[vtkusers] High memory cost of vtkDecimatePro for 3D model generation from DICOM series

Sat Apr 2 00:20:36 EDT 2016

Hi Liu,

You are thinking of a different definition of the word "rough".
I mean "having an irregular or bumpy surface".  I did not mean
"unfinished or lacking in detail".

 - David

On Fri, Apr 1, 2016 at 10:00 PM, Liu_tj <tjlp at netease.com> wrote:

> Hi, David,
>
> According to my understanding, smooth surface should have greater size
> than "rough" size, is my understanding wong?
> For the DICOM series of 512*512*190, if I shrink to 128*128*190, the
> generated 3D volume has worse quality than the one I don't shrink.
>
> Thanks
> Liu Peng
>
>
> 在2016-04-02，"David Gobbi" <david.gobbi at gmail.com> 写道：
>
> -----原始邮件-----
> *发件人:*"David Gobbi" <david.gobbi at gmail.com>
> *发送时间:*2016年04月2日 星期六
> *收件人:*"Liu_tj" <tjlp at netease.com>
> *抄送:*"vtkusers" <vtkusers at vtk.org>
> *主题:*Re: Re: [vtkusers] High memory cost of vtkDecimatePro for 3D model
> generation from DICOM series
>
>
> Hi Liu,
>
> For a volume of that size, I'd guess an STL file size of around 150MB for
> a smooth surface, so 520MB for a "rough" surface seems reasonable.   As I
> mentioned in my previous email, if vtkDecimatePro is running out of memory,
> you can try reducing the resolution of the image before running marching
> cubes.
>
>  - David
>
>
> On Wed, Mar 30, 2016 at 7:45 AM, Liu_tj <tjlp at netease.com> wrote:
>
>> Hi, David,
>>
>> I follow your advice and use the original vtkImageData for
>> vtkMarchingCubes, and the isovalue is 1000. Then I try to save the
>> generated 3D volume to stl file. For a 512*512*190 chest CT DICOM series,
>> the STL file is about 520M. Do you think the file size is rather bigger?
>>
>> Thanks.
>> Liu Peng
>>
>> 在2016-03-25，"Liu_tj" <tjlp at netease.com> 写道：
>>
>> -----原始邮件-----
>> *发件人:*"Liu_tj" <tjlp at netease.com>
>> *发送时间:*2016年03月25日 星期五
>> *收件人:*"David Gobbi" <david.gobbi at gmail.com>
>>
>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>> *主题:*Re: [vtkusers] High memory cost of vtkDecimatePro for 3D model
>> generation from DICOM series
>>
>> Hi, David,
>>
>> Continue this thread. For the 3D model generation, we have a preview
>> function. That means we need quick 3D model generation speed and don't need
>> high model precision. Only when really generating, we need a good 3D model
>> quality. So, for the preview, how to accelerate the generation speed?
>>
>> Thanks
>> Liu Peng
>>
>>
>>
>> 在2016-03-17，"David Gobbi" <david.gobbi at gmail.com> 写道：
>>
>> -----原始邮件-----
>> *发件人:*"David Gobbi" <david.gobbi at gmail.com>
>> *发送时间:*2016年03月17日 星期四
>> *收件人:*"Liu_tj" <tjlp at netease.com>
>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>> *主题:*Re: [vtkusers] High memory cost of vtkDecimatePro for 3D model
>> generation from DICOM series
>>
>> Hi Liu Peng,
>>
>> The vtkMarchingCubes algorithm is for greyscale images. Using
>> vtkImageThreshold before vtkMarchingCubes will give a poor result, because
>> the algorithm won't be able to properly interpolate the voxels to find the
>> best surface if it is given a binary image.
>>
>> When you call SetValue(0, isovalue), make sure that "isovalue" is set to
>> the value that corresponds to the desired isosurface.  If you don't know
>> what value to use, you can start at 1000, then try 250, then 125, etc.
>> until you get a reasonable result.  But the best way to choose a value is
>> to use Otsu's method or something similar.
>>
>>  - David
>>
>>
>> On Wed, Mar 16, 2016 at 7:42 PM, Liu_tj <tjlp at netease.com> wrote:
>>
>>> Hi, VTK guys,
>>>
>>> I use VTK 7.0 to generate 3D model from DICOM series. I just follow the
>>> code example from
>>>
>>> http://www.vtk.org/pipermail/vtkusers/2013-November/082109.html <http://www.vtk.org/Wiki/VTK/Examples/Cxx/Modelling/MarchingCubes%22.>. When I try to reduce the number of triangles by vtkDecimatePro, the Visual Studio 2015 monitor shows that the memory jump to over 10G and my computer has no response, I have to restart my computer rudely. See my code below, with my DICOM series, the marched->GetNumberOfPoints() return more than 20 millions:
>>>
>>>  vtkSmartPointer<vtkMarchingCubes> surface = vtkSmartPointer<vtkMarchingCubes>::New();
>>>   surface->SetInputData(volume);
>>>   surface->ComputeNormalsOn();
>>>   surface->ComputeScalarsOn();
>>>   surface->SetValue(0, 1);
>>>
>>>   // Create polydata from iso-surface
>>>   vtkSmartPointer<vtkPolyData> marched = vtkSmartPointer<vtkPolyData>::New();
>>>   surface->Update();
>>>   marched->DeepCopy(surface->GetOutput());
>>>   std::cout<<"Number of points: " << marched->GetNumberOfPoints() << std::endl;
>>>
>>>   // Decimation to reduce the number of triangles
>>>   vtkSmartPointer<vtkDecimatePro> decimator = vtkDecimatePro::New();
>>>   decimator->SetInputData(marched);
>>>   decimator->SetTargetReduction(0.5);
>>>   decimator->SetPreserveTopology(1);
>>>   decimator->Update(); <------------------memory cost jumps to more than 10G.
>>>
>>> Any suggestions to decrease the memory cost? I only know that using vtkImageThreshold.
>>> Thanks,
>>>
>>>
>>
>>
>>
>
>
>
>
>
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