[ITK] [ITK-users] itkSmoothingQuadEdgeMeshFilter Help!!
Mallikarjun K
mallikarjun49 at gmail.com
Thu Aug 7 11:20:44 EDT 2014
Hi Arnaud,
Thanks,Can you please tell me your machine confuguration. I am running 4GB
RAM,i3 on windows7.
I have downloaded your project and tried to execute it and it is still the
same problem Which I was facing earlier.Any suggestions .....
thank you
On Thu, Aug 7, 2014 at 8:10 PM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> It takes 29s on my machine in debug to run 5 iterations with Delaunay
> conforming set to true
>
> https://gist.github.com/arnaudgelas/0f20ebdaf53956f79997
>
>
> On Aug 7, 2014, at 3:45 PM, Mallikarjun K <mallikarjun49 at gmail.com> wrote:
>
> File path is correct.if it is '\'(backward slash) we have to add "D:\\"
> .since I used '/' it's not required to add "//".
>
> please find the attached .vtk file
>
> Thanks
>
>
> On Thu, Aug 7, 2014 at 7:01 PM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
>
>> Shouldn't it be D://temp.vtk ? Isn't it missing one '/' ?
>>
>> Can you send this vtk file?
>>
>>
>> On Aug 7, 2014, at 3:23 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>> Hi Arnaud,
>>
>> Kindly have a look in the below code ,the problem is that even after
>> QEMeshFilter output is saved as .stl file ,the program is still running for
>> long time.I have observed in my tests that MeshFileReader seems to be the
>> culprit. Any suggestions ?
>>
>> /////
>> #include<iostream>
>> #include<string>
>>
>> #include <vtkPolyDataWriter.h>
>> #include <vtkPolyDataReader.h>
>> #include <itkMeshFileWriter.h>
>> #include <itkMeshFileReader.h>
>> #include <itkMeshIOFactory.h>
>> #include <itkMeshIOBase.h>
>> #include <vtkTriangleFilter.h>
>> #include <vtkCleanPolyData.h>
>> #include "itkMesh.h"
>> #include "itkQuadEdgeMesh.h"
>> #include "itkQuadEdgeMeshTraits.h"
>> #include "itkSmoothingQuadEdgeMeshFilter.h"
>> #include "vtkSTLWriter.h"
>> #include <vtkSmartPointer.h>
>>
>> int main()
>> {
>> std::string Inputfilename="D:/temp.vtk"; //number of points of this
>> mesh file is around 78K
>>
>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double >
>> qetraits;
>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType
>> >SmoothingQuadEdgeMeshFilter;
>>
>> vtkSmartPointer<vtkPolyDataWriter>
>> polyDatawriter=vtkSmartPointer<vtkPolyDataWriter>::New();
>> vtkSmartPointer<vtkPolyDataReader>
>> polyDatareader=vtkSmartPointer<vtkPolyDataReader>::New();
>>
>> SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>> SmoothingQuadEdgeMeshFilter::New();
>> /* polyDatareader->SetFileName(Inputfilename.c_str() );
>> polyDatareader->ReleaseDataFlagOn();
>> polyDatareader->Update();*/
>>
>> /*vtkSmartPointer<vtkTriangleFilter> triangleFilter =
>> vtkSmartPointer<vtkTriangleFilter>::New();
>> triangleFilter->SetInput(polyDatareader->GetOutput());
>> triangleFilter->Update();*/
>>
>> //
>> /* vtkSmartPointer<vtkCleanPolyData> clean =
>> vtkSmartPointer<vtkCleanPolyData>::New();
>> #if (VTK_MAJOR_VERSION < 6)
>> clean->SetInput(triangleFilter->GetOutput() );
>> #else
>> clean->SetInputData(triangleFilter->GetOutput() );
>> #endif
>> clean->ConvertPolysToLinesOff();
>> clean->ConvertLinesToPointsOff();
>> clean->Update();
>>
