DICOM: simplify handling of parsing in context of multi-frame #2311
Conversation
When checking for matching gradient directions across reversed phase encoding acquisition in order to perform explicit volume recombination, do not rely on b=0 volumes having either nulled or equivalent gradient directions; instead, disable checking those directions if the shell to which both volumes are assigned is classified as b=0.
Use of broad Except clause resulted in obscuring AttributeError when testing for regeex matches. This meant that input strings that should ideally have been omitted due to an exclusion regex would nevertheless be included in the process list.
Changes to multiframe handling prompted by discussion on forum: https://community.mrtrix.org/t/mrconvert-directions-in-0018-9089-not-detected/ The idea is to parse all tags regardless of which level in the hierarchy they appear in, rather than only parsing when they're top-level or within a Functional Group Sequence. Instead, we just need to ignore the IconImageSequence, which contains tags that can conflict with the main image; indeed, this seems to be the only reason the parsing worked as it did so far.
dwifslpreproc: Fix to b=0 volume matching
population_template: replace whitespace in unique filename
for_each: Fix use of regex for entry exclusion
Transparently handle UTF-8 dashes as regular ones
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Opened a bunch of random DICOMs across my file system and didn't find an issue; outstanding question is whether or not you're concerned about changes in the parsing of key-values, and whether or not you want to check for that in your tests. |
Working on that as we speak. Lots of differences obviously, especially in the DW scheme as we're handling things slightly differently than previously, all of which requires careful double-checking... I'll hopefully have all this worked out by COB today. I'll be committing this to #2346 though. I'll merge this into #2346 so we can test everything in one go before merging. |
jdtournier
changed the base branch from
master
to
dicom_dict_better_initialisation
Changes to multiframe handling prompted by discussion on forum:
https://community.mrtrix.org/t/mrconvert-directions-in-0018-9089-not-detected/
The idea is to parse all tags regardless of which level in the hierarchy they appear in, rather than only parsing when they're top-level or within a Functional Group Sequence. Instead, we just need to ignore the IconImageSequence, which contains tags that can conflict with the main image; indeed, this seems to be the only reason the parsing worked as it did so far.
All DICOM tests pass fine with these changes.
Setting this up as a draft request for now as any changes to DICOM handling require quite a bit of double-checking...