Description

Most of the points here are because of unclear comments/header, the need for merging the two testing scripts that interleave one another, and the need for checking for empty folders (from updating the local FlavorDatabase)

Tasks fixed:

• line 115: logContent seems a variable that is not used. Fixed in cedf18d
• line 110: it says that it removes existing data (spelling error though), but in fact it removes the output, the tested data right? Not the input testdata. Was confusing to me ;) Fixed in cedf18d
• onlyRemoveResults should be a boolean; the code looks a bit quick and dirty all together? Fixed in cedf18d
• Why does xASL_test_Flavors exists as intermediary? It would increase readability if xASL_test_FullPipelineTest and xASL_test_Flavors would be merged, and renamed to xASL_test_Flavors. Done in 6361d45 a19027d d5b7c0e
• After going through all this, I note the issue is the empty folders. When git updates, it will keep the previous folders. So we simply have to include a check for empty folders, generate a warning, and skip them (remove them from the flavorlist). This should check for empty subfolders as well, so only check for the existence of files. If no files exist, don't include a folder to the flavor list for testing. Fixed in macOS dcm2nii hotfix #1271

Tasks answered:

• xASL_test_EscapeToUnixshould be merged with xASL_adm_UnixPath? JAN: It actually crawls across the whole BIDS structure. And also removes double backslash. So it has a bit broader functionality. So it cannot be simply replaced. Since it is just an internal function available in this script, I would keep it.
• line 40 xASL_test_Flavors_DCM2BIDSshould probably be x = ExploreASL; instead of ExploreASL; JAN: Fine as it is - x-struct shouldn't be there, because it is not used later in this function. ExploreASL is called as a short for ExploreASL_Initialize.

Tasks todo

• Am I right that the user is expected to put a non-repository file testConfig.json inside of the local clone of the repository? I thought we wanted to avoid this.
• For HENK:
  There is an illegal character issue for [ ]. Perhaps we can fix this by putting the paths in strings for Linux/macOS: " ", or by removing more illegal characters from the path with our replacement functions. But the latter would involve overwriting the sourcedata which should be read-only, so it has to be the " ". Or first testing if the folder names don't have illegal characters (BTW: Windows should be much worse for illegal characters...)

executing: [/Users/henk/ExploreASL/ExploreASL/External/MRIcron/20220720/dcm2niix-osx -o /Users/henk/ExploreASL/FlavorDatabase/GE_PCASL_3Dspiral_DV25.0_product_1/derivatives/ExploreASL/temp/001/ASL_1/dcm2nii_temp_ASL4D /Users/henk/ExploreASL/FlavorDatabase/GE_PCASL_3Dspiral_DV25.0_product_1/sourcedata/sub-001/20/S 007 [3D ASL]/Im181.0.dcm]
zsh:1: bad pattern: [3D

Release notes

Review issue, nothing to mention.