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Thanks Alan,

I will play with this tomorrow. Looking at the xml file there are local
points, world point, and points? What are the difference between them. I
notice that world point and points are the same. For my data the local and
world are the same and as I have no points I would similarly those would be
world points.

What surface is being shown for the difference. Is that just points from the
last ellipsoid or is that actually a surface?

I will put together a tarball for you that you can grab. If I put it out on
shell.sci I assume you can grab it.

Cheers,

Allen




> On Jun 8, 2020, at 4:16 PM, Alan Morris <amorris@sci.utah.edu> wrote:
>
> Hi Allen,
>
> You don't need the reconstructions to do the group difference. See
> the attached sample file and video. The difference vectors are shown
> at each correspondence point. The difference shows how to get from
> group2 to group1. In this example, the last ellipsoid is the only
> member of group 2 and requires squishing to get the mean of the other
> shapes.
>
> If you're not interested in the reconstructions, the only tags you
> need are <point_files> and <group_ids>
>
> If you're not getting good reconstructions though, I'd be worried that
> perhaps the optimization didn't go well. If you want to point me at
> your data set (inputs and outputs), I can take a look at it.
>
> Alan
>
> On Mon, Jun 8, 2020 at 12:59 PM Allen Sanderson <allen@sci.utah.edu> wrote:
>>
>> Hi Alan,
>>
>> That sounds about what I would like to do. So please do send an example.
>> That said does one have to have the actual reconstructions ??? What I
>> would almost prefer at this point is to see the correspondence particles
>> and far they are from the mean?
>>
>> Here is my line of thinking. The correspondence particles are placed on
>> the image voxels during the optimization process. That part is the
>> splitting. I am fuzzy on what actually happens during the “optimization
>> iterations”. Is this step where the actual correspondence is done? But
>> once done and go to the Analysis step I get a reconstructed image just
>> based on the correspondence particles which as Jadie notes is not very
>> good unless the distance transforms are used.
>>
>> I would actually like to visualize each individual dataset with its
>> correspondence particles but with a vector and colored by the magnitude.
>> This visualization is similar to the group but allows one to see
>> individual datasets compared to the mean. Most importantly it does not
>> rely on a reconstruction (which is problematic for thin surfaces).
>>
>> At this I understand, this visualization may not be possible but if I knew
>> which files contained the mean particles tat would be helpful. For
>> instance, not sure what these files contain:
>> -rw-r----- 1 allen admin 3024 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1_bad-sparse.particles
>> -rw-r----- 1 allen admin 192909 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1_good-sparse.particles
>> -rw-r----- 1 allen admin 16384 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1_goodPoints.txt
>> -rw-r----- 1 allen admin 195933 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1_sparse.particles
>>
>>
>> I noticed that each dataset had these files, but they were the same? These
>> should be the initial particles.
>> -rw-r----- 1 allen admin 245088 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1.lpts
>> -rw-r----- 1 allen admin 245088 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1.wpts
>>
>>
>> Also this appears to the reconstruction.
>> -rw-r----- 1 allen admin 330664 Jun 5 17:09
>> example_surface_1_00.rasterized_sp0.1_dense.vtk
>>
>> Oddly this morning when I started SWStudio it did not get loaded in which
>> I expected. I had to do the reconstruction again. Thought I may have
>> missed something.
>>
>>
>> Cheers,
>>
>> Allen
>>
>>
>>
>>
>> On Jun 7, 2020, at 5:24 PM, Alan Morris <amorris@sci.utah.edu> wrote:
>>
>> Allen,
>>
>> The mesh to mesh comparison tools are a little light at the moment. I
>> recently moved over the older group differences functionality into Studio,
