diff --git a/.claude/launch.json b/.claude/launch.json new file mode 100644 index 0000000..5570688 --- /dev/null +++ b/.claude/launch.json @@ -0,0 +1,11 @@ +{ + "version": "0.0.1", + "configurations": [ + { + "name": "docs", + "runtimeExecutable": ".venv/bin/mkdocs", + "runtimeArgs": ["serve", "--dev-addr", "127.0.0.1:8127"], + "port": 8127 + } + ] +} diff --git a/.github/scripts/osipi_badge_summary.py b/.github/scripts/osipi_badge_summary.py new file mode 100755 index 0000000..74f00cc --- /dev/null +++ b/.github/scripts/osipi_badge_summary.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python3 +"""Summarize a pytest JUnit XML run of the OSIPI suite into shields.io badge fields. + +Writes `message`, `color` and `failed` as GitHub Actions step outputs (stdout, meant to +be redirected into `$GITHUB_OUTPUT`). + +Skipped tests are excluded from the count rather than counted as passes. Six of the +OSIPI tests skip on a GitHub-hosted runner even with the acceleration wheels installed, +because they need real CUDA hardware; counting those as passes would advertise a +conformance level that was never measured. +""" + +from __future__ import annotations + +import sys +import xml.etree.ElementTree as ET +from pathlib import Path +from typing import Dict + + +def _totals(results_path: Path) -> Dict[str, int]: + root = ET.parse(results_path).getroot() + suites = [root] if root.tag == "testsuite" else list(root.iter("testsuite")) + totals = {"tests": 0, "failures": 0, "errors": 0, "skipped": 0} + for suite in suites: + for key in totals: + totals[key] += int(suite.get(key) or 0) + return totals + + +def main(argv: list[str]) -> int: + if len(argv) != 2: + print(f"usage: {Path(argv[0]).name} ", file=sys.stderr) + return 2 + + totals = _totals(Path(argv[1])) + failed = totals["failures"] + totals["errors"] + ran = totals["tests"] - totals["skipped"] + passed = ran - failed + + if ran <= 0: + message = "no tests run" + color = "lightgrey" + else: + message = f"{passed}/{ran} passing" + if totals["skipped"]: + message += f" ({totals['skipped']} skipped)" + color = "brightgreen" if failed == 0 else "red" + + print(f"message={message}") + print(f"color={color}") + print(f"failed={failed}") + return 0 + + +if __name__ == "__main__": + raise SystemExit(main(sys.argv)) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..bf47122 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,78 @@ +name: docs + +# Builds the ROCKETSHIP site with Zensical and publishes it to GitHub Pages. +# +# Zensical replaces Material for MkDocs, which reaches end of life on +# 5 November 2026. It reads the same mkdocs.yml and inherits the shared DCEasy +# theme from dceasy-base.yml, so the config here is unchanged by the switch. +# +# No CNAME file: this is a project site, and it inherits the custom domain from +# the organization site (petmri/petmri.github.io), which is where dceasy.org is +# configured. Adding one here would give the two copies a chance to disagree. +# +# Action majors are kept current because GitHub retires the Node runtime they +# run on, not because this workflow needs new features. Every action below is on +# node24; upload-pages-artifact pins upload-artifact internally. + +on: + push: + branches: + - main + - master + # Docs currently live on dev, so dev publishes the site. Remove this once + # dev merges, otherwise main and dev race for the Pages deployment and the + # last push wins. + - dev + pull_request: + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write + +# Deployments must not cancel each other. A push and a pull_request run can fire +# for the same commit; with cancel-in-progress the later one kills the former, and +# since deploy only runs on push, the site silently never updates. Matches DCEPrep +# and GitHub's own Pages starter workflow. +concurrency: + group: pages + cancel-in-progress: false + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v7 + + - name: Setup Python + uses: actions/setup-python@v7 + with: + python-version: "3.12" + + - name: Install docs dependencies + run: pip install -r requirements-docs.txt + + - name: Build docs + run: zensical build --strict + + - name: Configure Pages + uses: actions/configure-pages@v6 + + - name: Upload Pages artifact + uses: actions/upload-pages-artifact@v5 + with: + path: site + + deploy: + if: github.event_name == 'push' + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v5 diff --git a/.github/workflows/run_DCE.yml b/.github/workflows/run_DCE.yml index a429fee..b382583 100644 --- a/.github/workflows/run_DCE.yml +++ b/.github/workflows/run_DCE.yml @@ -11,20 +11,280 @@ on: - master - dev +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: - build: + python_checks: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v7 + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: '3.11' + + - name: Install Python dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -r requirements.txt + + - name: Run Python tests with coverage + run: | + python -m pytest tests/python -q \ + --cov=python \ + --cov-report=term-missing \ + --cov-report=xml \ + --cov-fail-under=60 + + - name: Run OSIPI primary merge-gate reliability summary + run: | + python tests/python/run_osipi_reliability.py \ + --suite all \ + --summary-json /tmp/osipi_primary_reliability_summary.json + + - name: Upload OSIPI primary reliability summary + uses: actions/upload-artifact@v7 + with: + name: osipi-primary-reliability-summary + path: /tmp/osipi_primary_reliability_summary.json + retention-days: 7 + if-no-files-found: error + + - name: Upload Python coverage report + uses: actions/upload-artifact@v7 + with: + name: python-coverage-xml + path: coverage.xml + retention-days: 7 + if-no-files-found: error + + python_portability: + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: [windows-latest, macos-latest, ubuntu-22.04] + python-version: ["3.11"] + + steps: + - uses: actions/checkout@v7 + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + + - name: Install Python dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -r requirements.txt + + - name: Run Python unit/integration tests (non-parity mode) + run: python -m pytest tests/python -m "not parity" -q + + # Every test that needs the accelerated backends, plus the OSIPI badge, in one job so the + # release download happens once. Kept out of python_checks so a flaky external download + # cannot fail the main Python job, and so this doubles as the only end-to-end exercise of + # the installer. python_checks still runs all of these tests; without the wheels they skip. + accelerated_backends: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v7 + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: '3.11' + + # Pulls prebuilt pyCpufit/pyGpufit from the Gpufit release into .venv. Runners have no + # CUDA, so pyGpufit imports but reports cuda_available=false and the gpufit half of the + # gate skips itself; pyCpufit is a pure-CPU library and runs. + - name: Install Python acceleration (pyCpufit/pyGpufit) + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: python install.py --no-matlab --no-gui --venv-path .venv + + # Runs before the equivalence gate so the badge