// BPW -- this really doesn't have anything to do with "edgemate" but
// it's commonly called with check_symmetry_of_the_edge_mates(), and
// they're both disabled.
//
void count_fragment_and_edge_labels(Tfragment frags[],
Tedge edges[],
char comment[]) {
FILE *fout = stderr;
fprintf(stderr, "count_fragment_and_edge_labels()-- Disabled.\n");
return;
const int nsample=500;
const int nbucket=500;
IntFragment_ID nfrag = GetNumFragments(frags);
IntFragment_ID vid;
Histogram_t *frag_lab_histogram = create_histogram(nsample,nbucket,TRUE,FALSE);
fprintf(fout,"*** Histogram Fragment Labels <%s> ***\n",comment);
for(vid=0; vid<nfrag; vid++) {
const Tlab ilab = get_lab_fragment(frags,vid);
add_to_histogram(frag_lab_histogram, (int)ilab, NULL);
}
fprintf(fout,"Histogram of the fragment label \n");
print_histogram(fout,frag_lab_histogram, 0, 1);
free_histogram(frag_lab_histogram);
IntEdge_ID ie;
IntEdge_ID nedge = GetNumEdges(edges);
Histogram_t *inter_chunk_edge_nes_histogram = create_histogram(nsample,nbucket,TRUE,FALSE);
Histogram_t *intra_chunk_edge_nes_histogram = create_histogram(nsample,nbucket,TRUE,FALSE);
fprintf(fout,
"*** Histogram Edge Labels (2 edges/overlap) <%s> ***\n",
comment);
for(ie=0; ie<nedge; ie++) {
const Tnes nes = get_nes_edge(edges,ie);
const IntFragment_ID avx = get_avx_edge(edges,ie);
const IntFragment_ID bvx = get_bvx_edge(edges,ie);
const IntChunk_ID a_cid = get_cid_fragment(frags,avx);
const IntChunk_ID b_cid = get_cid_fragment(frags,bvx);
if( a_cid == b_cid ) {
add_to_histogram(intra_chunk_edge_nes_histogram, (int)nes, NULL);
} else {
add_to_histogram(inter_chunk_edge_nes_histogram, (int)nes, NULL);
}
}
fprintf(fout,"Histogram of the inter-chunk overlap labels \n");
print_histogram(fout,inter_chunk_edge_nes_histogram, 0, 1);
free_histogram(inter_chunk_edge_nes_histogram);
fprintf(fout,"Histogram of the intra-chunk overlap labels \n");
print_histogram(fout,intra_chunk_edge_nes_histogram, 0, 1);
free_histogram(intra_chunk_edge_nes_histogram);
}
int read_histograms_x (HISTOGRAM **phisto, int nhisto, const long *xcld_ids, int nxcld, IO_BUFFER *iobuf)
{
int mhisto, ihisto, rc, ncounts;
char title[256];
char type, cdummy;
long ident;
double rlower[2] = {0., 0.}, rupper[2] = {0., 0.},
rsum[2] = {0., 0.}, rtsum[2] = {0., 0.};
long ilower[2] = {0,0}, iupper[2] = {0,0}, isum[2] = {0,0}, itsum[2] = {0,0};
long entries=0, tentries=0, underflow[2] = {0,0}, overflow[2] = {0,0};
int nbins=0, nbins_2d=0, ibin, mbins[2] = {0,0};
HISTOGRAM *thisto=NULL, *ohisto=NULL;
IO_ITEM_HEADER item_header;
int adding = 0;
if ( nhisto < 0 )
{
adding = 1;
nhisto = -nhisto;
}
if ( iobuf == (IO_BUFFER *) NULL )
return -1;
item_header.type = 100;
if ( (rc = get_item_begin(iobuf,&item_header)) != 0 )
return rc;
if ( item_header.version < 1 || item_header.version > 2 )
{
Warning("Wrong version no. of histogram data to be read");
return -1;
}
// fprintf(stderr,"Read histograms called, with %d histograms excluded\n",nxcld);
mhisto = get_short(iobuf);
for (ihisto=0; ihisto<mhisto; ihisto++)
{
int add_this = 0, exclude_this = 0;
type = (char) get_byte(iobuf);
if ( get_string(title,sizeof(title)-1,iobuf) % 2 == 0 )
cdummy = get_byte(iobuf); // Compiler may warn about it but this is OK.
ident = get_long(iobuf);
nbins = (int) get_short(iobuf);
nbins_2d = (int) get_short(iobuf);
entries = (uint32_t) get_long(iobuf);
tentries = (uint32_t) get_long(iobuf);
underflow[0] = (uint32_t) get_long(iobuf);
overflow[0] = (uint32_t) get_long(iobuf);
if ( type == 'R' || type == 'r' || type == 'F' || type == 'D' )
{
rlower[0] = get_real(iobuf);
rupper[0] = get_real(iobuf);
rsum[0] = get_real(iobuf);
rtsum[0] = get_real(iobuf);
}
else
{
ilower[0] = get_long(iobuf);
iupper[0] = get_long(iobuf);
isum[0] = get_long(iobuf);
itsum[0] = get_long(iobuf);
}
if ( nbins_2d > 0 )
{
underflow[1] = (uint32_t) get_long(iobuf);
overflow[1] = (uint32_t) get_long(iobuf);
if ( type == 'R' || type == 'r' || type == 'F' || type == 'D' )
{
rlower[1] = get_real(iobuf);
rupper[1] = get_real(iobuf);
rsum[1] = get_real(iobuf);
rtsum[1] = get_real(iobuf);
}
else
{
ilower[1] = get_long(iobuf);
iupper[1] = get_long(iobuf);
isum[1] = get_long(iobuf);
itsum[1] = get_long(iobuf);
}
ncounts = nbins * nbins_2d;
}
else
ncounts = nbins;
/* Don't attempt to allocate histograms without data. */
if ( ncounts <= 0 )
continue;
if ( xcld_ids != (const long *) NULL && nxcld > 0 )
{
int ixcld;
for ( ixcld=0; ixcld<nxcld && xcld_ids[ixcld] > 0; ixcld++ )
{
if ( xcld_ids[ixcld] == ident )
{
exclude_this = 1;
break;
}
}
}
/* If the histogram has a numerical identifier delete a */
/* previously existing histogram with the same identifier. */
ohisto = NULL;
if ( ident != 0 )
{
if ( (ohisto=get_histogram_by_ident(ident)) !=
(HISTOGRAM *)NULL )
{
if ( adding && ! exclude_this )
add_this = 1;
else
free_histogram(ohisto);
}
}
/* (Re-) Allocate the new histogram according to its type. */
thisto = NULL;
// if ( ! exclude_this ) /* Would really exclude all histograms of this ID but we just don't want to add it up */
{
if ( nbins_2d > 0 )
{
if ( type == 'R' || type == 'r' )
thisto = alloc_2d_real_histogram(rlower[0],rupper[0],nbins,
rlower[1],rupper[1],nbins_2d);
else if ( type == 'F' || type == 'D' )
{
mbins[0] = nbins;
mbins[1] = nbins_2d;
thisto = allocate_histogram(&type,2,rlower,rupper,mbins);
}
else
thisto = alloc_2d_int_histogram(ilower[0],iupper[0],nbins,
ilower[1],iupper[1],nbins_2d);
}
else
{
if ( type == 'R' || type == 'r' )
thisto = alloc_real_histogram(rlower[0],rupper[0],nbins);
else if ( type == 'F' || type == 'D' )
thisto = allocate_histogram(&type,1,rlower,rupper,&nbins);
else
thisto = alloc_int_histogram(ilower[0],iupper[0],nbins);
}
}
/* If the allocation failed or the histogram should be excluded, skip the histogram contents. */
/* This should guarantee that reading the input doesn't get */
/* confused when there is not enough memory available to allocate */
/* a histogram. The drawback is that, so far, there is no failure */
/* indicator for the caller. */
if ( thisto == (HISTOGRAM *) NULL )
{
if ( type == 'F' || type == 'D' )
for (ibin=0; ibin<10; ibin++ )
(void) get_real(iobuf); /* contents... in histogram extension */
if ( tentries > 0 )
for (ibin=0; ibin<ncounts; ibin++)
(void) get_long(iobuf); /* long and real is the same length */
continue;
}
else
thisto->type = type;
/* Give the histogram its title and identifier. */
if ( *title )
describe_histogram(thisto,title,add_this?0:ident);
#ifdef _REENTRANT
histogram_lock(thisto);
#endif
/* Set the values for histogram statistics. */
thisto->entries = entries;
