int main(int argc, char * argv[]) {
FSLIO *fslio;
FSLIO *fslioOutput;
void *buffer;
void *outputBuffer;
size_t buffsize;
char *inputpath = NULL;
char *outputpath = NULL;
char *maskpath = NULL;
int x=-1, y=-1, z=-1, t=0;
short xDim, yDim, zDim, vDim;
size_t pixtype;
short dt;
float inter = 0.0, slope = 1.0;
BOOL verbose = FALSE;
int threads = 1;
int ac;
if( argc < 2 ) {
rsMaskPrintHelp();
return 1;
}
/* parse parameters */
for( ac = 1; ac < argc; ac++ ) {
if( ! strncmp(argv[ac], "-h", 2) ) {
rsMaskPrintHelp();
return 1;
} else if ( ! strcmp(argv[ac], "-input") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -input\n");
return 1;
}
inputpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strncmp(argv[ac], "-m", 2) ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -m[ask]\n");
return 1;
}
maskpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strncmp(argv[ac], "-v", 2) ) {
verbose = TRUE;
} else if ( ! strcmp(argv[ac], "-output") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -output\n");
return 1;
}
outputpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strcmp(argv[ac], "-threads") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -threads\n");
return 1;
}
threads = atoi(argv[ac]); /* no string copy, just pointer assignment */
} else {
fprintf(stderr, "\nError, unrecognized command %s\n", argv[ac]);
}
}
rsSetThreadsNum(threads);
if ( inputpath == NULL ) {
fprintf(stderr, "No input volume specified!\n");
return 1;
}
if ( outputpath == NULL ) {
fprintf(stderr, "No output volume specified!\n");
return 1;
}
if ( maskpath == NULL ) {
fprintf(stderr, "A binary mask must be specified!\n");
return 1;
}
if ( verbose ) {
fprintf(stdout, "Input file: %s\n", inputpath);
fprintf(stdout, "Mask file: %s\n", maskpath);
fprintf(stdout, "Output file: %s\n", outputpath);
}
// Load file
/* open input file */
fslio = FslOpen(inputpath, "rb");
if (fslio == NULL) {
fprintf(stderr, "\nError, could not read header info for %s.\n", inputpath);
return 1;
}
/* determine dimensions */
FslGetDim(fslio, &xDim, &yDim, &zDim, &vDim);
if ( verbose ) {
fprintf(stdout, "Dim: %d %d %d (%d Volumes)\n", xDim, yDim, zDim, vDim);
}
if (fslio->niftiptr->scl_slope != 0) {
slope = fslio->niftiptr->scl_slope;
inter = fslio->niftiptr->scl_inter;
}
/* determine datatype and initalize buffer */
pixtype = FslGetDataType(fslio, &dt);
/* prepare centrality file */
fslioOutput = FslOpen(outputpath, "wb");
if (fslioOutput == NULL) {
fprintf(stderr, "\nError, could not read header info for %s.\n", outputpath);
return 1;
}
FslCloneHeader(fslioOutput, fslio);
FslSetDim(fslioOutput, xDim, yDim, zDim, vDim);
FslSetDimensionality(fslioOutput, 4);
FslSetDataType(fslioOutput, dt);
char *callString = rsMergeStringArray(argc, argv);
rsWriteNiftiHeader(fslioOutput, callString);
free(callString);
/* load mask */
unsigned long nPoints = 0L;
double ***mask = d3matrix(zDim-1, yDim-1, xDim-1);
Point3D *maskPoints = rsReadMask(maskpath, xDim, yDim, zDim, &nPoints, NULL, fslio, mask);
if ( maskPoints == NULL) {
fprintf(stderr, "\nError: Mask invalid.\n");
FslClose(fslio);
FslClose(fslioOutput);
return 1;
}
// Prepare buffer
buffsize = rsGetBufferSize(xDim, yDim, zDim, vDim, dt);
buffer = malloc(buffsize);
outputBuffer = malloc(buffsize);
if (buffer == NULL || outputBuffer == NULL) {
fprintf(stdout, "Not enough free memory :-(\n");
return 1;
}
FslReadVolumes(fslio, buffer, vDim);
rsResetBufferToValue(dt, outputBuffer, slope, inter, xDim, yDim, zDim, vDim, log(-1));
long p;
#pragma omp parallel num_threads(rsGetThreadsNum()) private(p) shared(buffer,fslio)
{
#pragma omp for schedule(guided, 1)
for (p = 0L; p<nPoints; p++) {
