[Dune-devel] Update on psurface

[Oliver Sander]

Hi Xiaoxue,
thanks for the update.  I just had another look at your code.

 >
> 1. The hdf5 file generated from amiramesh file are twice as large as the original file. Oliver suggest that moving out the redundant data in hdf5.  So I add a base hdf5 writer that store as much data
> as amiraio does. You can choose which hdf5 output type psurface_convert write using commend line options.

That seems to work only partly. The help message offers me three options  -t b, -t r, -t w.  However:

sander at affe:~/psurface_convert$ ./psurface_convert -i femur_distal_15mm.am -o femur.h5 -t w
the option need a value/nsander at affe:~/psurface_convert$

I suppose you put a /n in a string instead of \n.

But what is the value that is asked for?



> 2. Write the vtu writer that did not write planar graph into vtu. The output vtu file only display  base grid triangle.   You can also control it using line options.
>
> 3.  I modified the hdf5 writer so that the output h5 file have similar structure with amiramesh. I used to store x coordinate, y coordinate and z coordinate in 3 different arrays. Now I use on array
> to store them.

Hmm, I was really expecting hdf5 to support multidimensional arrays.  So instead of

X_1
Y_1
Z_1
X_2
Y_2
Z_2
X_3
...

one should have

X_1 Y_1 Z_1
X_2 Y_2 Z_2
X_3 ...

in the file.  Is that not possible?

As the next step we should get the new hdf5 files into dune-grid.  That should be very easy.
Can you please do the following: [I'll send you all necessary files in a separate mail]

- Install UG
- Install dune-grid, and make sure it builds UGGrid and AmiraMesh support.
- Add the test program that I'll send you.  It reads a grid from a file, and a PSurface
   boundary description from a second file.  Then the grid is refined once, and the result
   written to vtk.  That way, you can see whether the boundary parametrization works.
- Loading the PSurface object is done in a method 'read' in the file psurfaceboundary.hh.
   Currently, this method only supports AmiraMesh files.  Please extend this method to
   a) detect whether the file is an amiramesh file or an hdf5 file
   b) Read the PSurface object from hdf5 in the latter case

This should be pretty easy, as all the heavy lifting is already done in psurface itself.


Best,
Oliver


>
> Best,
> Xiaoxue
>
>
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