[Insight-users] Raw images reader

[Thibault Varacca]

Hi,
yes it works better ...
I have also another problem:  i have a 32-bit float image in input and the
filter generates an image of 8-bit unsigned integer. I want to have 32-bit
float in output.
Any way to do this?
Thanks !


2013/4/26 Bradley Lowekamp <blowekamp at mail.nih.gov>

> Hello,
>
> It appears you are not actually setting the seeds to the filter. There are
> two methods to choose from in C++:
>
> Self & SetSeed (std::vector< unsigned int > idx)
> Self & SetSeedList (std::vector< std::vector< unsigned int > > t)
>
> What you have as variable "seedList" is really just a single seed. In Java
> the types of the arguments for the above methods should be VectorUInt32,
> and VectorUIntList respectfully. You should be able to use the first one
> with your current variable.
>
> Brad
>
>
> On Apr 26, 2013, at 10:48 AM, Thibault Varacca <thibault.varacca at gmail.com>
> wrote:
>
> Ok the .mhd way to do this worked great.
>
> I have to do 3D segmentation on raw images. I tryed to do this with the
> ThresholdImageFilter but all my values are at zero after applying the
> filter ...
> My Raw images are Float32 3D 128x128x128, here is my code :
>
> import org.itk.simple.ConnectedThresholdImageFilter;
> import org.itk.simple.Image;
> import org.itk.simple.ImageFileReader;
> import org.itk.simple.ImageFileWriter;
> import org.itk.simple.VectorUInt32;
>
> public class ImageReader {
>
>     private static String inputFilename = "fdk.xy.mhd";
>     private static String outputFilename = "output.mhd";
>
>     public static void main(String[] args) {
>
>         VectorUInt32 seedList = new VectorUInt32(3);
>         ImageFileReader reader = new ImageFileReader();
>         ImageFileWriter writer = new ImageFileWriter();
>         ConnectedThresholdImageFilter filter = new
> ConnectedThresholdImageFilter();
>
>         reader.setFileName(inputFilename);
>         writer.setFileName(outputFilename);
>
>         Image input = reader.execute();
>
>         /* valeurs de seuil */
>         filter.setLower(0.003);
>         filter.setUpper(5);
>         filter.setReplaceValue((short) 5);
>
>         /* seed points */
>         seedList.clear();
>         seedList.push_back(100);
>         seedList.push_back(16);
>         seedList.push_back(46);
>
>
>         Image output = filter.execute(input);
>         writer.execute(output);
>
>     }
>
> Do you know how to make it work?
>
> Thank you !
>
>
> 2013/4/26 Samuel Pichardo <sammeuly at gmail.com>
>
>> Hi
>>
>> In Python, you could use rather numpy io function
>> http://docs.scipy.org/doc/numpy/reference/generated/numpy.fromfile.html
>> and convert the arrays to simpleITK with
>> *SimpleITK*.*GetImageFromArray*<http://www.nullege.com/codes/search/SimpleITK.GetImageFromArray>
>>
>> Regards
>>
>> Sam
>>
>>
>> On 2013-04-26, at 4:59 AM, Thibault Varacca <thibault.varacca at gmail.com>
>> wrote:
>>
>> Dear all,
>> I'm looking to load and read raw images with simpleITK but I didn't find
>> any RawReader().
>> How can i do this?
>> Thanks !
>>
>> --
>> Thibault Varacca
>> EFREI Promo 2014
>> 06 60 53 11 35
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>>
>
>
> --
> Thibault Varacca
> EFREI Promo 2014
> 06 60 53 11 35
>  _____________________________________
> 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
>
>
>


-- 
Thibault Varacca
EFREI Promo 2014
06 60 53 11 35
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