const Point3D *point = &maskPoints[p];
double *pointValues = (double*)malloc(sizeof(double)*vDim);
rsExtractTimecourseFromBuffer(dt, pointValues, buffer, slope, inter, point, xDim, yDim, zDim, vDim);
rsWriteTimecourseToBuffer(dt, pointValues, outputBuffer, slope, inter, point, xDim, yDim, zDim, vDim);
free(pointValues);
}
}
/* write output */
free(buffer);
FslWriteVolumes(fslioOutput, outputBuffer, vDim);
FslClose(fslioOutput);
free(outputBuffer);
free(fslioOutput);
free(maskPoints);
}
int main()
{
int i,z,d,w;
int billID, wordID, freq;
double sum;
double likelihood[10];
FILE *fp1 = fopen("../data/Bill_Term", "r");
FILE *fp2 = fopen("../data/Term_Bill", "r");
FILE *fpwrite = fopen("../Result/result6479/10topic_NoSeeds_zw", "w");
FILE *fpwrite2 = fopen("../Result/result6479/10topic_NoSeeds_zd", "w");
// initialize
double **n_dw1 = dmatrix(N_Bill_Term, 3);
double **n_dw2 = dmatrix(N_Bill_Term, 3);
double ***p_z_d = d3matrix(10, K, D);
double ***p_w_z = d3matrix(10, V, K);
// initialize n(d,w), p(z|d), p(w|z)
i = 0;
while (!feof(fp1))
{
fscanf(fp1, "%d\t%d\t%d\n", &billID, &wordID, &freq);
// n_dw[billID-1][wordID-1] = freq;
n_dw1[i][0] = billID;
n_dw1[i][1] = wordID;
n_dw1[i][2] = freq;
i++;
}
printf("%s%d\n%s%d\n", "i = ", i, "N_Bill_Term = ", N_Bill_Term);
i = 0;
while (!feof(fp2))
{
fscanf(fp2, "%d\t%d\t%d\n", &billID, &wordID, &freq);
n_dw2[i][0] = wordID;
n_dw2[i][1] = billID;
n_dw2[i][2] = freq;
i++;
}
printf("%s%d\n%s%d\n", "i = ", i, "N_Bill_Term = ", N_Bill_Term);
srand((unsigned)time(NULL));
for (i = 0; i < 10; i++)
{
for (d = 0; d < D; d++)
{
for (z = 0; z < K; z++)
p_z_d[i][z][d] = rand() / (double)RAND_MAX; // p(z|d)
// Normalization
sum = 0;
for (z = 0; z < K; z++)
sum += p_z_d[i][z][d];
if (sum != 0)
for (z = 0; z < K; z++)
p_z_d[i][z][d] /= sum;
else
printf("%s\n", "Need initialize again.");
sum = 0;
for (z = 0; z < K; z++)
sum += p_z_d[i][z][d];
if (fabs(sum-1)>0.0001) printf("%s\n", "abs(sum-1)>0.0001, Need initialize again.");
}
}
for (i = 0; i < 10; i++)
{
for (z = 0; z < K; z++)
{
for (w = 0; w < V; w++)
p_w_z[i][w][z] = rand() / (double)RAND_MAX; // p(w|z)
//Normalization
sum = 0;
for (w = 0; w < V; w++)
sum += p_w_z[i][w][z];
if (sum != 0)
for (w = 0; w < V; w++)
p_w_z[i][w][z] /= sum;
else
printf("%s\n", "Need initialize again.");
sum = 0;
for (w = 0; w < V; w++)
sum += p_w_z[i][w][z];
if (fabs(sum-1)>0.0001) printf("%s\n", "abs(sum-1)>0.0001, Need initialize again.");
}
}
// select the best one, after 50 iterations
for (i = 0; i < 10; i++)
{
printf("%s%d\n", "Initialization ", i);
pLSA(n_dw1, n_dw2, p_w_z[i], p_z_d[i], 50);
likelihood[i] = calLikelihood(n_dw1, p_z_d[i], p_w_z[i]);
printf("%s%d%s%f\n", "Likelihood", i, " is ", likelihood[i]);
}
int ml = 0;
for (i = 1; i < 10; i++)
if (likelihood[i] > likelihood[ml])
ml = i;
printf("%s%d\n", "ml = ", ml);
pLSA(n_dw1, n_dw2, p_w_z[ml], p_z_d[ml], 450);
// output
printf("%s\n", "Writing to file...");
// d: person, z: topic, w: bill
// topic-word
printf("%s\n", "p(w|z)");
for (z = 0; z < K; z++)
{
sum = 0;
for (w = 0; w < V; w++)
{
sum += p_w_z[ml][w][z];
fprintf(fpwrite, "%.12lf", p_w_z[ml][w][z]);
if (w != V-1)
fprintf(fpwrite, "%s", "\t");
}
printf("%lf\n", sum);
fprintf(fpwrite, "%s", "\n");
}
// topic-bill
printf("%s\n", "p(z|d)");
for (z = 0; z < K; z++)
{
for (d = 0; d < D; d++)
{
fprintf(fpwrite2, "%.12lf", p_z_d[ml][z][d]);
if (d != D-1)
fprintf(fpwrite2, "%s", "\t");
}
fprintf(fpwrite2, "%s", "\n");
}
// clear
fclose(fp1);
fclose(fp2);
fclose(fpwrite);
fclose(fpwrite2);
free_dmatrix(n_dw1, N_Bill_Term);
free_dmatrix(n_dw2, N_Bill_Term);
free_d3matrix(p_z_d, 10, K);
free_d3matrix(p_w_z, 10, V);
return 0;
}