publishes even when that gate is red. + # continue-on-error keeps a failing suite from skipping the publish; the final step + # restores the non-zero exit so the job status stays meaningful. + - name: Run OSIPI conformance tests + continue-on-error: true + run: .venv/bin/python -m pytest tests/python -m osipi -q -rs --junitxml=osipi-results.xml + + - name: Summarize OSIPI results for the badge + id: count + run: python .github/scripts/osipi_badge_summary.py osipi-results.xml >> "$GITHUB_OUTPUT" + + # Lets the job run cleanly on forks and before GIST_TOKEN is configured, instead of + # failing the publish step. + - name: Check badge credentials + id: creds + env: + GIST_TOKEN: ${{ secrets.GIST_TOKEN }} + run: | + if [ -n "$GIST_TOKEN" ]; then + echo "available=true" >> "$GITHUB_OUTPUT" + else + echo "available=false" >> "$GITHUB_OUTPUT" + echo "::warning::GIST_TOKEN is not set; skipping badge publish." + fi + + # GitHub's own Actions badges are binary and per-workflow, so reporting a pass *count* + # for the osipi-marked subset needs a value parked where shields.io can fetch it. + # Skipped on pull_request so PR runs cannot overwrite the branch status in the gist. + - name: Publish OSIPI badge + if: github.event_name != 'pull_request' && steps.creds.outputs.available == 'true' + uses: schneegans/dynamic-badges-action@v1.7.0 + with: + auth: ${{ secrets.GIST_TOKEN }} + gistID: b65ef98aadaa684f2d7d31e82137c4b4 + filename: osipi.json + label: OSIPI + message: ${{ steps.count.outputs.message }} + color: ${{ steps.count.outputs.color }} + + - name: Run backend-equivalence gate (cpu vs cpufit on frozen Stage-B arrays) + run: .venv/bin/python -m pytest tests/python/test_backend_equivalence.py -q -rs + + # always() so an OSIPI failure is still reported when the equivalence gate above failed. + - name: Fail if any OSIPI test failed + if: always() && steps.count.outputs.failed != '0' + run: | + echo "OSIPI suite reported ${{ steps.count.outputs.failed }} failure(s)/error(s)." + exit 1 + + parity_checks: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v7 + + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: '3.12' + cache: "pip" + + - name: Install Python dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -r requirements.txt + + - name: Set up MATLAB + uses: matlab-actions/setup-matlab@v3 + with: + products: Curve_Fitting_Toolbox Image_Processing_Toolbox Optimization_Toolbox Parallel_Computing_Toolbox Statistics_and_Machine_Learning_Toolbox + release: R2022a + + - name: Regenerate MATLAB parity baseline (for drift guard) + uses: matlab-actions/run-command@v2 + with: + command: addpath('tests/matlab'); addpath('tests/matlab/helpers'); export_parity_baseline('_ci_baseline_candidate'); + + - name: Check MATLAB baseline drift + # Fails if committed matlab_reference_v1.json no longer matches current MATLAB + # output, i.e. MATLAB algorithm code changed without regenerating the baseline. + # Together with the contract parity step below (Python vs committed baseline), + # this transitively verifies Python matches *current* MATLAB, not a stale snapshot. + run: | + python tests/contracts/check_baseline_drift.py \ + --candidate _ci_baseline_candidate/matlab_reference_v1.json + + - name: Regenerate MATLAB region-parity baseline (drift-check candidate) + uses: matlab-actions/run-command@v2 + with: + command: >- + addpath('.'); addpath('tests/matlab'); + generate_dce_tofts_parity_map( + 'outputRoot', '_ci_matlabref_candidate/sub-10bbbdownsample', + 'dynamicPath', 'tests/data/BIDS_test/rawdata/sub-10bbbdownsample/ses-01/dce/sub-10bbbdownsample_ses-01_DCE.nii', + 'aifRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/dce/sub-10bbbdownsample_ses-01_label-AIF_mask.nii', + 'brainRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_label-brain_mask.nii', + 't1MapPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_space-DCEref_T1map.nii', + 'noiseRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_label-noise_mask.nii', + 'models', {'tofts', 'patlak'}); + + - name: Check MATLAB region-parity baseline drift (sub-10bbbdownsample) + # Fails if a fresh MATLAB run of generate_dce_tofts_parity_map no longer matches + # the committed derivatives/matlabref/... maps, i.e. MATLAB's own pipeline + # (steady-state auto-detect, fitting, etc.) changed without regenerating the + # fixture. Complements the contract drift guard above, which never exercises + # A_make_R1maps_func/find_end_ss. + run: | + python tests/contracts/check_matlabref_map_drift.py \ + --candidate-root _ci_matlabref_candidate/sub-10bbbdownsample + + - name: Generate MATLAB parity baseline maps (downsample fixture) + uses: matlab-actions/run-command@v3 + with: + command: >- + addpath('.'); addpath('tests/matlab'); + generate_dce_tofts_parity_map( + 'outputRoot', 'tests/data/BIDS_test/derivatives/matlabref/sub-10bbbdownsample/ses-01/dce', + 'dynamicPath', 'tests/data/BIDS_test/rawdata/sub-10bbbdownsample/ses-01/dce/sub-10bbbdownsample_ses-01_DCE.nii', + 'aifRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/dce/sub-10bbbdownsample_ses-01_label-AIF_mask.nii', + 'brainRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_label-brain_mask.nii', + 't1MapPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_space-DCEref_T1map.nii', + 'noiseRoiPath', 'tests/data/BIDS_test/derivatives/sub-10bbbdownsample/ses-01/anat/sub-10bbbdownsample_ses-01_label-noise_mask.nii', + 'models', {'tofts', 'patlak'}); + + - name: Run Python contract parity checks + run: | + python tests/contracts/generate_python_results.py --output /tmp/python_results.json + python tests/contracts/compare_with_matlab_baseline.py --python-results /tmp/python_results.json --require-all + + # ROI-xls parity is a separate test; it runs unfiltered in python_checks, not here. + - name: Run Python DCE region parity (downsample fixture, gated tofts/patlak Ktrans) + run: | + python -m pytest tests/python/test_dce_pipeline_parity_metrics.py::test_bbb_p19_region_parity \ + --dataset-root tests/data/BIDS_test \ + -q + + # Also runs in python_checks, but against the *committed* payload. Here it runs after + # the regeneration step above, so it grades Python against current MATLAB instead. + - name: Run Python Stage-B AIF contract parity (Cp_use/step/timing/max_index) + run: | + python -m pytest tests/python/test_stage_b_aif_parity.py \ + --dataset-root tests/data/BIDS_test \ + -q + + - name: Generate MATLAB T1 parity map (small VFA fixture) + uses: matlab-actions/run-command@v2 + with: + command: >- + addpath('tests/matlab'); addpath('tests/matlab/helpers'); + generate_t1_parity_map( + 'vfaFiles', {'tests/data/BIDS_test/rawdata/sub-11tiny/ses-01/anat/sub-11tiny_ses-01_flip-01_VFA.nii.gz', + 'tests/data/BIDS_test/rawdata/sub-11tiny/ses-01/anat/sub-11tiny_ses-01_flip-02_VFA.nii.gz', + 'tests/data/BIDS_test/rawdata/sub-11tiny/ses-01/anat/sub-11tiny_ses-01_flip-03_VFA.nii.gz'}, + 'flipAngles', [2 5 10], 'trMs', 8.012, 'fitType', 't1_fa_fit', + 'outputPath', 'tests/data/BIDS_test/derivatives/matlabref/sub-11tiny/ses-01/anat/sub-11tiny_ses-01_desc-t1fafit_T1map.nii', + 'rsquaredThreshold', 0); + + - name: Run Python T1 map parity (small VFA