eegkno / Spharm

Installation of Spharm-mat and Spharm-pdm on OSX Yosemite

Installation of Spharm toolkit in MacOS

Tested on:

• OS X El Capitan version 10.11.6
• Matlab 2016b, 64-bit

Download, Installation and Tutorial

SPHARM-MAT http://imaging.indyrad.iupui.edu/projects/SPHARM/?page_id=22

Spharm-pdm https://www.nitrc.org/projects/spharm-pdm/

SPHARM-MAT Tutorial http://imaging.indyrad.iupui.edu/projects/SPHARM/SPHARM-docs/C01_Introduction.html

PRE-INSTALL

1. Setup mex: To setup, you need a C/C++ compiler. In the MATLAB Command Window, type:

mex -setup C

INSTALL SPHARM-MAT-v1-0-0

1. Go to the directory of the library (SpharmMatDir):

cd SpharmMatDir/code/C_sources

2. Compile compile simple.c

mex simple.c

If this warning is generated:

simple.c:485:3: warning: implicitly declaring library function 'memset' with type 'void *(void , int, unsigned long)' [-Wimplicit-function-declaration] memset(comp_table,0,MAX_COMPsizeof(int));

include the following headers in the file simple.c:

#include <string.h> /* memset */ #include <unistd.h> /* close */

3. compile LocalSmoothing.c

mex LocalSmoothing.c -lmwlapack -lmwblas

4. Add to Matlab the path of the new files SpharmMatDir/code/C_sources NOTE: I tried to copy the new mex files to SpharmMatDir/code, but for some reason, Matlab doesn't find them. LocalSmoothing.mexa64 LocalSmoothing.mexw32 simple.mexa64 simple.mexw32

5. Test SPHARM-MAT according to the manual. Source: http://www.iu.edu/~spharm/SPHARM-docs/C02_Data_Preparation.html#data-preparation

Matlab could display errors related to the function: [path, name, ext, ver] = fileparts(file);

This function returns 4 parameters. The last one (ver) needs to be removed from all the files in the source code. Now the function should look like

[path, name, ext] = fileparts(file);

6. To use SPHARM-MAT-v1-0-0 + Spharm-pdm

I downloaded the version 1.8 for Mac (MacOSX_10.5.8.zip). Source: https://www.nitrc.org/frs/?group_id=308

Add the path of the SPHARM-PDM according to the "install SPHARM-PDM" of the SPHARM-MAT manual

/home/user/MATLAB/Spharm_2/SPHARM-PDM-v10.5.8

##Troubleshooting

Error

union (line 106) Invalid input. Valid flags are 'rows', 'stable', 'sorted', 'legacy'.

Solution: In the file initParamCALD change

indDif = union(indDif1, indDif2, indDif3); to indDif = union(indDif1, indDif2);

Error

Error using  ./
Matrix dimensions must agree.
Error in get_vertexnormals (line 42)
vnorm = vnorm./vnlen(:,[1 1 1]);

Solution: The function get(p,'VertexNormals'); in get_vertexnormals.m doesn't return anything. Instead of it, I downloaded the function patchnormals() from https://www.mathworks.com/matlabcentral/fileexchange/24330-patch-normals.

The compiled mex file is included within SpharmMatDir/code/C_sources, a directory that was already in the MATLAB PATH (see step 4)

The code in get_vertexnormals(vs,fs) was modified as follows:

function vnorm = get_vertexnormals(vs,fs)
	f = figure;
    p = patch('vertices',vs,'faces',fs);
    %vnorm = - get(p,'VertexNormals');
    FV.vertices = p.Vertices;
    FV.faces = p.Faces;
    vnorm = - patchnormals(FV);
    vnlen = sqrt(sum(vnorm.^2,2));
    vnorm = vnorm./vnlen(:,[1 1 1]);
    vnlen = sqrt(sum(vnorm.^2,2));
    close(f);
return;

Error: SPHARM-MAT-v1-0-0 + Spharm-pdm

The new version of Spharm-pdm uses the functions SegPostProcessCLP and GenParaMeshCLP, but when they are invoked from SPHARM-MAT, it calls to the functions SegPostProcess and GenParaMesh that are deprecated. In order to have everything working togueter, it is necessary to do some changes in the files of SPHARM-MAT.

1. Install Spharm-pdm according to http://imaging.indyrad.iupui.edu/projects/SPHARM/SPHARM-docs/C01_Introduction.html#install-spharm-pdm
2. Change the call of the funtions

SegPostProcess to SegPostProcessCLP GenParaMesh to GenParaMeshCLP ParaToSPHARMMesh to ParaToSPHARMMeshCLP

in the files * SPHARM-MAT-v1-0-0/code/SpharmMatUtilBatchJobs.m * SPHARM-MAT-v1-0-0/code/initOptions.m * initParamCALD 3. Since the SegPostProcessCLP and GenParaMeshCLP are new versions, they have different flags used at the moment of the invokation, so in the file SpharmMatUtilTopologyFix.m it is necessary to change the lines:

from optionSTR=[optionSTR '-o' new_name]; to optionSTR=[optionSTR ' ' new_name];