mlx-reason-ct 0.1.0__tar.gz

mlx_reason_ct-0.1.0/.git

@@ -0,0 +1 @@
+gitdir: /Users/js/Developer/GitHub/NV-Reason-CT-MLX/.git/worktrees/NV-Reason-CT-MLX

mlx_reason_ct-0.1.0/.gitignore

@@ -0,0 +1,14 @@
+.venv/
+__pycache__/
+.pytest_cache/
+.ruff_cache/
+dist/
+build/
+*.egg-info/
+models/
+outputs/
+.cache/
+*.safetensors
+*.nii
+*.nii.gz
+.DS_Store

mlx_reason_ct-0.1.0/AGENTS.md

@@ -0,0 +1,14 @@
+# MLX-Reason-CT
+
+- Project: MLX-Reason-CT; package/CLI: `mlx-reason-ct`.
+- Repository: `sandovaljoseph/MLX-Reason-CT`; public code repository; retain separate model-material licensing.
+- Preset: base. Python 3.12; pinned dependencies in `pyproject.toml` and `uv.lock`.
+- Inference: macOS Apple Silicon Metal only, FP32 only. CPU preprocessing,
+  conversion and bundle verification are portable. No runtime fallback.
+- Port additions: Apache-2.0, Copyright (c) 2026 Joseph Sandoval.
+  Preserve upstream OpenMDW-1.1, Apache-2.0, MIT and BSD notices.
+- Keep the package independent of application registries and project/run frameworks.
+- Preserve pinned checkpoint, tokenizer, template, geometry and numerical contracts.
+- Run `make env`, `make qa`, and `make build` for package changes.
+- Use only synthetic CT fixtures; generated reports require human review.
+- Keep weights and local outputs outside Git. Do not add hosted CI.

mlx_reason_ct-0.1.0/LICENSE

@@ -0,0 +1,203 @@
+Copyright 2018- The Hugging Face team. All rights reserved.
+
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mlx_reason_ct-0.1.0/Makefile

@@ -0,0 +1,20 @@
+.PHONY: env lint typecheck test qa build
+
+env:
+	uv sync --locked --python 3.12
+
+lint:
+	uv run --locked ruff check .
+	uv run --locked ruff format --check .
+
+typecheck:
+	uv run --locked pyright --project . --warnings
+	uv run --locked pyright --verifytypes mlx_reason_ct --ignoreexternal
+
+test:
+	uv run --locked python -m pytest -q
+
+qa: lint typecheck test
+
+build:
+	uv build

