this doesn't work: sc.attrs.mget(['type','quality','xnat:mrScanData/parameters/te'])

[Sason Torosean]

Hello All
I am trying to execute the following code hoping to get both type and te from scan level.

    for sc  in interface.select.project(ss[0]).subject(ss[1]).experiment(ss[2]).scans('*'):
         print sc.attrs.mget(['type','quality','xnat:mrScanData/parameters/te'])

but this is the result I get...

>>>
['ncanda-localizer-v1', 'unknown', 'ncanda-localizer-v1']
['ncanda-calibration-v1', 'unknown', 'ncanda-calibration-v1']
['ncanda-t1spgr-v1', 'usable', 'ncanda-t1spgr-v1']
['ncanda-t2fse-v1', 'usable', 'ncanda-t2fse-v1']
['ncanda-dti6b500pepolar-v1', 'usable', 'ncanda-dti6b500pepolar-v1']
['ncanda-dti60b1000-v1', 'usable', 'ncanda-dti60b1000-v1']
['ncanda-grefieldmap-v1', 'usable', 'ncanda-grefieldmap-v1']
['ncanda-rsfmri-v1', 'usable', 'ncanda-rsfmri-v1']
>>>

now if I change 'te' with 'tr' it works just fine.
>>>
['ncanda-localizer-v1', 'unknown', '830.952']
['ncanda-calibration-v1', 'unknown', '150.0']
['ncanda-t1spgr-v1', 'usable', '5.904']
['ncanda-t2fse-v1', 'usable', '2500.0']
['ncanda-dti6b500pepolar-v1', 'usable', '8000.0']
['ncanda-dti60b1000-v1', 'usable', '8000.0']
['ncanda-grefieldmap-v1', 'usable', '1000.0']
['ncanda-rsfmri-v1', 'usable', '2200.0']
>>>


 I am hoping not to resort to getting this info from xml file, just because te isn't giving me the correct result!.
 Any help would be much appreciated.
Thanks

[Sason Torosean]

Ok so here is the "fix:"
If I remove 'type' from print sc.attrs.mget(['type','quality','xnat:mrScanData/parameters/te'])
and just put sc.attrs.mget(['quality','xnat:mrScanData/parameters/te'])
I get the right answer for 'te'

[David Gutman]

Sason there's something screwy with this... I had a very similar issue......  not sure how to trace this down but there must be something about the "type" label that breaks things.... under certain circumstances...

Has any one ever observed weird behavior when using XML shortcuts and an mget in pyxnat?  I am running 0.9.3... 

Basically it's overwriting one of the fields with the "type"....  I haven't gone through every iteration... but I can pull the parameter if I do it using simple the get..

It seems like specifically the "type" parameter and not the frames is "breaking" things... and when I switched it from the first to the second requested attribute it still was broken...

In [17]: xnat.select.project('NBIA_TCGA_PROD').subject('TCGA-02-0003').experiment('CCI_XNAT_PROD_E00001').scan('2').attrs.mget(['xnat:mrScanData/parameters/te'])

Out[17]: ['4.2']

In [18]: xnat.select.project('NBIA_TCGA_PROD').subject('TCGA-02-0003').experiment('CCI_XNAT_PROD_E00001').scan('2').attrs.mget(['type','frames','xnat:mrScanData/parameters/tr','xnat:mrScanata/parameters/te'])

Out[18]: ['Anatomy', '14', '80.0', 'Anatomy']

In [19]: xnat.select.project('NBIA_TCGA_PROD').subject('TCGA-02-0003').experiment('CCI_XNAT_PROD_E00001').scan('2').attrs.mget(['frames','xnat:mrScanData/parameters/tr','xnat:mrScanData/parameters/te'])

Out[19]: ['14', '80.0', '4.2']

In [20]: xnat.select.project('NBIA_TCGA_PROD').subject('TCGA-02-0003').experiment('CCI_XNAT_PROD_E00001').scan('2').attrs.mget([type,'frames','xnat:mrScanData/parameters/tr','xnat:mrScanData/parameters/te'])

In [26]: xnat.select.project('NBIA_TCGA_PROD').subject('TCGA-02-0003').experiment('CCI_XNAT_PROD_E00001').scan('2').attrs.mget(['frames','type','xnat:mrScanData/parameters/tr','xnat:mrScanData/parameters/te'])

Out[26]: ['14', 'Anatomy', '80.0', 'Anatomy']

In [24]: pyxnat.__version__

Out[24]: '0.9.3'

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David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine

[Sason Torosean]

Hi
It seems like I can't get
sc.attrs.get('xnat:mrScanData/parameters/fov')
 
sc.attrs.get('xnat:mrScanData/parameters/voxelRes')

to work either.....Are you able to get these parameters David ( or anyone else),  using just 'get'.
Thanks
S

[Sason Torosean]

[SOLVED] Ok I got it for the case of getting FOV, I need to ask for
sc.attrs.get('xnat:mrScanData/parameters/fov/x') instead, to get a number.
S