static void
erl_init(int ncpu)
{
init_benchmarking();
#ifdef ERTS_SMP
erts_system_block_init();
#endif
erts_init_monitors();
erts_init_gc();
erts_init_time();
erts_init_sys_common_misc();
erts_init_process(ncpu);
erts_init_scheduling(use_multi_run_queue,
no_schedulers,
no_schedulers_online);
erts_init_cpu_topology(); /* Must be after init_scheduling */
H_MIN_SIZE = erts_next_heap_size(H_MIN_SIZE, 0);
BIN_VH_MIN_SIZE = erts_next_heap_size(BIN_VH_MIN_SIZE, 0);
erts_init_trace();
erts_init_binary();
erts_init_bits();
erts_init_fun_table();
init_atom_table();
init_export_table();
init_module_table();
init_register_table();
init_message();
erts_bif_info_init();
erts_ddll_init();
init_emulator();
erts_bp_init();
init_db(); /* Must be after init_emulator */
erts_bif_timer_init();
erts_init_node_tables();
init_dist();
erl_drv_thr_init();
init_io();
init_copy();
init_load();
erts_init_bif();
erts_init_bif_chksum();
erts_init_bif_binary();
erts_init_bif_re();
erts_init_unicode(); /* after RE to get access to PCRE unicode */
erts_delay_trap = erts_export_put(am_erlang, am_delay_trap, 2);
erts_late_init_process();
#if HAVE_ERTS_MSEG
erts_mseg_late_init(); /* Must be after timer (erts_init_time()) and thread
initializations */
#endif
#ifdef HIPE
hipe_mode_switch_init(); /* Must be after init_load/beam_catches/init */
#endif
packet_parser_init();
erl_nif_init();
}
TSPsolver::TSPsolver(unsigned cities, unsigned amount_col)
{
amount_cities = cities;
W1 = 0.5;
W2 = 0.1;
init_chaotic(cities);
init_X_randomly(cities);
init_dist(amount_col);
}
void resolve(t_list *list, int ant)
{
int value;
t_list *l;
l = list;
value = 1;
init_dist(list);
valid_start(list);
((t_salle*)list->content)->dist = 0;
give_value((t_salle*)list->content);
while (l != NULL)
{
if (((t_salle *)l->content)->name[0] == 'L')
ft_error();
l = l->next;
}
if (ant <= 0)
ft_error();
omg(list, value, ant);
}
BITMAP *vecwrap_init_dist(int vec_mode, Params *p, BITMAP *a, BITMAP *b, BITMAP *ann, BITMAP *bmask, RegionMasks *region_masks, RegionMasks *amask, BITMAP *ann_sim) {
if (vec_mode == VEC_MODE_PATCH) {
return init_dist(p, a, b, ann, bmask, region_masks, amask);
}
else if (vec_mode == VEC_MODE_DESC) {
VECBITMAP<unsigned char> *av = bitmap_to_patches(p, a);
VECBITMAP<unsigned char> *bv = bitmap_to_patches(p, b);
VECBITMAP<int> *ans = vec_init_dist<unsigned char, int>(p, av, bv, ann, bmask, region_masks, amask);
delete av;
delete bv;
BITMAP *ansd = vecbitmap_to_bitmap(ans);
delete ans;
return ansd;
}
else if (vec_mode == VEC_MODE_SIM) {
if (!ann_sim) { fprintf(stderr, "vecwrap_init_dist: expected argument ann_sim\n"); exit(1); }
return sim_init_dist(p, a, b, ann, ann_sim);
}
else {
fprintf(stderr, "vecwrap_init_dist: unknown mode %d\n", vec_mode); exit(1);
}
