[vtkusers] AND-filter for vtkPolyData (was extract/selectcoincident points/cells)

[alex Dowson]

Hi


I also had check vtkBooleanOperationPolyDataFilter filter few month ago and 
I was not satisfied because it was not handling my some data while I was 
check another library was working
fine. May be it is not handling degenerated cases.  I had used carve CSG 
library was good. You can check also that with loading ply or stl file 
directly.


Alex


-----Original Message----- 
From: Dr. Roman Grothausmann
Sent: Tuesday, September 18, 2012 6:39 PM
To: alex Dowson
Cc: VTK Mailing List
Subject: Re: [vtkusers] AND-filter for vtkPolyData (was 
extract/selectcoincident points/cells)

Dear Alex,


Thanks for Your quick reply.

On 18/09/12 08:54, alex Dowson wrote:
> I seen your mesh data but I am not understand what you want to do ?

The two meshes originate from DiscreteMarchingCubes, which as Bill
wrote, generates coincident faces on two adjacent segmented surfaces,
i.e. adjacent labels in a voxel data set.

I want to extract all coincident faces, i.e. the faces that both meshes
share where they "touch".
The vtkBooleanOperationPolyDataFilter result
(intersec_3284-3307_raw.vtp) is very close, except for one triangle (the
blue one in intersec_3284-3307_raw_03_01.png), that does not meet this
requirement to have a coincident counter part in the other mesh. As it
is said in the article describing vtkBooleanOperationPolyDataFilter, it
has problems with coplanar trangles. Since coincident triangles are also
coplanar, I expect the inappropriate triangle in the result originates
from this unhandled coplanar cases. Amazingly, the result is nonetheless
quite good.

I noticed now, that the one vertex, that has no coincident
counter-vertex on the other mesh, has a "Distance" > 0 (as it should
be). Therefore, I can remove it (and the resulting inappropriate
triangle, blue) just with vtkThreshold.
However, when I run the code on many different meshes, I'd like to be
sure that no other similar cases arise (possible not handled properly
with just an additional vtkThreshold).

> 1) Do you want to join this two mesh in single ?

No. I want to extract their intersection that, in this special case,
only consists of coincident faces, i.e. has no volume.

> 2) Because there is only small part to intersection since it's boundary
> does not overlap. See in images has two parts you can see only small
> part is overlap and that will be ur final result
> from intersection and that's it producing right now.

Nearly, the one blue excess triangle (and the mentioned problems with
coplanar triangles in the describing text for
vtkBooleanOperationPolyDataFilter) worries me.

