On May 29, 2020, at 2:54 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Attached are the original vtk and ply file if anyone wants to look at them.

<example_surface_1_00.ply>

<example_surface_1_00.vtk>

On May 29, 2020, at 2:41 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Hi Shireen,

My VTK files contains polydata which I have converted over to ply files. See the image below from VIsIt of the ply data. However, the rasterization does not seen to be working correctly. I created an xml file based on the extents of the data :

<?xml version="1.0" ?>

<mesh>

example_surface_1_00.ply

</mesh>

<origin_x> -5.2</origin_x>

<origin_y>  0.0</origin_y>

<origin_z>-15.0</origin_z>

<size_x>10.4</size_x>

<size_y> 5.2</size_y>

<size_z>15.0</size_z>

<spacing_x>0.01</spacing_x>

<spacing_y>0.01</spacing_y>

<spacing_z>0.01</spacing_z>

I have tried different spacings, but that did not really change anything. I checked all of the surface normals and they are correct (pointing out of the volume). Does the rasterization strictly want triangles??? There were no complaints.

Cheers,

Allen 

<Screen Shot 2020-05-29 at 2.17.06 PM.png>

<Screen Shot 2020-05-29 at 2.33.02 PM.png>

On May 28, 2020, at 3:58 PM, Shireen Elhabian <shireen@sci.utah.edu> wrote:

Hi Allen,

Are your VTK files contain surface (triangular) meshes? Or volumetric meshes? As of now, ShapeWorks tools only support surface meshes. The femur use case (links below) should be a good starting point to see how you could groom/prep surface meshes to compute signed distance transforms as input to the Optimize phase. 

https://github.com/SCIInstitute/ShapeWorks/blob/master/Examples/Python/femur.py

https://github.com/SCIInstitute/ShapeWorks/blob/master/Documentation/UseCases.md#Femur-Use-Case

Though a bit late, happy Eid-ul-Fitr. Years ago I was in Egypt for Eid-ul-Fitr, then spent three weeks traveling around. I had a great time as it was the start of a three month tour around the Mediterranean Sea.

Thanks for your greeting! Hope you and your family are safe and healthy.

thanks and best regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor
School of Computing
Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513
Home Page: http://www.sci.utah.edu/~shireen

On May 28, 2020, at 3:13 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Hi,

It seems this script will process VTK data.

ShapeWorks/Examples/Scripts/FullPrepPipeline/FullPipelinePrepRunMeshtoDT.sh

However this sub script:

RasterizationVolumeOriginAndSize.sh 

Does not spit out the two files needed next:

# convert meshes to distance transforms

if [ $doMeshesToVolumes -eq 1 ]

then

    origin_filename=${parentDir}origin_size/origin_sp${spacing}_nb${narrow_band}.txt

    size_filename=${parentDir}origin_size/size_sp${spacing}_nb${narrow_band}.txt

I see the names in an xml file but not sure what to make of that. 

So at this point I am pretty lost. As such it would be really good to have a zoom chat so I can understand the pipeline. Especially as parts of the pipeline are not going to be needed - the data is located and oriented. But the bounding box is different. But for now I would just like to have and understand a working pipeline.

I can supply two VTK files that can be used for the initial setup. I have time tomorrow anytime to meet.

Cheers,

Allen

Allen Sanderson

SCI Institute

University of Utah

On May 27, 2020, at 2:49 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Hi Shireen,

Though a bit late, happy Eid-ul-Fitr. Years ago I was in Egypt for Eid-ul-Fitr, then spent three weeks traveling around. I had a great time as it was the start of a three month tour around the Mediterranean Sea.

I am finally working through all of the parts of ShapeWorks. I went through the ellipse example and now working with some of my VTK data. But I am not seeing documentation on starting with VTK files.  Just nrrd data. I have files that describe a closed surface (and as a volume elements) that I wanted to use for some initial testing and to familiarize myself with all the tools and steps.

I pinged Cam and Alan but they did not reply or did not know. Any pointers??


Cheers,

Allen