}
static void init_data(args_t *args)
{
bcf_srs_t *files = bcf_sr_init();
if ( args->regions_list )
{
if ( bcf_sr_set_regions(files, args->regions_list, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(files, args->targets_list, args->targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(files, args->fname) ) error("Failed to open %s: %s\n", args->fname,bcf_sr_strerror(files->errnum));
bcf_hdr_t *hdr = files->readers[0].header;
if ( !args->sample )
{
if ( bcf_hdr_nsamples(hdr)>1 ) error("Missing the option -s, --sample\n");
args->sample = hdr->samples[0];
}
else if ( bcf_hdr_id2int(hdr,BCF_DT_SAMPLE,args->sample)<0 ) error("No such sample: %s\n", args->sample);
int ret = bcf_hdr_set_samples(hdr, args->sample, 0);
if ( ret<0 ) error("Error setting the sample: %s\n", args->sample);
if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,bcf_hdr_id2int(hdr,BCF_DT_ID,"BAF")) )
error("The tag FORMAT/BAF is not present in the VCF: %s\n", args->fname);
int i;
args->xvals = (double*) calloc(args->nbins,sizeof(double));
for (i=0; i<args->nbins; i++) args->xvals[i] = 1.0*i/(args->nbins-1);
// collect BAF distributions for all chromosomes
int idist = -1, nbaf = 0, nprocessed = 0, ntotal = 0, prev_chr = -1;
float *baf = NULL;
while ( bcf_sr_next_line(files) )
{
ntotal++;
bcf1_t *line = bcf_sr_get_line(files,0);
if ( bcf_get_format_float(hdr,line,"BAF",&baf,&nbaf) != 1 ) continue;
if ( bcf_float_is_missing(baf[0]) ) continue;
nprocessed++;
if ( prev_chr==-1 || prev_chr!=line->rid )
{
// new chromosome
idist = args->ndist++;
args->dist = (dist_t*) realloc(args->dist, sizeof(dist_t)*args->ndist);
memset(&args->dist[idist],0,sizeof(dist_t));
args->dist[idist].chr = strdup(bcf_seqname(hdr,line));
args->dist[idist].yvals = (double*) calloc(args->nbins,sizeof(double));
args->dist[idist].xvals = args->xvals;
args->dist[idist].nvals = args->nbins;
prev_chr = line->rid;
}
int bin = baf[0]*(args->nbins-1);
args->dist[idist].yvals[bin]++; // the distribution
}
free(baf);
bcf_sr_destroy(files);
for (idist=0; idist<args->ndist; idist++)
{
#if 0
int j;
for (j=0; j<args->nbins; j++)
{
double x = args->dist[idist].xvals[j];
args->dist[idist].yvals[j] = exp(-(x-0.5)*(x-0.5)/1e-3);
}
#endif
init_dist(args, &args->dist[idist],args->verbose);
}
args->dat_fp = open_file(&args->dat_fname,"w","%s/dist.dat", args->output_dir);
fprintf(args->dat_fp, "# This file was produced by: bcftools polysomy(%s+htslib-%s), the command line was:\n", bcftools_version(),hts_version());
fprintf(args->dat_fp, "# \t bcftools %s ", args->argv[0]);
for (i=1; i<args->argc; i++)
fprintf(args->dat_fp, " %s",args->argv[i]);
fprintf(args->dat_fp,"\n#\n");
fprintf(args->dat_fp,"# DIST\t[2]Chrom\t[3]BAF\t[4]Normalized Count\n");
