[vtkusers] Fw: cutter for vtkGlyph3D
alex Dowson
alexdowson at hotmail.com
Wed Apr 25 01:07:06 EDT 2012
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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