>> std::string Inputfilename2="D:/cleaned.vtk";*/
>>
>> ////
>> /*polyDatawriter->SetInput(clean->GetOutput());
>> polyDatawriter->SetFileName(Inputfilename2.c_str());
>> polyDatawriter->ReleaseDataFlagOn();
>> polyDatawriter->Write(); */
>>
>> typedef itk::MeshFileReader<MeshType> MeshReaderType;
>> MeshReaderType::Pointer Meshreader = MeshReaderType::New();
>> Meshreader->SetFileName(Inputfilename.c_str( ));
>> Meshreader->Update();
>>
>> /*MeshType::Pointer mesh = Meshreader->GetOutput();
>> mesh->DisconnectPipeline();*/
>>
>> QEMeshSmoother->SetInput(Meshreader->GetOutput()/*mesh*/ );
>> QEMeshSmoother->SetNumberOfIterations(1 );
>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>> QEMeshSmoother->SetDelaunayConforming(true);
>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>
>> QEMeshSmoother->ReleaseDataFlagOn();
>>
>> QEMeshSmoother->Update();
>>
>> std::string Outputfilename="D:/tempOut.vtk";
>>
>> typedef itk::MeshFileWriter<MeshType> MeshWriterType;
>> MeshWriterType::Pointer Meshwriter = MeshWriterType::New();
>> Meshwriter->SetFileName(Outputfilename.c_str( ));
>> Meshwriter->SetInput(QEMeshSmoother->GetOutput());
>> Meshwriter->Update();
>>
>> polyDatareader->SetFileName(Outputfilename.c_str() );
>> polyDatareader->ReleaseDataFlagOn();
>> polyDatareader->Update();
>>
>> vtkSmartPointer<vtkSTLWriter>
>> stlWriter=vtkSmartPointer<vtkSTLWriter>::New();
>> stlWriter->SetInput( polyDatareader->GetOutput());
>> stlWriter->SetFileName("D:/QEoutput.stl");
>> stlWriter->SetFileTypeToASCII();
>> stlWriter->Write();
>> //Here it stops and taking long time
>>
>> return 0;
>>
>> }
>> ////
>>
>>
>>
>> On Thu, Aug 7, 2014 at 3:39 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>>> Hi Arnaud,
>>>
>>> Thanks for your reply and valuable suggestions.
>>>
>>> Number of points in my input mesh are 78928.In my pipeline I am already
>>> cleaning the polydata using vtkCleanPolyData filter.I will check the speed
>>> improvement and results with delaunay conforming turned OFF.
>>>
>>> Thank you
>>>
>>>
>>> On Thu, Aug 7, 2014 at 2:22 PM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> wrote:
>>>
>>>> Hi Malik,
>>>>
>>>> First of all, I would recommend using MeshFileReader instead of
>>>> VTKPolyDataReader (I guess VTKPolyDataReader will be deprecated in near
>>>> future?).
>>>>
>>>> Regarding now the smoothing procedure in itself. This class
>>>> definitively misses some documentation and I will be adding some in the
>>>> next few days (mainly extracted from the corresponding insight journal).
>>>>
>>>> At the end of each iteration, when the delaunay conforming flag is
>>>> turned ON, the conformation is performed. So depending on the mesh
>>>> configuration, mesh size and number of iterations, it can take ages…
>>>> How large is your input mesh (number of points)?
>>>>
>>>> You can also check results, by running first a smoothing without
>>>> delaunay conforming, then apply a delaunay conforming on the output.
>>>> Results won't be as nice, but you should get significant speed improvement.
>>>> Another possibility is to first do a clean poly data in vtk, with a
>>>> small threshold to remove small edges in the input meshes (which results in
>>>> lots of edge flipping after smoothing).