mlx_reason_ct-0.1.0/PKG-INFO

@@ -0,0 +1,110 @@
+Metadata-Version: 2.4
+Name: mlx-reason-ct
+Version: 0.1.0
+Summary: Native MLX port of NVIDIA NV-Reason-CT for 3D CT reasoning on Apple Silicon
+Project-URL: Homepage, https://github.com/sandovaljoseph/MLX-Reason-CT
+Project-URL: Repository, https://github.com/sandovaljoseph/MLX-Reason-CT
+Project-URL: Documentation, https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/docs/usage.md
+Project-URL: Issues, https://github.com/sandovaljoseph/MLX-Reason-CT/issues
+Project-URL: Weights, https://huggingface.co/josand/MLX-Reason-CT
+Author: Joseph Sandoval
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Keywords: apple-silicon,ct,medical-imaging,mlx,nv-reason-ct
+Requires-Python: <3.13,>=3.12
+Requires-Dist: huggingface-hub==1.23.0
+Requires-Dist: jinja2==3.1.6
+Requires-Dist: mlx==0.32.2; sys_platform == 'darwin' and platform_machine == 'arm64'
+Requires-Dist: nibabel==5.4.2
+Requires-Dist: numpy==2.3.5
+Requires-Dist: safetensors==0.8.0
+Requires-Dist: scipy==1.18.1
+Requires-Dist: tokenizers==0.22.2
+Description-Content-Type: text/markdown
+
+# MLX-Reason-CT
+
+Native MLX port of [NVIDIA NV-Reason-CT](https://huggingface.co/nvidia/NV-Reason-CT)
+for Apple Silicon. Run 3D CT reasoning and report generation locally on Mac.
+
+- Chest and abdomen CT
+- Structured reports and CT question answering
+- Local NIfTI input with Apple Silicon GPU acceleration
+- FP32 inference using MLX; no PyTorch or CUDA required
+
+MLX port by **Joseph Sandoval**.
+[PyPI](https://pypi.org/project/mlx-reason-ct/) ·
+[Weights](https://huggingface.co/josand/MLX-Reason-CT) ·
+[Usage](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/docs/usage.md)
+
+## Requirements
+
+Apple Silicon Mac, macOS, Python 3.12 and [uv](https://docs.astral.sh/uv/).
+Weights occupy 17.4 GB. Measured peak MLX memory use is about 22.7 GB;
+allow additional unified memory for preprocessing, macOS and other apps.
+
+## Quick start
+
+```bash
+uv tool install --python 3.12 mlx-reason-ct
+
+mlx-reason-ct download \
+  --revision e15558ae30c8ad6c25c0bfcce7467cc72cd0b2f2 \
+  --model-dir models
+```
+
+Generate a chest CT report:
+
+```bash
+mlx-reason-ct report \
+  --input ct.nii.gz --model-dir models --output-dir outputs
+```
+
+For abdomen CT:
+
+```bash
+mlx-reason-ct report \
+  --input ct.nii.gz --model-dir models --output-dir outputs \
+  --anatomy-region abdomen
+```
+
+To ask a question about the CT, set `--prompt` to your question.
+
+For an existing Python 3.12 environment, install with `pip install mlx-reason-ct`.
+For source development, clone [this repository](https://github.com/sandovaljoseph/MLX-Reason-CT)
+and run `make env`; use
+`uv run mlx-reason-ct` for the commands above.
+
+## Input and output
+
+Input is one 3D CT volume in NIfTI format (`.nii` or `.nii.gz`) with Hounsfield
+Unit values and valid spatial geometry. DICOM and 2D images are unsupported.
+
+The upstream crop locates the chest from enclosed air. On whole-body scans,
+especially with arms raised, it can select the head and neck instead; crop such
+volumes to the chest or abdomen before running.
+
+Each run writes:
+
+- `report.txt` — generated response
+- `model_response.json` — response, reasoning (with `--enable-thinking`) and generation metadata
+- `run.json` — execution metadata
+
+## Technical details
+
+This release uses FP32 inference with weights converted directly from the
+original BF16 checkpoint, without retraining. Implementation and verification
+details, including token-exact parity with the CUDA source model on real CT, are in
+[docs](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/docs/usage.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Code: [Apache-2.0](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/LICENSE), Joseph Sandoval.
+Weights: [OpenMDW-1.1](https://huggingface.co/josand/MLX-Reason-CT/blob/main/LICENSE), NVIDIA CORPORATION & AFFILIATES.
+[Third-party notices](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/THIRD_PARTY_NOTICES.md).

mlx_reason_ct-0.1.0/README.md

@@ -0,0 +1,85 @@
+# MLX-Reason-CT
+
+Native MLX port of [NVIDIA NV-Reason-CT](https://huggingface.co/nvidia/NV-Reason-CT)
+for Apple Silicon. Run 3D CT reasoning and report generation locally on Mac.
+
+- Chest and abdomen CT
+- Structured reports and CT question answering
+- Local NIfTI input with Apple Silicon GPU acceleration
+- FP32 inference using MLX; no PyTorch or CUDA required
+
+MLX port by **Joseph Sandoval**.
+[PyPI](https://pypi.org/project/mlx-reason-ct/) ·
+[Weights](https://huggingface.co/josand/MLX-Reason-CT) ·
+[Usage](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/docs/usage.md)
+
+## Requirements
+
+Apple Silicon Mac, macOS, Python 3.12 and [uv](https://docs.astral.sh/uv/).
+Weights occupy 17.4 GB. Measured peak MLX memory use is about 22.7 GB;
+allow additional unified memory for preprocessing, macOS and other apps.
+
+## Quick start
+
+```bash
+uv tool install --python 3.12 mlx-reason-ct
+
+mlx-reason-ct download \
+  --revision e15558ae30c8ad6c25c0bfcce7467cc72cd0b2f2 \
+  --model-dir models
+```
+
+Generate a chest CT report:
+
+```bash
+mlx-reason-ct report \
+  --input ct.nii.gz --model-dir models --output-dir outputs
+```
+
+For abdomen CT:
+
+```bash
+mlx-reason-ct report \
+  --input ct.nii.gz --model-dir models --output-dir outputs \
+  --anatomy-region abdomen
+```
+
+To ask a question about the CT, set `--prompt` to your question.
+
+For an existing Python 3.12 environment, install with `pip install mlx-reason-ct`.
+For source development, clone [this repository](https://github.com/sandovaljoseph/MLX-Reason-CT)
+and run `make env`; use
+`uv run mlx-reason-ct` for the commands above.
+
+## Input and output
+
+Input is one 3D CT volume in NIfTI format (`.nii` or `.nii.gz`) with Hounsfield
+Unit values and valid spatial geometry. DICOM and 2D images are unsupported.
+
+The upstream crop locates the chest from enclosed air. On whole-body scans,
+especially with arms raised, it can select the head and neck instead; crop such
+volumes to the chest or abdomen before running.
+
+Each run writes:
+
+- `report.txt` — generated response
+- `model_response.json` — response, reasoning (with `--enable-thinking`) and generation metadata
+- `run.json` — execution metadata
+
+## Technical details
+
+This release uses FP32 inference with weights converted directly from the
+original BF16 checkpoint, without retraining. Implementation and verification
+details, including token-exact parity with the CUDA source model on real CT, are in
+[docs](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/docs/usage.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Code: [Apache-2.0](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/LICENSE), Joseph Sandoval.
+Weights: [OpenMDW-1.1](https://huggingface.co/josand/MLX-Reason-CT/blob/main/LICENSE), NVIDIA CORPORATION & AFFILIATES.
+[Third-party notices](https://github.com/sandovaljoseph/MLX-Reason-CT/blob/main/THIRD_PARTY_NOTICES.md).