fixture) + run: | + python -m pytest tests/python/test_t1_map_parity.py::test_bids_t1_map_parity_nonlinear \ + -q + + matlab_checks: strategy: - #fail-fast: false + fail-fast: false matrix: os: [ubuntu-latest, ubuntu-22.04] - release: [R2020b, R2021a, R2022a] + release: [R2020b, R2022a, latest] runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up MATLAB - uses: matlab-actions/setup-matlab@v2 + uses: matlab-actions/setup-matlab@v3 with: products: Curve_Fitting_Toolbox Image_Processing_Toolbox Optimization_Toolbox Parallel_Computing_Toolbox Statistics_and_Machine_Learning_Toolbox release: ${{ matrix.release }} @@ -35,20 +295,29 @@ jobs: # chmod +x mpm # ./mpm install --release=${{ matrix.release }} --products MATLAB Statistics_and_Machine_Learning_Toolbox Parallel_Computing_Toolbox Curve_Fitting_Toolbox - name: Run T1 mapping - uses: matlab-actions/run-command@v2 + uses: matlab-actions/run-command@v3 with: - command: addpath .; addpath dce/; addpath external_programs/; addpath external_programs/niftitools/; addpath parametric_scripts/; addpath parametric_scripts/custom_scripts/; T1mapping_fit('test_data/BIDS_test/rawdata/sub-01/ses-01/anat/', 'test_data/BIDS_test/derivatives/sub-01/ses-01/anat/', 'sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii') + command: addpath .; addpath dce/; addpath external_programs/; addpath external_programs/niftitools/; addpath parametric_scripts/; addpath parametric_scripts/custom_scripts/; T1mapping_fit('tests/data/BIDS_test/rawdata/sub-01original/ses-01/anat/', 'tests/data/BIDS_test/derivatives/sub-01original/ses-01/anat/', 'sub-01original_ses-01_space-DCEref_desc-bfczunified_VFA.nii') - - name: Run DCE - uses: matlab-actions/run-command@v2 + - name: Run Algorithm Unit Tests + uses: matlab-actions/run-command@v3 with: - command: run_dce_cli('test_data/BIDS_test/rawdata/sub-01/ses-01/', 'test_data/BIDS_test/derivatives/sub-01/ses-01/') + command: addpath .; addpath tests/matlab/; addpath tests/matlab/helpers/; results = run_unit_tests(); assert(~any([results.Failed]), 'Unit tests failed.'); + + - name: Run Algorithm Integration Tests + uses: matlab-actions/run-command@v3 + with: + command: addpath .; addpath tests/matlab/; addpath tests/matlab/helpers/; results = run_all_tests('suite','integration'); assert(~any([results.Failed]), 'Integration tests failed.'); + + - name: Run DCE (Full) + uses: matlab-actions/run-command@v3 + with: + command: run_dce_cli('tests/data/BIDS_test/rawdata/sub-01original/ses-01/', 'tests/data/BIDS_test/derivatives/sub-01original/ses-01/') - name: Upload Ktrans result - uses: actions/upload-artifact@v6 + uses: actions/upload-artifact@v7 with: name: Ktrans_result_${{ matrix.os }}-${{ matrix.release }} - path: test_data/BIDS_test/derivatives/sub-01/ses-01/dce/dce_patlak_fit_Ktrans.nii + path: tests/data/BIDS_test/derivatives/sub-01original/ses-01/dce/dce_patlak_fit_Ktrans.nii retention-days: 7 if-no-files-found: error - diff --git a/.gitignore b/.gitignore index 5bdef65..d1ddd2e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,183 +1,231 @@ -################# -## Eclipse -################# - -*.pydevproject -.project -.metadata -bin/ -tmp/ -*.tmp -*.bak -*.swp -*~.nib -local.properties -.classpath -.settings/ -.loadpath - -# External tool builders -.externalToolBuilders/ - -# Locally stored "Eclipse launch configurations" -*.launch - -# CDT-specific -.cproject - -# PDT-specific -.buildpath - - -################# -## Visual Studio -################# - -## Ignore Visual Studio temporary files, build results, and -## files generated by popular Visual Studio add-ons. - -# User-specific files -*.suo -*.user -*.sln.docstates - -# Build results -[Dd]ebug/ -[Rr]elease/ -*_i.c -*_p.c -*.ilk -*.meta -*.obj -*.pch -*.pdb -*.pgc -*.pgd -*.rsp -*.sbr -*.tlb -*.tli -*.tlh -*.tmp -*.vspscc -.builds -*.dotCover - -## TODO: If you have NuGet Package Restore enabled, uncomment this -#packages/ - -# Visual C++ cache files -ipch/ -*.aps -*.ncb -*.opensdf -*.sdf - -# Visual Studio profiler -*.psess -*.vsp - -# ReSharper is a .NET coding add-in -_ReSharper* - -# Installshield output folder -[Ee]xpress - -# DocProject is a documentation generator add-in -DocProject/buildhelp/ -DocProject/Help/*.HxT -DocProject/Help/*.HxC -DocProject/Help/*.hhc -DocProject/Help/*.hhk -DocProject/Help/*.hhp -DocProject/Help/Html2 -DocProject/Help/html - -# Click-Once directory -publish - -# Others -[Bb]in -[Oo]bj -sql -TestResults -*.Cache -ClientBin -stylecop.* -~$* -*.dbmdl -Generated_Code #added for RIA/Silverlight projects - -# Backup & report files from converting an old project file to a newer -# Visual Studio version. Backup files are not needed, because we have git ;-) -_UpgradeReport_Files/ -Backup*/ -UpgradeLog*.XML - - - -############ -## Windows -############ - -# Windows image file caches -Thumbs.db - -# Folder config file -Desktop.ini - - -############# -## Python -############# - -*.py[co] - -# Packages -*.egg -*.egg-info -dist -build -eggs -parts -bin -var -sdist -develop-eggs -.installed.cfg - -# Installer logs -pip-log.txt - -# Unit test / coverage reports -.coverage -.tox - -#Translations -*.mo - -#Mr Developer -.mr.developer.cfg - -# Mac crap -.DS_Store - -############# -## Matlab -############# -*.asv - -############# -## Linux -############# -*~ - -############# -## Project Specific -############# -email_preferences.txt -dce_last_state.mat -*info.log -dce/*info.log -test_data/BIDS_test/derivatives - +################# +## Eclipse +################# + +*.pydevproject +.project +.metadata +bin/ +tmp/ +*.tmp +*.bak +*.swp +*~.nib +local.properties +.classpath +.settings/ +.loadpath + +# External tool builders +.externalToolBuilders/ + +# Locally stored "Eclipse launch configurations" +*.launch + +# CDT-specific +.cproject + +# PDT-specific +.buildpath + + +################# +## Visual Studio +################# + +## Ignore Visual Studio temporary files, build results, and +## files generated by popular Visual Studio add-ons. + +# User-specific files +*.suo +*.user +*.sln.docstates + +# Build results +[Dd]ebug/ +[Rr]elease/ +*_i.c +*_p.c +*.ilk +*.meta +*.obj +*.pch +*.pdb +*.pgc +*.pgd +*.rsp +*.sbr +*.tlb +*.tli +*.tlh +*.tmp +*.vspscc +.builds +*.dotCover + +## TODO: If you have NuGet Package Restore enabled, uncomment this +#packages/ + +# Visual C++ cache files +ipch/ +*.aps +*.ncb +*.opensdf +*.sdf + +# Visual Studio profiler +*.psess +*.vsp + +# ReSharper is a .NET coding add-in +_ReSharper* + +# Installshield output folder +[Ee]xpress + +# DocProject is a documentation generator add-in +DocProject/buildhelp/ +DocProject/Help/*.HxT +DocProject/Help/*.HxC +DocProject/Help/*.hhc +DocProject/Help/*.hhk +DocProject/Help/*.hhp +DocProject/Help/Html2 +DocProject/Help/html + +# Click-Once directory +publish + +# Others +[Bb]in +[Oo]bj +sql +TestResults +*.Cache +ClientBin +stylecop.