[Insight-users] Raw images reader

[Thibault Varacca]

I tried to apply CastImageFilter 8bit -> 32 bit float but nothing worked ...


2013/4/29 Thibault Varacca <thibault.varacca at gmail.com>

> 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
>>>  _____________________________________
>>> 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
>>  _____________________________________
>> 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
>



-- 
Thibault Varacca
EFREI Promo 2014
06 60 53 11 35
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20130429/46a8dc28/attachment.htm>