I investigated a bit.
The problem is with the mitkImageWriter.cpp that contains a code
segment like this:
// If the extension is NOT .pic and NOT .nrrd the following block is entered
if ( m_Extension.find(".pic") == std::string::npos
&& m_Extension.find(".nrrd") == std::string::npos)
{
if(input->GetDimension() > 3)
{
int t, timesteps;
timesteps = input->GetDimension(3);
...
So 3D+t images are split into 3D images and then saved one by one.
What is the motivation behind this? I suppose you wanted to split only
those image formats that do not support 4D images. If yes, I would
suggest to add the ".hdr" extension to the "if" condition.
Could somebody confirm this?
Thanks,
Miklos
On Wed, Sep 7, 2011 at 4:45 PM, Miklos Espak <[email protected]> wrote:
> I see. My case is different then.
>
> After that I registered the NiftiImageIOFactory by
> itk::NiftiImageIOFactory::RegisterOneFactory();
> I coul read and write images by the built-in mitk::ItkImageFileReader
> and mitk::ItkImageFileWriter, respectively. (Even the series reader
> works.)
>
> I mean, this works through the API. Opening a 3D/3D+t image from the
> GUI also works, the only thing is that I have to choose "all" instead
> of "known extension" because the ".hdr" extension is not listed.
>
> The bigger problem is saving via the datamanager view context menu.
> Even if saving through API works, when I use the menu item then a
> series of images is saved, and a warning is displayed about that.
>
> I am afraid that this should be fixed in either the menu action or the
> built-in object factories. I did not debug it, though.
>
> Miklos
>
> On Tue, Sep 6, 2011 at 11:14 PM, Clarkson, Matt <[email protected]> wrote:
>> Hi Miklos,
>>
>> Using the documents here: http://www.mitk.org/wiki/BugSquashingSeminars, and
>> specifically the "Defining your own MITK Datatypes" it was quite easy to
>> create the necessary Factory classes to create a reader for a specific file
>> format, and to have the file extensions appear in the Load/Save dialog boxes.
>>
>> However, my problem was that I wanted to NOT use the standard ITK Analyze
>> reader, which meant replacing the mitkItkImageFileReader, and replace it
>> with a modified version.
>> This turns out to be a bit trickier, as you would have to unregister the
>> MITK provided one, and provide your own.
>>
>> However, we could just ask for .img and .img.gz to be added to the file
>> dialog box (via mitkCoreObjectFactory.cpp), as this would probably suffice
>> for most people, and the image would be read using the standard
>> mitkImageFileReader.h
>>
>> Can you remind me again, why did you have to register a new Nifti file
>> reader when ITK and hence MITK already had one?
>>
>> Matt
>>
>>
>>
>>
>>
>>
>> On 6 Sep 2011, at 17:09, Miklos Espak wrote:
>>
>>> Hi,
>>>
>>> if I save a 3D+t image through the GUI (datamanager view context
>>> menu), a series of images is saved instead of a single image.
>>>
>>> I would like to use the Analyze format (.hdr + .img), it is not
>>> offered by the save dialog, so I chose Nifti.
>>>
>>> I registered the itk::NiftiImageIOFactory, and from the sources I can
>>> open and save 3D+t images properly. Is there a way to get around this?
>>>
>>> Matt!
>>> Have you succeeded with adding hdr to the open/save dialog?
>>>
>>> Thanks,
>>> Miklos
>>>
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