mlx_reason_ct-0.1.0/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,218 @@
+# Third-party notices
+
+MLX-Reason-CT
+Copyright (c) 2026 Joseph Sandoval
+
+The original contributions to this standalone port are licensed under Apache-2.0.
+This does not replace the licenses or notices of upstream portions or model materials.
+
+NV-Reason-CT model architecture, processor policy, tokenizer, template, configuration
+and converted parameters originate from NVIDIA CORPORATION & AFFILIATES.
+Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+These Model Materials retain OpenMDW-1.1; see the NVIDIA license below.
+
+The vendored MLX-LM gated_delta.py retains Copyright (c) 2025 Apple Inc. and MIT terms.
+The complete upstream license texts are retained below.
+
+| Material | Origin and pinned version | Terms |
+| --- | --- | --- |
+| Model architecture, converted weights, tokenizer, template, processor policy and configuration | [NVIDIA NV-Reason-CT](https://huggingface.co/nvidia/NV-Reason-CT/tree/386b93e034983f6c1fc841a43833a1b6a0cd9c13), revision `386b93e034983f6c1fc841a43833a1b6a0cd9c13`; Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES | [OpenMDW-1.1](#nvidia-openmdw-11) |
+| Physical resampling extent and spacing semantics | [MONAI](https://github.com/Project-MONAI/MONAI), 1.6.0; MONAI Consortium | [Apache-2.0](LICENSE) |
+| Primus EVA architecture semantics | [dynamic-network-architectures](https://github.com/MIC-DKFZ/dynamic-network-architectures), 0.4.3; MIC-DKFZ | Apache-2.0 |
+| EVA attention, rotary and SwiGLU semantics | [timm](https://github.com/huggingface/pytorch-image-models), 1.0.22; Ross Wightman and contributors | Apache-2.0 |
+| Qwen3.5 hybrid decoder, MRoPE and gated-delta chunk algebra | [Transformers](https://github.com/huggingface/transformers), 5.10.4; Hugging Face and contributors | Apache-2.0 |
+| CUDA Sklansky prefix-scan summation order and activation arithmetic | [PyTorch](https://github.com/pytorch/pytorch), 2.13.0, revision `cf30153c4c131c8164ee7798e5022d810682e2cb`; copyright holders listed in the retained license | [BSD](#pytorch-bsd) |
+| Vendored recurrent Metal kernel: `gated_delta.py` | [MLX-LM](https://github.com/ml-explore/mlx-lm), published 0.32.0 wheel; Copyright (c) 2025 Apple Inc.; SHA256 `f69e837ea68641dbb06fdb5dcc024a9a7e1d9353f08ae58c05275253a0c39428` | [MIT](#apple-mit) |
+
+The Apple module is copied verbatim from the published wheel. Runtime dependencies
+retain their package licenses. MONAI, timm, Transformers and PyTorch are provenance
+references, not runtime requirements. All learned arithmetic executes on Metal.
+
+The model is intended for research and education. It is not intended for clinical
+diagnosis or treatment decisions. Outputs require human review and are not ground truth.
+
+<details>
+<summary>NVIDIA OpenMDW-1.1: full license</summary>
+
+## NVIDIA OpenMDW-1.1
+
+```text
+Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+
+OpenMDW License Agreement, version 1.1 (OpenMDW-1.1)
+
+By exercising rights granted to you under this agreement, you accept and agree
+to its terms.
+
+As used in this agreement, "Model Materials" means the materials provided to
+you under this agreement, consisting of: (1) one or more machine learning
+models (including architecture and parameters); and (2) all related artifacts
+(including associated data, documentation and software) that are provided to
+you hereunder.
+
+Subject to your compliance with this agreement, permission is hereby granted,
+free of charge, to deal in the Model Materials without restriction, including
+under all copyright, patent, database, and trade secret rights included or
+embodied therein.
+
+If you distribute any portion of the Model Materials, you shall retain in your
+distribution (1) a copy of this agreement, and (2) all copyright notices and
+other notices of origin included in the Model Materials that are applicable to
+your distribution.
+
+If you file, maintain, or voluntarily participate in a lawsuit against any