fprintf(args->dat_fp,"# FIT\t[2]Goodness of Fit\t[3]iFrom\t[4]iTo\t[5]The Fitted Function\n");
fprintf(args->dat_fp,"# CN\t[2]Chrom\t[3]Estimated Copy Number\t[4]Absolute fit deviation\n");
char *fname = NULL;
FILE *fp = open_file(&fname,"w","%s/dist.py", args->output_dir);
//-------- matplotlib script --------------
fprintf(fp,
"#!/usr/bin/env python\n"
"#\n"
"import matplotlib as mpl\n"
"mpl.use('Agg')\n"
"import matplotlib.pyplot as plt\n"
"import csv,sys,argparse\n"
"from math import exp\n"
"\n"
"outdir = '%s'\n"
"\n"
"def read_dat(dat,fit,cn):\n"
" csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)\n"
" with open(outdir+'/dist.dat', 'rb') as f:\n"
" reader = csv.reader(f, 'tab')\n"
" for row in reader:\n"
" if row[0][0]=='#': continue\n"
" type = row[0]\n"
" chr = row[1]\n"
" if type=='DIST':\n"
" if chr not in dat: dat[chr] = []\n"
" dat[chr].append(row)\n"
" elif type=='FIT':\n"
" if chr not in fit: fit[chr] = []\n"
" fit[chr].append(row)\n"
" elif type=='CN':\n"
" cn[chr] = row[2]\n"
"\n"
"def plot_dist(dat,fit,chr):\n"
" fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
" ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'k-',label='Distribution')\n"
" if chr in fit:\n"
" for i in range(len(fit[chr])):\n"
" pfit = fit[chr][i]\n"
" exec('def xfit(x): return '+pfit[5])\n"
" istart = int(pfit[3])\n"
" iend = int(pfit[4])+1\n"
" vals = dat[chr][istart:iend]\n"
" args = {}\n"
" if i==0: args = {'label':'Target to Fit'}\n"
" ax.plot([x[2] for x in vals],[x[3] for x in vals],'r-',**args)\n"
" if i==0: args = {'label':'Best Fit'}\n"
" ax.plot([x[2] for x in vals],[xfit(float(x[2])) for x in vals],'g-',**args)\n"
" ax.set_title('BAF distribution, chr'+chr)\n"
" ax.set_xlabel('BAF')\n"
" ax.set_ylabel('Frequency')\n"
" ax.legend(loc='best',prop={'size':7},frameon=False)\n"
" plt.savefig(outdir+'/dist.chr'+chr+'.png')\n"
" plt.close()\n"
"\n"
"def plot_copy_number(cn):\n"
" fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
" xlabels = sorted(cn.keys())\n"
" xvals = range(len(xlabels))\n"
" yvals = [float(cn[x]) for x in xlabels]\n"
" ax.plot(xvals,yvals,'o',color='red')\n"
" for i in range(len(xvals)):\n"
" if yvals[i]==-1: ax.annotate('?', xy=(xvals[i],0.5),va='center',ha='center',color='red',fontweight='bold')\n"
" ax.tick_params(axis='both', which='major', labelsize=9)\n"
" ax.set_xticks(xvals)\n"
" ax.set_xticklabels(xlabels,rotation=45)\n"
" ax.set_xlim(-1,len(xlabels))\n"
" ax.set_ylim(0,5.0)\n"
" ax.set_yticks([1.0,2.0,3.0,4.0])\n"
" ax.set_xlabel('Chromosome')\n"
" ax.set_ylabel('Copy Number')\n"
" plt.savefig(outdir+'/copy-number.png')\n"
" plt.close()\n"
"\n"
"class myParser(argparse.ArgumentParser):\n"
" def error(self, message):\n"
" self.print_help()\n"
" sys.stderr.write('error: %%s\\n' %% message)\n"