Many thanks for looking into this.
Roman

>
>
> -----Original Message----- From: Dr. Roman Grothausmann
> Sent: Tuesday, September 18, 2012 11:29 AM
> To: alex Dowson
> Subject: Re: [vtkusers] AND-filter for vtkPolyData (was
> extract/selectcoincident points/cells)
>
> Dear Alex!
>
>
> n 18/09/12 06:43, alex Dowson wrote:
>> Dear Dr.Roman
>>
>> can you show picture of your two input mesh or vtp file ?
>
> An visualization and the vtp files are in the tbz of my last post. I
> attached them here as well.
>
> Many thanks for looking into this
> Roman
>
>
>>
>>
>> alex
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message----- From: Dr. Roman Grothausmann
>> Sent: Monday, September 17, 2012 7:03 PM
>> To: alexdowson at hotmail.com ; jothybasu at gmail.com
>> Cc: VTK Mailing List ; Cory Quammen
>> Subject: Re: Fwd: Re: [vtkusers] AND-filter for vtkPolyData (was
>> extract/selectcoincident points/cells)
>>
>> Dear Alex, dear Jothy,
>>
>>
>> Many thanks for Your hint to use vtkBooleanOperationPolyDataFilter for
>> this. It basically works but it seems not completely exact. I've
>> attached an image that shows two touching blobs (raw meshes generated by
>> discreteMarchingCubes, in attached tbz), one is rendered yellow, the
>> other as wire frame. The intersection result (code below) of
>> vtkBooleanOperationPolyDataFilter is rendered in blue, therefore it
>> looks grey where it overlaps with the yellow faces. As you can see, one
>> triangle is blue nonetheless. It exists on the blob rendered as wire
>> frame but has no counter part on the yellow one, therefore does not
>> belong to the set of coincident faces nor does the one corner point
>> belong to the set of coincident vertices.
>> Since I do not really need a boolean operation (including surface
>> intersections) and since Cory Quammen's publication on
>> vtkBooleanOperationPolyDataFilter mentions that coplanar face are
>> problematic and not treated specially, I thought that
>> vtkDistancePolyDataFilter combined with a ThresholdBetween(0.0,0.0) on
>> the point-data "Distance" would do the trick. However, I realized from a
>> test, that there can be coincident vertices that do not belong to
>> coincident faces. Now, I would need a method to find all faces in the
>> second mesh which are made up completely by all the vertices from the
>> first mesh with "Distance"==0. (Using GetPointCells for all verts with
>> "Distance"==0 seems not to help here, since this way "border"
>> cells/triangles incorporating only one ore two of the verts are selected
>> as well.)
>> Using "Distance"==0 for the cell-data, does not work either because it
>> contains cell-to-point distance (not cell-to-cell distance). Therefore,
>> it needs a ThresholdBetween(0.0, t) where t is slightly greater than 0
>> (I used t=0.01 in the code below). As the two meshes originate from
>> marching-cubes, I guess an upper limit for t could be deduced from the
>> theory which would still grantee that only coincident faces are selected
>> this way, but I do not know for sure how to deduce this upper limit
>> for t.
>>
>> Do You have any ideas how to solve this problem?
>>
>> Thanks for Your help or hints.
>> Roman
>>
>> /////find and extract coincident vertices and faces of two marching
>> cubes meshes
>>
>> #include <vtkXMLPolyDataReader.h>//for vtp-files
>> // #include <vtkPolyDataReader.h>//for vtk-files
>> #include <vtkBooleanOperationPolyDataFilter.h>
>> #include <vtkXMLPolyDataWriter.h>//for vtp-files
>>
>> int main(int argc, char* argv[]){
>> if( argc <= 3 )
>> {
