[Insight-users] Reading LSM images

[Luis Ibanez]

Hi Jesse,

Thanks for the clarification.

You are right, if the 3D image is in a single file, then
using the ImageFileReader is the correct way to
proceed.

Could you please post to the list the exact text
that you get from the Exceptions ?

If you need examples on how to catch exceptions
and print their error messages, you will find many
of them in the directories under

                     Insight/Examples


     Thanks


             Luis


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On Sat, Feb 13, 2010 at 12:33 PM, Jesse Stokum <jessestokum at gmail.com> wrote:
> Luis,
>
> Thanks for the quick reply, I really appreciate it. The lsm image
> stack that I'm working with are actually all in a single file - which
> is why I hesitated to use the ImageSeriesReader for this one. I
> suppose I could always split the stack into a series of slices imagej
> or something else, but it would be more time efficient to just read in
> the entire file. Also, intuitively I think that I would get better
> filtering results if I handled it as a 3d image, though I could be
> wrong about that. Thanks!
>
> Jesse
>
> On Fri, Feb 12, 2010 at 5:07 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>> Hi Jesse,
>>
>>
>> If you have the images in independent files (one file per slice),
>> you should use the itk::ImageSeriesReader (instead of the
>> itk::ImageFileReader).
>>
>>
>> The LSM reader in ITK should be able to manage three channels
>> (three components per pixel).
>>
>> You will find examples on how to use the ImageSeriesReader
>> in the ITK Software Guide
>>
>>                   http://www.itk.org/ItkSoftwareGuide.pdf
>>
>> in the chapter "Reading and Writing Images",
>>
>> and you will find source code examples in the directory:
>>
>>                           Insight/Examples/IO
>>
>> in particular, you may find interesting the example:
>>
>>            RGBImageSeriesReadWrite.cxx
>>
>> you probably only need to replace there the PNGImageIO
>> class with a LSMImageIO class.
>>
>>
>> Please give it a try and let us know if you find any problems.
>>
>> BTW: I you get any Exceptions, please post to the list
>> the *exact* error message that you get from the exception.
>>
>>
>>     Thanks
>>
>>
>>
>>           Luis
>>
>>
>>
>> -------------------------------------------------------------------------------------
>> On Fri, Feb 12, 2010 at 12:34 PM, Jesse Stokum <jessestokum at gmail.com> wrote:
>>> I'm trying to use ITK's ImageFileReader to read in LSM format images
>>> and my code is abruptly throwing exceptions. The images are three
>>> channel, and are ~30 slices. Should I consider them 3d images? Here's
>>> the code in my main() I've been trying:
>>>
>>>        typedef itk::RGBPixel<unsigned char> PixelType;
>>>        typedef itk::Image<PixelType, 3> ImageType;
>>>
>>>        typedef itk::ImageFileReader<ImageType> ReaderType;
>>>        typedef itk::LSMImageIO ImageIOType;
>>>        typedef itk::ImageFileWriter<ImageType> WriterType;
>>>
>>>        ReaderType::Pointer reader = ReaderType::New();
>>>        ImageIOType::Pointer lsmImageIO = ImageIOType::New();
>>>        reader->SetImageIO(lsmImageIO);
>>>        reader->SetFileName("Tests.lsm");
>>>
>>> Are lsm pixels vector pixels? I guess I'm just unsure how to handle
>>> this situation. Thanks in advance!
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>>
>