Hi Luca,
Ben Dickerhoff and I tried changing the extents to "dim -1" in the header file
of our image .vti and then running vmtkimagevoipainter. However the output
painted region was still in a different spatial location than originally
specified. We were just wondering if you had looked into this problem any
further and if you had any new insights...
Thanks for all your help. It is greatly appreciated!
Anna
________________________________
From: Luca Antiga [luca.ant...@gmail.com]
Sent: Wednesday, June 06, 2012 2:25 PM
To: Dickerhoff, Benjamin R
Cc: vmtk-users@lists.sourceforge.net
Subject: Re: [vmtk-users] Problem with vmtkimagevoipainter update
Hi Ben,
yes, you can do that directly and save the file back.
Just change both extents from 0 to dim-1 in each direction. Note that the
physical location of the image will change (unless you move the origin to
originalExtent[0] * spacing[0], originalExtent[2] * spacing[1],
originalExtent[4] * spacing[2]).
Best,
Luca
On 06/giu/2012, at 21:13, "Dickerhoff, Benjamin R"
<benjamin-dickerh...@uiowa.edu<mailto:benjamin-dickerh...@uiowa.edu>> wrote:
Luca-
Thanks for the response. When you say to set the origin of the image to 0 0
0 and the extent from 0 to dim-1 in all directions, do you mean to physically
change the header in the .vti? Below is the header from one of the image files.
The origin of the image appears already to be set to "0 0 0".
<VTKFile type="ImageData" version="0.1" byte_order="LittleEndian"
compressor="vtkZLibDataCompressor">
<ImageData WholeExtent="203 364 141 396 75 254" Origin="0 0 0"
Spacing="0.21838390827 0.21838390827 0.21838378906">
<Piece Extent="203 364 141 396 75 254">
<PointData Scalars="Scalars_">
<DataArray type="Float32" Name="Scalars_" format="appended"
RangeMin="-0.87353515625" RangeMax="0.87353515625" offset="0"
/>
</PointData>
<CellData>
</CellData>
</Piece>
</ImageData
Thanks,
Ben
________________________________
From: Luca Antiga [luca.ant...@gmail.com<mailto:luca.ant...@gmail.com>]
Sent: Wednesday, June 06, 2012 11:55 AM
To: Dickerhoff, Benjamin R
Cc: vmtk-users@lists.sourceforge.net<mailto:vmtk-users@lists.sourceforge.net>
Subject: Re: [vmtk-users] Problem with vmtkimagevoipainter update
Dear all,
I've been off-list for a few days. I'll look into this asap, in the meantime,
as a test, try setting the origin of the image to 0 0 0 and the extent from 0
to dim-1 in all directions. Then save the image and execute the vmtk script. I
suspect it's an extent related issue.
Keep in touch
Luca
On 06/giu/2012, at 16:51, "Dickerhoff, Benjamin R"
<benjamin-dickerh...@uiowa.edu<mailto:benjamin-dickerh...@uiowa.edu>> wrote:
VMTK Users,
With regards to the problem that I posted about trouble I was having with
vmtkimagevoipainter, I have not figured out how to resolve this yet. I have
figured out that the bounding box in the output has the same dimensions as the
bounding box chosen as an input, however, its output location in the image set
is offset towards the corner of the entire input VOI. Additionally, the output
paint value does correspond to the input value specified using the option
"-paintvalue".
Ben Berkowitz helped me simplify the vmtkimagevoipainter script by writing
the python script at the end of this email. It is intended to take in a vtk
image file and the bounding coordinates (min and max for x, y, and z) for the
region we wish to "paint". This script gives the same output as the
vmtkimagevoipainter script. It seems that the vtkvmtk.vtkvmtkImageBoxPainter()
script is reading in the input just fine, but can't process where to place the
region to be painted in the output image. I'm not exactly sure where to go from
here to help correct this. If anybody has any suggestions, I'd greatly
appreciate your input.
Thanks for your time,
Ben Dickerhoff
import vtk
import sys
import math
from vmtk import vtkvmtk
from vmtk import vmtkscripts
file = sys.argv[1]
reader = vmtkscripts.vmtkImageReader()
reader.InputFileName = file
reader.Execute()
xmin = float(sys.argv[2])
xmax = float(sys.argv[3])
ymin = float(sys.argv[4])
ymax = float(sys.argv[5])
zmin = float(sys.argv[6])
zmax = float(sys.argv[7])
extents = [xmin, xmax, ymin, ymax, zmin, zmax]
imageBoxPainter = vtkvmtk.vtkvmtkImageBoxPainter()
imageBoxPainter.SetInput(reader.Image)
imageBoxPainter.SetBoxExtent(extents)
imageBoxPainter.SetBoxDefinitionToUseExtent()
imageBoxPainter.SetPaintValue(10)
imageBoxPainter.Update()
writer = vmtkscripts.vmtkImageWriter()
writer.Image = imageBoxPainter.GetOutput()
writer.OutputFileName = file[:-4]+'_painted.vti'
writer.Execute()
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