[x3d-public] problem in nrrd example file header

Andreas Plesch andreasplesch at gmail.com
Wed Feb 14 05:32:37 PST 2018

I recall that I tested the fixed nrrd files with other volume rendering
capable browsers. Let me look for the corresponding X3D scenes and post
their URLs for further testing.

I remember it was pretty difficult to discover the files on savage.



On Feb 13, 2018 10:29 AM, "Don Brutzman" <brutzman at nps.edu> wrote:

Hi Nicholas... am following up on this lingering item from the holiday

Can you please confirm the correction by Andreas, and advise on how we are
handling the files?

I don't mind hosting at savage.nps.edu but often there are difficulties
with server certificates and cross-origin resource sharing (CORS).  Thus it
would be good to figure out how best to handle this large Web3D dataset.

If the "right answer" isn't immediately clear, perhaps a short session in
one of the regular teleconferences might be appropriate sometime, then we
can figure it out together.


On 1/2/2018 12:30 AM, Don Brutzman wrote:

> Thanks for further checking Andreas.
> Nicholas (cc:ed) is originator of these files.  Have also copied Medical
> working group since these are relevant examples.
> I will be happy to post updates to these files but am hoping that we all
> proceed consistently to avoid versionitis later.  Further most are large
> (indeed overwhelming usual .zip distributions) so it is good to get them
> all sorted out correctly together.
> v/r Don
> On 1/1/2018 5:32 PM, Andreas Plesch wrote:
>> It turns out that
>> http://savage.nps.edu/Savage/VolumeRendering/datasets/nrrd/m
>> ri_ventricles_segment.nrrd
>> has the same problem of a malformed header line, eg. an excess space
>> character in the spacings line.
>> Here is a corrected nrrd file:
>> https://cdn.glitch.com/405924cd-3c0d-476e-9b88-520a5610604c%
>> 2Fmri_ventricles_segment_fixed.nrrd?1514854259949
>> -Andreas
>> On Mon, Dec 18, 2017 at 4:18 PM, Andreas Plesch <andreasplesch at gmail.com>
>> wrote:
>>> I am working on ImageTexture3D support for x3dom using the existing
>>> ImageTextureAtlas node and https://github.com/scijs/nrrd-js as a
>>> parser.
>>> It turns out the the parser is very strict, and so discovered a
>>> malformed header line in
>>> https://savage.nps.edu/Savage/VolumeRendering/datasets/nrrd/
>>> mri_ventricles.nrrd
>>> used in http://www.web3d.org/x3d/content/examples/Basic/VolumeRender
>>> ing/BasicVentriclesIndex.html
>>> Specifically, the header line
>>> 'spacings:  NaN 0.009 0.009 0.009'
>>> has _two_ space character after the colon delimiter. Exactly _one_
>>> space is allowed, however, as described here:
>>> http://teem.sourceforge.net/nrrd/format.html#general.2
>>> second paragraph:
>>> ... a string "<field>" identifying the field (called the field
>>> identifier), then a colon followed by a single space ": ", and then
>>> the information describing the field "<desc>" (called the field
>>> descriptor) ...
>>> The second space then acts as a separator making the first value in
>>> the array an empty string which causes throwing when attempting to
>>> parse as a float.
>>> I made an attempt at fixing the header by removing one space and made
>>> the file available here:
>>> https://cdn.glitch.com/af228b45-6772-432d-a549-74f9f447b2c3%
>>> 2Fmri_ventricles2.nrrd?1513631507711
>>> -Andreas
>>> --
>>> Andreas Plesch
>>> Waltham, MA 02453
all the best, Don
Don Brutzman  Naval Postgraduate School, Code USW/Br       brutzman at nps.edu
Watkins 270,  MOVES Institute, Monterey CA 93943-5000 USA   +1.831.656.2149
X3D graphics, virtual worlds, navy robotics http://faculty.nps.edu/brutzman
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