" sys.exit(2)\n"
"\n"
"def main():\n"
" parser = myParser()\n"
" parser.add_argument('-a', '--all', action='store_true', help='Create all plots')\n"
" parser.add_argument('-c', '--copy-number', action='store_true', help='Create copy-number plot')\n"
" parser.add_argument('-d', '--distrib', metavar='CHR', help='Plot BAF distribution of a single chromosome')\n"
" args = parser.parse_args()\n"
" dat = {}; fit = {}; cn = {}\n"
" read_dat(dat,fit,cn)\n"
" if args.distrib!=None:\n"
" plot_dist(dat,fit,args.distrib)\n"
" if args.all:\n"
" for chr in dat: plot_dist(dat,fit,chr)\n"
" plot_copy_number(cn)\n"
" elif args.copy_number:\n"
" plot_copy_number(cn)\n"
" else:\n"
" for chr in dat: plot_dist(dat,fit,chr)\n"
"\n"
"if __name__ == '__main__':\n"
" main()\n",
args->output_dir);
//---------------------------------------
chmod(fname, S_IWUSR|S_IRUSR|S_IRGRP|S_IROTH|S_IXUSR|S_IXGRP|S_IXOTH);
free(fname);
fclose(fp);
}
void mexFunction(int nout, mxArray *pout[], int nin, const mxArray *pin[]) {
FILE *f = fopen("log.txt", "wt");
fclose(f);
if (nin < 2) { mexErrMsgTxt("nnmex called with < 2 input arguments"); }
const mxArray *A = pin[0], *B = pin[1];
const mxArray *ANN_PREV = NULL, *ANN_WINDOW = NULL, *AWINSIZE = NULL;
int aw = -1, ah = -1, bw = -1, bh = -1;
BITMAP *a = NULL, *b = NULL, *ann_prev = NULL, *ann_window = NULL, *awinsize = NULL;
VECBITMAP<unsigned char> *ab = NULL, *bb = NULL;
VECBITMAP<float> *af = NULL, *bf = NULL;
if (mxGetNumberOfDimensions(A) != 3 || mxGetNumberOfDimensions(B) != 3) { mexErrMsgTxt("dims != 3"); }
if (mxGetDimensions(A)[2] != mxGetDimensions(B)[2]) { mexErrMsgTxt("3rd dimension not same size"); }
int mode = MODE_IMAGE;
if (mxGetDimensions(A)[2] != 3) { // a discriptor rather than rgb
if (mxIsUint8(A) && mxIsUint8(B)) { mode = MODE_VECB; }
else if (is_float(A) && is_float(B)) { mode = MODE_VECF; }
else { mexErrMsgTxt("input not uint8, single, or double"); }
}
Params *p = new Params();
RecomposeParams *rp = new RecomposeParams();
BITMAP *borig = NULL;
if (mode == MODE_IMAGE) {
a = convert_bitmap(A);
b = convert_bitmap(B);
borig = b;
aw = a->w; ah = a->h;
bw = b->w; bh = b->h;
}
else if (mode == MODE_VECB) {
ab = convert_vecbitmap<unsigned char>(A);
bb = convert_vecbitmap<unsigned char>(B);
if (ab->n != bb->n) { mexErrMsgTxt("3rd dimension differs"); }
aw = ab->w; ah = ab->h;
bw = bb->w; bh = bb->h;
p->vec_len = ab->n;
}
else if (mode == MODE_VECF) {
af = convert_vecbitmap<float>(A);
bf = convert_vecbitmap<float>(B);
if (af->n != bf->n) { mexErrMsgTxt("3rd dimension differs"); }
aw = af->w; ah = af->h;
bw = bf->w; bh = bf->h;
p->vec_len = af->n;
}
double *win_size = NULL;
BITMAP *amask = NULL, *bmask = NULL;
double scalemin = 0.5, scalemax = 2.0; // The product of these must be one.
