[vtkusers] High memory cost of vtkDecimatePro for 3D model generation from DICOM series
Elvis Stansvik
elvis.stansvik at orexplore.com
Fri Mar 18 02:47:34 EDT 2016
2016-03-18 3:19 GMT+01:00 David Gobbi <david.gobbi at gmail.com>:
> You can segment an image with just one threshold (i.e. just the lower
> threshold). It is not necessary to set a range.
>
Sorry for jumping in here, but I'm also pretty new to VTK, and what Liu
describes sounds like something we will want to do soon: Allow the user to
set a grayscale range, and only show the parts of the volume that falls
within this range.
When you say "you can segment an image with just one threshold", do you
mean that it somehow doesn't make sense to use two thresholds? If so, why?
What if the use really wants to "extract" the parts of the volume where the
scalar values are within some range?
Thanks in advance,
Elvis
> But, regardless, vtkMarchingCubes is designed to take a greyscale image as
> input, not a binary image.
>
> - David
>
>
> On Thu, Mar 17, 2016 at 8:09 PM, Liu_tj <tjlp at netease.com> wrote:
>
>> Hi, David,
>>
>> The user scenario is that we allow the user to set segment threshold
>> which is a grayscale range. So at the 2D DICOM view, the pixels which fall
>> in this range will be shown by special color (I implement it with
>> vtkLookupTableand vtkImageMapToColors); then the user can preview the 3D
>> model generated by the points in this grayscale range.
>>
>> Thanks
>>
>>
>> 在2016-03-18，"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18日 星期五
>> *收件人:*"Liu_tj" <tjlp at netease.com>
>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>> *主题:*Re: Re: Re: Re: Re: [vtkusers] High memory cost of vtkDecimatePro
>> for 3D model generation from DICOM series
>>
>>
>> You only need one threshold to create a model from an image.
>> Why do you let the user set two thresholds?
>>
>>
>> On Thu, Mar 17, 2016 at 7:54 PM, Liu_tj <tjlp at netease.com> wrote:
>>
>>> Hi, David,
>>>
>>> If the user sets a upper value, what should we do?
>>>
>>> Thanks
>>> Liu Peng
>>>
>>>
>>>
>>> 在2016-03-18，"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18日 星期五
>>> *收件人:*"Liu_tj" <tjlp at netease.com>
>>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>>> *主题:*Re: Re: Re: Re: [vtkusers] High memory cost of vtkDecimatePro for
>>> 3D model generation from DICOM series
>>>
>>>
>>> Hi Liu Peng,
>>>
>>> Now that I have seen your code, you should definitely remove
>>> vtkImageThreshold and set the vtkMarchingCubes isovalue to around 1000.
>>> I'm certain that vtkImageThreshold does nothing useful in this pipeline.
>>>
>>> For vtkReverseSense, see the documentation page for the class for an
>>> explanation of what it does. I wrote that example code because I thought
>>> you might need an upper and a lower threshold, but now that I have seen
>>> your code, I think you only need one threshold (just the lower threshold).
>>> So you can ignore the code that I sent.
>>>
>>> As for the camera, it is usually a good idea to point it at the center
>>> of the volume. I do not always like VTK's default camera position, so I
>>> when I write VTK code, I almost always set the camera position myself.
>>>
>>> - David
>>>
>>>
>>>
>>> On Thu, Mar 17, 2016 at 7:07 PM, Liu_tj <tjlp at netease.com> wrote:
>>>
>>>> Hi, David,
>>>>
>>>> Below is my present C# code.You can see that I reset the camera
>>>> position, otherwise after rendering, the 3D model is not at the window
>>>> center, I have to pan it, any recommendation for the position issue also?
>>>>
>>>> private void Display(vtkRenderWindow aRenderWindow, vtkImageData
>>>> aData)
>>>> {
>>>> vtkImageData volume = vtkImageData.New();
>>>> double isoValue = 1;
>>>> volume.DeepCopy(aData);
>>>> vtkImageThreshold image_threshold = vtkImageThreshold.New();
>>>> image_threshold.SetInputData(volume);
>>>> image_threshold.ThresholdBetween(1000,20000);
>>>> image_threshold.ReplaceInOn();
>>>> image_threshold.SetInValue(1);
>>>> image_threshold.ReplaceOutOn();
>>>> image_threshold.SetOutValue(0);
>>>> image_threshold.Update();
>>>>
>>>> vtkMarchingCubes surface = vtkMarchingCubes.New();
>>>> surface.SetInputData(image_threshold.GetOutput());
>>>> surface.ComputeNormalsOn();
>>>> surface.ComputeScalarsOn();
>>>> surface.SetValue(0, isoValue);
>>>> surface.Update();
>>>>
>>>> vtkPolyData marched = vtkPolyData.New();
>>>> marched.DeepCopy(surface.GetOutput());
>>>>
>>>> long pointcnt = marched.GetNumberOfPoints();
>>>>
>>>> // Decimation to reduce the number of triangles
>>>> vtkDecimatePro decimator = vtkDecimatePro.New();
>>>> decimator.SetInputData(marched);
>>>> decimator.SetTargetReduction(0.5);
>>>> decimator.SetPreserveTopology(1);
>>>> decimator.Update();
>>>> //Smoothing
>>>> vtkSmoothPolyDataFilter smoother =
