[vtkusers] Extract a slice and save it as jpg/png
Chris Turner
cturnercomplex at googlemail.com
Wed Jul 14 12:22:01 EDT 2010
So I tried to volume render the VOI but I only saw a black rectangle
and as soon as i try to click into the window it disappeared.
Thats the code I added:
# create a rendering window and renderer
renderer = vtk.vtkRenderer()
window = vtk.vtkRenderWindow()
window.AddRenderer(renderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(window)
# enable user interface interactor
window.SetSize(500,500)
renderer.SetBackground(1,1,1)
caster = vtk.vtkImageCast()
caster.SetInput(voi.GetOutput())
caster.SetOutputScalarTypeToUnsignedShort()
rayCastFunction = vtk.vtkVolumeRayCastMIPFunction()
volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper.SetInput(caster.GetOutput())
volumeMapper.SetVolumeRayCastFunction(rayCastFunction)
volumeProperty = vtk.vtkVolumeProperty() #slicer.vtkVolumeProperty()
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint( 100.0, 1,1,1)
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint( 100, 1.0);
volumeProperty.SetColor(colorTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
Volume = vtk.vtkVolume()
Volume.SetMapper(volumeMapper)
Volume.SetProperty(volumeProperty)
renderer.AddViewProp(Volume)
iren.Start()
Also when I use "print str(image)" I get the following output:
vtkImageData (0x1bc4ef0)
Debug: Off
Modified Time: 404
Reference Count: 3
Registered Events: (none)
Source: (none)
Information: 0x1bc5060
Data Released: False
Global Release Data: Off
UpdateTime: 0
Release Data: Off
UpdateExtent: Not Initialized
WholeExtent: 0, 0, 0, 0, 0, 0
RequestExactExtent: Off
Field Data:
Debug: Off
Modified Time: 402
Reference Count: 1
Registered Events: (none)
Number Of Arrays: 0
Number Of Components: 0
Number Of Tuples: 0
Number Of Points: 1
Number Of Cells: 1
Cell Data:
Debug: Off
Modified Time: 392
Reference Count: 1
Registered Events: (none)
Number Of Arrays: 0
Number Of Components: 0
Number Of Tuples: 0
Copy Tuple Flags: ( 1 1 1 1 1 0 1 )
Interpolate Flags: ( 1 1 1 1 1 0 0 )
Pass Through Flags: ( 1 1 1 1 1 1 1 )
Scalars: (none)
Vectors: (none)
Normals: (none)
TCoords: (none)
Tensors: (none)
GlobalIds: (none)
PedigreeIds: (none)
Point Data:
Debug: Off
Modified Time: 398
Reference Count: 1
Registered Events: (none)
Number Of Arrays: 1
Array 0 name = ImageFile
Number Of Components: 1
Number Of Tuples: 1
Copy Tuple Flags: ( 1 1 1 1 1 0 1 )
Interpolate Flags: ( 1 1 1 1 1 0 0 )
Pass Through Flags: ( 1 1 1 1 1 1 1 )
Scalars:
Debug: Off
Modified Time: 397
Reference Count: 1
Registered Events: (none)
Name: ImageFile
Data type: short
Size: 1
MaxId: 0
NumberOfComponents: 1
Information: 0
Name: ImageFile
Number Of Components: 1
Number Of Tuples: 1
Size: 1
MaxId: 0
LookupTable: (none)
Array: 0x1bc9a10
Vectors: (none)
Normals: (none)
TCoords: (none)
Tensors: (none)
GlobalIds: (none)
PedigreeIds: (none)
Bounds:
Xmin,Xmax: (0, 0)
Ymin,Ymax: (0, 0)
Zmin,Zmax: (0, 0)
Compute Time: 0
ScalarType: 4
NumberOfScalarComponents: 1
Spacing: (1, 1, 1)
Origin: (0, 0, 0)
Dimensions: (1, 1, 1)
Increments: (1, 1, 1)
Extent: (0, 0, 0, 0, 0, 0)
But when I load it in ParaView the image has the correct parameters.
I'm confused.
Chris
On Wed, Jul 14, 2010 at 11:55 AM, Jothy <jothybasu at gmail.com> wrote:
> Are you able to render this atleast, before trying to save?
>
> Jothy
>
> On Wed, Jul 14, 2010 at 4:27 PM, Chris Turner
> <cturnercomplex at googlemail.com> wrote:
>>
>> bounds are (-69.3 ,323 ,332 ,9.68,468,448)
>> extents are (0,0,0,79,145,116)
>>
>> I changed the SetVOI to (-69,323,332,-68,468,448) but same result.
