked
+from unimri.optimization import conjugate_gradient
+
+maps = estimate_sensitivity(raw)
+F = (
+    NUFFTOperator(raw.trajectory, image_shape)
+    if not raw.is_cartesian
+    else FourierOperator(image_shape)
+)
+A = unchecked(F @ SensitivityOperator(maps))
+image = conjugate_gradient(A, raw.kspace, n_iter=30)
+```
+
+The reconstruction half works today (see `examples/`); `unimri.read` for vendor
+formats does not yet.
+
+## Installation (development)
+
+```bash
+git clone https://github.com/istiyakamin/UniMRI
+cd UniMRI
+python -m venv .venv && source .venv/bin/activate   # Windows: .venv\Scripts\activate
+pip install -e ".[dev]"
+pytest
+```
+
+GPU and vendor-specific support are optional extras: `pip install -e ".[gpu]"`,
+`".[torch]"`, `".[ismrmrd]"`.
+
+## Documentation
+
+- [Architecture](docs/architecture.md) — the layered design and the operator model
+- [Data model](docs/data-model.md) — `MRIData` schema and unit conventions
+- [I/O & format support](docs/io-format-support.md)
+- [Roadmap](docs/roadmap.md)
+- [Prior art](docs/prior-art.md) — how UniMRI relates to `mrpro`, `mri-nufft`,
+  `sigpy`, BART, ISMRMRD/Gadgetron, and others
+- [Acknowledgments](docs/acknowledgments.md) — every library, standard, and
+  method UniMRI uses, with credit
+
+## Contributing
+
+UniMRI is meant to grow as a community project. See
+[CONTRIBUTING.md](CONTRIBUTING.md) and the
+[good first issues](https://github.com/istiyakamin/UniMRI/labels/good%20first%20issue).
+
+## Acknowledgments
+
+UniMRI builds on the open-source scientific Python ecosystem — NumPy, SciPy,
+h5py, and (as it grows) ISMRMRD, MRI-NUFFT, SigPy, BART, twixtools, PyTorch, and
+others, plus published reconstruction methods credited to their originators. The
+full list with licenses is in [docs/acknowledgments.md](docs/acknowledgments.md).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

unimri-0.0.1a1/docs/acknowledgments.md

@@ -0,0 +1,109 @@
+# Acknowledgments
+
+UniMRI stands on a large body of open-source scientific software. This page
+credits every library, standard, and method the project uses or is built to use.
+Licenses are noted where known; consult each project for the authoritative terms.
+
+## Runtime dependencies
+
+Libraries imported by the UniMRI core (`pip install unimri`):
+
+| Library | Used for | License |
+| --- | --- | --- |
+| [NumPy](https://numpy.org) | n-dimensional arrays; the default compute backend | BSD-3-Clause |
+| [SciPy](https://scipy.org) | signal processing, linear algebra, spatial transforms | BSD-3-Clause |
+| [h5py](https://www.h5py.org) | reading/writing HDF5 (ISMRMRD, UniMRI's cache format) | BSD-3-Clause |
+
+UniMRI targets the [Python Array API standard](https://data-apis.org/array-api/)
+so that operators can run on NumPy, CuPy, or PyTorch arrays unchanged.
+
+## Optional integrations
+
+Enabled through extras (`pip install "unimri[...]"`):
+
+| Library | Extra | Used for | License |
+| --- | --- | --- | --- |
+| [FINUFFT](https://github.com/flatironinstitute/finufft) | `nufft` | the non-uniform FFT behind `NUFFTOperator` and non-Cartesian reconstruction | Apache-2.0 |
+| [Matplotlib](https://matplotlib.org) | `viz` | plotting in the examples | Matplotlib (BSD-style) |
+| [ISMRMRD (Python)](https://github.com/ismrmrd/ismrmrd-python) | `ismrmrd` | reading ISMRMRD raw data | permissive (see project) |
+| [PyTorch](https://pytorch.org) | `torch` | GPU / autograd array backend; unrolled-network reconstruction later | BSD-3-Clause |
+| [CuPy](https://cupy.dev) | `gpu` | CUDA array backend | MIT |
+
+## Planned dependencies
+
+These will be wrapped behind UniMRI interfaces as the corresponding milestones
+land (see the [roadmap](roadmap.md)); UniMRI does not reimplement them.