/* parse parameters */
int i = 2;
int sim_mode = 0;
int knn_chosen = -1;
p->algo = ALGO_CPU;
int enrich_mode = 0;
if (nin > i && !mxIsEmpty(pin[i])) {
if (mxStringEquals(pin[i], "cpu")) { p->algo = ALGO_CPU; }
else if (mxStringEquals(pin[i], "gpucpu")) { p->algo = ALGO_GPUCPU; }
else if (mxStringEquals(pin[i], "cputiled")) { p->algo = ALGO_CPUTILED; }
else if (mxStringEquals(pin[i], "rotscale")) { sim_mode = 1; }
else if (mxStringEquals(pin[i], "enrich")) { p->algo = ALGO_CPUTILED; enrich_mode = 1; }
else { mexErrMsgTxt("Unknown algorithm"); }
} i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->patch_w = int(mxGetScalar(pin[i])); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->nn_iters = int(mxGetScalar(pin[i])); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->rs_max = int(mxGetScalar(pin[i])); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->rs_min = int(mxGetScalar(pin[i])); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->rs_ratio = mxGetScalar(pin[i]); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->rs_iters = mxGetScalar(pin[i]); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { p->cores = int(mxGetScalar(pin[i])); } i++;
if (nin > i && !mxIsEmpty(pin[i])) { bmask = convert_bitmap(pin[i]); } i++; // XC+
if (nin > i && !mxIsEmpty(pin[i])) {
if (!mxIsDouble(pin[i])) { mexErrMsgTxt("\nwin_size should be of type double."); }
win_size = (double*)mxGetData(pin[i]);
if (mxGetNumberOfElements(pin[i])==1) { p->window_h = p->window_w = int(win_size[0]); }
else if (mxGetNumberOfElements(pin[i])==2) { p->window_h = int(win_size[0]); p->window_w = int(win_size[1]); }
else { mexErrMsgTxt("\nwin_size should be a scalar for square window or [h w] for a rectangular one."); }
} i++;
/* continue parsing parameters */
// [ann_prev=NULL], [ann_window=NULL], [awinsize=NULL],
if (nin > i && !mxIsEmpty(pin[i])) {
ANN_PREV = pin[i];
int clip_count = 0;
ann_prev = convert_field(p, ANN_PREV, bw, bh, clip_count); // Bug fixed by Connelly
} i++;
if (nin > i && !mxIsEmpty(pin[i])) {
ANN_WINDOW = pin[i];
int clip_count = 0;
ann_window = convert_field(p, ANN_WINDOW, bw, bh, clip_count);
} i++;
if (nin > i && !mxIsEmpty(pin[i])) {
AWINSIZE = pin[i];
awinsize = convert_winsize_field(p, AWINSIZE, aw, ah);
if (p->window_w==INT_MAX||p->window_h==INT_MAX) { p->window_w = -1; p->window_h = -1; }
} i++;
if (nin > i && !mxIsEmpty(pin[i])) {
knn_chosen = int(mxGetScalar(pin[i]));
if (knn_chosen == 1) { knn_chosen = -1; }
if (knn_chosen <= 0) { mexErrMsgTxt("\nknn is less than zero"); }
} i++;
if (nin > i && !mxIsEmpty(pin[i])) {
scalemax = mxGetScalar(pin[i]);
if (scalemax <= 0) { mexErrMsgTxt("\nscalerange is less than zero"); }
scalemin = 1.0/scalemax;
if (scalemax < scalemin) {
double temp = scalemax;
scalemax = scalemin;
scalemin = temp;
}
} i++;
if (ann_window&&!awinsize&&!win_size) {
mexErrMsgTxt("\nUsing ann_window - either awinsize or win_size should be defined.\n");
}
if (enrich_mode) {
int nn_iters = p->nn_iters;
p->enrich_iters = nn_iters/2;
p->nn_iters = 2;
