[Paraview] I can't read a binary 'raw' data image file

[Cory Quammen]

Robert,

I second Ken's suggestion of using the NRRD header. You might even be
able to export NRRD from ImageJ. I know you can export NRRD through
Fiji. I do this regularly.

- Cory

On Tue, Nov 6, 2012 at 9:54 AM, Moreland, Kenneth <kmorel at sandia.gov> wrote:
> This is a bit off the question you asked, but you might consider making a
> NRRD header file, which is a simple text file that provides the
> information you normally have to enter by hand in the raw file reader
> (http://teem.sourceforge.net/nrrd/).  I like using NRRD headers so that I
> don't have to continually enter this information (that I tend to forget)
> every time I load the file, and that don't have that gotcha with the
> dimensions/extent indexing that Cory describes.
>
> As an example, a NRRD header file for your file could be called
> snail_partial_348x250x348_float32.nhdr and contain the following:
>
> NRRD0004
> dimension: 3
> sizes: 348 250 348
> spacings: 1 1 1
> endian: little
> type: float (or `unsigned char' for the other version)
> encoding: raw
> data file: snail_partial_348x250x348_float32.raw
>
> -Ken
>
>
>
> On 11/6/12 7:00 AM, "Cory Quammen" <cquammen at cs.unc.edu> wrote:
>
>>Hi Robert,
>>
>>On Tue, Nov 6, 2012 at 8:37 AM,  <Robert.Atwood at diamond.ac.uk> wrote:
>>> Dear List
>>>
>>> I hope it's some silly 'newbie' issue, but I find myself completely
>>>unable to read a raw binary data file using the raw binary data file
>>>reader. I have saved a data file as 'raw data' from ImageJ to try, and
>>>loaded that same file in ImageJ to verify that data is present. I have
>>>saved two versions: 8 bit [0-255] binary data and floating point 32-bit
>>>data in little-endian format.
>>>
>>> Then in Paraview I try to open the file, then select
>>> File prefix : this contains the correct file name it appears to me
>>> C:\Documents and Settings\kny48981\My
>>>Documents\Experiments\snail\snail_partial_348x250x348_float32.raw
>>> Data Scalar Type: Float (or Unsigned char for the other version)
>>> Data Byte Order: LittleEndian
>>> File Dimensionality: 3
>>> Data Origin 0 0 0
>>> Data Spacing 1 1 1
>>> Data Extent 0 348
>>>             0 250
>>>             0 348
>>> Number of Scalar Components: 1
>>> Scalar Array Name: ImageFile
>>> File Lower Left (ticked)
>>
>>It looks like the image you are reading has the size 348x250x348. A
>>definite gotcha in the RAW file reader is that the maximum extent in
>>x, for example, has to be one less than the size of the image in x.
>>The same is true for the y and z dimensions.
>>
>>Hope that helps,
>>Cory
>>
>>--
>>Cory Quammen
>>Research Associate
>>Department of Computer Science
>>The University of North Carolina at Chapel Hill
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>
>



-- 
Cory Quammen
Research Associate
Department of Computer Science
The University of North Carolina at Chapel Hill