[Insight-users] Example of ITK
Ing. Arturo Vargas Olivares
ing.arturo.vargas at gmail.com
Thu May 10 16:01:50 EDT 2012
Ohhh I didn't know that... I think I need to read and test more, more and
more. I don't know how to do the print and the castings, I'm lost, I need
to read, test and research more.
On Thu, May 10, 2012 at 3:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
> Hello Arturo,
>
> You can use the print function in Python to print the ITK information
> about the image. This will tell you that the image is being loaded as an
> itk::VectorImage, most likely of three components.
>
> There is no obvious way to convert a VectorImage to a scalar image of
> float as you requested, which is why you are getting this error message.
> Additionally, as already noted the CurvatureFlow image filter expects a
> floating point image as input which is why are doing this cast.
>
> So, why is the image getting loaded into a VectorImage, and not a scalar.
> That is because the ITK ImageIO is reporting the image has having
> multi-components. Even if the image looks grayscale it may have been saved
> as an RGB image.
>
> I hope that helps explain what is going on. While SimpleITK is pixel type
> less, it is type aware and so there needs to be a certain level of
> understanding of the pixel types that are loaded, and some times casts need
> to be made.
>
> Brad
>
>
>
> On May 10, 2012, at 3:28 PM, Ing. Arturo Vargas Olivares wrote:
>
> Hello again.
>
> I tried the command but I still have problems, it says it is not supported
> (see below).
>
>
> image = sitk.Cast( image, sitk.sitkFloat32 )
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (7489, 0))
> ---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call last)
> C:\Users\Student3\Desktop\MRI images\<ipython-input-165-9a6139d5ca18> in
> <module>()
> ----> 1 image = sitk.Cast( image, sitk.sitkFloat32 )
> C:\Python27\lib\site-packages\simpleitk-0.4.0-py2.7-win-amd64.egg\SimpleITK.pyc
> in Cast(*args, **kwargs)
> 3597 def Cast(*args, **kwargs):
> 3598 """Cast(Image image, PixelIDValueType pixelID) -> Image"""
> -> 3599 return _SimpleITK.Cast(*args, **kwargs)
> 3600 class Version(_object):
> 3601 """Proxy of C++ itk::simple::Version class"""
> RuntimeError: Exception thrown in SimpleITK Cast: C:\Users\Bradley
> Lowekamp\Documents\Source\SimpleITK\Code\BasicFilters\src\sitkCastImageFilter.cxx:75:
> sitk::ERROR: Filter does not support casting from casting vector of 8-bit
> unsigned integer to 32-bit float
>
> On Thu, May 10, 2012 at 3:13 PM, Cagatay Bilgin <bilgincc at gmail.com>wrote:
>
>> Hi Arturo,
>>
>> the following line should cast the image to float
>> image = sitk.Cast( image, sitk.sitkFloat32 )
>>
>> Let us know how it goes
>>
>> Cagatay
>>
>> On Thu, May 10, 2012 at 11:36 AM, Ing. Arturo Vargas Olivares <
>> ing.arturo.vargas at gmail.com> wrote:
>>
>>> I'm new in this...
>>> how do I cast my image to float?
>>>
>>>
>>>
>>> On Thu, May 10, 2012 at 2:31 PM, Cagatay Bilgin <bilgincc at gmail.com>wrote:
>>>
>>>> Try casting your image to float type before
>>>> you feed to the smoother. That should do it
>>>> I guess.
>>>>
>>>> Cagatay
>>>>
>>>> On Thu, May 10, 2012 at 11:27 AM, Ing. Arturo Vargas Olivares <
>>>> ing.arturo.vargas at gmail.com> wrote:
>>>>
>>>>> Hello to all !!
>>>>>
>>>>> I have implemented this code in order to test an example from the ITK
>>>>> software guide.
>>>>>
>>>>> import numpy as np
>>>>> import scipy.io as ios
>>>>> import matplotlib.pyplot as mplot
>>>>> import matplotlib.cm as cm
>>>>> import SimpleITK as sitk
>>>>> import sys
>>>>> #
>>>>> # Read the image
>>>>> #
>>>>> reader = sitk.ImageFileReader()
>>>>> reader.SetFileName( 'BrainProtonDensitySlice.png' )
>>>>> image = reader.Execute();
>>>>> #
>>>>> # Set up the writer
>>>>> #
>>>>> writer = sitk.ImageFileWriter()
>>>>> writer.SetFileName( 'BrainProtonDensitySlice_out.png' )
>>>>> #
>>>>> # Blur using CurvatureFlowImageFilter
>>>>> #
>>>>> blurFilter = sitk.CurvatureFlowImageFilter()
>>>>> blurFilter.SetNumberOfIterations( 5 )
>>>>> blurFilter.SetTimeStep( 0.125 )
>>>>> image = blurFilter.Execute( image )
>>>>> #
>>>>> # Set up ConnectedImageFilter for segmentation
>>>>> #
>>>>> segmentationFilter = sitk.ConnectedThresholdImageFilter()
>>>>> segmentationFilter.SetLower(150)
>>>>> segmentationFilter.SetUpper(180)
>>>>> segmentationFilter.SetReplaceValue(255)
>>>>> segmentationFilter.SetSeed((60,116))
>>>>> image = segmentationFilter.Execute( image )
>>>>> writer.Execute( image )
>>>>>
>>>>>
>>>>> It seems that everything is OK except the execution of my filters (see
>>>>> below). It says that the Pixel Type is the problem but I don't know how to
>>>>> fix this.
>>>>>
>>>>> Guys, do you have any ideas?
>>>>>
>>>>>
>>>>> ---------------------------------------------------------------------------
>>>>> RuntimeError Traceback (most recent call
>>>>> last)
>>>>> C:\Users\Student3\Desktop\MRI images\test8.py in <module>()
>>>>> 22 blurFilter.SetNumberOfIterations( 5 )
>>>>> 23 blurFilter.SetTimeStep( 0.125 )
>>>>> ---> 24 image = blurFilter.Execute( image )
>>>>> 25 #
>>>>> 26 # Set up ConnectedImageFilter for segmentation
>>>>>
>>>>> C:\Python27\lib\site-packages\simpleitk-0.4.0-py2.7-win-amd64.egg\SimpleITK.pyc
>>>>> in Execute(self, *args)
>>>>> 8050
>>>>> 8051 """
>>>>> -> 8052 return
>>>>> _SimpleITK.CurvatureFlowImageFilter_Execute(self, *args)
>>>>> 8053
>>>>> 8054 __swig_destroy__ =
>>>>> _SimpleITK.delete_CurvatureFlowImageFilter
>>>>> RuntimeError: Exception thrown in SimpleITK
>>>>> CurvatureFlowImageFilter_Execute: c:\users\bradley
>>>>> lowekamp\documents\source\simpleitk\code\common\include\sitkMemberFunctionFactory.txx:174:
>>>>> sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not
>>>>> supported in 2D byclass itk::simple::CurvatureFlowImageFilter
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> 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:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>
>>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> 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:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
>
> ========================================================
>
> Bradley Lowekamp
>
> Medical Science and Computing for
>
> Office of High Performance Computing and Communications
>
> National Library of Medicine
>
> blowekamp at mail.nih.gov
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20120510/11e6c2ab/attachment.htm>
More information about the Insight-users
mailing list