if (A != B) { mexErrMsgTxt("\nOur implementation of enrichment requires that image A = image B.\n"); }
if (mode == MODE_IMAGE) {
b = a;
} else {
mexErrMsgTxt("\nEnrichment only implemented for 3 channel uint8 inputs.\n");
}
}
init_params(p);
if (sim_mode) {
init_xform_tables(scalemin, scalemax, 1);
}
RegionMasks *amaskm = amask ? new RegionMasks(p, amask): NULL;
BITMAP *ann = NULL; // NN field
BITMAP *annd_final = NULL; // NN patch distance field
BITMAP *ann_sim_final = NULL;
VBMP *vann_sim = NULL;
VBMP *vann = NULL;
VBMP *vannd = NULL;
if (mode == MODE_IMAGE) {
// input as RGB image
if (!a || !b) { mexErrMsgTxt("internal error: no a or b image"); }
if (knn_chosen > 1) {
p->knn = knn_chosen;
if (sim_mode) { mexErrMsgTxt("rotating+scaling patches not implemented with knn (actually it is implemented it is not exposed by the wrapper)"); }
PRINCIPAL_ANGLE *pa = NULL;
vann_sim = NULL;
vann = knn_init_nn(p, a, b, vann_sim, pa);
vannd = knn_init_dist(p, a, b, vann, vann_sim);
knn(p, a, b, vann, vann_sim, vannd, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, pa);
// sort_knn(p, vann, vann_sim, vannd);
} else if (sim_mode) {
BITMAP *ann_sim = NULL;
ann = sim_init_nn(p, a, b, ann_sim);
BITMAP *annd = sim_init_dist(p, a, b, ann, ann_sim);
sim_nn(p, a, b, ann, ann_sim, annd);
if (ann_prev) { mexErrMsgTxt("when searching over rotations+scales, previous guess is not supported"); }
annd_final = annd;
ann_sim_final = ann_sim;
} else {
ann = init_nn(p, a, b, bmask, NULL, amaskm, 1, ann_window, awinsize);
BITMAP *annd = init_dist(p, a, b, ann, bmask, NULL, amaskm);
nn(p, a, b, ann, annd, amaskm, bmask, 0, 0, rp, 0, 0, 0, NULL, p->cores, ann_window, awinsize);
if (ann_prev) minnn(p, a, b, ann, annd, ann_prev, bmask, 0, 0, rp, NULL, amaskm, p->cores);
annd_final = annd;
}
}
/*
else if (mode == MODE_VECB) {
// mexPrintf("mode vecb %dx%dx%d, %dx%dx%d\n", ab->w, ab->h, ab->n, bb->w, bb->h, bb->n);
// mexPrintf(" %d %d %d %d\n", ab->get(0,0)[0], ab->get(1,0)[0], ab->get(0,1)[0], ab->get(0,0)[1]);
if (!ab || !bb) { mexErrMsgTxt("internal error: no a or b image"); }
ann = vec_init_nn<unsigned char>(p, ab, bb, bmask, NULL, amaskm);
VECBITMAP<int> *annd = vec_init_dist<unsigned char, int>(p, ab, bb, ann, bmask, NULL, amaskm);
// mexPrintf(" %d %d %d %p %p\n", annd->get(0,0)[0], annd->get(1,0)[0], annd->get(0,1)[0], amaskm, bmask);
vec_nn<unsigned char, int>(p, ab, bb, ann, annd, amaskm, bmask, 0, 0, rp, 0, 0, 0, NULL, p->cores);
if (ann_prev) vec_minnn<unsigned char, int>(p, ab, bb, ann, annd, ann_prev, bmask, 0, 0, rp, NULL, amaskm, p->cores);
annd_final = vecbitmap_to_bitmap(annd);
delete annd;
}
else if (mode == MODE_VECF) {
// mexPrintf("mode vecf %dx%dx%d, %dx%dx%d\n", af->w, af->h, af->n, bf->w, bf->h, bf->n);
// mexPrintf(" %f %f %f %f\n", af->get(0,0)[0], af->get(1,0)[0], af->get(0,1)[0], af->get(0,0)[1]);
if (!af || !bf) { mexErrMsgTxt("internal error: no a or b image"); }
ann = vec_init_nn<float>(p, af, bf, bmask, NULL, amaskm);
VECBITMAP<float> *annd = vec_init_dist<float, float>(p, af, bf, ann, bmask, NULL, amaskm);
