[vtk-developers] Discrete contouring classes

Sat Dec 23 19:31:36 EST 2017

The image on the right has some texture but looks mostly flat (as if there was no shading at all). In contrast, in the left image shapes are nicely visible. Can you remove edges completely and estimate surface normals from voxel values in a small neighborhood?

Andras

-----Original Message-----
From: Bill Lorensen [mailto:bill.lorensen at gmail.com] 
Sent: Saturday, December 23, 2017 7:18 PM
To: Andras Lasso <lasso at queensu.ca>
Cc: Will Schroeder <will.schroeder at kitware.com>; vtk-developers <vtk-developers at vtk.org>
Subject: Re: [vtk-developers] Discrete contouring classes

I brightened the edges rather than darkening them.
See
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2Florensen%2FSPLBrainAtlas%2Fmaster%2FModels%2FScreenshot%2Fwhite_matter_of_left_cerebral_hemisphere.png&data=02%7C01%7Classo%40queensu.ca%7C6e05c878eb634666e41a08d54a63bfb5%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636496714637148564&sdata=JsXf9yOP6WQu7xa82bU%2FS64iwyJIGcIW9Vs1v0pg76I%3D&reserved=0

On Sat, Dec 23, 2017 at 11:53 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> There are no normals in the cube files I generate. I do color the 
> edges, so on large poly models, the dark edges may be causing the 
> problem.
>
> For example, see this lower poly count model:
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.g
> ithubusercontent.com%2Florensen%2FSPLBrainAtlas%2Fmaster%2FModels%2FSc
> reenshot%2Fright_putamen.png&data=02%7C01%7Classo%40queensu.ca%7C6e05c
> 878eb634666e41a08d54a63bfb5%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0
> %7C636496714637148564&sdata=jeeJF3UcOimQ3qesRBVqMVNd%2Bq%2F9OR4Tsr1u1Q
> xKJ%2FQ%3D&reserved=0
>
> On Sat, Dec 23, 2017 at 10:45 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> I'll take a look to fix normals on cube models.
>>
>> On Sat, Dec 23, 2017 at 10:28 AM, Andras Lasso <lasso at queensu.ca> wrote:
>>> Hi Will and Bill,
>>>
>>>
>>>
>>> Surface generation from binary labelmap is an important task for us 
>>> in 3D Slicer, to display segmentation results in 3D while it is 
>>> being edited in 2D, We are very interested in any potential improvements.
>>>
>>>
>>>
>>> Currently, we use discrete marching cubes and sinc smoothing, which 
>>> gives good results, but sometimes it can be quite slow (especially 
>>> the smoothing step).
>>>
>>>
>>>
>>> We tried cube models but surface normals always pointed to x/y/z 
>>> direction instead of actual surface normal direction, so it was very 
>>> hard to see 3D shapes. This flat look is visible in your examples, too:
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2Florensen%2FSPLBrainAtlas%2Fmaster%2FModels%2FScreenshot%2Fwhite_matter_of_left_cerebral_hemisphere.png&data=02%7C01%7Classo%40queensu.ca%7C6e05c878eb634666e41a08d54a63bfb5%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636496714637148564&sdata=JsXf9yOP6WQu7xa82bU%2FS64iwyJIGcIW9Vs1v0pg76I%3D&reserved=0.
>>>
>>>
>>>
>>> We use discrete marching cubes, but as far as I remember, we did not 
>>> see huge differences between regular and discrete marching cubes. Is 
>>> there a study or examples that compares them (visual appearance, 
>>> accuracy, computation time, etc.)? Is there a solution that provides 
>>> smooth surfaces (that would not require further smoothing step to 
>>> remove staircase artifacts)?
>>>
>>>
>>>
>>> We also plan to evaluate how well we can visualize binary labelmaps 
>>> in 3D using the new multi-volume-rendering feature that is being 
>>> integrated into VTK now.
>>>
>>>
>>>
>>> Andras
>>>
>>>
>>>
>>> From: vtk-developers [mailto:vtk-developers-bounces at vtk.org] On 
>>> Behalf Of Will Schroeder
>>> Sent: Saturday, December 23, 2017 8:35 AM
>>> To: vtk-developers <vtk-developers at vtk.org>
>>> Subject: Re: [vtk-developers] Discrete contouring classes
>>>
>>>
>>>
>>> FYI here is an example of discrete marching cubes at work. From Bill:
>>>
>>>
>>>
>>> Here is the SPLBrainAtlas;
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit
>>> hub.com%2Florensen%2FSPLBrainAtlas%2Fwiki%2FAtlas-Summary&data=02%7C
>>> 01%7Classo%40queensu.ca%7C6e05c878eb634666e41a08d54a63bfb5%7Cd61ecb3
>>> b38b142d582c4efb2838b925c%7C1%7C0%7C636496714637148564&sdata=SflCrfK
>>> aKUbhYoX2DkqCbM4a8V6UAiUNF08%2F9BYjb5Q%3D&reserved=0
>>>
>>> The two-paned images show Discrete on left, Cube's Model (also
>>> undersold) on right. STL files created using discrete followed by 
>>> non-manifold joint smoothing.
>>>
>>>
>>>
>>> On Sat, Dec 23, 2017 at 8:30 AM, Will Schroeder 
>>> <will.schroeder at kitware.com>
>>> wrote:
>>>
>>> FYI- Back in the day (2004) Jim Miller and Bill Lorensen added the 
>>> vtkDiscreteMarchingCubes class. This is used to generate contours 
>>> for label masks (as you would find in segmentation). The key here is 
>>> that the labels are non-continuous (i.e., scalar field is not 
>>> smooth) so the regular edge interpolation of something like marching 
>>> cubes doesn't work. Long story short, this class interpolates on the 
>>> mid-edge point between regions, and it generates different regions (i.e., meshes) for each label.
>>>
>>>
>>>
>>> This class and approach is woefully underappreciated and underused.
>>>
>>>
>>>
>>> I am just adding flying edges versions (2D and 3D) of this 
>>> functionality (MR 3739). These are of course much faster and scalable across multiple cores.
>>> They also produce slightly different results. Principally they do 
>>> not merge coincident points belonging to different regions (since 
>>> flying edges does not use a point locator) -- this is both good and 
>>> bad depending on the application. Also normals are generated by the 
>>> flying edges algorithm, not by vtkDiscreteMarchingCubes.
>>>
>>>
>>>
>>> See the docs for more info.
>>>
>>>
>>>
>>> Best,
>>>
>>> W
>>>
>>>
>>>
>>> --
>>>
>>> William J. Schroeder, PhD
>>> Kitware, Inc. - Building the World's Technical Computing Software
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>>>
>>>
>>>
>>>
>>> --
>>>
>>> William J. Schroeder, PhD
>>> Kitware, Inc. - Building the World's Technical Computing Software
>>> 28 Corporate Drive
>>> Clifton Park, NY 12065
>>> will.schroeder at kitware.com
>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
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>>
>>
>>
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