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[IV3D-USERS] Re: Re: Re: Re: NRRD import


Chronological Thread 
  • From: Dave Chen <dchen@mail.nih.gov>
  • To: "iv3d-users@sci.utah.edu" <iv3d-users@sci.utah.edu>
  • Subject: [IV3D-USERS] Re: Re: Re: Re: NRRD import
  • Date: Thu, 21 Jan 2010 13:57:26 -0500

Hi.  I'm also interested in viewing color volumes, particularly the Visible Human dataset

Looking at the example volumes at the OpenQVis web page, they seem to all say "RGBA" but aren't, in fact,
color volumes.  The examples seem to be greyscale voxels with a color lookup table.

But you are talking about color volumes, right?

Thanks,
Dave Chen

On Jan 21, 2010, at 1:43 PM, tom fogal wrote:

Tim Holy <holy@wustl.edu> writes:
On Thursday 21 January 2010 10:45:13 am Jens Krueger wrote:
Currently dat/raw pairs (Qvis) are the only supported way of
getting RGBA into imagevis3d. If you can write your data into nrrd,
you can also easily create QVis files.
[snip]
However, the documentation of the format on this page
http://openqvis.sourceforge.net/docu/fileformat.html seems not to
specify anything about the order of color values in the file.  Should
it be all 4 RGBA values for the first pixel, then all 4 for the
second pixel, etc? Or should it be the red channel for the whole
volume, followed by the green channel for the whole volume, etc?

It should be RGBA, RGBA, RGBA, etc.

Here's a QVis format header that I use to load up an RGBA dataset into
ImageVis3D:

 ObjectFileName: fullbody1728x1008x1878_old.raw
 TaggedFileName: ---
 Resolution:     1728 1008 1878
 SliceThickness: 1 1 3
 Format:         UCHAR4
 NbrTags:        0
 ObjectType:     TEXTURE_VOLUME_OBJECT
 ObjectModel:    RGBA
 GridType:       EQUIDISTANT

You should hopefully be able to just change the filename and use that
file.  Place it in a .dat file so that ImageVis3D will recognize it as
QVis format.

-tom

Am 21.01.2010 um 17:40 schrieb Tim Holy:
Hi again,

In experimenting further with NRRD import, it also appears that the NRRD
importer does not make use of the "space directions" tag. Consequently,
the user has to manually enter the spacing along each coordinate axis.
There are a number of other NRRD0004 features that could also be of
potential interest.

If I'm not barking up the wrong tree in terms of choosing NRRD as a data
interchange format (i.e., with respect to my previous post re RGBA
support), there's a chance I can help with simple bugfixes/extensions
(obviously, in consultation with those who have developed iv3d in the
first place!).

Best,
--Tim


David T. Chen, PhD                      [Lockheed Martin contractor]
phone:301.435.3264                      iphone:301.524.3174
Office of High Performance Computing and Communications
National Library of Medicine




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