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[IV3D-USERS] Re: RE: Re: imagevis3D data format


Chronological Thread 
  • From: tom fogal <tfogal@sci.utah.edu>
  • To: iv3d-users@sci.utah.edu
  • Subject: [IV3D-USERS] Re: RE: Re: imagevis3D data format
  • Date: Wed, 07 Dec 2011 15:23:29 -0700
On 12/07/2011 02:23 PM, Yang, Hui wrote:
Thank you for your promt reply. I am totally new to the volume
rendering. I don't know if it is a volume data set. All those numbers
after @1 represent the electron density values. It is a 3D scalar
fields defined on a uniform grid. I will try the obj format. But I
have almost 200 am files, so I really want to convert them to another
type of file by keeping those data after @1 and only changing the
head.

Ahh, okay, if it's really a 3D scalar field on a uniform grid, then you just want to load the data as-is without trying to convert or export it into anything.

You can use the "Header skip" in the raw conversion dialog to skip past the junk at the beginning of the file. Of course, you'll have to know exactly how many bytes that is.

If you send me a few files I can probably write a more convenient loader for them in short order. We have an ftp setup for people to upload data into; contact me off-list if you want to pursue this route.

Cheers,

-tom

________________________________________
From: tom fogal [tfogal@sci.utah.edu]
Sent: Wednesday, December 07, 2011 3:42 PM
To: iv3d-users@sci.utah.edu
Subject: [IV3D-USERS] Re: imagevis3D data format

Is an "AmiraMesh" file actually a mesh?  If so, you want to export to
OBJ (.obj) format.   I hear Amira can export in that format.

If it's actually a volume data set, my guess is you just want a file
that is everything after that "@1".  Then you can manually instruct
ImageVis3D what the volume sizes, etc. are and load the file that way.

Unfortunately I do not think we support loading only a mesh into
ImageVis3D at present -- it has to be associated with some volume data.
   This should arguably be changed.  In the meantime, just create a 1x1x1
"volume" and load it into ImageVis3D, then use 'File | Add Geometry to
this Data Set' to import your OBJ-format mesh.

Cheers,

-tom

On 12/07/2011 01:30 PM, hui.yang@rockets.utoledo.edu wrote:
Hello,

I am trying to use iv3D to do the volume rendering of electron density data of
a formaldehyde molecule.  The electron density data is stored in a AmiraMesh
file. I would like to ask which format should I change to? I tried to load it
as raw data, but I couldn't see any shape of of the molecule at all.

Any help will be appreciated.

-Hui

Here is the part of my        AmiraMesh file.

# AmiraMesh ASCII 1.0

define Lattice             78      41      76

Parameters {
      BoundingBox      -1.925136           1.924864     -1.000101      
0.999899
-1.567035      2.182965,
      CoordType "uniform"
}

Lattice { float Data } = @1

@1
    0.1705088760E-02  0.1930265808E-02  0.2177519857E-02       
0.2447091951E-02
0.2738759561E-02  0.3051764319E-02
    0.3384750565E-02  0.3735719626E-02  0.4102004485E-02       
0.4480269015E-02
0.4866535091E-02  0.5256239877E-02
    0.5644324265E-02  0.6025351931E-02  0.6393656808E-02       
0.6743514942E-02
0.7069334839E-02  0.7365858635E-02
    0.7628364894E-02  0.7852862814E-02  0.8036267207E-02       
0.8176544061E-02
0.8272817757E-02  0.8325433077E-02
...


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