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Hi Shireen,

In my experience downsampled volumes didn't proceed any faster than full
sized ones. But anyways, the full resolution execution finished. Increasing
the iterations made it much longer, but results are more consistent, so
that's good.

I am wondering if you can elaborate a bit more on the Procrustes fitting done
in SW.

I see in the log file the setting were:
m_procrustes_interval = 0
m_recompute_regularization_interval = 1
m_procrustes_scaling = 1
m_adaptivity_mode = 0
m_keep_checkpoints = 0

I thought when Procrustes interval is set to 0, it doesn't do Procrustes
alignment. Am I mistaken?
If they are indeed Procrustes aligned, what are the coordinates reported? Are
they the tangent approximations? If I take do a SVD of the reported
coordinates, I get a very different result of shape variance decomposition
than SW reports. Below is the first 10 from SW

mode 0 : 1359.87, 33.5901%, 33.5901%
mode 1 : 599.133, 14.7992%, 48.3893%
mode 2 : 359.544, 8.88109%, 57.2704%
mode 3 : 265.742, 6.56408%, 63.8344%
mode 4 : 216.873, 5.35698%, 69.1914%
mode 5 : 191.874, 4.73947%, 73.9309%
mode 6 : 166.742, 4.11869%, 78.0496%
mode 7 : 112.695, 2.78369%, 80.8333%
mode 8 : 71.9164, 1.77641%, 82.6097%
mode 9 : 70.1653, 1.73315%, 84.3428%
mode 10 : 64.4909, 1.59299%, 85.9358%

what I get is:
75.3%
1.33%
1.254%
...

I appreciate any insight you can provide.
Best,
M



-----Original Message-----
From: Shireen Elhabian [mailto:shireen@sci.utah.edu]
Sent: Monday, February 22, 2016 10:24 AM
To: shapeworks-users@sci.utah.edu; Murat Maga
Subject: Re: [shapeworks-users] Downsampling groomed volumes

Hi Murat,

It would be the volume size ... reducing it will hugely speed things up ...
however, you might want at least to visual QC the downsampled volumes to make
sure that this step didn't introduce holes in the resulting shapes or eroded
thin structures ....

best regards
Shireen

On 02/22/2016 11:19 AM, Murat Maga wrote:
> Hello,
>
> After three days of non-stop crunching on 32 core system with openMP,
> particle distribution hasn't finished yet (it still has two more splits to
> go). I don't want to cancel the job but I also need some results to take a
> look for an upcoming conference.
>
> I am wondering if I can simply down sample groomed files and submit a new
> job with the new parameters? Or stated differently, what would have more
> impact on the compute time at the particle distribution stage? The size of
> the volume or specific parameters (shown below)?
>
> <iterations_per_split>1000</iterations_per_split>
> <starting_regularization>100</starting_regularization>
> <ending_regularization>0.1</ending_regularization>
> <number_of_particles>1024</number_of_particles>
> <optimization_iterations>5000</optimization_iterations>
>
> Best,
> M

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• [shapeworks-users] Downsampling groomed volumes, Murat Maga, 02/22/2016
  • Re: [shapeworks-users] Downsampling groomed volumes, Shireen Elhabian, 02/22/2016
    • RE: [shapeworks-users] Downsampling groomed volumes, Murat Maga, 02/24/2016
      • Re: [shapeworks-users] Downsampling groomed volumes, Shireen Elhabian, 02/25/2016

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