[Insight-developers] Reading vector images
Stephen R. Aylward
aylward at unc.edu
Thu, 13 May 2004 18:26:36 -0400
Hi,
I dunno, is a multi-channel image of floats the same as an image of
vectors of floats? :) Right now, I think, metaImage handles them the
same, but I think MetaImage is wrong in this regard and we should
perhaps distinguish them.
The idea behind using FLOAT instead of FLOAT_ARRAY is based on how the
data is read. Basically the size (in memory) of an image is set as
numberOfPixel*numberOfChannels*sizeOfPixelType
For the simple case of multiple values per pixel this works with
PixelType = FLOAT.
The question becomes what should we return for SizeOf(FLOAT_ARRAY).
UGH - right now it returns 4 (bad Stephen). Yup, sometimes metaImage
sucks. There isn't a simple fix. But, I'd rather fix this in
metaImage than accept the convention that sizeOf(FLOAT_ARRAY) = 4 and
that numberOfChannels is the number of components in that array - it
seems wrong that SizeOf(FLOAT) = SizeOf(FLOAT_ARRAY). So, until we fix
that, perhaps we should keep using an image of vectors as a
multi-channel image instead of a single channel image of a pixelType
that returns the wrong SizeOf. That way, if we fix the
sizeOf(FLOAT_ARRAY) problem then we'll be able to have multi-channel
images where each channel is an array of floats...
Lessor of evils...your choice...take the blue pill....
Stephen
Miller, James V (Research) wrote:
> A bug was reported in the beginning of February and another bug was
> reported in Oct 2003. And I just verified it again yesterday :)
>
> The meta library was pretty much okay. The MetaIO object was pretty much
> okay. The ImageIOBase and ImageFileReader were not.
>
> My interpretation of ImageIO object is that PixelType could be any of
> CHAR, UCHAR, SHORT, USHORT, ...., RGB, RGBA, VECTOR, COVARIANTVECTOR, ...
>
> ComponentType could be any native type (but not VECTOR, COVARIANTVECTOR,
> RGB...)
>
> So a vector image would have a PixelType of VECTOR and ComponentType of
> (for instance) float.
>
> Currently, if you asked an ImageFileReader for an Image<Vector<float, 2>,
> 2>,
> you get a block of raw memory. The ImageIO object says the PixelType
> is float while the reader is told to output Vector<float, 2>. These types
> are not the same, so a call to DoConvertBuffer is made. But there is no
> case in DoConvertBuffer for an output pixel type with two components.
>
> DoConvertBuffer does make a number of assumptions that a multiple component
> pixel is RGB. A potentially dangerous decision.
>
> In terms of the Meta format. I thought an image of MET_FLOAT_ARRAY would
> be equivalent to a Vector<float, NumComponents> whereas an image of
> MET_FLOAT
> would be an image of scalar floats. Is this not the case? If not, how does
> Meta
> treat pixels with multiple components? And what is a MET_FLOAT_ARRAY?
>
> Jim
>
>
>
>
> -----Original Message-----
> From: Stephen R. Aylward [mailto:aylward at unc.edu]
> Sent: Thursday, May 13, 2004 10:51 AM
> To: Miller, James V (Research)
> Cc: 'Luis Ibanez'; Insight-developers (E-mail); Julien Jomier
> Subject: Re: [Insight-developers] Reading vector images
>
>
> Hi,
>
> I think we need to think about this more for consistency.
>
> I've traditionally distinguished multi-component images from images of
> vectors. MetaImage supports multi-component images - that is, an image
> of float with multiple channels per pixel. Versus an image of float_arrays.
>
> MetaImage has been working for multi-channel images perhaps it has been
> broken recently, but I know it has worked in the past ai-is.
>
> If you make changes, please ensure backward compatibility with what has
> been working in the past. We and others have been using it by
> by-passing itk's IO classes and using MetaIO direct.
>
> Thanks,
> Stephen
>
> Miller, James V (Research) wrote:
>
>
>>Okay.
