diff --git a/.github/workflows/run.yml b/.github/workflows/run.yml index 58bf984..6567ed2 100644 --- a/.github/workflows/run.yml +++ b/.github/workflows/run.yml @@ -33,14 +33,24 @@ jobs: shell: bash -el {0} run: | source /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh + dataset=Siemens_mMR_NEMA_IQ + curl -sfSL -o ${dataset}.zip https://petric.tomography.stfc.ac.uk/data/${dataset}.zip + mkdir -p data; cd data; unzip -u ../${dataset}.zip; cd .. + # petric.py seems to need the data in the current dir curl -fsSL https://raw.githubusercontent.com/SyneRBI/PETRIC/main/petric.py > petric.py test -f main.py || ln -s main_ISTA.py main.py python < 0 + assert data.reference_image.max() > 0 + assert data.FOV_mask.max() > 0 EOF full: if: startsWith(github.ref, 'refs/tags') diff --git a/SIRF_data_preparation/plot_BSREM_metrics.py b/SIRF_data_preparation/plot_BSREM_metrics.py index 39bb828..74c2273 100644 --- a/SIRF_data_preparation/plot_BSREM_metrics.py +++ b/SIRF_data_preparation/plot_BSREM_metrics.py @@ -23,7 +23,9 @@ # scanID = 'Siemens_Vision600_thorax' # scanID = 'NeuroLF_Hoffman_Dataset' # scanID = 'Siemens_mMR_NEMA_IQ' -scanID = 'Mediso_NEMA_IQ' +# scanID = 'Mediso_NEMA_IQ' +# scanID = 'GE_DMI3_Torso' +scanID = 'Siemens_mMR_NEMA_IQ_lowcounts' srcdir = SRCDIR / scanID outdir = OUTDIR / scanID @@ -126,3 +128,5 @@ plt.figure() data_QC.plot_image(image - reference_image, **slices, vmin=-cmax / 100, vmax=cmax / 100) plt.savefig(outdir / f'{scanID}_ref_diff_image_at_0.01_0.005.png') + +# %%