>>>>
>>>> HTH
>>>> Arnaud
>>>>
>>>>
>>>> On Aug 6, 2014, at 10:42 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>>>> wrote:
>>>>
>>>> Hi All,
>>>>
>>>> Can anyone suggest me if anything wrong I am doing in this below
>>>> pipeline ,Where I used itkVtkPolydataReader to convert vtk Surface polydata
>>>> to Itk QuadedgeMesh. Execution loop is being hung up for sometime(4 to 5
>>>> mins in release mode) at itkVtkPolydataReader .
>>>>
>>>>
>>>> ////
>>>>
>>>> typedef itk::QuadEdgeMeshTraits<double, 3,double, double, double,double
>>>> > qetraits;
>>>>
>>>> typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits > MeshType;
>>>>
>>>> itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>
>>>> typedef itk::VTKPolyDataReader< MeshType >VTKPolyDataReaderType;
>>>> //typedef itk::VTKPolyDataWriter< MeshType >VTKPolyDataWriterType;
>>>>
>>>> //VTKPolyDataWriterType::Pointer
>>>> ItkToVtkWriter=VTKPolyDataWriterType::New();
>>>> VTKPolyDataReaderType::Pointer
>>>> VtkToItkReader=VTKPolyDataReaderType::New();
>>>>
>>>> VtkToItkReader->SetFileName("abc.vtk");
>>>> VtkToItkReader->Update();
>>>>
>>>> typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>> SmoothingQuadEdgeMeshFilter;
>>>>
>>>> SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>>>> SmoothingQuadEdgeMeshFilter::New();
>>>>
>>>> QEMeshSmoother->SetInput(VtkToItkReader->GetOutPut());
>>>> QEMeshSmoother->SetNumberOfIterations(5 );
>>>> QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>> QEMeshSmoother->SetDelaunayConforming(true );
>>>> QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>>> QEMeshSmoother->Update();
>>>>
>>>> ////
>>>>
>>>>
>>>> On Fri, Aug 1, 2014 at 4:36 PM, Mallikarjun K <mallikarjun49 at gmail.com>
>>>> wrote:
>>>>
>>>>> Thanks Bill for your answer.
>>>>>
>>>>> The reason I am using this pipeline is that SmoothingQEMeshFilter has
>>>>> an additional parameter for smoothing which is delaunay conforming which
>>>>> helps to optimize aspect ratio of triangles while smoothing and thus
>>>>> produces better output.Is there anything similar filter in the vtk
>>>>> pipeline.I used vtkWindowedSincPolydatafilter which is not giving the
>>>>> output as good as QEMeshSmoothing filter.
>>>>>
>>>>> Thanks for your help
>>>>>
>>>>>
>>>>> On Thu, Jul 31, 2014 at 5:14 PM, Bill Lorensen <
>>>>> bill.lorensen at gmail.com> wrote:
>>>>>
>>>>>> If you have it in vtk, I suggest using the vtk pipeline to smooth the
>>>>>> data.
>>>>>>
>>>>>> On Thu, Jul 31, 2014 at 1:35 AM, Mallikarjun K <
>>>>>> mallikarjun49 at gmail.com> wrote:
>>>>>> > Hi Bill,
>>>>>> > Thanks for the replay.
>>>>>> >
>>>>>> > Yes,I built both ITK and my app with Release ,I forgot to mention
>>>>>> it in the
>>>>>> > previous post.Actually the data set is the output of
>>>>>> > vtkDiscreteMarchingCubes algorithm(around 5MB) and need to smooth
>>>>>> .I saved
>>>>>> > this marching cube's output as .vtk file and read it using
>>>>>> > itkVTKPolyDataReader and then I am giving this reader's output to
>>>>>> > itkSmoothingQuadEdgeMeshFilter's input.
>>>>>> >
>>>>>> > I checked the execution time of each step in the pipeline ,after
>>>>>> > SmothingQEMeshFilter has got it's input ,it is taking time to
>>>>>> process the
>>>>>> > data.
