From bc3a08637cb83304988e103076a7c6b5574fa9ad Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sun, 7 Jun 2026 13:13:48 -0400 Subject: [PATCH] re-license to Apache 2.0 and properly attribute and note changes from dcmri --- LICENSE | 201 ++++++++++++++++++ NOTICE | 31 +++ PRD.md | 2 +- README.md | 2 +- docs/prd.md | 2 +- mkdocs.yml | 1 + osipy/common/convolution/__init__.py | 3 + osipy/common/convolution/conv.py | 8 +- osipy/common/convolution/expconv.py | 8 +- pyproject.toml | 6 +- tests/fixtures/osipi_codecollection/README.md | 11 +- tests/fixtures/osipi_dro/MANIFEST.md | 2 +- 12 files changed, 262 insertions(+), 15 deletions(-) create mode 100644 LICENSE create mode 100644 NOTICE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/NOTICE b/NOTICE new file mode 100644 index 0000000..18b73cc --- /dev/null +++ b/NOTICE @@ -0,0 +1,31 @@ +osipy +Copyright 2026 OSIPI and the osipy developers + +This product is licensed under the Apache License, Version 2.0 (the "License"). +See the LICENSE file for the full license text. You may obtain a copy of the +License at http://www.apache.org/licenses/LICENSE-2.0. + +================================================================================ +Third-party attributions +================================================================================ + +dcmri — https://github.com/dcmri/dcmri + Licensed under the Apache License, Version 2.0. + + The expconv function in osipy/common/convolution/expconv.py is a derivative + work MODIFIED from dcmri version 0.6.20 (Apache-2.0 Section 4(b)): it adapts + dcmri's recursive exponential-convolution algorithm (module dcmri/utils.py). + Modified: an (f, T, t) signature, batched/GPU-capable execution via the + array-module abstraction, and non-normalized output. + +OSIPI TF6.2 DCE-DSC-MRI Challenges + https://github.com/OSIPI/TF6.2_DCE-DSC-MRI_Challenges + Licensed under the Apache License, Version 2.0. + The DCE digital reference object data under tests/fixtures/osipi_dro/dce/ is + redistributed from this source. + +OSIPI DCE-DSC-MRI CodeCollection + https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection + Licensed under the Apache License, Version 2.0. + The reference concentration CSV data under + tests/fixtures/osipi_codecollection/dce/csv/ is redistributed from this source. diff --git a/PRD.md b/PRD.md index f6c1d19..947a00e 100644 --- a/PRD.md +++ b/PRD.md @@ -3,7 +3,7 @@ **Version**: 0.0.1 **Date**: 2026-03-02 **Status**: Active -**License**: MIT +**License**: Apache-2.0 --- diff --git a/README.md b/README.md index b3ed393..31eaaa0 100644 --- a/README.md +++ b/README.md @@ -182,7 +182,7 @@ mkdocs serve # Local docs at http://127.0.0.1:8000 ## License -MIT License +This project is licensed under the [Apache License 2.0](LICENSE). See [NOTICE](NOTICE) for third-party attributions. ## References diff --git a/docs/prd.md b/docs/prd.md index 7707494..b15cd3c 100644 --- a/docs/prd.md +++ b/docs/prd.md @@ -3,7 +3,7 @@ **Version**: 1.0.0 **Date**: 2026-02-14 **Status**: Active -**License**: MIT +**License**: Apache-2.0 --- diff --git a/mkdocs.yml b/mkdocs.yml index 14b4d7a..a8187d2 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,6 +3,7 @@ site_description: OSIPI-compliant MRI perfusion analysis library site_url: https://osipy.readthedocs.io repo_url: https://github.com/OSIPI/osipy repo_name: OSIPI/osipy +copyright: "Copyright 2026 OSIPI and the osipy developers — Apache-2.0" theme: name: material diff --git a/osipy/common/convolution/__init__.py b/osipy/common/convolution/__init__.py index 666a27f..5d71007 100644 --- a/osipy/common/convolution/__init__.py +++ b/osipy/common/convolution/__init__.py @@ -24,6 +24,9 @@ contrast-enhanced MRI. NMR Biomed. 