>> but it only compares the means of two groups. In the near future we’ll be
>> enhancing this quite a bit.
>>
>> At the moment, I can think of one possible way to do what you want, once
>> you have good reconstructions. In the old analysis parameter file format,
>> you can specify <group_ids> and list 1’s and 2’s (I can send an example).
>> To compare one sample against the mean, you could list all shapes in group
>> 1 and then just the sample in question as group 2. This sample could also
>> be in group 1 to make it the mean of all shapes. The group difference
>> functionality would then show you what you’re looking for, I believe.
>> You’d have to make a separate parameter file for each one and load them in
>> separate sessions.
>>
>> I’ll add this as a feature request.
>>
>> Alan
>>
>>
>> On Fri, Jun 5, 2020 at 5:52 PM Allen Sanderson <allen@sci.utah.edu> wrote:
>>>
>>> Thanks Alan and Jadie,
>>>
>>> I think for now the construction may be problematic. Here is what I would
>>> like to see but not sure how to get it and may not without a good
>>> reconstruction. But I would like to see is the difference from the mean
>>> on each original mesh. That should be possible, no?
>>>
>>> Cheers,
>>>
>>> Allen
>>>
>>>
>>>
>>>
>>>> On Jun 5, 2020, at 3:11 PM, Alan Morris <akenmorris@gmail.com> wrote:
>>>>
>>>> I found the documentation in a Studio PDF:
>>>>
>>>> -Max Angle:This is the largent angle between particle normals (from
>>>> respective sam-ples) permitted to label the particle as a good
>>>> corresponding particle across the given population, and is useful for
>>>> surface reconstruction.
>>>>
>>>> -Mesh Decimation:The PreView library code can decimate the number of
>>>> triangles to the value set here. The default is 0.30 or 30 percent.
>>>>
>>>> -# Clusters:To help speed up reconstruction, you can define how many
>>>> samples/clus-ters are used to warp their image volumed into the mean
>>>> space. 0 indicates to use all of the samples.
>>>>
>>>> -Run Reconstruction:Click this to run the reconstruction step. If it
>>>> fails, the iso-surface filter from the visualization toolkit (VTK) is
>>>> used instead to generate the finalsurface reconstructions. You can
>>>> re-run with different Optimizations as needed.
>>>>
>>>> -----------------
>>>> In general, you need a good correspondence for the surface
>>>> reconstruction to work well.
>>>>
>>>> Alan
>>>>
>>>>
>>>>
>>>> On Fri, Jun 5, 2020 at 2:31 PM Jadie Adams <jadieraeadams@gmail.com>
>>>> wrote:
>>>>>
>>>>> Hi Allen,
>>>>>
>>>>> From my understanding the initial surface is constructed just based on
>>>>> the particles which is why it looks so bad. If you hit Run
>>>>> Reconstruction it uses the distance transforms to reconstruct the
>>>>> surface which makes it look much better.
>>>>> The surfaces in the analyze part of Studio are just for visualization.
>>>>> You can always load your original mesh and the .particles file into a
>>>>> tool like Paraview to help visualize as well.
>>>>>
>>>>> @Alan do you know if the reconstruction parameters are documented
>>>>> anywhere?
>>>>>
>>>>> Thanks,
>>>>> Jadie
>>>>>
>>>>> On Fri, Jun 5, 2020 at 12:47 PM Allen Sanderson <allen@sci.utah.edu>
>>>>> wrote:
>>>>>>
>>>>>> Hi Jadie,
>>>>>>
>>>>>> Questions for you, after the optimization is completed and one goes to
>>>>>> the analysis there is an initial surface. I assumed that it was the
>>>>>> reconstructed surface. I got a really bad surface so I decided to
>>>>>> change the Max from 10 to 5 and got a much improved surface but still
>>>>>> not as expected.
>>>>>>
>>>>>> Would these results be expected?? and can you point me to any
>>>>>> documentation on the various parameters.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Allen
>>>>>>
>>>
>>
> <Group_Difference.mp4><groups.xml>

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• Re: [shapeworks-dev-support] initial surface after optimization, Alan Morris, 06/08/2020
  • Re: [shapeworks-dev-support] initial surface after optimization, Allen Sanderson, 06/08/2020
    • Re: [shapeworks-dev-support] initial surface after optimization, Alan Morris, 06/08/2020

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