[vtkusers] Extract a slice and save it as jpg/png
Jothy
jothybasu at gmail.com
Wed Jul 14 12:28:53 EDT 2010
You are not setting the opaccity/color transfer function properly
try this , my scalar values range from 0-100.
# The following class is used to store transparencyv-values for later
retrival. In our case, we want the value 0 to be
# completly opaque whereas the three different cubes are given different
transperancy-values to show how it works.
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
alphaChannelFunc.AddPoint(10, 0.005)
alphaChannelFunc.AddPoint(50, 0.1)
alphaChannelFunc.AddPoint(100, 0.15)
# This class stores color data and can create color tables from a few
color points. For this demo, we want the three cubes
# to be of the colors red green and blue.
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(0, 1.0, 0.0, 0.0)
colorFunc.AddRGBPoint(50, 0.0, 1.0, 0.0)
colorFunc.AddRGBPoint(100, 0.0, 0.0, 1.0)
Jothy
On Wed, Jul 14, 2010 at 5:22 PM, Chris Turner <cturnercomplex at googlemail.com
> wrote:
> 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
> >> >> >> >>
> >> >> >> >> 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
> >> >> >>
> >> >> >> 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
> >> >>
> >> >> 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
> >>
> >> 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
>
> Follow this link to subscribe/unsubscribe:
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