* +~$* +*.dbmdl +Generated_Code #added for RIA/Silverlight projects + +# Backup & report files from converting an old project file to a newer +# Visual Studio version. Backup files are not needed, because we have git ;-) +_UpgradeReport_Files/ +Backup*/ +UpgradeLog*.XML + + + +############ +## Windows +############ + +# Windows image file caches +Thumbs.db + +# Folder config file +Desktop.ini + + +############# +## Python +############# + +*.py[co] +__pycache__/ +.venv/ + +# Packages +*.egg +*.egg-info +dist +build +eggs +parts +bin +var +sdist +develop-eggs +.installed.cfg + +# Installer logs +pip-log.txt + +# Unit test / coverage reports +.coverage +.tox +# Also holds the parity-summary JSONs (conftest.py's --parity-summary-dir default) +.pytest_cache/ + +#Translations +*.mo + +#Mr Developer +.mr.developer.cfg + +# Mac crap +.DS_Store + +############# +## Matlab +############# +*.asv + +############# +## Linux +############# +*~ + +############# +## Project Specific +############# +email_preferences.txt +dce_last_state.mat +*info.log +dce/*info.log +tests/data/synthetic/generated +tests/data/BBB data p19/Dyn-1_timecurves.fig +tests/data/BBB data p19/Dyn-1dynamicCt.nii.gz +tests/data/BBB data p19/processed/python_out/ +tests/data/BBB data p19/processed/python_out_tofts_kmax100/ +tests/data/BBB data p19/processed/results_matlab/ +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/A_* +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/B_* +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/dceAIF_fitting.* +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/dce_timecurves.* +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/dcedynamicCt.nii.gz +tests/data/ci_fixtures/dce/downsample_x2_bids/derivatives/sub-01/ses-01/dce/dce_patlak_fit* +out/ +site/ + +# Installer-generated acceleration artifacts +external_programs/CpufitMex* +external_programs/GpufitCudaAvailableMex* +external_programs/Gpufit*Mex* +external_programs/cpufit*.m +external_programs/gpufit*.m +external_programs/Gpufit*.m +external_programs/ConstraintType.m +external_programs/EstimatorID.m +external_programs/ModelID.m +external_programs/libCpufit.* +external_programs/libGpufit.* + +# Installer-generated GUI launchers (contain machine-local venv paths) +rocketship_dce.sh +rocketship_dce.bat +rocketship_parametric.sh +rocketship_parametric.bat +# Superseded single launcher; install.py deletes it, this keeps a stale copy untracked. +rocketship.sh +rocketship.bat + + +# CI drift-guard: freshly regenerated baseline candidate (never committed) +_ci_baseline_candidate/ + +# Local runner scratch output (never committed) +RUNNER_DATA/ + +# Reference papers (copyrighted PDFs; cited by DOI, not committed) +tests/data/osipi/reference/*.pdf diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 0000000..2759b3d --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,379 @@ +# ROCKETSHIP Agent Guidance + +## What this is + +ROCKETSHIP is a toolbox for processing and analyzing parametric MRI and DCE-MRI +(dynamic contrast-enhanced) data. It has two parallel implementations: + +- **MATLAB** (`dce/`, `parametric_scripts/`, `external_programs/`, `dsc/`) — the original, + still-maintained implementation. GUIs (`dce.m`, `fitting_gui.m`) and CLI entry points + (`run_dce.m`, `run_parametric.m`, `run_dce_cli.m`). +- **Python** (`python/`) — the actively-developed port and the recommended path for new + work. No production users yet, so prioritize correctness and clean architecture over + preserving legacy MATLAB behavior that isn't required for parity. + +Because the Python port must reproduce MATLAB's numeric behavior, most non-trivial +changes touch both sides and get validated by the MATLAB-vs-Python parity test suite +(see Testing below). When MATLAB and Python disagree, prefer fixing whichever one +deviates from the *intended* algorithm rather than tuning tolerances to paper over it. + +## Setup + +```bash +python3 install.py # creates .venv, installs deps + pyGpufit/pyCpufit, writes rocketship.sh +``` + +MATLAB is optional here: without it on `PATH` the installer warns that the MATLAB MEX files +could not be verified and still exits 0. `rocketship_dce.sh` and `rocketship_parametric.sh` +(`.bat` on Windows) are generated, machine-local, gitignored wrappers that activate the venv +and launch one GUI each; `install.py` writes both from one template (`LAUNCHERS`) and deletes +the superseded single `rocketship.sh`. One launcher per GUI rather than one taking +`[dce|parametric]`, because the subcommand form left the parametric GUI unmentioned in the +installer's own next-steps output and nobody found it. + +Manual alternative: `python3 -m venv .venv && .venv/bin/pip install -r requirements.txt` +(add `-r requirements_gui.txt` for the PySide6 GUI). MATLAB toolboxes required: Curve +Fitting, Parallel Computing, Statistics and Machine Learning, Image Processing. + +## Running the pipelines + +```bash +# DCE (Python), shipped example config (sub-02downsample, ~11 s): +.venv/bin/python run_dce_python_cli.py +# DCE smoke test on the tiny fixture (~0.5 s): +.venv/bin/python run_dce_python_cli.py --config tests/python/dce_run_tiny.json +# DCE with an explicit config + overrides: +.venv/bin/python run_dce_python_cli.py --config tests/python/dce_cli_config.example.json --set voxel_MaxFunEvals=100 + +# Parametric T1 (Python): +.venv/bin/python run_parametric_python_cli.py + +# BIDS batch processing across a dataset: +.venv/bin/python run_dce_bids_batch.py --bids-root --pipeline-folder dceprep --backend gpufit +.venv/bin/python run_parametric_bids_batch.py --bids-root --pipeline-folder t1prep + +# MATLAB (from the MATLAB command line, repo root on path): +run_dce_cli('rawdata/sub-01/ses-01/', 'derivatives/sub-01/ses-01/') +``` + +Full CLI reference, config precedence, and output formats: `python/README.md` and +`docs/dce_options.md`. + +## Testing + +```bash +# Fast Python unit/integration suite (the default; includes gated DCE parity): +.venv/bin/python -m pytest tests/python + +# With coverage (matches CI's python_checks job, --cov-fail-under=60): +.venv/bin/python -m pytest tests/python -q --cov=python --cov-report=term-missing --cov-fail-under=60 + +# Single test: +.venv/bin/python -m pytest tests/python/test_dce_pipeline.py::TestDcePipeline::test_resolve_baseline_window_accepts_glr_alias -v + +# DCE parity vs MATLAB (Tofts/Patlak Ktrans, gated on corr+RMSE over brain/GM/WM): +.venv/bin/python -m pytest tests/python -m parity +.venv/bin/python -m pytest tests/python -m parity --parity-suite=allmodels -s # + reported-only extras + +# ROI-summary .xls parity (separate, default-on, few seconds): +.venv/bin/python -m pytest tests/python/test_dce_pipeline_parity_metrics.py::test_bbb_p19_roi_xls_parity + +# Runtime parity vs a live MATLAB run (needs MATLAB on PATH): +.venv/bin/python -m pytest tests/python/test_runtime_parity.py --run-runtime-parity + +# OSIPI reliability (ground truth vs published peer tolerances): +.venv/bin/python -m pytest tests/python -m osipi -v + +# MATLAB tests (from MATLAB): +results = run_unit_tests(); +results = run_all_tests('suite', 'all', 'includeIntegration', true); +``` + +Full test-suite docs (regions, gated-vs-reported split, thresholds, fixture regeneration +commands): `tests/README.md`. Pytest markers are declared in `pytest.ini` +(`unit`, `integration`, `parity`, `slow`, `portability`, `osipi`, `fast`). + +CI (`.github/workflows/run_DCE.yml`) runs, per push/PR to `master`/`dev`: `python_checks` +(unit tests + coverage + OSIPI summary), `parity_checks` (MATLAB contract/baseline drift +guards + Python-vs-MATLAB dataset parity), `python_portability` (Windows/macOS, non-parity), +and `matlab_checks` (a MATLAB release × OS matrix: unit/integration tests + a full DCE CLI +run). `matlab_checks` runners have no GPU — `backend="auto"` always resolves to plain CPU +there, so accelerated-backend-only issues won't surface in CI. + +## Architecture + +### DCE pipeline stages (both languages implement the same A → B → D shape) + +- **Stage A** — signal-to-concentration conversion from dynamic images + T1 maps + AIF/ROI + masks, and steady-state baseline window resolution. MATLAB: `A_make_R1maps_func.m`. + Python: `run_dce_pipeline`'s Stage A path in `python/dce_pipeline.py`. +- **Stage B** — AIF fitting/timing (biexponential fit or reference-region). MATLAB: + `B_AIF_fitting_func.m`. Python: same file, `_fit_aif_biexp` and friends. +- **Stage D** — per-voxel or per-ROI kinetic model fitting, producing parameter maps. + MATLAB: `D_fit_voxels_func.m` + `FXLfit_generic.m` + per-model `model_*.m`/`model_*_cfit.m`. + Python: same file, dispatching to `python/dce_models.py` (CPU/scipy) or the accelerated + path (see below). +- **Part E** (post-fit statistical comparison, f-test/AIC) is Python-only so far: + `python/dce_postfit_analysis.py`. + +`python/dce_pipeline.py` is the core (~4500 lines) — nearly everything for Stage A/B/D +config resolution, metadata/sidecar discovery, and backend dispatch lives there. +`python/dce_models.py` holds the CPU/scipy model implementations (ports of the MATLAB +`model_*.m` math). `python/dce_cli.py` is a thin CLI wrapper; `python/parametric_pipeline.py` ++ `python/parametric_models.py` are the equivalent stack for VFA T1 mapping. + +### Config resolution + +Every DCE default, limit and preference lives in **`python/dce_defaults.json`**. Source +code carries no fallback values: precedence is CLI `--set` → `stage_overrides` in the run +config → `dce_defaults.json` → **error**. A key missing everywhere raises `DceConfigError` +naming the key and the file; a key in the run config that the defaults file does not +declare is rejected as a typo. `python/dce_config.py` is the resolver. + +Parametric T1 follows the same rule with its own pair: **`python/parametric_defaults.json`** +holds the defaults and `python/parametric_config.py` resolves against it, with the same +`required`/`optional`/`defaults` sections and the same typo guard. Its config is flat -- there +is no `stage_overrides` block -- so a run config's own top-level keys are the overrides. Input +paths (`output_dir`, `vfa_files`, `mask_file`, `b1_map_file`) describe one study rather than +how the software behaves, so they belong in a run config and never in the defaults file; +`python/parametric_run_example.json` is the runnable example. + +`relaxivity` and `hematocrit` are per-scan values, so for those two the DCE image's JSON +sidecar wins over the run config: sidecar → run config → defaults file → error. +`relaxivity` deliberately has **no default** — the right value depends on the contrast +agent, so a run without one stops rather than guessing. (MATLAB keeps its +`script_preferences.txt` fallback; that divergence is intentional and documented in +`docs/dce_options.md`.) Scan parameters (TR/FA/time-resolution) are resolved strictly from +the metadata sidecar when present; partial manual override alongside a sidecar is rejected +(all three or none — no silent per-field fallback). + +A run config names its inputs in `dynamic_files`/`aif_files`/`roi_files`/`t1map_files`, but +any of those left empty is filled from the dceprep naming convention under `subject_tp_path` +when one is set (`dce_file_discovery.DISCOVERABLE_FILE_LISTS`, applied in +`DcePipelineConfig.from_dict`, reported as "Found by BIDS convention"). Naming a +file wins; only empty lists are filled, and `drift_files` is never discovered. The batch +driver and the GUI's auto-find use the same discovery, so all three interfaces select the +same files. `subject_source_path`/`subject_tp_path` are optional -- omitting them is the +non-BIDS case, where every input must be named and TR/FA/time-resolution/relaxivity stated. + +Relative paths in a run config are anchored to **the directory holding that config file**, +not the process cwd, so a config runs the same from anywhere. Paths given on the command +line (`--output-dir`, `--set dce_metadata_path=...`) are anchored to the cwd, where they +were typed. Entry points pass the anchor as `from_dict(..., base_dir=...)`; the path-valued +preference keys are listed in `dce_config.PATH_VALUED_KEYS` and resolved by +`dce_config.resolve_override_paths`. The parametric side follows the same rule. + +The steady-state/baseline window follows its own precedence in `_resolve_baseline_window` +(`python/dce_pipeline.py`): explicit `stage_overrides.steady_state_end` → a +`SteadyStateEndTimeIndex` field in the AIF file's JSON sidecar (the documented mechanism +for a fixed/reproducible run — same discovery convention as the metadata sidecar, `.nii`/ +`.nii.gz` swapped for `.json`) → auto-detect via `stage_overrides.steady_state_auto_method`. +`tv` is the default (MATLAB `dce/find_end_ss_tv.m`): a total-variation denoise followed by the +first significant upward jump. `biexp_fit` (MATLAB `dce/find_end_ss_biexp.m`) fits a 6-parameter +biexponential to the mean AIF *signal* curve and, unlike the shape heuristics, also reports where +the injection ends — but on 280 human-rated sessions it is right 74.6% of the time against `tv`'s +95.0%, always erring one frame late, so it is selectable rather than default (see S11 in +`project-management/projects/archived/batch-parity/aif_fitting_parity.md`). `piecewise_constant` ports +MATLAB `find_end_ss`; `legacy_sobel` ports the different `dce_auto_aif.m` heuristic; `glr` is an +additional ported detector. + +Stage B's AIF fit (`_fit_aif_biexp`, `dce/AIFbiexpfithelp.m`) always holds `t_base_end` at the +resolved baseline end and always fits the upslope duration as `t0_exp = t_base_end + delta`, +with `delta` floored at one frame. There is no `start_injection_min` option: the injection start +*is* the baseline end. Background and rationale: +`project-management/projects/archived/batch-parity/aif_fitting_parity.md`. + +### Run output + +The pipelines emit a structured event stream (`_emit_progress` in `dce_pipeline.py`, +`_emit_event` in `parametric_pipeline.py`). That stream is the machine record and always +lands in full in `/*_events.jsonl`. `python/run_reporting.py` is the only place +that turns it into text for people, and the CLIs, both batch drivers and both GUI log views +all render through it, so every interface describes a run the same way. + +Verbosity (`--verbosity quiet|normal|detailed|debug`, `-v`/`-vv`/`-q`) selects how much of +that stream is rendered, never how much is recorded. `normal` is the default; the GUI log +renders at `detailed` (`run_reporting.GUI_VERBOSITY`). `--events on` puts the raw JSON +stream on stdout *instead of* human progress -- stdout carries one audience at a time -- +and is how