>>
>>
>> On Wed, Jul 14, 2010 at 11:01 AM, Jothy <jothybasu at gmail.com> wrote:
>> > Have you checked that your setVOi is with the bounds of the Image. What
>> > are
>> > your bounds?
>> >
>> > Jothy
>> >
>> > On Wed, Jul 14, 2010 at 3:58 PM, Chris Turner
>> > <cturnercomplex at googlemail.com> wrote:
>> >>
>> >> No didn't do the trick either.
>> >>
>> >> No file, no error/warning message.
>> >>
>> >> Thanks though!
>> >>
>> >> On Wed, Jul 14, 2010 at 10:54 AM, Jothy <jothybasu at gmail.com> wrote:
>> >> > Try SetVOI(0,0,0,79,1,146)
>> >> >
>> >> > Jothy
>> >> >
>> >> > On Wed, Jul 14, 2010 at 3:44 PM, Chris Turner
>> >> > <cturnercomplex at googlemail.com> wrote:
>> >> >>
>> >> >> Hi David & Bill,
>> >> >>
>> >> >> thanks for your patience and your help I appreciate it a lot! So
>> >> >> this
>> >> >> is the code with David's suggestion:
>> >> >>
>> >> >> import os
>> >> >> import vtk
>> >> >> import sys
>> >> >>
>> >> >>
>> >> >> reader=vtk.vtkImageReader()
>> >> >> reader.SetFileName("/tmp/lungROI.vtk")
>> >> >> reader.Update()
>> >> >>
>> >> >> lut=vtk.vtkLookupTable()
>> >> >> lut.SetRange(-1024, +4095)
>> >> >>
>> >> >> map=vtk.vtkImageMapToColors()
>> >> >> map.SetInput(reader.GetOutput())
>> >> >> map.SetLookupTable(lut)
>> >> >>
>> >> >>
>> >> >> voi=vtk.vtkExtractVOI()
>> >> >> voi.SetInput(map.GetOutput())
>> >> >> voi.SetVOI(0,0,0,79,146,1)
>> >> >> voi.Update()
>> >> >>
>> >> >> writerp=vtk.vtkPNGWriter()
>> >> >> writerp.SetInput(voi.GetOutput())
>> >> >> writerp.SetFileName("/tmp/out.png")
>> >> >> writerp.Write()
>> >> >>
>> >> >> print "done"
>> >> >>
>> >> >>
>> >> >> .... but still no output nor an error message. You can take a look
>> >> >> at
>> >> >> the Image here:
>> >> >>
>> >> >> http://www.load.to/t8MWurwasf/lungROI.vtk (~10mb)
>> >> >>
>> >> >> Thanks Again,
>> >> >> Chris
>> >> >>
>> >> >>
>> >> >> On Tue, Jul 13, 2010 at 4:38 PM, David Gobbi <david.gobbi at gmail.com>
>> >> >> wrote:
>> >> >> > Hi Chris,
>> >> >> >
>> >> >> > This could be an instance of trying to write 16-bit data to a JPEG
>> >> >> > file. Try adding vtkImageMapToColors with a suitable
>> >> >> > vtkLookupTable.
>> >> >> > The Range of the lookup table will have to be set to something
>> >> >> > reasonable for the image, a range of (-1024, +4095) is a good
>> >> >> > place
>> >> >> > to
>> >> >> > start and then you can increase or decrease the range in order to
>> >> >> > get
>> >> >> > the contrast right.
>> >> >> >
>> >> >> > David
>> >> >> >
>> >> >> >
>> >> >> > On Tue, Jul 13, 2010 at 2:15 PM, Bill Lorensen
>> >> >> > <bill.lorensen at gmail.com>
>> >> >> > wrote:
>> >> >> >> Post you entire example. And, if you can post a link to your
>> >> >> >> data...
>> >> >> >>
>> >> >> >> On Tue, Jul 13, 2010 at 3:57 PM, Chris Turner
>> >> >> >> <cturnercomplex at googlemail.com> wrote:
>> >> >> >>> Hi Bill,
>> >> >> >>>
>> >> >> >>> thanks for your answer! But didn't do the trick.
>> >> >> >>> So strange I thought this was a standard question and procedure.
>> >> >> >>> And
>> >> >> >>> that there has to be a easy way to do that.
