[ITK] Bruker Format

[Dženan Zukić]

This alternation of behavior is accomplished by this check:
  if ( this->MustRescale() )
    {
    if ( this->m_ComponentType == CHAR
         || this->m_ComponentType == UCHAR
         || this->m_ComponentType == SHORT
         || this->m_ComponentType == USHORT
         || this->m_ComponentType == INT
         || this->m_ComponentType == UINT
         || this->m_ComponentType == LONG
         || this->m_ComponentType == ULONG )
      {
      this->m_ComponentType = FLOAT;
      }
    }

Regards

On Fri, Feb 10, 2017 at 6:43 PM, Dženan Zukić <dzenanz at gmail.com> wrote:

> Hi Tobias,
>
> reading is done in function void NiftiImageIO::Read(void *buffer) in
> file C:\Dev\ITK-git\Modules\IO\NIFTI\src\itkNiftiImageIO.cxx
>
> This function is supposed to read image data from disk into the given
> buffer pointer. The data type of this buffer is of this->m_ComponentType.
> In case that NIFTI reader detects it needs to do rescale/slope
> transformation (in function ReadImageInformation), it says that
> this->m_ComponentType=FLOAT, no matter what is the real component type on
> disk. Then Read reads the image data, converts it to float, does
> rescale/slope transformation in place (float to float).
>
> Later ImageFileReader (which calls ImageIO::Read()) does C++ cast from
> this->m_ComponentType into the type with which ImageFileReader was
> instantiated.
>
> Regards,
> Dženan
>
> On Fri, Feb 10, 2017 at 5:02 PM, Wood, Tobias <tobias.wood at kcl.ac.uk>
> wrote:
>
>> Hello,
>>
>> I’ve made some progress on rewriting the Bruker code. I’m stuck on when
>> the ImageIO classes should apply scalings/offsets.
>>
>> Bruker’s default data type is INT16. They store a scaling and offset that
>> must be applied to the data. For whatever reason, the scaling tends to very
>> small - about 1e-5. Hence a lot of values should be scaled down to < 1.
>> Obviously, if this is done at INT16 precision then most of the data is
>> rounded to zero and lost.
>>
>> I tried to copy the NifiIO class which also applies scaling (See lines
>> 707 onwarsds in itkNiftiImageIO.cxx). However - if I read this correctly,
>> it is applying the scaling at the precision/datatype of the image file, not
>> the PixelType requested by the itkImage template parameter to
>> itkImageFileReader.
>>
>> At what point is the buffer read by the ImageIO classes converted to the
>> PixelType of the requested itkImage? How do I supply the scaling and offset
>> to this conversion?
>>
>> As always, I hope I’m missing something obvious.
>> Thanks,
>> Toby
>>
>> On 16/01/2017, 09:27, "Wood, Tobias" <tobias.wood at kcl.ac.uk> wrote:
>>
>>     >    In addition to Dženan's suggestion, the code could be cleaned
>> up, moved out of the ITKReview module, and placed in its own module in the
>> IO group. This will enable it to be automatically registered like the other
>> ImageIOs.
>>
>>     Thanks Matt and Dženan, that’s what I was wondering. I will
>> experiment with the code and submit a patch if I find time.
>>
>>     Best wishes,
>>     Toby
>>
>>
>>
>>
>
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