Hi all,

I am new to ShapeWorks and is having troubles to get it working. I downloaded the executables for windows (since I cannot find the source code I assume it is sufficient) and tried to run it on my own dataset (.vtk format).

My problem is simple: nothing comes up. I wrote a .params file (and a .xml as well) similar to the one in the torus example, add the folder to my system path, cd to the data folder and run

..\ShapeWorksGroom ID.preprocess1.params isolate hole_fill center auto_crop  (note I only changed the name of parameter file and names of input and output files inside)
just like in the example. However, nothing happens.
(I mean there are no output files, and it does not feel like running anyrthing)

But if I only type in

..\ShapeWorksGroom

Then the prompt returns a string of the usage of ShapeWorksGroom, so I know it recognize the command.

I think there may be some steps I am missing. Any ideas?

P.S.: I also tried to type in some random strings behind ..\ShapeWorksGroom, something like

..\ShapeWorksGroom sfdvgsbvdsf

And the outcome was the same, no output, no error prompt, nothing. Hope this information helps.

Thanks in advance.

Regards,
Long

Hi Long

At present, ShapeWorks does not support data in .vtk format.
ShapeWorksGroom works with binary surfaces in an ITK-reader-friendly format (e.g. .NRRD or .MHA). i'm afraid you may need to scan convert your .vtk meshes into an ITK compatible format...

HTH
Regards
manasi

P.S. please use the XML parameter files. the "params" version is not supported any more.

Hi Manasi,

Thanks for the reply. This time re-make the .mha models (and verified them by viewing them in another software), wrote a .xml file, and run again.

Still no good. Nothing comes up, not even an error prompt. Just like how it was.

A question: Does ShapeWorks throw any exceptions or any other bits of info to help me track the problem?

Hi Long

A command line like: ShapeWorksGroom preprocess.xml
will not work unless at least one filter is specified. Please try a command line like: ShapeWorksGroom preprocess.xml isolate
and let me know if that does not work...

Please not that this version of ShapeWorks is not a professional piece of code, and may not have exceptions/error messages defined for every situation.

HTH
Regards
manasi

Hi Manasi,

No it doesn't. I suspect I made some mistakes in writing up my .xml, so I uploaded it here.

The data files are named ID5x.mha, in the same folder as the .xml.

Thanks a lot Manasi. You are a star :)

Regards,
Long

Hi Long

The parameter file you attached is not in XML format !
Please look at the attached file for details...

HTH
Regards
manasi

To Manasi,

Thanks a lot! After (learning and) rewriting my xml file I finally got the thing running. It would have taken me forever if it wasn't you.

By the way, I think the developers should really consider rewriting the manual... much of the things inside had changed.

And for anyone who clicked at the attachment above, you may see an error page. This is normal, since the xml file seems to have a syntax error. This error shows up in my xml editor, the file cannot be displayed correctly in web browser, but works for the purpose.


Thanks again Manasi!

Regards,
Long

Me again. This time "missing transform file parameter" for the command "center". What parameter does it take? I cannot find it in manual.

Cheers,
Long

Hi Long

i thought we updated the XML parameter files in the Torus example with all the parameters. But i'll double-check that, and also work on the documentation.

Meanwhile, the parameter you are looking for is: < transform_file > filename < / transform_file >
of course, no spaces in the tag :)

HTH
Thanks for your patience !
Regards
manasi

Talking of the Torus example, I didn't seem to see it anywhere.
=========
Oh I found it. Hidden so well...

Did anyone ever encounter a problem with the center and auto_crop command? While running these command with my binary volumes, I came across a "failure to allocate memory" error. Checking the prompt, I saw something like:

Reading xxx.mha...
ImageRegion (00B9F708)
Dimension: 3
Index: [213 213 46]
Size: [4294967083, 4294967083, 4294967025]

What is in the Index field matches my volume size, but the field in "Size" does not make any sense, and is different from what I saw in the torus example. I guess it miscalculate something. Any ideas?