[Insight-users] Displaying .mat files

[Bradley Lowekamp]

Hello,

I see that you are running the 0.4.0 release. Are you running window as well? Is the error message truncated?

Did you download and install ImageJ?

http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Recommended_Software

There also is a bug in that binary release where on windows it may not find the ImageJ executable. The work around is to install ImageJ into C:\ImageJ, and then add that path the the executable into your PATH environmental variable. Alternatively you could compile a more recent version from the source.

We debated if we should release a patched version for this fix, but decided that we should continue out effort on development instead of packaging, and since it was only called a beta release its not unexpected to have a couple small bug. But if people clamor too much a couple patched versions could be made.

Brad

On May 8, 2012, at 2:23 PM, Ing. Arturo Vargas Olivares wrote:

> I'm trying to display a picture but I'm not sure why I can't.
> (Commands in blue, outputs in green)
>  
> Any ideas?
>  
>  
> inputImage = sitk.ReadImage( 'lena_color.bmp' )
> inputImage
> Out[89]: <SimpleITK.Image; proxy of <Swig Object of type 'std::vector< itk::simple::Image >::value_type *' at 0x0000000019BE6C60> >
> sitk.Show( inputImage )
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
> C:\Users\Student3\Desktop\MRI images\<ipython-input-90-868b377c2eaa> in <module>()
> ----> 1 sitk.Show( inputImage )
> C:\Python27\lib\site-packages\simpleitk-0.4.0-py2.7-win-amd64.egg\SimpleITK.pyc in Show(*args, **kwargs)
>    3155 def Show(*args, **kwargs):
>    3156   """Show(Image image, string title = "")"""
> -> 3157   return _SimpleITK.Show(*args, **kwargs)
>    3158 class ImageFilter(_object):
>    3159     """Proxy of C++ itk::simple::ImageFilter class"""
> RuntimeError: Exception thrown in SimpleITK Show: C:\Users\Bradley Lowekamp\Documents\Source\SimpleITK\Code\IO\src\sitkShow.cxx:54:
> sitk::ERROR: Can not find location of
>  
>  
> 
> 
>  
> On Tue, May 8, 2012 at 11:16 AM, Ing. Arturo Vargas Olivares <ing.arturo.vargas at gmail.com> wrote:
> Hi Bradley
>  
> Have you ever tried to test the 'SimpleGaussian.py' example? how can I test it?
>  
> I'm interested in test this example, I think it has sitk methods that can help me to understand the tool. I'm new in ITK and I'm trying with SimpleITK first.
>  
> 
> 
>  
> On Mon, May 7, 2012 at 10:24 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:
> Hello,
> 
> I am not sure that ITK can directly read all .mat images. There is the HDF5 image IO that may work for a subset, but I have never tried this combination my self.
> 
> If you are using SimpleITK with Python, you may look for mat image reader in another python package such as scipy. They should be able to export the image to a numpy array, then this can be imported into SimpleITK with the sitk.CreateimageFromArray() method.
> 
> By default SimpleITK uses ImageJ to display images from the sitk.Show method. More information about getting this setup can be found here:
> 
> http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Recommended_Software
> 
> Brad
> 
> On May 7, 2012, at 8:56 AM, Ing. Arturo Vargas Olivares wrote:
> 
> > Hello friends.
> > I need your help.
> > I'm new in the world of SimpleITK and I'm starting a PhD research and I need to know more about image segmentation tools. By the mean time I'd like to know how to open or display images using SimpleITK. The images are in the .mat format (MATLAB) and I also have python and installed in my PC.
> > Any help will be very appreciated.
> > BR
> > Arturo V.
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> 
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> http://www.kitware.com/products/protraining.php
> 
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========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov



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