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Hi Liam,

On 4/5/19 9:34 AM, Liam M. Healy wrote:

I have a regular grid of Cartesian x, y, z values on which is
defined a set of values that I want to plot. I have read this write-up
https://github.com/SCIInstitute/ImageVis3D/blob/master/doc/import.adoc,
and I'm lost in a sea of possibilities.

I think a .nhdr is easiest. You won't have to change anything, just write another secondary file of metadata. I attached a couple examples that should help you get started; for more details see:

http://teem.sourceforge.net/nrrd/format.html

You can then import it as normal, or use the command line 'uvfconvert' to convert on the command line. If you're generating this data from a simulation, it might be valuable to invoke uvfconvert after 'mpirun', i.e. as part of your batch job. Conversion benefits from large amounts of available memory.

In fact I would just write the program to generate a UVF directly,
but since I don't know what that format is, I can't do that.

The format itself is probably not for the faint of heart: it's an ordered(ish) collection of regular sub-volumes, each with their own ghost data ("halo cells" in some domains), in addition to some indexing structures, so it would be hard to generate directly from your simulation.

> It sounds like the "raw data converter" you mention is helpful;
> where can I get it and information on it?

The raw converter will pop up anytime the interactive (non-script-mode) IV3D does not recognize the type of input file it is given. It's really just a dialog that specifies the kind of metadata in a .nhdr.

HTH,
-tom

On Fri, Apr 5, 2019 at 12:28 AM tom fogal
< >
wrote:

Hi Liam, sorry for the slow response!

As you've found, that paper is now quite out of date.

Unfortunately, there is not a great route to import hdf5 data at this
time. In the past, I have used h5dump to dump the raw data, and then
used the raw data converter to import this into ImageVis3D. If you want
to script it, it is not too hard to write a .nhdr from a shell script
that references the raw data that h5dump produces.

HTH,
-tom

On 4/3/19 10:41 AM, Liam Healy wrote:

Hello,

I am interested in using ImageVis3D for volume ray-casting of a non-biomedical
application. I have data in an HDF5 file. I have read this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954506/, and in it, it is stated
that the UVF format is documented at ftp://datex.sci.utah.edu/UVF and
converters are available there too, but I find that the domain name is not
currently registered. Is there a new site where these things may be
downloaded?

Thank you.
Liam Healy

NRRD0004
encoding: raw
dimension: 3
type: float
sizes: 380 2200 2200
spacings: 1 1 1
endian: little
data file: 05120
NRRD0001
encoding: raw
dimension: 3
type: uint16
sizes: 501 501 925
spacings: 1 1 1
data file: Filtered_501x501x925_16bits.raw

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• [IV3D-USERS] Documentation for UVF, Liam Healy, 04/03/2019
  • Re: [IV3D-USERS] Documentation for UVF, tom fogal, 04/04/2019
    • Re: [IV3D-USERS] Documentation for UVF, Liam M. Healy, 04/05/2019
      • Re: [IV3D-USERS] Documentation for UVF, tom fogal, 04/06/2019

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