the GUI drives its progress bar. Below `debug`, a failed run reports the error +and exits non-zero without a traceback. + +Every run records which ROCKETSHIP produced it. `python/version.py` is the single source: +`__version__` plus `git_revision()`, the short commit with `-dirty` when the tree has +uncommitted changes, or `None` outside a checkout. `version.build_identity()` returns both +as one dict, and that dict goes into the `cli_config` and `run_start` events and into the +run summary JSON. The rendered header shows the version at every level and the revision at +`detailed` and above. Readers take it from the *event*, never by importing `version` +themselves, so a GUI rendering a subprocess or a replay of an old log reports the build that +produced the run rather than the one doing the reading. + +A few messages come from call sites with no event callback in scope (config-time BIDS +discovery, per-scan value provenance, Stage-D backend choice). They call +`run_reporting.notice(text, level)`, which the entry point routes to a reporter or into the +event stream; with no sink installed it prints, so the pipeline stays usable as a library. +Do not add bare `print` calls to the pipelines -- they bypass verbosity and reach every +interface. + +### GUI structure + +Both GUIs are one interface over two pipelines. `python/gui_common.py` holds everything that +is the same by nature -- the window palette and `WINDOW_QSS`, path resolution against the +config that holds a path, browse dialogs, the collapsible section, the log view and its +reporter, the run bar, the figures panel, and the `QProcess` lifecycle including the event +demux -- exposed as `GuiCommonMixin` plus a few builders. Each window keeps only what differs: +which settings exist, how a config payload is assembled, and what an event means for the +progress bar. + +Do not re-add a local copy of a mixin method to a window. Two copies of "how a GUI drives a +CLI" is what produced four different `--set` parsers; `tests/python/test_gui_common.py` fails +if one comes back. Both windows show the same four tabs (Inputs, CLI Output, QC Figures, +Results) and share `dce_volume_viewer.py`, which is pipeline-agnostic despite its name. + +### Backend selection (Stage D acceleration) + +`backend` is `auto` | `cpu` | `gpufit`. `auto` tries `pygpufit`+CUDA, then `pycpufit` +(CPU), then falls back to the pure Python/scipy path — see `probe_acceleration_backend`/ +`_resolve_backend_selection` in `dce_pipeline.py`. Accelerated models (`tofts`, `ex_tofts`, +`patlak`, `tissue_uptake`, `2cxm`) all fit through the shared `python/dce_fit_backends.py` +multi-start machinery (`FitInputs`, per-model `assemble_*_candidates`, `fit_with_multistart`), +so every backend — cpufit/gpufit or plain Python — sees the same candidate starting points +and the same bounds clamp; `tissue_uptake`/`2cxm` are fit in E-space (`E = Ktrans/Fp`) and +converted back on output. `pygpufit`/`pycpufit` are not in `requirements.txt` (installed +separately via `install.py`), so CI's `auto` always resolves to pure CPU. + +### Data layout and fixtures + +BIDS-style `rawdata/` (raw images, scan-parameter sidecars) + `derivatives/` (masks, T1 +maps, pipeline outputs) trees, discovered via `python/bids_discovery.py`. Test fixtures +live under `tests/data/BIDS_test/`, committed and lightweight (no per-run regeneration in +CI) — key subjects: `sub-10bbbdownsample` (DCE Tofts/Patlak parity), `sub-11tiny` (T1/DCE +settings matrix), `sub-0Xphantom` (synthetic ground-truth reliability, diagnostic only). +MATLAB reference maps live under `derivatives/matlabref/...`; regenerate them only when +the MATLAB algorithm actually changes (commands in `tests/README.md`), and expect to +update the committed maps in the same change — a stale committed baseline vs. a +freshly-regenerated one is a real, previously-hit failure mode +(`tests/contracts/check_matlabref_map_drift.py` guards against it in CI). + +### Cross-language parity contracts + +`tests/contracts/` holds the MATLAB↔Python numeric contract: `export_parity_baseline.m` +(MATLAB) writes `tests/contracts/baselines/matlab_reference_v1.json` from synthetic +curves fed straight to the model math (no imaging pipeline involved); +`generate_python_results.py` + `compare_with_matlab_baseline.py` check Python against it. +`check_baseline_drift.py` catches MATLAB algorithm drift at that (synthetic-curve) layer; +`check_matlabref_map_drift.py` catches drift at the full-pipeline NIfTI-map layer — these +are deliberately separate because the synthetic-curve contract never exercises +`A_make_R1maps_func`/`find_end_ss` (steady-state detection, AIF extraction, etc.). + +## Documentation Discipline + +Canonical planning and status docs: +- `project-management/ROADMAP.md` — strategy/sequencing, merge-readiness criteria. +- `project-management/TODO.md` — active open tasks/blockers only. +- `project-management/COMPLETED.md` — historical completion log. + +Current measurable state is the test suite itself, not a document. Run it rather than +consulting a snapshot; a checked-in status file went stale between reads and was removed. + +Keep planning docs non-overlapping. Do not update all planning docs by default. + +Document roles: +- `ROADMAP.md`: strategy and sequencing only. + - Includes merge-readiness criteria, long-horizon workstreams, and delivery order. + - Excludes day-to-day checklists and historical changelog entries. +- `TODO.md`: active actionable tasks only. + - Includes open blockers, open follow-ups, and open external handoff items. + - Excludes completed history and broad strategic narrative. +- `COMPLETED.md`: historical completion log only. + - Includes resolved milestones, completed work packages, and retired status notes. + - Excludes open tasks. + +Update decision rule (apply smallest necessary set): +- Strategy changed: update `ROADMAP.md`. +- Open work changed: update `TODO.md`. +- Work finished or historical status archived: update `COMPLETED.md`. + +Do not leave important caveats only in commit messages or chat; record them in the single appropriate document above. + +When you discover a problem that cannot be fixed immediately, document it before moving on: +- Write it up under `project-management/projects//` -- integrate it into + an existing initiative folder if the problem clearly belongs to one (e.g. a Stage-D + backend divergence found while working on batch parity goes in `projects/archived/batch-parity/`), + or create a new `projects//` folder if it doesn't fit any existing initiative. + Include what's confirmed (root cause, evidence), what's still open, and any agreed + near-term mitigation, so the next person (or your future self) doesn't have to + re-derive it from scratch. +- Still add a one-line pointer in `TODO.md` per the update rule above, since undocumented + open work is easy to lose track of and `TODO.md` is where open work is expected to be + discoverable; keep the actual detail in the project folder, not duplicated in `TODO.md`. + +When asked to plan or estimate a new initiative, also write it up under `project-management/projects//`. Upon completion, move the initiative