thisto->tentries = tentries;
thisto->underflow = underflow[0];
thisto->overflow = overflow[0];
if ( type == 'R' || type == 'r' || type == 'F' || type == 'D' )
{
thisto->specific.real.sum = rsum[0];
thisto->specific.real.tsum = rtsum[0];
}
else
{
thisto->specific.integer.sum = isum[0];
thisto->specific.integer.tsum = itsum[0];
}
if ( nbins_2d > 0 )
{
thisto->underflow_2d = underflow[1];
thisto->overflow_2d = overflow[1];
if ( type == 'R' || type == 'r' || type == 'F' || type == 'D' )
{
thisto->specific_2d.real.sum = rsum[1];
thisto->specific_2d.real.tsum = rtsum[1];
}
else
{
thisto->specific_2d.integer.sum = isum[1];
thisto->specific_2d.integer.tsum = itsum[1];
}
}
/* If wanted and possible, return the pointer to caller. */
if ( phisto != (HISTOGRAM **) NULL && ihisto < nhisto )
phisto[ihisto] = (add_this ? ohisto : thisto);
/* Finally, read the histogram contents. */
if ( type == 'F' || type == 'D' )
{
struct Histogram_Extension *he = thisto->extension;
he->content_all = get_real(iobuf);
he->content_inside = get_real(iobuf);
get_vector_of_real(he->content_outside,8,iobuf);
if ( type == 'F' )
{
if ( thisto->tentries > 0 )
for ( ibin=0; ibin<ncounts; ibin++ )
he->fdata[ibin] = (float) get_real(iobuf);
else
for ( ibin=0; ibin<ncounts; ibin++ )
he->fdata[ibin] = (float) 0.;
}
else
{
if ( thisto->tentries > 0 )
get_vector_of_real(he->ddata,ncounts,iobuf);
else
for ( ibin=0; ibin<ncounts; ibin++ )
he->ddata[ibin] = 0.;
}
}
else
{
if ( thisto->tentries > 0 )
get_vector_of_long((long *)thisto->counts,ncounts,iobuf);
else
for ( ibin=0; ibin<nbins; ibin++ )
thisto->counts[ibin] = 0;
}
#ifdef _REENTRANT
histogram_unlock(thisto);
#endif
if ( add_this )
{
// fprintf(stderr,"Adding histogram ID %ld\n", ident);
add_histogram(ohisto,thisto);
free_histogram(thisto);
}
}
if ( (rc = get_item_end(iobuf,&item_header)) != 0 )
return rc;
return(mhisto);
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *xset , *cset, *mset=NULL ;
int nopt=1 , method=PEARSON , do_autoclip=0 ;
int nvox , nvals , ii, jj, kout, kin, polort=1 ;
int ix1,jy1,kz1, ix2, jy2, kz2 ;
char *prefix = "degree_centrality" ;
byte *mask=NULL;
int nmask , abuc=1 ;
int all_source=0; /* output all source voxels 25 Jun 2010 [rickr] */
char str[32] , *cpt ;
int *imap = NULL ; MRI_vectim *xvectim ;
float (*corfun)(int,float *,float*) = NULL ;
/* djc - add 1d file output for similarity matrix */
FILE *fout1D=NULL;
/* CC - we will have two subbricks: binary and weighted centrality */
int nsubbriks = 2;
int subbrik = 0;
float * bodset;
float * wodset;
int nb_ctr = 0;
/* CC - added flags for thresholding correlations */
double thresh = 0.0;
double othresh = 0.0;
int dothresh = 0;
double sparsity = 0.0;
int dosparsity = 0;
/* variables for calculating degree centrality */
long * binaryDC = NULL;
double * weightedDC = NULL;
/* variables for histogram */
hist_node_head* histogram=NULL;
hist_node* hptr=NULL;
hist_node* pptr=NULL;
int bottom_node_idx = 0;
int totNumCor = 0;
long totPosCor = 0;
int ngoal = 0;
int nretain = 0;
float binwidth = 0.0;
int nhistnodes = 50;
/*----*/
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dDegreeCentrality [options] dset\n"
" Computes voxelwise weighted and binary degree centrality and\n"
" stores the result in a new 3D bucket dataset as floats to\n"
" preserve their values. Degree centrality reflects the strength and\n"
" extent of the correlation of a voxel with every other voxel in\n"
" the brain.\n\n"
" Conceptually the process involves: \n"
" 1. Calculating the correlation between voxel time series for\n"
" every pair of voxels in the brain (as determined by masking)\n"
" 2. Applying a threshold to the resulting correlations to exclude\n"
" those that might have arisen by chance, or to sparsify the\n"
" connectivity graph.\n"
" 3. At each voxel, summarizing its correlation with other voxels\n"
" in the brain, by either counting the number of voxels correlated\n"
" with the seed voxel (binary) or by summing the correlation \n"
" coefficients (weighted).\n"
" Practically the algorithm is ordered differently to optimize for\n"
" computational time and memory usage.\n\n"
" The threshold can be supplied as a correlation coefficient, \n"
" or a sparsity threshold. The sparsity threshold reflects the fraction\n"
" of connections that should be retained after the threshold has been\n"
" applied. To minimize resource consumption, using a sparsity threshold\n"
" involves a two-step procedure. In the first step, a correlation\n"
" coefficient threshold is applied to substantially reduce the number\n"
" of correlations. Next, the remaining correlations are sorted and a\n"
" threshold is calculated so that only the specified fraction of \n"
" possible correlations are above threshold. Due to ties between\n"
" correlations, the fraction of correlations that pass the sparsity\n"
" threshold might be slightly more than the number specified.\n\n"
" Regardless of the thresholding procedure employed, negative \n"
" correlations are excluded from the calculations.\n"
"\n"
"Options:\n"
" -pearson = Correlation is the normal Pearson (product moment)\n"
" correlation coefficient [default].\n"
#if 0
" -spearman = Correlation is the Spearman (rank) correlation\n"
" coefficient.\n"
" -quadrant = Correlation is the quadrant correlation coefficient.\n"
#else
" -spearman AND -quadrant are disabled at this time :-(\n"
#endif
"\n"
" -thresh r = exclude correlations <= r from calculations\n"
" -sparsity s = only use top s percent of correlations in calculations\n"
" s should be an integer between 0 and 100. Uses an\n"
" an adaptive thresholding procedure to reduce memory.\n"
" The speed of determining the adaptive threshold can\n"
" be improved by specifying an initial threshold with\n"
" the -thresh flag.\n"
"\n"
" -polort m = Remove polynomical trend of order 'm', for m=-1..3.\n"
" [default is m=1; removal is by least squares].\n"
" Using m=-1 means no detrending; this is only useful\n"
" for data/information that has been pre-processed.\n"
"\n"
" -autoclip = Clip off low-intensity regions in the dataset,\n"
" -automask = so that the correlation is only computed between\n"
" high-intensity (presumably brain) voxels. The\n"
" mask is determined the same way that 3dAutomask works.\n"
"\n"
" -mask mmm = Mask to define 'in-brain' voxels. Reducing the number\n"
" the number of voxels included in the calculation will\n"
" significantly speedup the calculation. Consider using\n"
" a mask to constrain the calculations to the grey matter\n"
" rather than the whole brain. This is also preferrable\n"