26(8):1004-1027. doi:10.1002/nbm.2940 .. [3] OSIPI CAPLEX, https://osipi.github.io/OSIPI_CAPLEX/ + +The expconv function in this package is a derivative work adapted from dcmri +(Apache-2.0); see the project NOTICE file for attribution. """ from osipy.common.convolution.conv import conv, uconv diff --git a/osipy/common/convolution/conv.py b/osipy/common/convolution/conv.py index 2ca1ecc..cb56a5b 100644 --- a/osipy/common/convolution/conv.py +++ b/osipy/common/convolution/conv.py @@ -1,9 +1,9 @@ -"""Piecewise-linear convolution with analytic integration. +"""Piecewise-linear convolution with trapezoidal integration. This module implements convolution using piecewise-linear interpolation -with analytical integration between time points. This approach is more -accurate than FFT-based methods for pharmacokinetic modeling, particularly -when time sampling is non-uniform. +and trapezoidal integration between time points, supporting non-uniform +time sampling. (Note: this is an approximate trapezoidal scheme; it does +not perform the exact product-of-linears integration used by dcmri.) References ---------- diff --git a/osipy/common/convolution/expconv.py b/osipy/common/convolution/expconv.py index cd1ce79..d339a9c 100644 --- a/osipy/common/convolution/expconv.py +++ b/osipy/common/convolution/expconv.py @@ -13,7 +13,13 @@ model in DCE-MRI by linear inversion. Magn Reson Med. 76(3):998-1006. doi:10.1002/mrm.25991 -dcmri library: https://github.com/dcmri/dcmri +Attribution +----------- +``expconv`` adapts the recursive exponential-convolution algorithm from +dcmri v0.6.20 (https://github.com/dcmri/dcmri, module ``dcmri/utils.py``), +licensed under the Apache License, Version 2.0. Modified: ``(f, T, t)`` +signature, batched/GPU array-module path, and non-normalized output. See the +project NOTICE file. """ from __future__ import annotations diff --git a/pyproject.toml b/pyproject.toml index 8406c8a..2d0bb94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,10 +7,11 @@ name = "osipy" dynamic = ["version"] description = "OSIPI-compliant MRI perfusion analysis library" readme = "README.md" -license = "MIT" +license = "Apache-2.0" +license-files = ["LICENSE", "NOTICE"] requires-python = ">=3.12" authors = [ - { name = "osipy contributors" }, + { name = "OSIPI and the osipy developers" }, ] keywords = [ "mri", @@ -25,7 +26,6 @@ keywords = [ classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.12", diff --git a/tests/fixtures/osipi_codecollection/README.md b/tests/fixtures/osipi_codecollection/README.md index 425341c..7cf5e3e 100644 --- a/tests/fixtures/osipi_codecollection/README.md +++ b/tests/fixtures/osipi_codecollection/README.md @@ -4,8 +4,11 @@ Reference data for cross-implementation testing of DCE-MRI pharmacokinetic model ## Source -Parameter combinations are drawn from the OSIPI DCE-DSC-MRI CodeCollection patterns. -Concentration curves are generated using osipy's own forward models with the Parker AIF. +The reference concentration **CSV** files under `dce/csv/` are externally generated +data redistributed from the OSIPI DCE-DSC-MRI CodeCollection +(https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection), licensed under the Apache +License 2.0. The **JSON** reference cases are generated by osipy's own forward +models with the Parker AIF (see `scripts/generate_osipi_reference.py`). ## Structure @@ -26,4 +29,6 @@ python3 scripts/generate_osipi_reference.py ## License -Same as osipy. +Apache License 2.0. The osipy-generated JSON is under the osipy project license +(Apache-2.0); the redistributed CodeCollection CSV data is Apache-2.0 (OSIPI). +See the project NOTICE file. diff --git a/tests/fixtures/osipi_dro/MANIFEST.md b/tests/fixtures/osipi_dro/MANIFEST.md index 2f11b7c..7660ab7 100644 --- a/tests/fixtures/osipi_dro/MANIFEST.md +++ b/tests/fixtures/osipi_dro/MANIFEST.md @@ -93,4 +93,4 @@ d = np.load(ivim_dir / "d.npy") ## License - DCE data: Apache 2.0 (OSIPI) -- DSC/ASL/IVIM synthetic data: MIT (osipy) +- DSC/ASL/IVIM synthetic data: Apache 2.0 (osipy)