+
+| Library | Will be used for | License |
+| --- | --- | --- |
+| [twixtools](https://github.com/pehses/twixtools) (P. Ehses) | parsing Siemens TWIX `.dat` files | MIT |
+| [MRI-NUFFT](https://github.com/mind-inria/mri-nufft) | broader NUFFT backend (GPU, more kernels) behind the same `NUFFTOperator` interface | BSD-3-Clause |
+| [cufinufft](https://github.com/flatironinstitute/finufft) | GPU NUFFT backend | Apache-2.0 |
+| [gpuNUFFT](https://github.com/andyschwarzl/gpuNUFFT) | GPU gridding backend (via MRI-NUFFT) | MIT |
+| [torchkbnufft](https://github.com/mmuckley/torchkbnufft) (M. Muckley) | differentiable Kaiser–Bessel NUFFT (via MRI-NUFFT) | MIT |
+| [SigPy](https://github.com/mikgroup/sigpy) | reference parallel-imaging / compressed-sensing recon, ESPIRiT | BSD-3-Clause |
+| [BART](https://mrirecon.github.io/bart/) | optional reference calibration & iterative reconstruction | BSD-3-Clause |
+| [array-api-compat](https://github.com/data-apis/array-api-compat) | array-backend compatibility, if a full shim becomes necessary | MIT |
+
+## Development and documentation tooling
+
+| Tool | Role | License |
+| --- | --- | --- |
+| [Hatch / hatchling](https://hatch.pypa.io) | build backend | MIT |
+| [pytest](https://pytest.org) + [pytest-cov](https://github.com/pytest-dev/pytest-cov) | test runner and coverage | MIT |
+| [Ruff](https://docs.astral.sh/ruff/) | linter and formatter | MIT |
+| [mypy](https://mypy-lang.org) | static type checking | MIT |
+| [MkDocs](https://www.mkdocs.org) + [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) | documentation site | BSD-2-Clause / MIT |
+| [mkdocstrings](https://mkdocstrings.github.io) | API docs from docstrings | ISC |
+| [pre-commit](https://pre-commit.com) | git hook management | MIT |
+| [GitHub Actions](https://github.com/features/actions) | continuous integration | — |
+
+## Standards and community templates
+
+- [ISMRMRD](https://ismrmrd.github.io) — the raw-data interchange format UniMRI
+  interoperates with (Inati et al., *Magn Reson Med* 2017).
+- [Python Array API standard](https://data-apis.org/array-api/) — the backend
+  abstraction contract.
+- [Contributor Covenant](https://www.contributor-covenant.org) — the Code of
+  Conduct.
+- [Keep a Changelog](https://keepachangelog.com) and
+  [Semantic Versioning](https://semver.org) — changelog and version scheme.
+- [Citation File Format](https://citation-file-format.github.io) — `CITATION.cff`.
+
+## Methods and algorithms
+
+UniMRI implements or will implement the following published methods; credit is to
+their originators, with full citations added alongside each implementation:
+
+- **Shepp–Logan phantom** — Shepp & Logan (1974); the modified (Toft) variant
+  used by `unimri.testing.phantoms`.
+- **Golden-angle radial sampling** — Winkelmann et al. (2007).
+- **Density-adapted 3D projection reconstruction** — Nagel et al. (2009); the
+  primary non-Cartesian / X-nuclei target.
+- **Sampling density compensation (iterative)** — Pipe & Menon (1999).
+- **ESPIRiT** coil-sensitivity calibration — Uecker et al. (2014).
+- **POCS / homodyne** partial-Fourier reconstruction — Haacke et al.; Noll et al.
+- **CG-SENSE** — Pruessmann et al. (2001).
+
+## Inspiration and prior art
+
+UniMRI's unified-data-model + operator-based design follows earlier work,
+discussed in detail in [Prior art](prior-art.md):
+
+- [MRIReco.jl](https://github.com/MagneticResonanceImaging/MRIReco.jl) — the same
+  thesis, in Julia (Knopp & Grosser, *Magn Reson Med* 2021).
+- [mrpro](https://github.com/PTB-MR/mrpro) — a PyTorch MR reconstruction
+  framework with a closely related architecture.
+- [Gadgetron](https://github.com/gadgetron/gadgetron) — streaming reconstruction
+  and vendor converters (Hansen & Sørensen, *Magn Reson Med* 2013).
+- [fastMRI](https://github.com/facebookresearch/fastMRI),
+  [PyQMRI](https://github.com/IMTtugraz/PyQMRI),
+  [DIRECT](https://github.com/NKI-AI/direct) — adjacent toolkits.
+- [mapVBVD](https://github.com/CIC-methods/FID-A) / pymapVBVD — Siemens raw
+  reading, the lineage `twixtools` comes from.
+
+## Getting credit right
+
+If your library or method is used by UniMRI and is missing, mis-licensed, or
+mis-attributed here, please open an issue or pull request — corrections are
+welcome and appreciated.