" to using -autoclip or -automask.\n"
"\n"
" -prefix p = Save output into dataset with prefix 'p', this file will\n"
" contain bricks for both 'weighted' or 'degree' centrality\n"
" [default prefix is 'deg_centrality'].\n"
"\n"
" -out1D f = Save information about the above threshold correlations to\n"
" 1D file 'f'. Each row of this file will contain:\n"
" Voxel1 Voxel2 i1 j1 k1 i2 j2 k2 Corr\n"
" Where voxel1 and voxel2 are the 1D indices of the pair of\n"
" voxels, i j k correspond to their 3D coordinates, and Corr\n"
" is the value of the correlation between the voxel time courses.\n"
"\n"
"Notes:\n"
" * The output dataset is a bucket type of floats.\n"
" * The program prints out an estimate of its memory used\n"
" when it ends. It also prints out a progress 'meter'\n"
" to keep you pacified.\n"
"\n"
"-- RWCox - 31 Jan 2002 and 16 Jul 2010\n"
"-- Cameron Craddock - 26 Sept 2015 \n"
) ;
PRINT_AFNI_OMP_USAGE("3dDegreeCentrality",NULL) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
mainENTRY("3dDegreeCentrality main"); machdep(); PRINT_VERSION("3dDegreeCentrality");
AFNI_logger("3dDegreeCentrality",argc,argv);
/*-- option processing --*/
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-time") == 0 ){
abuc = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-autoclip") == 0 ||
strcmp(argv[nopt],"-automask") == 0 ){
do_autoclip = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mask") == 0 ){
mset = THD_open_dataset(argv[++nopt]);
CHECK_OPEN_ERROR(mset,argv[nopt]);
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-pearson") == 0 ){
method = PEARSON ; nopt++ ; continue ;
}
#if 0
if( strcmp(argv[nopt],"-spearman") == 0 ){
method = SPEARMAN ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-quadrant") == 0 ){
method = QUADRANT ; nopt++ ; continue ;
}
#endif
if( strcmp(argv[nopt],"-eta2") == 0 ){
method = ETA2 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
prefix = strdup(argv[++nopt]) ;
if( !THD_filename_ok(prefix) ){
ERROR_exit("Illegal value after -prefix!") ;
}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-thresh") == 0 ){
double val = (double)strtod(argv[++nopt],&cpt) ;
if( *cpt != '\0' || val >= 1.0 || val < 0.0 ){
ERROR_exit("Illegal value (%f) after -thresh!", val) ;
}
dothresh = 1;
thresh = val ; othresh = val ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-sparsity") == 0 ){
double val = (double)strtod(argv[++nopt],&cpt) ;
if( *cpt != '\0' || val > 100 || val <= 0 ){
ERROR_exit("Illegal value (%f) after -sparsity!", val) ;
}
if( val > 5.0 )
{
WARNING_message("Sparsity %3.2f%% is large and will require alot of memory and time, consider using a smaller value. ", val);
}
dosparsity = 1 ;
sparsity = val ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-polort") == 0 ){
int val = (int)strtod(argv[++nopt],&cpt) ;
if( *cpt != '\0' || val < -1 || val > 3 ){
ERROR_exit("Illegal value after -polort!") ;
}
polort = val ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-mem_stat") == 0 ){
MEM_STAT = 1 ; nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-mem_profile",8) == 0 ){
MEM_PROF = 1 ; nopt++ ; continue ;
}
/* check for 1d argument */
if ( strcmp(argv[nopt],"-out1D") == 0 ){
if (!(fout1D = fopen(argv[++nopt], "w"))) {
ERROR_message("Failed to open %s for writing", argv[nopt]);
exit(1);
}
nopt++ ; continue ;
}
ERROR_exit("Illegal option: %s",argv[nopt]) ;
}
/*-- open dataset, check for legality --*/
if( nopt >= argc ) ERROR_exit("Need a dataset on command line!?") ;
xset = THD_open_dataset(argv[nopt]); CHECK_OPEN_ERROR(xset,argv[nopt]);
if( DSET_NVALS(xset) < 3 )
ERROR_exit("Input dataset %s does not have 3 or more sub-bricks!",argv[nopt]) ;
DSET_load(xset) ; CHECK_LOAD_ERROR(xset) ;
/*-- compute mask array, if desired --*/
nvox = DSET_NVOX(xset) ; nvals = DSET_NVALS(xset) ;
INC_MEM_STATS((nvox * nvals * sizeof(double)), "input dset");
PRINT_MEM_STATS("inset");
/* if a mask was specified make sure it is appropriate */
if( mset ){
if( DSET_NVOX(mset) != nvox )
ERROR_exit("Input and mask dataset differ in number of voxels!") ;
mask = THD_makemask(mset, 0, 1.0, 0.0) ;
/* update running memory statistics to reflect loading the image */
INC_MEM_STATS( mset->dblk->total_bytes, "mask dset" );
PRINT_MEM_STATS( "mset load" );
nmask = THD_countmask( nvox , mask ) ;
INC_MEM_STATS( nmask * sizeof(byte), "mask array" );
PRINT_MEM_STATS( "mask" );
INFO_message("%d voxels in -mask dataset",nmask) ;
if( nmask < 2 ) ERROR_exit("Only %d voxels in -mask, exiting...",nmask);
/* update running memory statistics to reflect loading the image */
DEC_MEM_STATS( mset->dblk->total_bytes, "mask dset" );
DSET_unload(mset) ;
PRINT_MEM_STATS( "mset unload" );
}
/* if automasking is requested, handle that now */
else if( do_autoclip ){
mask = THD_automask( xset ) ;
nmask = THD_countmask( nvox , mask ) ;
INFO_message("%d voxels survive -autoclip",nmask) ;
if( nmask < 2 ) ERROR_exit("Only %d voxels in -automask!",nmask);
}
/* otherwise we use all of the voxels in the image */
else {
nmask = nvox ;
INFO_message("computing for all %d voxels",nmask) ;
}
if( method == ETA2 && polort >= 0 )
WARNING_message("Polort for -eta2 should probably be -1...");
/* djc - 1d file out init */
if (fout1D != NULL) {
/* define affine matrix */
mat44 affine_mat = xset->daxes->ijk_to_dicom;
/* print command line statement */
fprintf(fout1D,"#Similarity matrix from command:\n#");
for(ii=0; ii<argc; ++ii) fprintf(fout1D,"%s ", argv[ii]);
/* Print affine matrix */
fprintf(fout1D,"\n");
fprintf(fout1D,"#[ ");
int mi, mj;
for(mi = 0; mi < 4; mi++) {
for(mj = 0; mj < 4; mj++) {
fprintf(fout1D, "%.6f ", affine_mat.m[mi][mj]);
}
}
fprintf(fout1D, "]\n");
/* Print image extents*/
THD_dataxes *xset_daxes = xset->daxes;
fprintf(fout1D, "#Image dimensions:\n");
fprintf(fout1D, "#[%d, %d, %d]\n",
xset_daxes->nxx, xset_daxes->nyy, xset_daxes->nzz);
/* Similarity matrix headers */
fprintf(fout1D,"#Voxel1 Voxel2 i1 j1 k1 i2 j2 k2 Corr\n");
}
/* CC calculate the total number of possible correlations, will be
usefule down the road */
totPosCor = (.5*((float)nmask))*((float)(nmask-1));
/** For the case of Pearson correlation, we make sure the **/
/** data time series have their mean removed (polort >= 0) **/
/** and are normalized, so that correlation = dot product, **/
/** and we can use function zm_THD_pearson_corr for speed. **/
switch( method ){
default:
case PEARSON: corfun = zm_THD_pearson_corr ; break ;
case ETA2: corfun = my_THD_eta_squared ; break ;
}
/*-- create vectim from input dataset --*/
INFO_message("vectim-izing input dataset") ;
