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A graph library for Matlab based on the boost graph library

Home Page: http://dgleich.github.com/matlab-bgl

C 14.29% C++ 62.72% MATLAB 22.20% Shell 0.30% Batchfile 0.33% Makefile 0.16%

matlab-bgl's Introduction

MatlabBGL

A C library wrapping the Boost graph library and a Matlab wrapper for the Boost graph library.

Features

  • Wrappers around most of the Boost graph library functions
  • Copy-free implementations of many graph algorithms on Matlab's native sparse matrix type.
  • Works effeciently on huge problems

Synopsis

[coming soon]

Installation

Ideally, you download, unzip and it works. Reality is almost never ideal though.

There are some fantastic instructions from others on how to compile here. https://answers.launchpad.net/matlab-bgl/+question/69161

License

Matlab code: BSD libmbgl code: GPLv2

Copyright David F. Gleich, 2006-2011

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matlab-bgl's Issues

Investigate 64-bit integers in max-flow

Hi,
I am working on minimum cut problem with a large data set. In my problem, I have a constraint that a node will not be in the minimum cut unless some perticular blocks are in cut. I fixed those constraints by putting a infinite capacity arcs ( by giving a large numeric value like 9.9e+17) from those nodes to its precedence nodes. I have total 230000 nodes in total. When I am running the push relable algorithm I am getting follwoing warning:
"Warning: The rounded (unrounded) value of the minimum cut is -2147483648 (1.2969e+017),but
the value of the max-flow is 371223564. These values should be equal "

I am sure that the minimum cut providing after this warning is not the true minimum cut. I have tried by reduceing the value of the infinite capacity arcs value. On that case the progrm is running without warning but it is not respect my constraints.

Could you plese help me to solve this problem.
If you need more information I am ready to provide.

With regards,

Matlab error in Computing Edge-Betweenness Centrality

Hello
I'm trying to calculate the betweenness centrality for all edges in an adjacency matrix. I download matlabbgl from https://www.cs.purdue.edu/homes/dgleich/packages/matlab_bgl/ that includes betweenness_centrality.m file and unzip it to a directory. Then I open matlab and change directory until I get to the directory where I unzipped matlabbgl.

Well I'm not 100% sure, but I think that this can be my solution. However, I'm still new to matlab and can't get the code running very well. when I call betweenness centrality with a sparse matrix argument in another file and run it, the matlab gives error :

Undefined function 'betweenness_centrality_mex' for input arguments of type 'double'.
Error in betweenness_centrality (line 110)
bc = betweenness_centrality_mex(A,weight_arg);

OS is Windows 7 enterprise 64-bit and Matlab 2013a
Any help is highly appreciated. I'm currently writing my thesis and desperately need betweenness for my network :) Thanks a lot!!!

kuratowski_subgraph crashes on R2008b

The kuratowski_subgraph function crashes Matlab R2008b completely. This occurs because the mex file allocates 3n-6 entries of memory, but the output graph takes 3n-6+1 entries.

max_flow() error on Matlab R2018b and windows 10

Hello
the max_flow() will report an error when running max_flow_example saying that there is no such function or method called max_flow_mex(). The c and mexw64 files called max_flow_mex dont seem to work even if I put them in the folder where max_flow.m is. Could I get some help with it? Thank you

Problem in matlab-bgl testing

Dear,
Thanks a lot for previous answer in (https://answers.launchpad.net/matlab-bgl/+question/280846) to my question.
When I installed BGL package and test that, I see the below error, please help me to solve that:

addpath H:\thesis\simulation\matlab-bgl-master
clustering_coefficients(sparse(ones(5)))
Undefined function or variable 'clustering_coefficients_mex'.

Error in clustering_coefficients (line 99)
ccfs=clustering_coefficients_mex(A,options.undirected,weight_arg);

OS is Windows 10 enterprise 64-bit
Matlab 2015a

kuratowski_subgraph fails on R2010b

The Kuratowski example fails when libmbgl is compiled with g++-4.1 and the matlab files are mexed with g++-4.3.

A = clique_graph([3,3]); % Generate K_3,3
K = kuratowski_subgraph(A);
isequal(A,K) % K_3,3 is a Kuratowski graph!

inconsistent history comment formatting

The history information in the files is inconsistent. The format should be:

for C/C++ files:
/** History

  • yyyy-mm-dd: Note
    */

and

for Matlab files:
%% History
% yyyy-mm-dd: Note
%%

inplace function error

Hello Dear
Thanks a lot for previous guidance and response.
When I run function that use inplace, I see below error please guide me to solve that:
[d dt pred] = bfs_in_mbgl_efficient(A,1);
Undefined function or variable 'inplace'.

Error in ipdouble (line 9)
ip = inplace(a);

Error in bfs_in_mbgl_efficient (line 13)
ip_d = ipdouble(-ones(num_vertices(A),1));

Best regard

c file not recognized : 'matlab_bgl_sp_mex'

Hello,

Thank you for creating this algorithm! I downloaded it because it seems to be a dependency for the code of directional connectivity index (DCI). I want to calculate the DCI for a riparian ecosystem in two directions (along the river axis and perpendicular to the river axis).

I'm new to Matlab, but I get this error when running the code:

Error in shortest_paths (line 131)
[d pred] =
matlab_bgl_sp_mex(A,u,target,lower(options.algname),options.inf,...

