Commit c060ad85 authored by Devin OKelly's avatar Devin OKelly
Browse files

Test addition of astrocyte_cli tests

parent a6845b16
......@@ -252,6 +252,7 @@ test_nextflow:
script:
- set -x
- cd workflow
# Copy all of the data files in the test data folder into the workflow folder.
- find "$V36_PHANTOM_DATA_FOLDER" -maxdepth 1 -type f -exec cp -t ./ {} +
- ls -lah
- |
......@@ -291,8 +292,33 @@ test_nextflow:
test_astrocyte:
stage: astrocyte
script:
- echo "PASS"
- module add astrocyte/0.3.1
- pwd
- ls -lah
- find "$V36_PHANTOM_DATA_FOLDER" -maxdepth 1 -type f -exec cp -t ./workflow {} +
- |
astrocyte_cli run . --verbose
--param=msotFile,"Scan_3.msot" \
--param=binFile,"Scan_3.bin" \
--param=irfFile,"Scan_3.irf" \
--param=nodFile,"Scan_3.nod" \
--param=reconModel,"backproject2D" \
--param=reconSolver,"lsqr" \
--param=fieldOfView,"25" \
--param=pixelResolution,"200" \
--param=tuneSpeedOfSound,"auto" \
--param=userSpeedOfSound,"1520" \
--param=unmixingEndmembers,"{['hbo2', 'hb']}" \
--param=multispectralPrefilter,"slidingFunction" \
--param=reconSettings.FramesToReconstruct,"[1,2,3,4,5,6,7,8,9,10]" \
--param=unmixingSolver,"direct" \
--param=parallelizationSettings,"local" \
--param=doDebug,"false"
artifacts:
- ./*/*/*/*/*/recons.h5
- ./*/*/*/*/*/unmixed.h5
- ./output/*/recons.h5
- ./output/*/unmixed.h5
##########################################
......
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