>>>> vtkSmoothPolyDataFilter.New();
>>>> smoother.SetInputData(decimator.GetOutput());
>>>> smoother.SetNumberOfIterations(5);
>>>> smoother.SetFeatureAngle(60);
>>>> smoother.SetRelaxationFactor(0.05);
>>>> smoother.FeatureEdgeSmoothingOff();
>>>>
>>>> //Select the largest region
>>>> vtkPolyDataConnectivityFilter connectivityFilter =
>>>> vtkPolyDataConnectivityFilter.New();
>>>>
>>>> connectivityFilter.SetInputConnection(decimator.GetOutputPort());
>>>> connectivityFilter.ScalarConnectivityOff();
>>>> connectivityFilter.SetExtractionModeToLargestRegion();
>>>> connectivityFilter.Update();
>>>>
>>>> // Create final polygon mesh
>>>> vtkPolyData mesh = vtkPolyData.New();
>>>> mesh.ShallowCopy(connectivityFilter.GetOutput());
>>>>
>>>> // Visualization
>>>> vtkRenderer renderer =
>>>> aRenderWindow.GetRenderers().GetFirstRenderer();
>>>> renderer.SetBackground(0.0, 0.0, 0.0);
>>>>
>>>> vtkPolyDataMapper mapper = vtkPolyDataMapper.New();
>>>> mapper.SetInputData(mesh);
>>>> mapper.ScalarVisibilityOff();
>>>>
>>>> vtkActor actor = vtkActor.New();
>>>> actor.SetMapper(mapper);
>>>> renderer.AddActor(actor);
>>>>
>>>> vtkCamera camera = renderer.MakeCamera();
>>>> camera.SetPosition(-500.0, 245.5, 122.0);
>>>> camera.SetFocalPoint(301.0, 245.5, 122.0);
>>>> camera.SetViewAngle(30.0);
>>>> camera.SetRoll(-90.0);
>>>> renderer.SetActiveCamera(camera);
>>>>
>>>> aRenderWindow.Render();
>>>>
>>>> vtkRenderWindowInteractor interactor =
>>>> aRenderWindow.GetInteractor();
>>>> interactor.Start();
>>>> }
>>>>
>>>>
>>>>
>>>> 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: Re: Re: [vtkusers] High memory cost of vtkDecimatePro for 3D
>>>> model generation from DICOM series
>>>>
>>>>
>>>> And I should add: if it is necessary to use a range (instead of just a
>>>> lower threshold), then the pipeline can use vtkMarchingCubes twice:
>>>>
>>>> vtkSmartPointer<vtkMarchingCubes> cubes1 =
>>>> vtkSmartPointer<vtkMarchingCubes>::New();
>>>> cubes1->SetInputData(imagedata);
>>>> cubes1->SetValue(0, lowerThreshold);
>>>>
>>>> vtkSmartPointer<vtkMarchingCubes> cubes2 =
>>>> vtkSmartPointer<vtkMarchingCubes>::New();
>>>> cubes2->SetInputData(imagedata);
>>>> cubes2->SetValue(0, upperThreshold);
>>>>
>>>> vtkSmartPointer<vtkReverseSense> reverse =
>>>> vtkSmartPointer<vtkReverseSense>::New();
>>>> reverse->SetInputConnection(cubes2->GetOutputPort());
>>>>
>>>> vtkSmartPointer<vtkAppendPolyData> surface =
>>>> vtkSmartPointer<vtkAppendPolyData>::New();
>>>> surface->SetInputConnection(cubes1->GetOutputPort());
>>>> surface->AddInputConnection(cubes2->GetOutputPort());
>>>> surface->Update();
>>>>
>>>>
>>>> On Thu, Mar 17, 2016 at 6:06 AM, David Gobbi <david.gobbi at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Liu Peng,
>>>>>
>>>>> For creating a model, it is common to allow the user to set just a
>>>>> lower threshold (rather than a range), and to use the lower threshold as
>>>>> the isovalue. If you send the code for the whole pipeline, that might help.
>>>>>
>>>>> - David
>>>>>
>>>>> On Wed, Mar 16, 2016 at 11:27 PM, Liu_tj <tjlp at netease.com> wrote:
>>>>>
>>>>>> Hi, David,
>>>>>>
>>>>>> If I don't use vtkImageThreshol, how to generate 3D model from the
>>>>>> points whose grayscale is in some specific range? This range can be changed
>>>>>> by the user.
>>>>>>
>>>>>> 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: Re: [vtkusers] High memory cost of vtkDecimatePro for 3D
>>>>>> model generation from DICOM series
>>>>>>
>>>>>>
>>>>>> On Wed, Mar 16, 2016 at 10:35 PM, Liu_tj <tjlp at netease.com> wrote:
>>>>>>
>>>>>>> Hi,David,
>>>>>>>
>>>>>>> If using vtkImageThreshold before vtkMarchingCubes is not a good
>>>>>>> option, what other better way do you have?
>>>>>>>
>>>>>>
>>>>>> The output of the reader should go directly into vtkMarchingCubes.
>>>>>>
>>>>>>
>>>>>>> Beside, for the isovalue, I try 2,3,4 and
>>>>>>> marched->GetNumberOfPoints() return 0, only isovalue is 1 and
>>>>>>> marched->GetNumberOfPoints() return a number greater than 0. I have no idea
>>>>>>> this is relating to the DICOM series or other problem.
>>>>>>>
>>>>>>
>>>>>> If you remove vtkImageThreshold, and put the output of the reader
>>>>>> directly into vtkMarchingCubes, then you should be able to use an isovalue
>>>>>> somewhere between 100 and 2000 and get a good result.
>>>>>>
>>>>>> Also, after vtkMarchingCubes, you can use vtkConnectivityFilter to
>>>>>> clean up the polydata before you decimate it.
>>>>>>
>>>>>> - David
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
> _______________________________________________
> 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
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/vtkusers/attachments/20160318/2e656751/attachment-0001.html>
More information about the vtkusers
mailing list