>>
>>I have part of this working now. There was a minor error in the MetaIO
>>object wrt to setting ComponentType verses setting PixelType for arrays.
>>
>>I need to go back and check whether MetaIO writes pixel type in its header
>>as META_FLOAT_ARRAY when writing vector images. I may have editted a
>>meta header by hand to change a META_FLOAT to a META_FLOAT_ARRAY.
>>
>>However, most of bug is in the ImageFileReader and ImageIOBase. My current
>>solution relies on the memory layout for a Vector<T, N> being equivalent to
>>the
>>memory layout of an array T[N]. If we can assume this, then I have most
>>of the trivial case working (I was able to read a meta image with 2D
>>vectors).
>>
>>One hurdle is going to be if a file has vectors of floats and the reader is
>>asked to produce a vector of ints. I'll need to modify
>
> DoConvertPixelBuffer
>
>>to handle this.
>>
>>Interesting that we have a number of examples that read vector images.
>
> What
>
>>file formats were these tested on?
>>
>>Jim
>>
>>
>>
>>-----Original Message-----
>>From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>Sent: Wednesday, May 12, 2004 7:10 PM
>>To: Miller, James V (Research)
>>Cc: Insight-developers (E-mail); Julien Jomier
>>Subject: Re: [Insight-developers] Reading vector images
>>
>>
>>
>>Hi Jim,
>>
>>Yes, this is a known bug in the MetaImage reader.
>>
>> http://www.itk.org/Bug/bug.php?op=show&bugid=580&pos=12
>>
>>Although, as you pointed out, the error may actually
>>be in the ImageFileReader<> class.
>>
>>
>>If you have any hints of how to solve it,
>>please go ahead :-)
>>
>>
>>Your suggestion seem to be in the right direction.
>>We certainly have a lot more types defined in
>>
>>
>> ImageIOBase::SetPixelType()
>>
>>that in
>>
>> ImageIOBase::GetPixelType()
>>
>>
>>They should probably be made symmetrical...
>>
>>
>>
>> Luis
>>
>>
>>
>>
>>------------------------------------
>>Miller, James V (Research) wrote:
>>
>>
>>
>>
>>>I just tried to read an image of two component vectors into ITK using
>>>the Meta format.
>>>
>>>I get all zeros.
>>>
>>>It looks to me that in ImageFileReader::GenerateData() there is a test for
>>>
>>> m_ImageIO->GetPixelType() == typeid(TOutputImage::PixelType)
>>>
>>>TOutputImage::PixelType should be Vector<float, 2>
>>>
>>>m_ImageIO->GetPixelType() returns float
>>>
>>>The above check for equality fails and a data conversion occurs. The
>>>result is all zeros.
>>>
>>>It looks as though people have asked this on the list before but I did
>>>not find a response.
>>>I seem to recall people reading vectors as RGB pixels.
>>>
>>>Perhaps if I add a GetPixelType() method to MetaImageIO that checks the
>>>m_PixelType to be VECTOR?
>>>
>>>
>>>
>>>
>>>*Jim Miller*
>>>*/_____________________________________/*
>>>/Visualization & Computer Vision//
>>>/GE Research/
>>>/Bldg. KW, Room C218B/
>>>/P.O. Box 8, Schenectady NY 12301/
>>>
>>>//_millerjv at research.ge.com <mailto:millerjv at research.ge.com>_/
>>>
>>>/_james.miller at research.ge.com_/
>>>/(518) 387-4005, Dial Comm: 8*833-4005, /
>>>/Cell: (518) 505-7065, Fax: (518) 387-6981/
>>>
>>>
>>>
>>>
>>
>>
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>>Insight-developers at itk.org
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>>
>>
>
>
>
--
===========================================================
Dr. Stephen R. Aylward
Associate Professor of Radiology
Adjunct Associate Professor of Computer Science and Surgery
http://caddlab.rad.unc.edu
aylward at unc.edu
(919) 966-9695