Hi Yves,
Thanks for your report. The mitk::ExtractDirectedPlaneImageFilter is
mostly based on code from the MITK rendering module, namely from
mitk::ImageMapper2D. Part of this code may be rendering-specific and
therefore appear cumbersome when just using this filter to extract
slices.
You are mentioning that the output extent is sometimes set to negative
values. Which values of xMin/xMax, yMin/yMax do you get in this case?
Also, is "boundsInitialized" set to true in your case (lines 314ff in
the current MITK SVN checkout)?
We recently discovered a bug due to which a shift of one pixel appears
in some cases of 2D image rendering which might be related to the
behavior you observed (see http://bugs.mitk.org/show_bug.cgi?id=2401).
We plan to look into this within the next one or two weeks.
Regards,
Mathias
From: Yves Martelli [mailto:ymarte...@cistib.upf.edu]
Sent: Thursday, September 17, 2009 11:47 AM
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] Segmentation on reoriented planes
Hi,
I'm part of the UPF in Barcelona and we are working on segmentations on
reoriented planes. We are using the mitkExtractDirectedPlaneImageFilter
to extract a slice from the mask volume to then write the user
selected/deleted pixels on it. We then write them back to the mask
volume using the slice index to world and then volume world to index
transformations.
Regarding the extraction, we were having troubles with black stripes in
the extracted segmentation from the mask volume. We think we solved it
by upsampling the extracted slice by a factor of two (no theory behind
this!). But we are having troubles with the extent that is given to the
output image of the VtkImageReslice filter. It can contain negative
values which seem to result in strange output slices. Whenever we try to
draw on this slice (using the
mitk::ContourUtils::ProjectContourTo2DSlice method), previously created
masks are shifted. When using the extent calculated by the
VtkImageReslice filter (maximum range of int), this shift disappears.
When thinking a bit on this strategy, it is a bit risky in the sense
that you reprocess previously saved data and take the risk of modifying
it (different resampling results), so we are thinking of not extracting
the slice from the mask volume, but just create one with the proper
geometry.
These two modifications seem to fix our biggest problems but we still
have issues: one being that there is a shift between the drawn contour
and the saved one (roughly one pixel) and the second one with big angles
which disable parts of the image (no contour can be drawn).
Sorry for the long email, my question will be: is there a reason to set
the extent of the output slice after the VtkImageReslice filter? And if
you have any ideas on the drawing shift...
Regards,
Yves
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