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> 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]
> Sent: Wednesday, June 06, 2012 11:55 AM
> To: Dickerhoff, Benjamin R
> Cc: 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> 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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