folder to `project-management/projects/archived/` and add a one-line pointer in `COMPLETED.md` per the update rule above. + +Other reference docs: +- `docs/dce_options.md` — full `stage_overrides` field reference (shared by CLI + GUI). +- `docs/parametric_options.md` — parametric T1 field reference (shared by CLI + GUI + batch). +- `python/README.md` — Python usage guide (CLIs, batch processing, GUI, output formats). +- `tests/README.md` — full test-suite reference. + +OSIPI reference repos available locally for verification work: +- `~/code/DCE-DSC-MRI_CodeCollection` +- `~/code/DCE-DSC-MRI_TestResults` + +## Engineering Priorities +- The Python code path is still in development and has no production users yet. +- Prioritize correctness, numerical reliability, and clean architecture over preserving legacy behavior that is not needed. +- Do not keep unnecessary Python files/functions just for historical symmetry; remove dead code aggressively once replacements are validated. +- Keep MATLAB and Python comparisons explicit when parity is required, but do not preserve obsolete MATLAB UX patterns that add maintenance overhead. + +## Academic Software Standards +This is an academic software project. Favor: +- readable code with clear naming and unit-aware variables +- modular design that supports future method updates and extensions +- transparent algorithm choices and testable interfaces +- documentation that makes assumptions and limitations explicit + +### Comment style +Keep code comments brief — one or two lines is the norm, and prefer none over restating +what the code already says. Explain *why*, not *what*. + +Multi-line comment blocks need to earn their length. A short pointer to the durable record +beats an inline retelling: cite the commit, the issue, or the file in +`project-management/` and let that carry the detail. Narrative belongs in those docs +and in commit messages, not in the source. + +The exception is a non-obvious constraint that will be silently broken by someone editing +nearby — a numerical-stability requirement, a MATLAB-parity contract, a guard whose +condition is subtler than it looks. State it in a sentence or two, then link out. + +### Commit messages +Keep them shorter than the instinct to be thorough suggests. A subject line that states the +change, then a body of a few short paragraphs — roughly 150-250 words — covering *why* the +change was made and anything a reader could not infer from the diff. One paragraph per +substantive change, not per file, per defect and per detail. + +The diff already says what moved. The durable record for reasoning, evidence and open +caveats is `project-management/` (see Documentation Discipline above) — cite it and let +it carry the detail rather than restating it here. A message that runs past a screen is +usually a document that was written in the wrong place. + +## Porting Focus +Primary focus: +- Parametric maps, especially T1 fitting (with GUI support) +- DCE model reliability for Patlak, Tofts, and Extended Tofts +- DCE Part E post-fitting analysis workflow + +Secondary focus: +- further refinement of 2CXM and tissue uptake +- DSC workflow expansion + +## OSIPI Verification Expectations +- Keep OSIPI-labeled tests additive; do not replace existing ROCKETSHIP tests. +- Maintain explicit provenance for imported OSIPI data and peer-result CSVs in `tests/data/osipi/README.md`. +- During T1 workflow work, prioritize both: + - T1 mapping reliability checks against OSIPI reference datasets/peer result summaries. + - Signal-intensity to concentration conversion checks against OSIPI SI2Conc datasets/peer result summaries. + +Explicitly not targeted for Python parity unless scope changes: +- legacy neuroecon execution path +- legacy email notification flow +- manual click-based MATLAB AIF tools and ImageJ `.roi` compatibility paths diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..93a18ee --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,56 @@ +cff-version: 1.2.0 +message: "If you use ROCKETSHIP in your research, please cite the article below." +title: ROCKETSHIP +abstract: >- + An open source toolbox for the processing and analysis of dynamic + contrast-enhanced (DCE) and parametric MRI data. Provides quantitative + pharmacokinetic modelling, parametric mapping of T1, T2, T2* and the apparent + diffusion coefficient, and the supporting workflow required to take a study + from acquired images to parameter maps. +type: software +authors: + - family-names: Barnes + given-names: Samuel R. + orcid: "https://orcid.org/0000-0002-1065-8442" + affiliation: Loma Linda University + - family-names: Saca + given-names: Lucas + orcid: "https://orcid.org/0009-0008-3291-0750" + affiliation: Loma Linda University + - family-names: Ng + given-names: Thomas S. C. + affiliation: California Institute of Technology +license: GPL-3.0-or-later +repository-code: "https://github.com/petmri/ROCKETSHIP" +url: "https://petmri.github.io/ROCKETSHIP/" +keywords: + - DCE-MRI + - pharmacokinetic modelling + - parametric mapping + - Ktrans + - MRI +preferred-citation: + type: article + title: >- + ROCKETSHIP: a flexible and modular software tool for the planning, + processing and analysis of dynamic MRI studies + authors: + - family-names: Barnes + given-names: Samuel R. + - family-names: Ng + given-names: Thomas S. C. + - family-names: Santa-Maria + given-names: Naomi + - family-names: Montagne + given-names: Axel + - family-names: Zlokovic + given-names: Berislav V. + - family-names: Jacobs + given-names: Russell E. + journal: BMC Medical Imaging + volume: 15 + issue: 1 + start: 19 + year: 2015 + month: 6 + doi: 10.1186/s12880-015-0062-3 diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 0000000..505624c --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,7 @@ +# CLAUDE.md + +This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. + +All project guidance — what this is, setup, running the pipelines, testing, architecture, +documentation discipline, engineering priorities, and porting focus — lives in `AGENTS.md`. +Read it before doing any work here; it is the authoritative doc, not this file. diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/README.md b/README.md index 04efb96..ed00fa1 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,9 @@ -# ROCKETSHIP v1.3 +# ROCKETSHIP v2.0.rc +--- +[![OSIPI](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/ironictoo/b65ef98aadaa684f2d7d31e82137c4b4/raw/osipi.json)](https://github.com/petmri/ROCKETSHIP/actions/workflows/run_DCE.yml) +[![CI](https://github.com/petmri/ROCKETSHIP/actions/workflows/run_DCE.yml/badge.svg?branch=dev)](https://github.com/petmri/ROCKETSHIP/actions/workflows/run_DCE.yml) +[![Docs](https://github.com/petmri/ROCKETSHIP/actions/workflows/docs.yml/badge.svg)](https://petmri.github.io/ROCKETSHIP/) + ROCKETSHIP is a toolbox for processing and analyzing parametric MRI and DCE-MRI data. It was developed at the Biological Imaging Center at the California Institute of Technology and Loma Linda University. @@ -15,8 +20,9 @@ For documentation and how-to guides, use the project docs site: The GitHub Wiki is being migrated and