/*-- CC added in mask to reduce the size of xvectim -- */
xvectim = THD_dset_to_vectim( xset , mask , 0 ) ;
if( xvectim == NULL ) ERROR_exit("Can't create vectim?!") ;
/*-- CC update our memory stats to reflect vectim -- */
INC_MEM_STATS((xvectim->nvec*sizeof(int)) +
((xvectim->nvec)*(xvectim->nvals))*sizeof(float) +
sizeof(MRI_vectim), "vectim");
PRINT_MEM_STATS( "vectim" );
/*--- CC the vectim contains a mapping between voxel index and mask index,
tap into that here to avoid duplicating memory usage ---*/
if( mask != NULL )
{
imap = xvectim->ivec;
/* --- CC free the mask */
DEC_MEM_STATS( nmask*sizeof(byte), "mask array" );
free(mask); mask=NULL;
PRINT_MEM_STATS( "mask unload" );
}
/* -- CC unloading the dataset to reduce memory usage ?? -- */
DEC_MEM_STATS((DSET_NVOX(xset) * DSET_NVALS(xset) * sizeof(double)), "input dset");
DSET_unload(xset) ;
PRINT_MEM_STATS("inset unload");
/* -- CC configure detrending --*/
if( polort < 0 && method == PEARSON ){
polort = 0; WARNING_message("Pearson correlation always uses polort >= 0");
}
if( polort >= 0 ){
for( ii=0 ; ii < xvectim->nvec ; ii++ ){ /* remove polynomial trend */
DETREND_polort(polort,nvals,VECTIM_PTR(xvectim,ii)) ;
}
}
/* -- this procedure does not change time series that have zero variance -- */
if( method == PEARSON ) THD_vectim_normalize(xvectim) ; /* L2 norm = 1 */
/* -- CC create arrays to hold degree and weighted centrality while
they are being calculated -- */
if( dosparsity == 0 )
{
if( ( binaryDC = (long*)calloc( nmask, sizeof(long) )) == NULL )
{
ERROR_message( "Could not allocate %d byte array for binary DC calculation\n",
nmask*sizeof(long));
}
/* -- update running memory estimate to reflect memory allocation */
INC_MEM_STATS( nmask*sizeof(long), "binary DC array" );
PRINT_MEM_STATS( "binaryDC" );
if( ( weightedDC = (double*)calloc( nmask, sizeof(double) )) == NULL )
{
if (binaryDC){ free(binaryDC); binaryDC = NULL; }
ERROR_message( "Could not allocate %d byte array for weighted DC calculation\n",
nmask*sizeof(double));
}
/* -- update running memory estimate to reflect memory allocation */
INC_MEM_STATS( nmask*sizeof(double), "weighted DC array" );
PRINT_MEM_STATS( "weightedDC" );
}
/* -- CC if we are using a sparsity threshold, build a histogram to calculate the
threshold */
if (dosparsity == 1)
{
/* make sure that there is a bin for correlation values that == 1.0 */
binwidth = (1.005-thresh)/nhistnodes;
/* calculate the number of correlations we wish to retain */
ngoal = nretain = (int)(((double)totPosCor)*((double)sparsity) / 100.0);
/* allocate memory for the histogram bins */
if(( histogram = (hist_node_head*)malloc(nhistnodes*sizeof(hist_node_head))) == NULL )
{
/* if the allocation fails, free all memory and exit */
if (binaryDC){ free(binaryDC); binaryDC = NULL; }
if (weightedDC){ free(weightedDC); weightedDC = NULL; }
ERROR_message( "Could not allocate %d byte array for histogram\n",
nhistnodes*sizeof(hist_node_head));
}
else {
/* -- update running memory estimate to reflect memory allocation */
INC_MEM_STATS( nhistnodes*sizeof(hist_node_head), "hist bins" );
PRINT_MEM_STATS( "hist1" );
}
/* initialize history bins */
for( kout = 0; kout < nhistnodes; kout++ )
{
histogram[ kout ].bin_low = thresh+kout*binwidth;
histogram[ kout ].bin_high = histogram[ kout ].bin_low+binwidth;
histogram[ kout ].nbin = 0;
histogram[ kout ].nodes = NULL;
/*INFO_message("Hist bin %d [%3.3f, %3.3f) [%d, %p]\n",
kout, histogram[ kout ].bin_low, histogram[ kout ].bin_high,
histogram[ kout ].nbin, histogram[ kout ].nodes );*/
}
}
/*-- tell the user what we are about to do --*/
if (dosparsity == 0 )
{
INFO_message( "Calculating degree centrality with threshold = %f.\n", thresh);
}
else
{
INFO_message( "Calculating degree centrality with threshold = %f and sparsity = %3.2f%% (%d)\n",
thresh, sparsity, nretain);
}
/*---------- loop over mask voxels, correlate ----------*/
AFNI_OMP_START ;
#pragma omp parallel if( nmask > 999 )
{
int lii,ljj,lin,lout,ithr,nthr,vstep,vii ;
float *xsar , *ysar ;
hist_node* new_node = NULL ;
hist_node* tptr = NULL ;
hist_node* rptr = NULL ;
int new_node_idx = 0;
double car = 0.0 ;
/*-- get information about who we are --*/
#ifdef USE_OMP
ithr = omp_get_thread_num() ;
nthr = omp_get_num_threads() ;
if( ithr == 0 ) INFO_message("%d OpenMP threads started",nthr) ;
#else
ithr = 0 ; nthr = 1 ;
#endif
/*-- For the progress tracker, we want to print out 50 numbers,
figure out a number of loop iterations that will make this easy */
vstep = (int)( nmask / (nthr*50.0f) + 0.901f ) ; vii = 0 ;
if((MEM_STAT==0) && (ithr == 0 )) fprintf(stderr,"Looping:") ;
#pragma omp for schedule(static, 1)
for( lout=0 ; lout < xvectim->nvec ; lout++ ){ /*----- outer voxel loop -----*/
if( ithr == 0 && vstep > 2 ) /* allow small dsets 16 Jun 2011 [rickr] */
{ vii++ ; if( vii%vstep == vstep/2 && MEM_STAT == 0 ) vstep_print(); }
/* get ref time series from this voxel */
xsar = VECTIM_PTR(xvectim,lout) ;
/* try to make calculation more efficient by only calculating the unique
correlations */
for( lin=(lout+1) ; lin < xvectim->nvec ; lin++ ){ /*----- inner loop over voxels -----*/
/* extract the voxel time series */
ysar = VECTIM_PTR(xvectim,lin) ;
/* now correlate the time series */
car = (double)(corfun(nvals,xsar,ysar)) ;
if ( car <= thresh )
{
continue ;
}
/* update degree centrality values, hopefully the pragma
will handle mutual exclusion */
#pragma omp critical(dataupdate)
{
/* if the correlation is less than threshold, ignore it */
if ( car > thresh )
{
totNumCor += 1;
if ( dosparsity == 0 )
{
binaryDC[lout] += 1; binaryDC[lin] += 1;
weightedDC[lout] += car; weightedDC[lin] += car;
/* print correlation out to the 1D file */
if ( fout1D != NULL )
{
/* determine the i,j,k coords */
ix1 = DSET_index_to_ix(xset,lii) ;
jy1 = DSET_index_to_jy(xset,lii) ;
kz1 = DSET_index_to_kz(xset,lii) ;
ix2 = DSET_index_to_ix(xset,ljj) ;
jy2 = DSET_index_to_jy(xset,ljj) ;
kz2 = DSET_index_to_kz(xset,ljj) ;
/* add source, dest, correlation to 1D file */
fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n",
lii, ljj, ix1, jy1, kz1, ix2, jy2, kz2, car);
}
}
else
{
/* determine the index in the histogram to add the node */
new_node_idx = (int)floor((double)(car-othresh)/(double)binwidth);
if ((new_node_idx > nhistnodes) || (new_node_idx < bottom_node_idx))
{
/* this error should indicate a programming error and should not happen */
WARNING_message("Node index %d is out of range [%d,%d)!",new_node_idx,
bottom_node_idx, nhistnodes);
}
else
{
/* create a node to add to the histogram */
