[ITK] [ITK-users] Resampling after SetDirection() and SetOrigin()
Mathew Guilfoyle
mrguilfoyle at gmail.com
Wed Jul 2 12:14:03 EDT 2014
Hi Matt
Sorry to labour this point but I'm still confused as to what is going on;
my misunderstanding may well be to do with how the pipelines work.
As an example:
import itk
fileNameIn = '/route/to/input.nii'
fileNameOut = '/route/to/output.nii'
image_type = itk.Image[itk.F, 3]
reader = itk.ImageFileReader[image_type].New()
reader.SetFileName(fileNameIn)
reader.Update()
image = reader.GetOutput()
#image.GetOrigin() gives [-148, -153, 55]
#image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
#gives matrix: 1.0 0 0
# 0 0.95 0.3
# 0 -0.3 0.95
image.GetOrigin().Fill(0)
image.GetDirection().SetIdentity()
#image.GetOrigin() gives [0, 0, 0]
#image.GetDirection().GetVnlMatrix().get(0,0)....(2,2)
#gives matrix: 1.0 0 0
# 0 1.0 0
# 0 0 1.0
writer = itk.ImageFileWriter[image_type].New()
writer.SetFileName(fileNameOut)
writer.SetInput(image)
writer.Update()
*#output image volume is unchanged when viewed in (e.g.) ImageJ*
resampler = itk.ResampleImageFilter[image_type, image_type].New()
resampler.SetInput(image)
resampler.SetSize(image.GetLargestPossibleRegion().GetSize())
resampler.SetOutputOrigin(image.GetOrigin())
resampler.SetOutputSpacing(image.GetSpacing())
resampler.SetOutputDirection(image.GetDirection())
resampler.Update()
writer.SetInput(resampler.GetOutput())
writer.Update()
*#now output is translated and rotated by the (inverse) values of the
original#origin vector and direction matrix##However,
resampler.GetInput().GetOrigin() gives [0,0,0]#and similarly the direction
of the input is a 3x3 identity matrix*
I don't understand why the resampler changes the image volume since it
should not be 'aware' of the original origin/direction.
>From your previous reply you suggest that the call to resampler.Update()
might cause the reader to re-import the file from disk. Is this the case
even when the reader and resampler are not connected in a pipeline (as
here). Further, if the reader does re-import the original image and
origin/direction parameters why does resampler.GetInput().GetOrigin()
report [0, 0, 0] and the input direction matrix is an identity?
I want to understand why this is happening as it is clearly important for
ensuring I set up more complex pipelines correctly.
Many thanks
Mathew
On 30 June 2014 03:28, Matt McCormick <matt.mccormick at kitware.com> wrote:
> Hi Mathew,
>
> The image does not retain the original parameters somewhere. However,
> can must be take, because if the image is generated by a filter in a
> pipeline, that filter will reset the original value when the pipeline
> is re-run. ChangeInformationImageFilter will ensure this reset does
> not happen during a pipeline update.
>
> The Set methods doo reorient/reposition the whole image volume in
> world space. The resampling filter does not select a subregion or
> rotates the images -- to get the same out, the sampling locations of
> the output image for the ResampleImageFilter must be set as desired.
> Set SetOutputOrigin [1], SetOutputDirection [2], etc.
>
> Hope this helps to clarify.
>
> I checked by wrapped install, and I have ChangeInformationImageFilter
> instantiations for float images.
>
> Hope this helps,
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#ac4b197ddefd3b3344bd9c9471acd5b00
>
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html#a9fdd6b862ab6cbaa03702da393bd0474
>
>
> On Sun, Jun 29, 2014 at 10:01 PM, Mathew Guilfoyle
> <mrguilfoyle at gmail.com> wrote:
> > Matt, thanks for the reply.
> >
> > I would be grateful if you could you explain why this is the desired
> > behaviour. If I use the SetDirection() or SetOrigin() methods does the
> > image object retain the original parameters somewhere? Subsequently
> calling
> > GetDirection() or GetOrigin() reports the changed parameters.
> >
> > Intuitively you would expect both Set methods to reorient/reposition the
> > whole image volume in world space, and on the face of it that is what
> they
> > seem to do. However, on passing the image to a resampling filter they
> act
> > to select a subregion or to rotate the image. I would have thought that
> > rotations and region selections should be options passed to the filter
> and
> > not set in the image itself?
> >
> > How does the ChangeInformationImageFilter do it differently?
> Incidentally I
> > have wrapped for float but don't get this as an option for this filter.
> >
> > Thanks
> > Mathew
> >
> >
> >
> > On 30 June 2014 01:45, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
> >>
> >> Hi Mathew,
> >>
> >> Yes, that is the correct and expected behavior. I do not know if
> >> ImageJ is using the actual location in world space.
> >>
> >> It sounds like ChangeInformationImageFilter is what you are looking
> >> for. It will be wrapped for float images if wrapped for float images
> >> is enabled in you CMake configuration (ITK_WRAP_float).
> >>
> >> Hope this helps,
> >> Matt
> >>
> >>
> >> On Sat, Jun 28, 2014 at 9:55 PM, Mathew Guilfoyle <
> mrguilfoyle at gmail.com>
> >> wrote:
> >> > If I change an image's direction and origin using SetDirection() and
> >> > SetOrigin() methods and then write the image back to a file, the
> volume
> >> > stack viewed in (e.g.) ImageJ is unchanged. This is the behaviour I
> >> > would
> >> > expect as changing the direction and origin shouldn't alter the array
> of
> >> > image pixels, just its location and orientation in 'world space'?
> >> >
> >> > However, if I take the same image, adjust the origin and direction as
> >> > before, and then input it to ResampleImageFilter with an identity
> >> > transform
> >> > (and set spacing, origin, direction, and size to those of the input
> >> > image)
> >> > the output is a translated and rotated image.
> >> >
> >> > It seems the difference between the original and adjusted origin and
> >> > direction are applied as a translation and rotation during resampling,
> >> > even
> >> > though GetOrigin() and GetDirection() on the input image to the
> >> > resampler
> >> > return the adjusted parameters.
> >> >
> >> > Is this the expected behaviour? Is there another image parameter that
> >> > needs
> >> > to be changed to correctly alter origin and direction?
> >> >
> >> > (ChangeInformationImageFilter is not wrapped for float images so I
> can't
> >> > use
> >> > it for my application)
> >> >
> >> > Thanks
> >> >
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