>> std::cerr << "Usage: " << argv[0];
>> std::cerr << " inputMesh0";
>> std::cerr << " inputMesh1";
>> std::cerr << " outputMesh";
>> std::cerr << std::endl;
>> return EXIT_FAILURE;
>> }
>>
>> if(!(strcasestr(argv[1],".vtp"))) {
>> std::cout << "The input should end with .vtp" << std::endl;
>> return -1;
>> }
>>
>> if(!(strcasestr(argv[2],".vtp"))) {
>> std::cout << "The input should end with .vtp" << std::endl;
>> return -1;
>> }
>>
>> //vtkPolyDataReader *reader = vtkPolyDataReader::New(); //*.vtk
>> vtkXMLPolyDataReader *reader0 = vtkXMLPolyDataReader::New(); //*.vtp
>>
>> reader0->SetFileName(argv[1]);
>> reader0->Update();
>>
>> vtkXMLPolyDataReader *reader1 = vtkXMLPolyDataReader::New(); //*.vtp
>>
>> reader1->SetFileName(argv[2]);
>> reader1->Update();
>>
>> vtkBooleanOperationPolyDataFilter *boolean=
>> vtkBooleanOperationPolyDataFilter::New();
>> boolean->SetInputConnection(0, reader0->GetOutputPort());
>> boolean->SetInputConnection(1, reader1->GetOutputPort());
>> boolean->SetOperationToIntersection();
>>
>> vtkXMLPolyDataWriter *Pwriter = vtkXMLPolyDataWriter::New();
>> //vtkDataSetWriter *Pwriter = vtkDataSetWriter::New();
>>
>> Pwriter->SetFileName(argv[3]);
>> Pwriter->SetInputConnection(boolean->GetOutputPort(0));
>> Pwriter->Update();
>>
>>
>> return EXIT_SUCCESS;
>> }
>>
>> ___________________________________________________________________
>>
>>
>> /////find and extract coincident vertices and faces of two marching
>> cubes meshes
>> //// there can be coincident verts that do not belong to coincident
>> faces!!!
>>
>>
>> #include <vtkXMLPolyDataReader.h>//for vtp-files
>> // #include <vtkPolyDataReader.h>//for vtk-files
>> //#include <vtkBooleanOperationPolyDataFilter.h>
>> #include <vtkDistancePolyDataFilter.h>
>> #include <vtkThreshold.h>
>> #include <vtkGeometryFilter.h>
>> #include <vtkXMLPolyDataWriter.h>//for vtp-files
>>
>> int main(int argc, char* argv[]){
>> if( argc != 4 )
>> {
>> std::cerr << "Usage: " << argv[0];
>> std::cerr << " inputMesh0";
>> std::cerr << " inputMesh1";
>> std::cerr << " outputMesh";
>> std::cerr << std::endl;
>> return EXIT_FAILURE;
>> }
>>
>> if(!(strcasestr(argv[1],".vtp"))) {
>> std::cout << "The input should end with .vtp" << std::endl;
>> return -1;
>> }
>>
>> if(!(strcasestr(argv[2],".vtp"))) {
>> std::cout << "The input should end with .vtp" << std::endl;
>> return -1;
>> }
>>
>> if(!(strcasestr(argv[3],".vtp"))) {
>> std::cout << "The input should end with .vtp" << std::endl;
>> return -1;
>> }
>>
>> //vtkPolyDataReader *reader = vtkPolyDataReader::New(); //*.vtk
>> vtkXMLPolyDataReader *reader0 = vtkXMLPolyDataReader::New(); //*.vtp
>>
>> reader0->SetFileName(argv[1]);
>> reader0->Update();
>>
>> vtkXMLPolyDataReader *reader1 = vtkXMLPolyDataReader::New(); //*.vtp
>>
>> reader1->SetFileName(argv[2]);
>> reader1->Update();
>>
>> vtkDistancePolyDataFilter *polydist= vtkDistancePolyDataFilter::New();
>> polydist->SetInputConnection(0, reader0->GetOutputPort());
>> polydist->SetInputConnection(1, reader1->GetOutputPort());
>> polydist->SignedDistanceOff();
>> //polydist->ComputeSecondDistanceOff(); //causes:
>> /*
>> ERROR: In
>> /home/grothama/sda8/programme/VTK/Filtering/vtkExecutive.cxx, line 756
>> vtkStreamingDemandDrivenPipeline (0x1d2a800): Algorithm
>> vtkDistancePolyDataFilter(0x1d29890) returned failure for request:
>> vtkInformation (0x1d4e040)
>> Debug: Off
>> Modified Time: 757
>> Reference Count: 1
>> Registered Events: (none)
>> Request: REQUEST_DATA
>> ALGORITHM_AFTER_FORWARD: 1
>> FROM_OUTPUT_PORT: 0
>> FORWARD_DIRECTION: 0
>> */