+person or entity asserting that the Model Materials directly or indirectly
+infringe any patent or copyright, then all rights and grants made to you
+hereunder are terminated, unless that lawsuit was in response to a
+corresponding lawsuit first brought against you.
+
+This agreement does not impose any restrictions or obligations with respect to
+any use, modification, or sharing of any outputs generated by using the Model
+Materials.
+
+THE MODEL MATERIALS ARE 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, TITLE, NONINFRINGEMENT, ACCURACY, OR THE
+ABSENCE OF LATENT OR OTHER DEFECTS OR ERRORS, WHETHER OR NOT DISCOVERABLE, ALL
+TO THE GREATEST EXTENT PERMISSIBLE UNDER APPLICABLE LAW.
+
+YOU ARE SOLELY RESPONSIBLE FOR (1) CLEARING RIGHTS OF OTHER PERSONS THAT MAY
+APPLY TO THE MODEL MATERIALS OR ANY USE THEREOF, INCLUDING WITHOUT LIMITATION
+ANY PERSON'S COPYRIGHTS OR OTHER RIGHTS INCLUDED OR EMBODIED IN THE MODEL
+MATERIALS; (2) OBTAINING ANY NECESSARY CONSENTS, PERMISSIONS OR OTHER RIGHTS
+REQUIRED FOR ANY USE OF THE MODEL MATERIALS; OR (3) PERFORMING ANY DUE
+DILIGENCE OR UNDERTAKING ANY OTHER INVESTIGATIONS INTO THE MODEL MATERIALS OR
+ANYTHING INCORPORATED OR EMBODIED THEREIN.
+
+IN NO EVENT SHALL THE PROVIDERS OF THE MODEL MATERIALS 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 MODEL MATERIALS, THE
+USE THEREOF OR OTHER DEALINGS THEREIN.
+```
+
+</details>
+
+<details>
+<summary>Apple MIT: full license</summary>
+
+## Apple MIT
+
+```text
+MIT License
+
+Copyright © 2023 Apple Inc.
+
+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.
+```
+
+</details>
+
+<details>
+<summary>PyTorch BSD: full license</summary>
+
+## PyTorch BSD
+
+```text
+From PyTorch:
+
+Copyright (c) 2016-     Facebook, Inc            (Adam Paszke)
+Copyright (c) 2014-     Facebook, Inc            (Soumith Chintala)
+Copyright (c) 2011-2014 Idiap Research Institute (Ronan Collobert)
+Copyright (c) 2012-2014 Deepmind Technologies    (Koray Kavukcuoglu)
+Copyright (c) 2011-2012 NEC Laboratories America (Koray Kavukcuoglu)
+Copyright (c) 2011-2013 NYU                      (Clement Farabet)
+Copyright (c) 2006-2010 NEC Laboratories America (Ronan Collobert, Leon Bottou, Iain Melvin, Jason Weston)
+Copyright (c) 2006      Idiap Research Institute (Samy Bengio)
+Copyright (c) 2001-2004 Idiap Research Institute (Ronan Collobert, Samy Bengio, Johnny Mariethoz)
+
+From Caffe2:
+
+Copyright (c) 2016-present, Facebook Inc. All rights reserved.
+
+All contributions by Facebook:
+Copyright (c) 2016 Facebook Inc.
+
+All contributions by Google:
+Copyright (c) 2015 Google Inc.
+All rights reserved.
+
+All contributions by Yangqing Jia:
+Copyright (c) 2015 Yangqing Jia
+All rights reserved.
+
+All contributions by Kakao Brain:
+Copyright 2019-2020 Kakao Brain
+
+All contributions by Cruise LLC:
+Copyright (c) 2022 Cruise LLC.
+All rights reserved.
+
+All contributions by Tri Dao:
+Copyright (c) 2024 Tri Dao.
+All rights reserved.
+
+All contributions by Arm:
+Copyright (c) 2021, 2023-2025 Arm Limited and/or its affiliates
+
+All contributions from Caffe:
+Copyright(c) 2013, 2014, 2015, the respective contributors
+All rights reserved.
+
+All other contributions:
+Copyright(c) 2015, 2016 the respective contributors
+All rights reserved.
+
+Caffe2 uses a copyright model similar to Caffe: each contributor holds
+copyright over their contributions to Caffe2. The project versioning records
+all such contribution and copyright details. If a contributor wants to further
+mark their specific copyright on a particular contribution, they should
+indicate their copyright solely in the commit message of the change when it is
+committed.
+
+All rights reserved.
+
+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 names of Facebook, Deepmind Technologies, NYU, NEC Laboratories America
+   and IDIAP Research Institute 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 OWNER 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.
+```
+
+</details>