>>>>>> >
>>>>>> > Thank you
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > On Wed, Jul 30, 2014 at 9:29 PM, Bill Lorensen <
>>>>>> bill.lorensen at gmail.com>
>>>>>> > wrote:
>>>>>> >>
>>>>>> >> First, make sure you are building ITK and your app with Release. A
>>>>>> >> Debug build can be 10-50 times slower.
>>>>>> >>
>>>>>> >>
>>>>>> >> On Wed, Jul 30, 2014 at 10:18 AM, Mallikarjun K <
>>>>>> mallikarjun49 at gmail.com>
>>>>>> >> wrote:
>>>>>> >> > Hi All,
>>>>>> >> > I am using itkSmoothingQuadEdgeMeshFilter for Surface Mesh
>>>>>> >> > smoothing.This
>>>>>> >> > filter is giving good results what I expected but taking more
>>>>>> execution
>>>>>> >> > time.can any one suggest me to reduce the execution time( multi
>>>>>> >> > threading
>>>>>> >> > or any parameters to add/remove )?
>>>>>> >> >
>>>>>> >> > Below is the code snippet
>>>>>> >> > ///////
>>>>>> >> > typedef itk::QuadEdgeMeshTraits<double, 3,double, double,
>>>>>> double,double
>>>>>> >> > >
>>>>>> >> > qetraits;
>>>>>> >> > typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3,qetraits >
>>>>>> MeshType;
>>>>>> >> >
>>>>>> >> > //typedef itk::QuadEdgeMesh< vtkFloatingPointType, 3 > MeshType;
>>>>>> >> >
>>>>>> >> > itk::OnesMatrixCoefficients< MeshType > coeff0;
>>>>>> >> >
>>>>>> >> > typedef itk::SmoothingQuadEdgeMeshFilter< MeshType, MeshType >
>>>>>> >> > SmoothingQuadEdgeMeshFilter;
>>>>>> >> >
>>>>>> >> > SmoothingQuadEdgeMeshFilter::Pointer QEMeshSmoother =
>>>>>> >> > SmoothingQuadEdgeMeshFilter::New();
>>>>>> >> >
>>>>>> >> > QEMeshSmoother->SetInput("abc.vtk");
>>>>>> >> > QEMeshSmoother->SetNumberOfIterations(5 );
>>>>>> >> > QEMeshSmoother->SetRelaxationFactor( 0.5 );
>>>>>> >> > QEMeshSmoother->SetDelaunayConforming(true );
>>>>>> >> > QEMeshSmoother->SetCoefficientsMethod( &coeff0 );
>>>>>> >> > QEMeshSmoother->Update();
>>>>>> >> > ////
>>>>>> >> >
>>>>>> >> > --
>>>>>> >> > Regards:
>>>>>> >> > Mallik
>>>>>> >> >
>>>>>> >> >
>>>>>> >> > _____________________________________
>>>>>> >> > Powered by www.kitware.com
>>>>>> >> >
>>>>>> >> > Visit other Kitware open-source projects at
>>>>>> >> > http://www.kitware.com/opensource/opensource.html
>>>>>> >> >
>>>>>> >> > Kitware offers ITK Training Courses, for more information visit:
>>>>>> >> > http://www.kitware.com/products/protraining.php
>>>>>> >> >
>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at:
>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ
>>>>>> >> >
>>>>>> >> > Follow this link to subscribe/unsubscribe:
>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users
>>>>>> >> >
>>>>>> >>
>>>>>> >>
>>>>>> >>
>>>>>> >> --
>>>>>> >> Unpaid intern in BillsBasement at noware dot com
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > --
>>>>>> > Regards:
>>>>>> > Mallik
>>>>>> >
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Unpaid intern in BillsBasement at noware dot com
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Regards:*
>>>>> Mallik
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> *Regards:*
>>>> Mallik
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> *Regards:*
>>> Mallik
>>>
>>>
>>
>>
>> --
>> *Regards:*
>> Mallik
>>
>>
>>
>
>
> --
> *Regards:*
> Mallik
>
> <temp.vtk>
>
>
>
--
*Regards:*
Mallik
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