new_node = (hist_node*)calloc(1,sizeof(hist_node));
if( new_node == NULL )
{
/* allocate memory for this node, rather than fiddling with
error handling here, lets just move on */
WARNING_message("Could not allocate a new node!");
}
else
{
/* populate histogram node */
new_node->i = lout;
new_node->j = lin;
new_node->corr = car;
new_node->next = NULL;
/* -- update running memory estimate to reflect memory allocation */
INC_MEM_STATS( sizeof(hist_node), "hist nodes" );
if ((totNumCor % (1024*1024)) == 0) PRINT_MEM_STATS( "hist nodes" );
/* populate histogram */
new_node->next = histogram[new_node_idx].nodes;
histogram[new_node_idx].nodes = new_node;
histogram[new_node_idx].nbin++;
/* see if there are enough correlations in the histogram
for the sparsity */
if ((totNumCor - histogram[bottom_node_idx].nbin) > nretain)
{
/* delete the list of nodes */
rptr = histogram[bottom_node_idx].nodes;
while(rptr != NULL)
{
tptr = rptr;
rptr = rptr->next;
/* check that the ptr is not null before freeing it*/
if(tptr!= NULL)
{
DEC_MEM_STATS( sizeof(hist_node), "hist nodes" );
free(tptr);
}
}
PRINT_MEM_STATS( "unloaded hist nodes - thresh increase" );
histogram[bottom_node_idx].nodes = NULL;
totNumCor -= histogram[bottom_node_idx].nbin;
histogram[bottom_node_idx].nbin=0;
/* get the new threshold */
thresh = (double)histogram[++bottom_node_idx].bin_low;
if(MEM_STAT == 1) INFO_message("Increasing threshold to %3.2f (%d)\n",
thresh,bottom_node_idx);
}
} /* else, newptr != NULL */
} /* else, new_node_idx in range */
} /* else, do_sparsity == 1 */
} /* car > thresh */
} /* this is the end of the critical section */
} /* end of inner loop over voxels */
} /* end of outer loop over ref voxels */
if( ithr == 0 ) fprintf(stderr,".\n") ;
} /* end OpenMP */
AFNI_OMP_END ;
/* update the user so that they know what we are up to */
INFO_message ("AFNI_OMP finished\n");
INFO_message ("Found %d (%3.2f%%) correlations above threshold (%f)\n",
totNumCor, 100.0*((float)totNumCor)/((float)totPosCor), thresh);
/*---------- Finish up ---------*/
/*if( dosparsity == 1 )
{
for( kout = 0; kout < nhistnodes; kout++ )
{
INFO_message("Hist bin %d [%3.3f, %3.3f) [%d, %p]\n",
kout, histogram[ kout ].bin_low, histogram[ kout ].bin_high,
histogram[ kout ].nbin, histogram[ kout ].nodes );
}
}*/
/*-- create output dataset --*/
cset = EDIT_empty_copy( xset ) ;
/*-- configure the output dataset */
if( abuc ){
EDIT_dset_items( cset ,
ADN_prefix , prefix ,
ADN_nvals , nsubbriks , /* 2 subbricks, degree and weighted centrality */
ADN_ntt , 0 , /* no time axis */
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_BUCK_TYPE ,
ADN_datum_all , MRI_float ,
ADN_none ) ;
} else {
EDIT_dset_items( cset ,
ADN_prefix , prefix ,
ADN_nvals , nsubbriks , /* 2 subbricks, degree and weighted centrality */
ADN_ntt , nsubbriks , /* num times */
ADN_ttdel , 1.0 , /* fake TR */
ADN_nsl , 0 , /* no slice offsets */
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_EPI_TYPE ,
ADN_datum_all , MRI_float ,
ADN_none ) ;
}
/* add history information to the hearder */
tross_Make_History( "3dDegreeCentrality" , argc,argv , cset ) ;
ININFO_message("creating output dataset in memory") ;
/* -- Configure the subbriks: Binary Degree Centrality */
subbrik = 0;
EDIT_BRICK_TO_NOSTAT(cset,subbrik) ; /* stat params */
/* CC this sets the subbrik scaling factor, which we will probably want
to do again after we calculate the voxel values */
EDIT_BRICK_FACTOR(cset,subbrik,1.0) ; /* scale factor */
sprintf(str,"Binary Degree Centrality") ;
EDIT_BRICK_LABEL(cset,subbrik,str) ;
EDIT_substitute_brick(cset,subbrik,MRI_float,NULL) ; /* make array */
/* copy measure data into the subbrik */
bodset = DSET_ARRAY(cset,subbrik);
/* -- Configure the subbriks: Weighted Degree Centrality */
subbrik = 1;
EDIT_BRICK_TO_NOSTAT(cset,subbrik) ; /* stat params */
/* CC this sets the subbrik scaling factor, which we will probably want
to do again after we calculate the voxel values */
EDIT_BRICK_FACTOR(cset,subbrik,1.0) ; /* scale factor */
sprintf(str,"Weighted Degree Centrality") ;
EDIT_BRICK_LABEL(cset,subbrik,str) ;
EDIT_substitute_brick(cset,subbrik,MRI_float,NULL) ; /* make array */
/* copy measure data into the subbrik */
wodset = DSET_ARRAY(cset,subbrik);
/* increment memory stats */
INC_MEM_STATS( (DSET_NVOX(cset)*DSET_NVALS(cset)*sizeof(float)), "output dset");
PRINT_MEM_STATS( "outset" );
/* pull the values out of the histogram */
if( dosparsity == 0 )
{
for( kout = 0; kout < nmask; kout++ )
{
if ( imap != NULL )
{
ii = imap[kout] ; /* ii= source voxel (we know that ii is in the mask) */
}
else
{
ii = kout ;
}
if( ii >= DSET_NVOX(cset) )
{
WARNING_message("Avoiding bodset, wodset overflow %d > %d (%s,%d)\n",
ii,DSET_NVOX(cset),__FILE__,__LINE__ );
}
else
{
bodset[ ii ] = (float)(binaryDC[kout]);
wodset[ ii ] = (float)(weightedDC[kout]);
}
}
/* we are done with this memory, and can kill it now*/
if(binaryDC)
{
free(binaryDC);
binaryDC=NULL;
/* -- update running memory estimate to reflect memory allocation */
DEC_MEM_STATS( nmask*sizeof(long), "binary DC array" );
PRINT_MEM_STATS( "binaryDC" );
}
if(weightedDC)
{
free(weightedDC);
weightedDC=NULL;
/* -- update running memory estimate to reflect memory allocation */
DEC_MEM_STATS( nmask*sizeof(double), "weighted DC array" );
PRINT_MEM_STATS( "weightedDC" );
}
}
else
{
/* add in the values from the histogram, this is a two stage procedure:
at first we add in values a whole bin at the time until we get to a point
where we need to add in a partial bin, then we create a new histogram
to sort the values in the bin and then add those bins at a time */
kout = nhistnodes - 1;
while (( histogram[kout].nbin < nretain ) && ( kout >= 0 ))
{
hptr = pptr = histogram[kout].nodes;
while( hptr != NULL )
{
/* determine the indices corresponding to this node */
if ( imap != NULL )
{
ii = imap[hptr->i] ; /* ii= source voxel (we know that ii is in the mask) */
}
else
{
ii = hptr->i ;
}
if ( imap != NULL )
{
jj = imap[hptr->j] ; /* ii= source voxel (we know that ii is in the mask) */
}
else
{
jj = hptr->j ;
}
/* add in the values */
if(( ii >= DSET_NVOX(cset) ) || ( jj >= DSET_NVOX(cset)))
{
if( ii >= DSET_NVOX(cset))
{
WARNING_message("Avoiding bodset, wodset overflow (ii) %d > %d\n (%s,%d)\n",
ii,DSET_NVOX(cset),__FILE__,__LINE__ );
}
if( jj >= DSET_NVOX(cset))
{
WARNING_message("Avoiding bodset, wodset overflow (jj) %d > %d\n (%s,%d)\n",
jj,DSET_NVOX(cset),__FILE__,__LINE__ );
}
}
else
{
bodset[ ii ] += 1.0 ;
wodset[ ii ] += (float)(hptr->corr);
bodset[ jj ] += 1.0 ;
wodset[ jj ] += (float)(hptr->corr);
}
if( fout1D != NULL )