>> >> >> >>>
>> >> >> >>> And why don't I even get a error message or something. Even when
>> >> >> >>> I
>> >> >> >>> turn on the debug mode there is nothing suspicious.
>> >> >> >>>
>> >> >> >>> Anybody has another approach?
>> >> >> >>>
>> >> >> >>> Thanks
>> >> >> >>> Chris
>> >> >> >>>
>> >> >> >>> On Mon, Jul 12, 2010 at 10:16 AM, Bill Lorensen
>> >> >> >>> <bill.lorensen at gmail.com> wrote:
>> >> >> >>>> Try,
>> >> >> >>>> voi.SetVOI(0,0,0,511,511,0)
>> >> >> >>>>
>> >> >> >>>> On Mon, Jul 12, 2010 at 10:07 AM, Chris Turner
>> >> >> >>>> <cturnercomplex at googlemail.com> wrote:
>> >> >> >>>>> Really? Am I the only one with that problem?
>> >> >> >>>>>
>> >> >> >>>>> On Fri, Jul 9, 2010 at 5:02 PM, Chris Turner
>> >> >> >>>>> <cturnercomplex at googlemail.com> wrote:
>> >> >> >>>>>> Hi Everyone!
>> >> >> >>>>>>
>> >> >> >>>>>> I'm trying to extract a slice from a vtkImageData object and
>> >> >> >>>>>> save
>> >> >> >>>>>> it as picture.
>> >> >> >>>>>>
>> >> >> >>>>>> That's how I do it:
>> >> >> >>>>>>
>> >> >> >>>>>> voi=vtkExtractVOI()
>> >> >> >>>>>> voi.SetInput(imageData)
>> >> >> >>>>>> voi.SetVOI(0,0,0,512,512,1)
>> >> >> >>>>>> voi.Update()
>> >> >> >>>>>>
>> >> >> >>>>>> writer=vtkJPEGWriter()
>> >> >> >>>>>> writer.SetInput(voi.GetOutput())
>> >> >> >>>>>> writer.SetFileName("slice.jpg")
>> >> >> >>>>>> writer.Write()
>> >> >> >>>>>>
>> >> >> >>>>>> ImageData is 512x512x40 spacing 1,1,1
>> >> >> >>>>>>
>> >> >> >>>>>> The strange thing is I don't get an output nor an error
>> >> >> >>>>>> message.
>> >> >> >>>>>> So
>> >> >> >>>>>> I
>> >> >> >>>>>> think I'm missing something here.... but it can't figure out
>> >> >> >>>>>> what.
>> >> >> >>>>>>
>> >> >> >>>>>> So does anybody have an idea or a better solution?
>> >> >> >>>>>>
>> >> >> >>>>>> Thanks
>> >> >> >>>>>> Chris
>> >> >> >>>>>>
>> >> >> >>>>> _______________________________________________
>> >> >> >>>>> Powered by www.kitware.com
>> >> >> >>>>>
>> >> >> >>>>> Visit other Kitware open-source projects at
>> >> >> >>>>> http://www.kitware.com/opensource/opensource.html
>> >> >> >>>>>
>> >> >> >>>>> Please keep messages on-topic and check the VTK FAQ at:
>> >> >> >>>>> http://www.vtk.org/Wiki/VTK_FAQ
>> >> >> >>>>>
>> >> >> >>>>> Follow this link to subscribe/unsubscribe:
>> >> >> >>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>> >> >> >>>>>
>> >> >> >>>>
>> >> >> >>>
>> >> >> >> _______________________________________________
>> >> >> >> Powered by www.kitware.com
>> >> >> >>
>> >> >> >> Visit other Kitware open-source projects at
>> >> >> >> http://www.kitware.com/opensource/opensource.html
>> >> >> >>
>> >> >> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> >> >> http://www.vtk.org/Wiki/VTK_FAQ
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>> >> >> >> Follow this link to subscribe/unsubscribe:
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>> >> >> >>
>> >> >> >
>> >> >> _______________________________________________
>> >> >> Powered by www.kitware.com
>> >> >>
>> >> >> Visit other Kitware open-source projects at
>> >> >> http://www.kitware.com/opensource/opensource.html
>> >> >>
>> >> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >> >>
>> >> >> Follow this link to subscribe/unsubscribe:
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>> >> >
>> >> >
>> >> _______________________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
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>> >
>> >
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.vtk.org/mailman/listinfo/vtkusers
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