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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
>> >>>
>>
>

Attachment: Group_Difference.mp4
Description: video/mp4

<distance_transform_files>
ellipsoid_9_DT.nrrd
ellipsoid_8_DT.nrrd
ellipsoid_7_DT.nrrd
ellipsoid_6_DT.nrrd
ellipsoid_5_DT.nrrd
ellipsoid_4_DT.nrrd
ellipsoid_3_DT.nrrd
ellipsoid_2_DT.nrrd
ellipsoid_1_DT.nrrd
</distance_transform_files>

<local_point_files>
ellipsoid_9.dt.local.particles
ellipsoid_8.dt.local.particles
ellipsoid_7.dt.local.particles
ellipsoid_6.dt.local.particles
ellipsoid_5.dt.local.particles
ellipsoid_4.dt.local.particles
ellipsoid_3.dt.local.particles
ellipsoid_2.dt.local.particles
ellipsoid_1.dt.local.particles
</local_point_files>

<world_point_files>
ellipsoid_9.dt.world.particles
ellipsoid_8.dt.world.particles
ellipsoid_7.dt.world.particles
ellipsoid_6.dt.world.particles
ellipsoid_5.dt.world.particles
ellipsoid_4.dt.world.particles
ellipsoid_3.dt.world.particles
ellipsoid_2.dt.world.particles
ellipsoid_1.dt.world.particles
</world_point_files>

<point_files>
ellipsoid_9.dt.world.particles
ellipsoid_8.dt.world.particles
ellipsoid_7.dt.world.particles
ellipsoid_6.dt.world.particles
ellipsoid_5.dt.world.particles
ellipsoid_4.dt.world.particles
ellipsoid_3.dt.world.particles
ellipsoid_2.dt.world.particles
ellipsoid_1.dt.world.particles
</point_files>

<group_ids>
  1
  1
  1
  1
  1
  1
  1
  1
  2
</group_ids>

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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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