{
/* add source, dest, correlation to 1D file */
ix1 = DSET_index_to_ix(cset,ii) ;
jy1 = DSET_index_to_jy(cset,ii) ;
kz1 = DSET_index_to_kz(cset,ii) ;
ix2 = DSET_index_to_ix(cset,jj) ;
jy2 = DSET_index_to_jy(cset,jj) ;
kz2 = DSET_index_to_kz(cset,jj) ;
fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n",
ii, jj, ix1, jy1, kz1, ix2, jy2, kz2, (float)(hptr->corr));
}
/* increment node pointers */
pptr = hptr;
hptr = hptr->next;
/* delete the node */
if(pptr)
{
/* -- update running memory estimate to reflect memory allocation */
DEC_MEM_STATS(sizeof( hist_node ), "hist nodes" );
/* free the mem */
free(pptr);
pptr=NULL;
}
}
/* decrement the number of correlations we wish to retain */
nretain -= histogram[kout].nbin;
histogram[kout].nodes = NULL;
/* go on to the next bin */
kout--;
}
PRINT_MEM_STATS( "hist1 bins free - inc into output" );
/* if we haven't used all of the correlations that are available, go through and
add a subset of the voxels from the remaining bin */
if(( nretain > 0 ) && (kout >= 0))
{
hist_node_head* histogram2 = NULL;
hist_node_head* histogram2_save = NULL;
int h2nbins = 100;
float h2binwidth = 0.0;
int h2ndx=0;
h2binwidth = (((1.0+binwidth/((float)h2nbins))*histogram[kout].bin_high) - histogram[kout].bin_low) /
((float)h2nbins);
/* allocate the bins */
if(( histogram2 = (hist_node_head*)malloc(h2nbins*sizeof(hist_node_head))) == NULL )
{
if (binaryDC){ free(binaryDC); binaryDC = NULL; }
if (weightedDC){ free(weightedDC); weightedDC = NULL; }
if (histogram){ histogram = free_histogram(histogram, nhistnodes); }
ERROR_message( "Could not allocate %d byte array for histogram2\n",
h2nbins*sizeof(hist_node_head));
}
else {
/* -- update running memory estimate to reflect memory allocation */
histogram2_save = histogram2;
INC_MEM_STATS(( h2nbins*sizeof(hist_node_head )), "hist bins");
PRINT_MEM_STATS( "hist2" );
}
/* initiatize the bins */
for( kin = 0; kin < h2nbins; kin++ )
{
histogram2[ kin ].bin_low = histogram[kout].bin_low + kin*h2binwidth;
histogram2[ kin ].bin_high = histogram2[ kin ].bin_low + h2binwidth;
histogram2[ kin ].nbin = 0;
histogram2[ kin ].nodes = NULL;
/*INFO_message("Hist2 bin %d [%3.3f, %3.3f) [%d, %p]\n",
kin, histogram2[ kin ].bin_low, histogram2[ kin ].bin_high,
histogram2[ kin ].nbin, histogram2[ kin ].nodes );*/
}
/* move correlations from histogram to histgram2 */
INFO_message ("Adding %d nodes from histogram to histogram2",histogram[kout].nbin);
while ( histogram[kout].nodes != NULL )
{
hptr = histogram[kout].nodes;
h2ndx = (int)floor((double)(hptr->corr - histogram[kout].bin_low)/(double)h2binwidth);
if(( h2ndx < h2nbins ) && ( h2ndx >= 0 ))
{
histogram[kout].nodes = hptr->next;
hptr->next = histogram2[h2ndx].nodes;
histogram2[h2ndx].nodes = hptr;
histogram2[h2ndx].nbin++;
histogram[kout].nbin--;
}
else
{
WARNING_message("h2ndx %d is not in range [0,%d) :: %.10f,%.10f\n",h2ndx,h2nbins,hptr->corr, histogram[kout].bin_low);
}
}
/* free the remainder of histogram */
{
int nbins_rem = 0;
for(ii = 0; ii < nhistnodes; ii++) nbins_rem+=histogram[ii].nbin;
histogram = free_histogram(histogram, nhistnodes);
PRINT_MEM_STATS( "free remainder of histogram1" );
}
kin = h2nbins - 1;
while (( nretain > 0 ) && ( kin >= 0 ))
{
hptr = pptr = histogram2[kin].nodes;
while( hptr != NULL )
{
/* determine the indices corresponding to this node */
if ( imap != NULL )
{
ii = imap[hptr->i] ;
}
else
{
ii = hptr->i ;
}
if ( imap != NULL )
{
jj = imap[hptr->j] ;
}
else
{
jj = hptr->j ;
}
/* add in the values */
if(( ii >= DSET_NVOX(cset) ) || ( jj >= DSET_NVOX(cset)))
{
if( ii >= DSET_NVOX(cset))
{
WARNING_message("Avoiding bodset, wodset overflow (ii) %d > %d\n (%s,%d)\n",
ii,DSET_NVOX(cset),__FILE__,__LINE__ );
}
if( jj >= DSET_NVOX(cset))
{
WARNING_message("Avoiding bodset, wodset overflow (jj) %d > %d\n (%s,%d)\n",
jj,DSET_NVOX(cset),__FILE__,__LINE__ );
}
}
else
{
bodset[ ii ] += 1.0 ;
wodset[ ii ] += (float)(hptr->corr);
bodset[ jj ] += 1.0 ;
wodset[ jj ] += (float)(hptr->corr);
}
if( fout1D != NULL )
{
/* add source, dest, correlation to 1D file */
ix1 = DSET_index_to_ix(cset,ii) ;
jy1 = DSET_index_to_jy(cset,ii) ;
kz1 = DSET_index_to_kz(cset,ii) ;
ix2 = DSET_index_to_ix(cset,jj) ;
jy2 = DSET_index_to_jy(cset,jj) ;
kz2 = DSET_index_to_kz(cset,jj) ;
fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n",
ii, jj, ix1, jy1, kz1, ix2, jy2, kz2, (float)(hptr->corr));
}
/* increment node pointers */
pptr = hptr;
hptr = hptr->next;
/* delete the node */
if(pptr)
{
free(pptr);
DEC_MEM_STATS(( sizeof(hist_node) ), "hist nodes");
pptr=NULL;
}
}
/* decrement the number of correlations we wish to retain */
nretain -= histogram2[kin].nbin;
histogram2[kin].nodes = NULL;
/* go on to the next bin */
kin--;
}
PRINT_MEM_STATS("hist2 nodes free - incorporated into output");
/* we are finished with histogram2 */
{
histogram2 = free_histogram(histogram2, h2nbins);
/* -- update running memory estimate to reflect memory allocation */
PRINT_MEM_STATS( "free hist2" );
}
if (nretain < 0 )
{
WARNING_message( "Went over sparsity goal %d by %d, with a resolution of %f",
ngoal, -1*nretain, h2binwidth);
}
}
if (nretain > 0 )
{
WARNING_message( "Was not able to meet goal of %d (%3.2f%%) correlations, %d (%3.2f%%) correlations passed the threshold of %3.2f, maybe you need to change the threshold or the desired sparsity?",
ngoal, 100.0*((float)ngoal)/((float)totPosCor), totNumCor, 100.0*((float)totNumCor)/((float)totPosCor), thresh);
}
}
INFO_message("Done..\n") ;
/* update running memory statistics to reflect freeing the vectim */
DEC_MEM_STATS(((xvectim->nvec*sizeof(int)) +
((xvectim->nvec)*(xvectim->nvals))*sizeof(float) +
sizeof(MRI_vectim)), "vectim");
/* toss some trash */
VECTIM_destroy(xvectim) ;
DSET_delete(xset) ;
if(fout1D!=NULL)fclose(fout1D);
PRINT_MEM_STATS( "vectim unload" );
if (weightedDC) free(weightedDC) ; weightedDC = NULL;
if (binaryDC) free(binaryDC) ; binaryDC = NULL;
/* finito */
INFO_message("Writing output dataset to disk [%s bytes]",
commaized_integer_string(cset->dblk->total_bytes)) ;
/* write the dataset */
DSET_write(cset) ;
WROTE_DSET(cset) ;
/* increment our memory stats, since we are relying on the header for this
information, we update the stats before actually freeing the memory */
DEC_MEM_STATS( (DSET_NVOX(cset)*DSET_NVALS(cset)*sizeof(float)), "output dset");
/* free up the output dataset memory */
DSET_unload(cset) ;
DSET_delete(cset) ;
/* force a print */
MEM_STAT = 1;
PRINT_MEM_STATS( "Fin" );
exit(0) ;
}
/* function for creating a sparse array from the thresholded
correlation matrix of a vectim.
