[Rtk-users] using rtk in matlab : input images for filters from matlab data types

[Julia Semyakishkina]

thanks for the fast reply.

Oops, it seems i missed that there is a backward operation of
GetArrayFromImage, i.e. GetImageFromArray..
However, forward still doesn't work for me.
This example code

% geometry
g = py.SimpleRTK.ThreeDCircularProjectionGeometry();
for i=0:359,
    g.AddProjection(500,1000,i);
end

% what projects
cube1 = zeros(128,128,128);
cube = single(cube1);

cube(17:112,17:112,17:112) = 1;
cube(33:96,33:96,33:96) = 0;

data_size = size(cube);
result = py.numpy.reshape(cube(:)', int32(fliplr(size(transpose))));
volume = py.SimpleRTK.GetImageFromArray(result);

const = py.SimpleRTK.ConstantImageSource();
const.SetSpacing(py.list([1,1,1]));
const.SetSize(py.list(int32(data_size)));
const.SetOrigin(py.list([-64.5,-64.5,-64.5]));
volume_meta = const.Execute();

volume.CopyInformation(volume_meta);

% projections

const2 = py.SimpleRTK.ConstantImageSource();
const2.SetSpacing(py.list([1,1,1]));
const2.SetSize(py.list(int32([512,1,360])));
const2.SetOrigin(py.list([-255.5,0,0]));
proj = const2.Execute();

% forward

forward = py.SimpleRTK.JosephForwardProjectionImageFilter();
forward.SetGeometry(g);
proj = forward.Execute(proj, img);

caused the following error :
Error using SimpleRTK>Execute (line 6218)
Python Error: RuntimeError: Exception thrown in SimpleRTK
JosephForwardProjectionImageFilter_Execute:
$RTK_BUILD$/SimpleRTK-build/Code/BasicFilters/src/srtkJosephForwardProjectionImageFilter.cxx:100:
srtk::ERROR: Image2 for JosephForwardProjectionImageFilter doesnt match
type or dimension!

I tried different types of cube, but with no success.


On Thu, Mar 23, 2017 at 11:01 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi Julia,
> I would have used
> volume = py.GetImageFromArray(result)
> instead of your last line. Does this work? If it does, then you have
> to be sure that you set correctly the origin, spacing and direction
> (the ITK meta information). One way to do this if you already have an
> image with the correct meta information would be to use
> py.volume.CopyInformation(volume)
> Simon
>
> On Thu, Mar 23, 2017 at 11:14 AM, Julia Semyakishkina
> <prekrasnaya1985 at gmail.com> wrote:
> > Hello.
> > In matlab example from http://wiki.openrtk.org/index.php/SimpleRTK
> volume
> > which is projected generates in SheppLoganPhantomFilter(). But i have my
> own
> > volume, that is stored in matlab regular matrix for example.
> >
> > What i want to do:
> > forward = py.JosephForwardProjectionImageFilter();
> > forward.SetGeometry(g);
> > projs = forward.Execute(projs, volume);
> >
> > The problem is to initialize the volume parameter.
> > By this code
> > data_size = size(matimg);
> > transpose = matimg';
> > result=py.numpy.reshape(transpose(:)', int32(data_size));
> > volume = py.Image.fromarray(result);
> >
> > i store volume in type of py.Image, but in Execute() method i have to
> pass
> > py.SimpleRTK.SimpleRTK.Image type. So, is there way to do such
> convertation
> > ? Or is there some another way to init py.SimpleRTK.SimpleRTK.Image with
> my
> > own matlab data ?
> >
> >
> >
> > _______________________________________________
> > Rtk-users mailing list
> > Rtk-users at public.kitware.com
> > http://public.kitware.com/mailman/listinfo/rtk-users
> >
>
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