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

[Robert.Atwood at diamond.ac.uk]

Thanks, that NRRD is good to know about as a workaround, though I also used MHD in the past. 

But correctly interpreting the zero-indexed array dimension is a start, I can see some snail shell now

Ideally, the best case would be to have the HDF5 reader to read the HDF5 files that we propose to use to store data in the extremely near future. First I need to just understand what Paraview can really do for our data


> -----Original Message-----
> From: Cory Quammen [mailto:cquammen at cs.unc.edu]
> Sent: 06 November 2012 14:58
> To: Moreland, Kenneth
> Cc: Atwood, Robert (DLSLtd,RAL,DIA); paraview at paraview.org
> Subject: Re: [Paraview] I can't read a binary 'raw' data image file
> 
> 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
> >>_______________________________________________
> >>Powered by www.kitware.com
> >>
> >>Visit other Kitware open-source projects at
> >>http://www.kitware.com/opensource/opensource.html
> >>
> >>Please keep messages on-topic and check the ParaView Wiki at:
> >>http://paraview.org/Wiki/ParaView
> >>
> >>Follow this link to subscribe/unsubscribe:
> >>http://www.paraview.org/mailman/listinfo/paraview
> >>
> >
> >
> 
> 
> 
> --
> Cory Quammen
> Research Associate
> Department of Computer Science
> The University of North Carolina at Chapel Hill

-- 
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom