[vtkusers] Fw: cutter for vtkGlyph3D

Wed Apr 25 18:23:33 EDT 2012

Change
cutter.SetInput(pdb.GetInput())
to
cutter.SetInput(pdb.GetOutput())

On Wed, Apr 25, 2012 at 1:07 AM, alex Dowson <alexdowson at hotmail.com> wrote:
> Hi
>
> For visibility of plane you need widget for that.  check the vtkPlaneWidget
> .
>
>
> alex
>
>
> From: zhixiu li
> Sent: Wednesday, April 25, 2012 10:15 AM
> To: alex Dowson
> Subject: Re: [vtkusers] Fw: cutter for vtkGlyph3D
>
> Thank you. I correct but can't see the plain. And I also set the
> ren.SetBackground(0, 0.1, 0.5)
> but the background is still black....
>
> On Wed, Apr 25, 2012 at 12:38 AM, alex Dowson <alexdowson at hotmail.com>
> wrote:
>>
>> Hi
>>
>> In Cutter code there is problem
>>
>> cutter.SetInput(pdb.GetInput())
>> should be
>> cutter.SetInput(pdb.GetOutput())
>>
>>
>> Alex
>>
>>
>>
>> From: zhixiu li
>> Sent: Wednesday, April 25, 2012 9:35 AM
>> To: alex Dowson
>> Subject: Re: [vtkusers] cutter for vtkGlyph3D
>>
>> Here is my code.
>> PDB format is a format for protein structure.
>> Basicly it has n atoms and each atom has x.y,z coordinate. It is like a
>> network. I attach a pdb file for you~
>> The visualization of the pdb is fine. The only thing is the cutting
>> doesn't work
>>
>> Thank you very much!
>>
>>
>>
>> import vtk
>> import sys
>>
>>
>> pdb = vtk.vtkPDBReader()
>> pdb.SetFileName(sys.argv[1])
>> pdb.SetHBScale(1.0)
>> pdb.SetBScale(1.0)
>> pdb.Update()
>>
>> #create a plane to cut,here it cuts in the XZ direction (xz
>> normal=(1,0,0);XY =(0,0,1),YZ =(0,1,0)
>> plane=vtk.vtkPlane()
>> plane.SetOrigin(0,0,0)
>> plane.SetNormal(10,0,0)
>>
>> #create cutter
>> cutter=vtk.vtkCutter()
>> cutter.SetCutFunction(plane)
>> cutter.SetInput(pdb.GetInput())
>> cutter.Update()
>> cutterMapper=vtk.vtkPolyDataMapper()
>> cutterMapper.SetInputConnection(cutter.GetOutputPort())
>>
>> #create plane actor
>> planeActor=vtk.vtkActor()
>> planeActor.GetProperty().SetColor(1.0,0.8,0)
>> planeActor.GetProperty().SetLineWidth(2)
>> planeActor.SetMapper(cutterMapper)
>>
>>
>> #create renderers and add actors of plane and cube
>> ren = vtk.vtkRenderer()
>> ren.AddActor(planeActor)
>>
>>
>> #creat atom sphere
>> sphere = vtk.vtkSphereSource()
>> sphere.SetCenter(0, 0, 0)
>> sphere.SetRadius(1)
>> sphere.SetThetaResolution(10)
>> sphere.SetPhiResolution(10)
>>
>> glyph = vtk.vtkGlyph3D()
>> glyph.SetInputConnection(pdb.GetOutputPort())
>> glyph.SetOrient(1)
>> glyph.SetColorMode(1)
>> # // glyph.ScalingOn()
>> glyph.SetScaleMode(2)
>> glyph.SetScaleFactor(.25)
>> glyph.SetSourceConnection(sphere.GetOutputPort())
>>
>> atomMapper = vtk.vtkPolyDataMapper()
>> atomMapper.SetInputConnection(glyph.GetOutputPort())
>> atomMapper.ImmediateModeRenderingOn()
>> atomMapper.UseLookupTableScalarRangeOff()
>> atomMapper.ScalarVisibilityOn()
>> atomMapper.SetScalarModeToDefault()
>>
>> atom = vtk.vtkLODActor()
>> atom.SetMapper(atomMapper)
>> atom.GetProperty().SetRepresentationToSurface()
>> atom.GetProperty().SetInterpolationToGouraud()
>> atom.GetProperty().SetAmbient(0.15)
>> atom.GetProperty().SetDiffuse(0.85)
>> atom.GetProperty().SetSpecular(0.1)
>> atom.GetProperty().SetSpecularPower(30)
>> atom.GetProperty().SetSpecularColor(1, 1, 1)
>> atom.SetNumberOfCloudPoints(30000)
>> ren.AddActor(atom)
>>
>>
>> #connection between atoms
>> tube = vtk.vtkTubeFilter()
>> tube.SetInputConnection(pdb.GetOutputPort())
>> tube.SetNumberOfSides(10)
>> tube.CappingOff()
>> tube.SetRadius(0.2)
>> tube.SetVaryRadius(0)
>> tube.SetRadiusFactor(10)
>>
>> bondMapper = vtk.vtkPolyDataMapper()
>> bondMapper.SetInputConnection(tube.GetOutputPort())
>> bondMapper.ImmediateModeRenderingOn()
>> bondMapper.UseLookupTableScalarRangeOff()
>> bondMapper.ScalarVisibilityOff()
>> bondMapper.SetScalarModeToDefault()
>>
>> bond = vtk.vtkLODActor()
>> bond.SetMapper(bondMapper)
>> bond.GetProperty().SetRepresentationToSurface()
>> bond.GetProperty().SetInterpolationToGouraud()
>> bond.GetProperty().SetAmbient(0.15)
>> bond.GetProperty().SetDiffuse(0.85)
>> bond.GetProperty().SetSpecular(0.1)
>> bond.GetProperty().SetSpecularPower(30)
>> bond.GetProperty().SetSpecularColor(1, 1, 1)
>> bond.GetProperty().SetDiffuseColor(1.0000, 0.8941, 0.70981)
>>
>> ren.AddActor(bond)
>>
>> #Add renderer to renderwindow and render
>> renWin = vtk.vtkRenderWindow()
>> renWin.AddRenderer(ren)
>> renWin.SetSize(600, 600)
>> iren = vtk.vtkRenderWindowInteractor()
>> iren.SetRenderWindow(renWin)
>> ren.SetBackground(0,0,0)
>> renWin.Render()
>> iren.Start()
>>
>>
>> On Tue, Apr 24, 2012 at 11:48 PM, alex Dowson <alexdowson at hotmail.com>
>> wrote:
>>>
>>> Hi
>>>
>>> Check you PDBReader FileName path . If is not locating file then output
>>> will be empty and you will get this error due to empty output. Also I still
>>> donot know
>>> what is PDB format so is it triangulated polydata ?
>>>
>>>
>>> Alex
>>>
>>>
>>>
>>> From: zhixiu li
>>> Sent: Wednesday, April 25, 2012 9:14 AM
>>> To: alex Dowson
>>> Subject: Re: [vtkusers] cutter for vtkGlyph3D
>>>
>>> Thank you.
>>> But after I tried your method,I got this kind of error:
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkExecutive.cxx, line 377
>>> vtkStreamingDemandDrivenPipeline (02B1D470): Attempt to get input
>>> information vector from input port index 0 for algorithm
>>> vtkPDBReader(02B1D150), which has 0 input ports.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkExecutive.cxx, line 377
>>> vtkStreamingDemandDrivenPipeline (02B1D470): Attempt to get input
>>> information vector from input port index 0 for algorithm
>>> vtkPDBReader(02B1D150), which has 0 input ports.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkExecutive.cxx, line 377
>>> vtkStreamingDemandDrivenPipeline (02B1D470): Attempt to get input
>>> information vector from input port index 0 for algorithm
>>> vtkPDBReader(02B1D150), which has 0 input ports.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B360A8): Input port 0 of algorithm
>>> vtkStructuredGridOutlineFilter(02B24EB0) has 0 connections but is not
>>> optional.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B33170): Input port 0 of algorithm
>>> vtkStructuredGridGeometryFilter(02B32C00) has 0 connections but is not
>>> optional.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B2FEB8): Input port 0 of algorithm
>>> vtkCutter(02B2BE00) has 0 connections but is not optional.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B360A8): Input port 0 of algorithm
>>> vtkStructuredGridOutlineFilter(02B24EB0) has 0 connections but is not
>>> optional.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B33170): Input port 0 of algorithm
>>> vtkStructuredGridGeometryFilter(02B32C00) has 0 connections but is not
>>> optional.
>>>
>>> ERROR: In ..\..\vtk-5.8.0\Filtering\vtkDemandDrivenPipeline.cxx, line 727
>>> vtkStreamingDemandDrivenPipeline (02B2FEB8): Input port 0 of algorithm
>>> vtkCutter(02B2BE00) has 0 connections but is not optional.
>>>
>>>
>>> On Tue, Apr 24, 2012 at 11:38 PM, alex Dowson <alexdowson at hotmail.com>
>>> wrote:
>>>>
>>>> Hi
>>>>
>>>> You can try like this
>>>>
>>>> plane = vtk.vtkPlane()
>>>> plane.SetOrigin(0,0,0)
>>>>
>>>> plane.SetNormal(0.17, 0, 0.9579)
>>>> planeCut = vtk.vtkCutter()
>>>> planeCut.SetInput(pdb.GetOutput())
>>>> planeCut.SetCutFunction(plane)
>>>>
>>>>
>>>>
>>>>
>>>> From: zhixiu li
>>>> Sent: Wednesday, April 25, 2012 8:48 AM
>>>> To: vtkusers
>>>> Subject: Re: [vtkusers] cutter for vtkGlyph3D
>>>>
>>>> Sorry, I didn't say it clearly.
>>>> I read the pdb by
>>>> pdb = vtk.vtkPDBReader()
>>>> pdb.SetFileName(sys.argv[1])
>>>>
>>>> And I want to cut the pdb by the plain and its cutter
>>>>
>>>> plane = vtk.vtkPlane()
>>>> plane.SetOrigin(??????????????????????what should I put in here)
>>>> plane.SetNormal(0.17, 0, 0.9579)
>>>> planeCut = vtk.vtkCutter()
>>>> planeCut.SetInput(????????????????????what should I put in here)
>>>> planeCut.SetCutFunction(plane)
>>>>
>>>>
>>>> Thank you!
>>>>
>>>>
>>>> On Tue, Apr 24, 2012 at 11:04 PM, zhixiu li <zhixiuli at gmail.com> wrote:
>>>>>
>>>>> Dear ALL,
>>>>> I have a pdb file and I want to use the pdbreader to read the pdb file.
>>>>> And use use vtkGlyph3D for each atom (each points ) of the pdb. I want to
>>>>> use a plain to cut this pdb and show the cutting plain of the pdb. How do I
>>>>> combine vtkCutter and vtkGlyph3D to achieve the aim? Thank you.
>>>>
>>>>
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>>>
>>>
>>
>>
>>
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>
>
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