>> polydist->Update();
>>
>> vtkThreshold *thresh= vtkThreshold::New();
>> thresh->SetInputConnection(polydist->GetOutputPort());
>> //thresh->SetInputArrayToProcess(0, 0, 0,
>> vtkDataObject::FIELD_ASSOCIATION_POINTS, "Distance"); //
>> FIELD_ASSOCIATION_VERTICES
>> //thresh->SetInputArrayToProcess(0, 0, 0,
>> vtkDataObject::FIELD_ASSOCIATION_POINTS, vtkDataSetAttributes::SCALARS);
>> // FIELD_ASSOCIATION_VERTICES
>> thresh->SetInputArrayToProcess(0, 0, 0,
>> vtkDataObject::FIELD_ASSOCIATION_CELLS, "Distance"); //
>> FIELD_ASSOCIATION_VERTICES
>> //thresh->SetAttributeModeToUsePointData();
>> thresh->ThresholdBetween(0.0,0.01);
>>
>> vtkGeometryFilter *usg2poly= vtkGeometryFilter::New();
>> usg2poly->SetInputConnection(thresh->GetOutputPort());
>>
>> vtkXMLPolyDataWriter *Pwriter = vtkXMLPolyDataWriter::New();
>> //vtkDataSetWriter *Pwriter = vtkDataSetWriter::New();
>>
>> Pwriter->SetFileName(argv[3]);
>> //Pwriter->SetInputConnection(polydist->GetOutputPort());
>> Pwriter->SetInputConnection(usg2poly->GetOutputPort());
>> Pwriter->Update();
>>
>>
>> return EXIT_SUCCESS;
>> }
>>
>>
>>
>> On 17/09/12 10:10, Roman Grothausmann wrote:
>>>
>>>
>>>
>>> -------- Original Message --------
>>> Subject: Re: [vtkusers] AND-filter for vtkPolyData (was
>>> extract/selectcoincident points/cells)
>>> Date: Wed, 5 Sep 2012 10:49:20 +0200
>>> From: Roman Grothausmann <roman.grothausmann at helmholtz-berlin.de>
>>> To: alex Dowson <alexdowson at hotmail.com>, VTK Mailing List
>>> <vtkusers at vtk.org>
>>>
>>> Hello Alex,
>>>
>>>
>>> Many thanks for the hint, I had not thought of boolean operation for
>>> this since the only overlap, ie the union, would consist only of a
>>> surface, not a volume. I'll give it a try and see if it results in what
>>> I need. It could work since for the meshes I look at I can rule out that
>>> they could also have volume unions.
>>>
>>> Thanks again for Your hint
>>> Roman
>>>
>>> On 05.09.2012 09:15, alex Dowson wrote:
>>>> Hi
>>>>
>>>> Have you tried CSG Boolean filter in VTK ? Check this class
>>>>
>>>> http://www.vtk.org/doc/nightly/html/classvtkBooleanOperationPolyDataFilter.html
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Also you can use implicit boolean operation filter for that.
>>>>
>>>>
>>>>
>>>>
>>>> -----Original Message----- From: Roman Grothausmann
>>>> Sent: Wednesday, September 05, 2012 12:42 PM
>>>> To: VTK Mailing List
>>>> Subject: [vtkusers] AND-filter for vtkPolyData (was
>>>> extract/selectcoincident points/cells)
>>>>
>>>> Dear mailing list members,
>>>>
>>>>
>>>> Is there a kind of AND-filter for vtkPolyData-meshes which I could use
>>>> to extract/select coincident points/cells of two meshes?
>>>>
>>>> Thanks for any hints or help
>>>> Roman
>>>>
>>>> On 31.08.2012 14:53, Roman Grothausmann wrote:
>>>>> Dear mailing list members,
>>>>>
>>>>>
>>>>> There are many filters in VTK to clean/merge coincident points but I
>>>>> could not find a single filter that extracts/selects coincident
>>>>> points/cells.
>>>>> I would need it to extract the sub-mesh of two or more
>>>>> vtkPolyData-meshes where these meshes overlap, e.g. when a
>>>>> vtkDiscreteMarchingCubes surface is generated of two or more labels
>>>>> that
>>>>> directly touch each other in voxel space.
>>>>> Or is there a way to just generate a mesh of the area where both
>>>>> labels
>>>>> touch?
>>>>>
>>>>> Any help or hints are very much appreciated
>>>>> Roman
>>>>>
>>>>
>>>
>>
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
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