[Insight-users] Displaying .mat files

Wed May 9 09:19:56 EDT 2012

Hi Bradley

OK, I'll try the points you're telling me.
I'll come back with my comments.

Arturo V.

On Wed, May 9, 2012 at 8:43 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:

> 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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>
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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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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