will be kept for transition notices. +If you are using ROCKETSHIP for DCE-MRI, please cite this paper, which also has detailed information about the DCE models used in this project: -## ROCKETSHIP Papers +Ng, T.S.C., et al. [ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies](https://doi.org/10.1186/s12880-015-0062-3). *BMC Medical Imaging*, 15, 19 (2015). PMID: 26076957 If you are using ROCKETSHIP for DCE-MRI, please cite this paper, which also has detailed information about the DCE models used in this project: @@ -42,7 +48,243 @@ Other publications using ROCKETSHIP (for a more complete list, see [Google Schol - Boehm-Sturm, P., et al. [Low-Molecular-Weight Iron Chelates May Be an Alternative to Gadolinium-based Contrast Agents for T1-weighted Contrast-enhanced MR Imaging](https://pubmed.ncbi.nlm.nih.gov/28880786/). *Radiology*, 286(2), 537-546 (2018). PMID: 28880786 - Sta Maria, N.S., et al. [Low Dose Focused Ultrasound Induces Enhanced Tumor Accumulation of Natural Killer Cells](https://doi.org/10.1371/journal.pone.0142767). *PLOS ONE*, 10(11), e0142767 (2015). PMID: 26556731 -## ROCKETSHIP MATLAB +## ROCKETSHIP Python + +The newly developed Python module provides a command-line interface (CLI) and GUI for DCE-MRI and parametric mapping workflows, with optional GPU acceleration via `pyGpufit` and CPU fallback via `pyCpufit`. The Python scripts are designed to be modular and scriptable, allowing users to run the same core processing stages as the MATLAB version, but with more flexible configuration and automation options. The MATLAB scripts remain available for users who prefer that environment or have existing workflows built around it, but the Python module is the recommended path forward for new users and projects. + +### Automated setup, recommended for most users + +Recommended setup (default): + +```bash +cd /path/to/ROCKETSHIP +python3 install.py +``` + +What this script does: + +- creates/reuses `.venv` (use `--recreate-venv` to rebuild) +- installs Python requirements (including GUI by default) +- downloads latest stable release package from `ironictoo/Gpufit` +- auto-detects host platform/arch and picks matching release asset +- detects local CUDA version (when available) and prefers the closest matching CUDA asset for your host +- falls back to CPU asset IDs when CUDA builds are not a good local match +- installs both `pyCpufit` and `pyGpufit` into the venv +- installs the MATLAB MEX files from the bundle and verifies them when MATLAB is on `PATH` + (if MATLAB is not found the installer warns and still finishes successfully) +- verifies imports and reports CUDA availability +- writes the `rocketship_dce.sh` and `rocketship_parametric.sh` launchers (`.bat` on Windows), which activate the + virtual environment and starts a GUI + +Common installer options: + +- `--release-tag `: pin to a specific Gpufit release +- `--asset-id `: force specific asset id +- `--venv-path `: custom venv path +- `--no-gui`: skip GUI dependency install + +### Manual setup + +Use this path only if you do not want to use the automated installer. + +```bash +cd /path/to/ROCKETSHIP +python3 -m venv .venv +.venv/bin/python -m pip install --upgrade pip setuptools wheel +.venv/bin/python -m pip install -r requirements.txt +.venv/bin/python -m pip install -r requirements_gui.txt +``` + +Manual acceleration package install (from local wheel/source paths): + +```bash +cd /path/to/ROCKETSHIP +.venv/bin/python -m pip install /path/to/pyCpufit-*.whl +.venv/bin/python -m pip install /path/to/pyGpufit-*.whl +``` + +### Run the Python DCE CLI + +Two example configs ship, one per data layout. Both run as they stand, from the ROCKETSHIP +root: + +```bash +source .venv/bin/activate + +# BIDS layout (tests/data/BIDS_test, subject sub-02downsample) +python run_dce_python_cli.py --config python/dce_run_example_bids.json + +# Not BIDS -- a flat folder of NIfTIs (tests/data/BBB data p19) +python run_dce_python_cli.py --config python/dce_run_example_nonbids.json +``` + +BIDS is not required, and the two examples show the difference. The BIDS one names two +folders and no files: the images and masks are found by the dceprep naming convention, and +the acquisition parameters come from the sidecar. The non-BIDS one names every file outright +and states `tr_ms`, `fa_deg`, `time_resolution_sec` and `relaxivity` in `stage_overrides`, +because there is no convention to read them from. + +Naming a file always wins over the convention, so a BIDS config can discover most of its +inputs and override one. See `docs/dce_options.md` for the full comparison. + +Run with the built-in default config template: + +```bash +source .venv/bin/activate +python run_dce_python_cli.py +``` + +Default template location: + +- `/path/to/ROCKETSHIP/python/dce_run_example_bids.json` +- This default is prewired to a conforming example session: + - `/path/to/ROCKETSHIP/tests/data/BIDS_test` (subject `sub-02downsample`, session `ses-01`) + - outputs to `/path/to/ROCKETSHIP/out/dce_run_example_bids` + +Optional runtime overrides: + +```bash +python run_dce_python_cli.py \ + --config tests/python/dce_cli_config.example.json \ + --set voxel_MaxFunEvals=100 \ + --set blood_t1_ms=1600 +``` + +Runs print readable progress by default. Use `-v` for more detail (settings, per-scan value +provenance, backend choice, every file written), `-vv` to add the raw event stream, or `-q` +for errors only. Verbosity changes only what is printed -- the JSONL event log below always +records the run in full. See `python/README.md` for the full table. + +Typical outputs: + +- Stage summary JSON: `/dce_pipeline_run.json` +- Event log JSONL: `/dce_pipeline_events.jsonl` +- Stage checkpoints (optional): `/a_out.json`, `b_out.json`, `d_out.json` +- DCE model maps (NIfTI when possible; fallback `.npy`) +- ROI spreadsheet output (`.xls`) for ROI-enabled runs +- QC figures for Stage A/B real runs + +### Run the Python Parametric T1 CLI + +Run with built-in default config template: + +```bash +source .venv/bin/activate +python run_parametric_python_cli.py +``` + +Run a single subject/session with path-first input discovery: + +```bash +source .venv/bin/activate +python run_parametric_python_case.py \ + --subject-source /path/to/rawdata/sub-01/ses-01 \ + --subject-tp /path/to/derivatives/t1prep/sub-01/ses-01 \ + --output-dir /path/to/output/sub-01/ses-01 +``` + +Single-case discovery behavior: + +- prefers unified DCEref VFA stacks under `derivatives/.../anat/*space-DCEref_desc-bfczunified_VFA.nii*` +- otherwise uses canonical per-flip DCEref VFA files under `derivatives/.../anat/*_flip-XX_space-DCEref_VFA.nii*` +- falls back to raw VFA files under `rawdata/.../anat/*flip-*_VFA.nii*` +- uses raw VFA sidecars for `FlipAngle` and `RepetitionTime` when available +- auto-detects `B1_scaled_FAreg.nii[.gz]` in derivatives first, then raw anat +- defaults to `t1_fa_fit`; override with `--fit-type` if needed + +Default template location: + +- `/path/to/ROCKETSHIP/python/parametric_run_example.json` + +Typical outputs: + +- Run summary JSON: `/parametric_t1_run.json` +- Event log JSONL: `/parametric_t1_events.jsonl` +- T1 map NIfTI: `/T1_map__