Error in DCIu (line 29)
d = shortest_paths(distance, start_nodes(ii)); %A vector
of the shortest path between starting/source node and
all other nodes

Error in connectivity_at_angle (line 117)
fval = DCIu(distance, dx, pixelx)

the 'matlab_bgl_sp_mex.c' function seems to be written in c, and Matlab doesn't recognize it. There should be a matlab_bgl_sp_mex.h file associated to it?

Thank you for any help!
Meghana

Causing MATLAB shuts down

The most simplified script to make this problem reappear:

x = zeros(2);
x = sparse(x);
c = clustering_coefficients(x);

It doesn't raise an error, instead, MATLAB shuts down.

compilation issues of libmbgl with boost 1.47 and gcc 4.6.2 in archlinux

  1. some things changed in boost.
    a. boost/property_map.hpp no longer exsits. Change to boost/property_map/property_map.hpp seems work.
    b. boost/graph/edmunds_karp_max_flow.hpp is deprecated,boost/graph/edmonds_karp_max_flow.hpp should be used.Function edmunds_karp_max_flow is changed to edmonds_karp_max_flow.Maybe function names in libmbgl should also use edmonds instead of edmunds.
  2. A const version of reverse_edge_pmap_helper::operator[] in max_flow.cc is needed or compilation fails.
  3. shortest_paths.cc and layouts.cc can not be compiled.I cannot tell the reasons.

Unrecognized function or variable 'planar_test_mex'.

Hello,

I installed the matlabBGL package from Matlab add-ons, but I cannot use the planarity testing algorithm. I got:

Unrecognized function or variable 'planar_test_mex'.

Error in boyer_myrvold_planarity_test (line 41)
    is_planar = planar_test_mex(A,0);

I am using Mac with MATLAB R2021a. Does anyone know why this happens? Thanks!

qpssvm_mex

hello,
i had a error like below:
Error in qpssvm (line 82)
[x,exitflag,t,access,History] = qpssvm_mex(H,f,b,uint16(I),x0,...

and i couldn't run the demo.m file

Help need

When , I install BLG package and test, I see the below error, please guide me:

addpath H:\thesis\simulation\matlab-bgl-master
clustering_coefficients(sparse(ones(5)))
Undefined function or variable 'clustering_coefficients_mex'.

Error in clustering_coefficients (line 99)
ccfs=clustering_coefficients_mex(A,options.undirected,weight_arg);

MEX file errors - matlab_bgl_sp_mex.c (macOS Monterey 12.5.1)

Hi,

Thanks for setting all of this up. I am seeking to use the BGL library for calculating directional connectivity index (DCI) on a binary matrix. I have successfully downloaded and unzipped the package folder, but I get an error message when I seek to compile the matlab_bgl_sp_mex.c file. I seek to compile the mex script with:

mex matlab_bgl_sp_mex.c -lmwlapack -lmwblas

And I get the error string below. It is a lot of text, but I figure maybe necessary to establish what is wrong. Apologies for any newbie misunderstanding.



Building with 'Xcode with Clang'.
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:246:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,initialize_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:247:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,discover_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:248:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:249:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,finish_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:251:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_edge,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:252:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_relaxed,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:253:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_relaxed,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:255:36: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp_visitor(n, ja, ia, a,
                                   ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:190:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:255:40: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp_visitor(n, ja, ia, a,
                                       ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:190:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:257:20: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
                d, (mwIndex
)pred, dinf, d_vis);
                   ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:192:27: note: passing argument to parameter 'pred' here
    double
d, mbglIndex *pred, double dinf,
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:261:28: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp(n, ja, ia, a,
                           ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:185:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:261:32: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp(n, ja, ia, a,
                               ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:185:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:263:20: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
                d, (mwIndex
)pred, dinf);
                   ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:187:27: note: passing argument to parameter 'pred' here
    double
d, mbglIndex *pred, double dinf);
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:275:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,initialize_vertex,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:277:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_edge,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:278:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_relaxed,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:279:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_relaxed,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:280:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_minimized,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:281:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_minimized,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:283:40: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp_visitor(n, ja, ia, a,
                                       ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:201:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:283:44: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp_visitor(n, ja, ia, a,
                                           ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:201:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:285:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex
)pred, dinf, bf_vis);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:203:27: note: passing argument to parameter 'pred' here
    double
d, mbglIndex *pred, double dinf,
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:289:32: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp(n, ja, ia, a,
                               ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:196:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:289:36: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp(n, ja, ia, a,
                                   ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:196:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:291:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex
)pred, dinf);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:198:27: note: passing argument to parameter 'pred' here
    double
d, mbglIndex *pred, double dinf);
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:298:19: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
        dag_sp(n, ja, ia, a,
                  ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:207:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:298:23: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
        dag_sp(n, ja, ia, a,
                      ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:207:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:300:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex
)pred, dinf);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:209:27: note: passing argument to parameter 'pred' here
    double
d, mbglIndex *pred, double dinf);
                          ^
28 warnings generated.

Error using mex
Undefined symbols for architecture x86_64:
  "_bellman_ford_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_bellman_ford_sp_visitor", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dag_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dijkstra_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dijkstra_sp_visitor", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)


Thanks!
-Daniel Kozar
PhD Student
UC Davis

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