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Nifti misc improvements #7

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@AnnaBeers AnnaBeers commented Feb 22, 2017

This pull requests represents a few of QTIM lab's contributions to glue medical, especially pertaining to Nifti file formats and exporting subsets. More to come.

Remaining things to do:

  • Create small test NIFTI and NRRD files

@astrofrog astrofrog force-pushed the nifti-misc-improvements branch from 3c0caae to 9a72c39 Compare February 22, 2017 22:04
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@AndrewBeers - I had forgotten to commit utils.py, which I've done now - sorry!

.travis.yml Outdated
@@ -10,7 +10,7 @@ env:
- SETUP_XVFB=True
- CONDA_CHANNELS="conda-forge"
- CONDA_DEPENDENCIES="glueviz pytest mock requests"
- PIP_DEPENDENCIES="pydicom"
- PIP_DEPENDENCIES="pydicom, nibabel"
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remove the comma here

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astrofrog commented Mar 21, 2017

There are some files that were added here that shouldn't be - specifically all the files in glue_medical.egg-info - can you remove these? By the way, I've just pushed a commit to master to add a .gitignore file (which was missing previously). I also fixed the DICOM tests. Could you rebase this branch?

EDIT: just remembered we had added a .gitignore file here, oops

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@AndrewBeers - thanks for continuing work on this! Just so you know, since we last worked on this I've now added the ability to write custom subset mask importers/exporters:

http://glueviz.org/en/stable/customizing_guide/customization.html#custom-subset-mask-importers

This is different from the Data/Subset exporter:

http://glueviz.org/en/stable/customizing_guide/customization.html#custom-data-subset-exporters

because in the latter, the values of the subset should be exported, as opposed to the mask.

@AnnaBeers AnnaBeers force-pushed the nifti-misc-improvements branch from 26835b5 to ceb851d Compare January 19, 2018 16:06
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