[Insight-users] sparse images?

[Darren Weber]

Hi Dan,

The proposal is very interesting.  Having read the PDF, I'll take a look at
the code.  I may be able to offer a review (time permitting).

Do you have any recent examples of using either the SliceContiguous or the
Sparse images to compose a 3D volume from a series of 2D image files?  Do
you somehow

a) Allocate the custom image memory (if known size & pixtype)
b) Create an IO object to read data from an image file
c) manually iterate over the IO object data with Get/Set accessors to put
data into custom image memory
d) Filter, etc. (if possible)
e) Write out image data to disk (somehow)

I can take the performance hit for the sparse image with Setting values.

Should I be looking into streaming data models?  Essentially all I need to
do is stream a set of 2D input data straight out to a 3D output data file.
I'm currently using a series reader (with a regex to define the image
series) and piping it straight to a writer (with vtkIO for the writer).  If
a streaming model is available for this data transfer, it might avoid the
segfaults due to allocation limits (I have plenty of disk space, just not
enough RAM).

Thanks!
Darren





On Wed, Nov 4, 2009 at 1:54 PM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Darren,
>
> You might want to investigate the following Insight Journal submission:
>    http://www.insight-journal.org/browse/publication/646
>
> <shameless plug>
> Make sure you leave a review!
> </shameless plug>
>
> Cheers, Dan
>
> 2009/11/4 Darren Weber <darren.weber.lists at gmail.com>:
> >
> > I'm working with a very large dataset (1000's of 2D images, size >
> 1024x1024
> > pixels, ushort RGB pixels).  A large portion of these images is
> background.
> >
> > A few routines, like saving all the 2D images into a 3D volume, fail with
> > segfaults due to malloc errors (on OSX 10.5.8 with 24Gb RAM; using ITK
> > 3.16.0).
> >
> > Is there an image format that provides 'sparse' images?  This implies
> there
> > are no data values for some of the image pixels (is this the same thing
> as
> > transparent background?).
> >
> > What is an optimal image format for working with this data?
> >
> > Thanks in advance (TIA),
> > Darren
> >
> >
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