This approach uses a histogram approach to implement a sparsity threshold if
it is so desired.
inputs:
xvectim: the input time courses that will be correlated
sparsity: the percentage of the top correlations that should be retained
threshold: a threshold that should be applied to determine if a correlation
should be retained. For sparsity thresholding this value will be used
as an initial guess to speed calculation and a higher threshold may
ultimately be calculated through the adaptive process.
output:
sparse_array_node: the list of remaining correlation values, or NULL if there
was an error
note:
this function can use a _lot_ of memory if you the sparsity is too high, we tell
the user how much memory we anticipate using, but this doesn't work for threshold only!*/
sparse_array_head_node* create_sparse_corr_array( MRI_vectim* xvectim, double sparsity, double thresh,
double (*corfun)(long,float*,float*), long mem_allowance )
{
/* random counters etc... */
long kout = 0;
/* variables for histogram */
hist_node_head* histogram=NULL;
sparse_array_head_node* sparse_array=NULL;
sparse_array_node* recycled_nodes=NULL;
long bottom_node_idx = 0;
long totNumCor = 0;
long totPosCor = 0;
long ngoal = 0;
long nretain = 0;
float binwidth = 0.0;
long nhistbins = 10000;
long mem_budget = 0;
/* retain the original threshold*/
double othresh = thresh;
/* set the memory budget from the allowance */
mem_budget = mem_allowance;
INFO_message( "Starting create_sparse_corr_array with a memory allowance of %ld", mem_budget);
/* calculate the total number of possible correlations */
totPosCor = .5 * ( xvectim->nvec -1 ) * ( xvectim->nvec );
/* create a head node for the sparse array */
sparse_array = (sparse_array_head_node*)calloc(1,sizeof(sparse_array_head_node));
if( sparse_array == NULL )
{
ERROR_message( "Could not allocate header for sparse array\n" );
return(NULL);
}
/* decrement the memory budget to account for the sparse array header */
mem_budget = mem_budget - sizeof(sparse_array_head_node);
/* check if we can do what is asked of us with the budget provided */
if( sparsity < 100.0 )
{
/* figure the cost of the histogram into the memory budget */
mem_budget = mem_budget - nhistbins*sizeof(hist_node_head);
/* and the number of desired correlations */
ngoal = nretain = (long)ceil(((double)totPosCor)*((double)sparsity) / 100.0);
/* check to see if we want to use more memory than would be used by the
full correlation matrix, if so, the we should probably just use full
correlation - or min memory func */
if((ngoal * sizeof( sparse_array_node )) > mem_budget)
{
WARNING_message( "The sparse array with %3.2lf%% of the %ld total"
" would exceed the memory budget (%3.2lf MB) refusing to proceed\n",
sparsity, totPosCor,((double)mem_budget)/(1024.0*1024.0));
return( NULL );
}
else
{
INFO_message( "The sparse array with %ld values will take %3.2lf"
" MB of memory (budget = %3.2lf MB)\n", ngoal,
(double)(ngoal * sizeof(sparse_array_node))
/(1024.0*1024.0), ((double)mem_budget)/(1024.0*1024.0));
}
}
else
{
WARNING_message( "Cannot pre-calculate the memory required for a sparse"
" matrix when only a correlation threshold is used. "
"Instead the mem is tracked and if we exceed what "
"would be used by the non-sparse array, the operation"
" will be aborted.");
}
INFO_message( "Extracting sparse correlation array with threshold = %f and"
" sparsity = %3.2f%% (%d)\n", thresh, sparsity, nretain);
/* if we are using a sparsity threshold, setup the histogram to sort the values */
if ( sparsity < 100.0 )
{
/* make sure that there is a bin for correlation values that == 1.0 */
binwidth = (1.005-thresh)/nhistbins;
/* allocate memory for the histogram bins */
if(( histogram = (hist_node_head*)malloc(nhistbins*sizeof(hist_node_head))) == NULL )
{
/* if the allocation fails, free all memory and exit */
ERROR_message( "Could not allocate %d byte array for histogram\n",
nhistbins*sizeof(hist_node_head));
return( NULL );
}
/* initialize history bins */
for( kout = 0; kout < nhistbins; kout++ )
{
histogram[ kout ].bin_low = thresh+kout*binwidth;
histogram[ kout ].bin_high = histogram[ kout ].bin_low+binwidth;
histogram[ kout ].nbin = 0;
histogram[ kout ].nodes = NULL;
histogram[ kout ].tail = NULL;
/*
INFO_message("Hist bin %d [%3.3f, %3.3f) [%d, %p]\n",
kout, histogram[ kout ].bin_low, histogram[ kout ].bin_high,
histogram[ kout ].nbin, histogram[ kout ].nodes );
*/
}
}
/*---------- loop over mask voxels, correlate ----------*/
AFNI_OMP_START ;
#pragma omp parallel if( xvectim->nvec > 999 )
{
int lii,ljj,lin,lout,ithr,nthr,vstep,vii ;
float *xsar , *ysar ;
sparse_array_node* new_node = NULL ;
int new_node_idx = 0;
double car = 0.0 ;
/*-- get information about who we are --*/
#ifdef USE_OMP
ithr = omp_get_thread_num() ;
nthr = omp_get_num_threads() ;
if( ithr == 0 ) INFO_message("%d OpenMP threads started",nthr) ;
#else
ithr = 0 ; nthr = 1 ;
#endif
/*-- For the progress tracker, we want to print out 50 numbers,
figure out a number of loop iterations that will make this easy */
vstep = (int)( xvectim->nvec / (nthr*50.0f) + 0.901f ) ; vii = 0 ;
if(ithr == 0 ) fprintf(stderr,"Looping:") ;
#pragma omp for schedule(static, 1)
for( lout=0 ; lout < xvectim->nvec ; lout++ )
{ /*----- outer voxel loop -----*/
if( ithr == 0 && vstep > 2 ) /* allow small dsets 16 Jun 2011 [rickr] */
{
vii++;
if( vii%vstep == vstep/2 )
{
vstep_print();
}
}
/* if the amount of memory exceeds budget, dont do anything more */
if ( mem_budget >= 0 )
{
/* get ref time series from this voxel */
xsar = VECTIM_PTR(xvectim,lout);
/* try to make calculation more efficient by only calculating the unique
correlations */
for( lin=(lout+1) ; lin < xvectim->nvec ; lin++ )
{ /*----- inner loop over voxels -----*/
if ( mem_budget >= 0 )
{
/* extract the voxel time series */
ysar = VECTIM_PTR(xvectim,lin);
/* now correlate the time series */
car = (double)(corfun(xvectim->nvals,xsar,ysar));
if ( car < thresh )
{
continue;
}
#pragma omp critical(dataupdate)
{
/* the threshold might have changed while we were waiting,
so check it again */
if (car >= thresh )
{
/* create a node to add to the histogram, try to use a
recycled node to save time and memory */
if ( recycled_nodes == NULL )
{
mem_budget = mem_budget - sizeof(sparse_array_node);
if( mem_budget >= 0 )
{
new_node = (sparse_array_node*)calloc(1,sizeof(sparse_array_node));
}
else
{
new_node = NULL;
}
}
else
{
new_node = recycled_nodes;
recycled_nodes = recycled_nodes->next;
new_node->next = NULL;
}
if( new_node == NULL )
{
/* allocate memory for this node, rather than fiddling with
error handling here, lets just move on */
WARNING_message("Could not allocate a new node!");
}
else
{
new_node->weight = car;
new_node->row = lout;
new_node->column = lin;
totNumCor += 1;
/* if keeping all connections, just add to linked list */
if ( sparsity >= 100.0 )
{
new_node->next = sparse_array->nodes;
sparse_array->nodes = new_node;
sparse_array->num_nodes = sparse_array->num_nodes + 1;
new_node = NULL;
}
/* otherwise, populate to proper bin of histogram */
else
{
/* determine the index in the histogram to add the node */
new_node_idx = (int)floor((double)(car-othresh)/(double)binwidth);
if ((new_node_idx > nhistbins) || (new_node_idx < bottom_node_idx))
{
/* this error should indicate a programming error and should not happen */
/*WARNING_message("Node index %d (%3.4lf >= %3.4lf) is out of range [%d,%d)"
" {[%3.4lf, %3.4lf)}!",new_node_idx, car, thresh, bottom_node_idx,
nhistbins, histogram[bottom_node_idx].bin_low,
histogram[bottom_node_idx].bin_high ); */
}
else
{
/* populate histogram node */
new_node->row = lout;
new_node->column = lin;
new_node->weight = car;
new_node->next = NULL;
/* update histogram bin linked-list */
new_node->next = histogram[new_node_idx].nodes;
histogram[new_node_idx].nodes = new_node;
/* if first node in bin, point tail to node */
if (histogram[new_node_idx].tail == NULL)
{
histogram[new_node_idx].tail = new_node;
}
/* increment bin count */
histogram[new_node_idx].nbin++;
/* see if there are enough correlations in the histogram
for the sparsity - prune un-needed hist bins*/
while ((totNumCor - histogram[bottom_node_idx].nbin) > nretain)
{
/* push the histogram nodes onto the list of recycled nodes, it could be
that this hist bin is empty, in which case we have nothing to add */
if( histogram[bottom_node_idx].tail != NULL )
{
histogram[bottom_node_idx].tail->next = recycled_nodes;
recycled_nodes = histogram[bottom_node_idx].nodes;
}
else
{
if( histogram[bottom_node_idx].nbin != 0 )
{
WARNING_message("Trying to remove histogram bin that contains"
" %d values, but whose tail pointer is NULL\n",
histogram[bottom_node_idx].nbin);
}
}
/* bookkeeping */
histogram[bottom_node_idx].nodes = NULL;
histogram[bottom_node_idx].tail = NULL;
totNumCor -= histogram[bottom_node_idx].nbin;
histogram[bottom_node_idx].nbin = 0;
/* get the new threshold */
thresh = (double)histogram[++bottom_node_idx].bin_low;
/*INFO_message("Increasing threshold to %3.2f (%d)\n",
thresh,bottom_node_idx); */
} /* while */
} /* else, new_node_idx in range */
} /* else, sparsity >= 100.0 */
} /* else, new_node != NULL */
} /* if (car >= thresh ) */
} /* this is the end of the critical section */
} /* if ( mem_budget >= 0 ) */
} /* end of inner loop over voxels */
} /* if ( mem_budget >= 0 ) */
} /* end of outer loop over ref voxels */
if( ithr == 0 ) fprintf(stderr,".\n") ;
} /* end OpenMP */
AFNI_OMP_END ;
/* check to see if we exceeded memory or didn't get any
correlations > threshold */
if (( mem_budget < 0 ) || ( totNumCor == 0 ))
{
if ( mem_budget < 0 )
{
ERROR_message( "Memory budget (%lf MB) exceeded, consider using a"
"higher correlation or lower sparsity threshold",
((double)mem_allowance/(1024.0*1024.0)));
}
else
{
ERROR_message( "No correlations exceeded threshold, consider using"
" a lower correlation threshold");
}
sparse_array = free_sparse_array( sparse_array );
}
else
{
/* if using sparsity threshold, construct sparse array from
the histogram */
if ( sparsity < 100.0 )
{
/* pull the requested number of nodes off of the histogram */
for ( kout = (nhistbins-1); kout >= bottom_node_idx; kout-- )
{
if((histogram[ kout ].nodes != NULL ) &&
(histogram[ kout ].nbin > 0))
{
if( histogram[ kout ].tail == NULL )
{
ERROR_message("Head is not null, but tail is?? (%ld)\n",
kout);
}
/* push the list onto sparse array */
histogram[ kout ].tail->next = sparse_array->nodes;
sparse_array->nodes = histogram[ kout ].nodes;
/* increment the number of nodes */
sparse_array->num_nodes = sparse_array->num_nodes +
histogram[ kout ].nbin;
/* remove the references from the histogram,
this is super important considering we don't want
to accidently free any nodes that are on the sparse_array
when we free the histogram later */
histogram[ kout ].nodes = NULL;
histogram[ kout ].tail = NULL;
histogram[ kout ].nbin = 0;
}
/* dont take more than we want */
if ( sparse_array->num_nodes > nretain ) break;
}
INFO_message( "Sparsity requested %ld and received %ld correlations"
" (%3.2lf%% sparsity) final threshold = %3.4lf.\n",
nretain, sparse_array->num_nodes,
100.0*((double)sparse_array->num_nodes)/((double)totPosCor),
thresh);
if( sparse_array->num_nodes < nretain )
{
INFO_message( "Consider lowering the initial correlation"
"threshold (%3.2lf) to retain more correlations.\n",
othresh);
}
}
else
{
INFO_message( "Correlation threshold (%3.2lf) resulted in %ld"
" correlations (%3.2lf%% sparsity).\n", thresh,
sparse_array->num_nodes,
100.0*((double)sparse_array->num_nodes)/((double)totPosCor));
}
}
/* free residual mem */
histogram = free_histogram( histogram, nhistbins );
recycled_nodes = free_sparse_list( recycled_nodes );
return( sparse_array );
}