On Oct 28, 2020, at 3:17 PM, Alan Morris <amorris@sci.utah.edu> wrote:

Hi Shireen,  Allen,

Great feedback Allen.  I've added the following issues:

https://github.com/SCIInstitute/ShapeWorks/issues/800

https://github.com/SCIInstitute/ShapeWorks/issues/801

> When running a python script to launchShapeWorksStudio the parameterDictionary used to runShapeWorksOptimize should optionally be passed in as well so that the optimize values are populated for the Particle System Parameters. This way if one saves the Project the optimize values are saved as well.

Yes, this is planned.  We will get there when the new Project file format is integrated in with the python and optimizer.

The studio_mesh branch will load VTK files (will add other formats later).  Lots of things won't work, it's still preliminary.  Don't be surprised if it crashes when you push certain buttons.  You must 'skip' the grooming step.  I think all of the optimization stuff will work properly.  Surface reconstruction will crash right now.

I'll look at the layout with Group Boxes.

For these parameters :

recompute_regularization_interval -> Yes, this needs to be added.  There are some issue with it (see https://github.com/SCIInstitute/ShapeWorks/issues/802)

save splits

checkpointing

I'm still planning to add a more comprehensive checkpointing and replay feature to Studio and the command line tools.

Thanks,

Alan

On Wed, Oct 28, 2020 at 1:43 PM Shireen Elhabian <shireen@sci.utah.edu> wrote:

Forwarding this to the dev support email list. Thanks Allen for the feedback. @Alan please find useful comments for Studio interface below. Could you also point Allen to the branch where studio can load meshes? studio_mesh?

Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor, School of Computing
Research Computer Scientist, 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

From: Allen Sanderson <allen@sci.utah.edu>

Subject: Suggestions

Date: October 27, 2020 at 3:01:48 PM MDT

To: shapeworks-dev@sci.utah.edu

Hi,

I am back working with the latest versions and have some suggestions for the SWStudio UI.

The orientation cube is very helpful. Except not all data is medical data. As such, the L/R S/I P/A does not make sense for those cases. In the Preferences it would be nice to have three options, Axis: “None” “Triad” and “Cube.”  The triad would have XYZ along each axis. It would even be nice to be able to locate it to any of the four corners.

When running a python script to launchShapeWorksStudio the parameterDictionary used to runShapeWorksOptimize should optionally be passed in as well so that the optimize values are populated for the Particle System Parameters. This way if one saves the Project the optimize values are saved as well. 

When working with meshes I get the following error:

ERROR: Error during mesh construction:

Exception: /Projects/ShapeWorks/ShapeWorks/dependencies/install/include/ITK-5.0/itkImageFileReader.hxx:136:

 Could not create IO object for reading file /Projects/Data/Sandia/SurfaceOnlyTest/example1_srf_only_00.triangles.ply

  Tried to create one of the following:

    BMPImageIO

    BioRadImageIO

    Bruker2dseqImageIO

    GDCMImageIO

    GE4ImageIO

    GE5ImageIO

    GiplImageIO

    HDF5ImageIO

    JPEGImageIO

    JPEG2000ImageIO

    LSMImageIO

    MINCImageIO

    MRCImageIO

    MetaImageIO

    NiftiImageIO

    NrrdImageIO

    PNGImageIO

    StimulateImageIO

    TIFFImageIO

    VTKImageIO

  You probably failed to set a file suffix, or

    set the suffix to an unsupported type.

Further messages will be suppressed

I am assuming the SWStudio is not quite fully functional with meshes.

The Optimize UI could use some sprucing up using Group Box with Check Box.

<Screen Shot 2020-10-27 at 2.14.40 PM.png>

See the bottom two group box examples in the first image:  https://doc.qt.io/qt-5/qtwidgets-widgets-groupbox-example.html

It would be nice to be able to set all of the optimization parameters in the UI:

recompute_regularization_interval

save splits

checkpointing

etc.

Also all of the inputs need to have tooltips. 

I noticed that the documentation (http://sciinstitute.github.io/ShapeWorks/workflow/optimize.html) has incorporated the inter- an intra- nomenclature. This addition is very helpful (at least for me). And the overall improvements are very helpful.

Cheers,

Allen

Allen Sanderson

SCI Institute

University of Utah