vec_nn<float, float>(p, af, bf, ann, annd, amaskm, bmask, 0, 0, rp, 0, 0, 0, NULL, p->cores);
if (ann_prev) vec_minnn<float, float>(p, af, bf, ann, annd, ann_prev, bmask, 0, 0, rp, NULL, amaskm, p->cores);
annd_final = create_bitmap(annd->w, annd->h);
clear(annd_final);
delete annd;
}
*/
else if(mode == MODE_VECB) {
if (sim_mode) { mexErrMsgTxt("internal error: rotation+scales not implemented with descriptor mode"); }
if (knn_chosen > 1) { mexErrMsgTxt("internal error: kNN not implemented with descriptor mode"); }
// mexPrintf("mode vecb_xc %dx%dx%d, %dx%dx%d\n", ab->w, ab->h, ab->n, bb->w, bb->h, bb->n);
// input as uint8 discriptors per pixel
if (!ab || !bb) { mexErrMsgTxt("internal error: no a or b image"); }
ann = XCvec_init_nn<unsigned char>(p, ab, bb, bmask, NULL, amaskm);
VECBITMAP<int> *annd = XCvec_init_dist<unsigned char, int>(p, ab, bb, ann, bmask, NULL, amaskm);
XCvec_nn<unsigned char, int>(p, ab, bb, ann, annd, amaskm, bmask, 0, 0, rp, 0, 0, 0, NULL, p->cores);
if (ann_prev) XCvec_minnn<unsigned char, int>(p, ab, bb, ann, annd, ann_prev, bmask, 0, 0, rp, NULL, amaskm, p->cores);
annd_final = vecbitmap_to_bitmap(annd);
delete annd;
} else if(mode == MODE_VECF) {
if (sim_mode) { mexErrMsgTxt("internal error: rotation+scales not implemented with descriptor mode"); }
if (knn_chosen > 1) { mexErrMsgTxt("internal error: kNN not implemented with descriptor mode"); }
// input as float/double discriptors per pixel
if (!af || !bf) { mexErrMsgTxt("internal error: no a or b image"); }
ann = XCvec_init_nn<float>(p, af, bf, bmask, NULL, amaskm);
VECBITMAP<float> *annd = XCvec_init_dist<float, float>(p, af, bf, ann, bmask, NULL, amaskm);
XCvec_nn<float, float>(p, af, bf, ann, annd, amaskm, bmask, 0, 0, rp, 0, 0, 0, NULL, p->cores);
if (ann_prev) XCvec_minnn<float, float>(p, af, bf, ann, annd, ann_prev, bmask, 0, 0, rp, NULL, amaskm, p->cores);
annd_final = create_bitmap(annd->w, annd->h);
clear(annd_final);
delete annd;
}
destroy_region_masks(amaskm);
// output ann: x | y | patch_distance
if(nout >= 1) {
mxArray *ans = NULL;
if (knn_chosen > 1) {
if (sim_mode) { mexErrMsgTxt("rotating+scaling patches return value not implemented with knn"); }
mwSize dims[4] = { ah, aw, 3, knn_chosen };
ans = mxCreateNumericArray(4, dims, mxINT32_CLASS, mxREAL);
int *data = (int *) mxGetData(ans);
for (int kval = 0; kval < knn_chosen; kval++) {
int *xchan = &data[aw*ah*3*kval+0];
int *ychan = &data[aw*ah*3*kval+aw*ah];
int *dchan = &data[aw*ah*3*kval+2*aw*ah];
for (int y = 0; y < ah; y++) {
// int *ann_row = (int *) ann->line[y];
// int *annd_row = (int *) annd_final->line[y];
for (int x = 0; x < aw; x++) {
// int pp = ann_row[x];
int pp = vann->get(x, y)[kval];
int pos = y + x * ah;
xchan[pos] = INT_TO_X(pp);
ychan[pos] = INT_TO_Y(pp);
dchan[pos] = vannd->get(x, y)[kval];
}
}
}
} else if (ann_sim_final) {
mwSize dims[3] = { ah, aw, 5 };
ans = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL);
float *data = (float *) mxGetData(ans);
float *xchan = &data[0];
float *ychan = &data[aw*ah];
float *dchan = &data[2*aw*ah];
float *tchan = &data[3*aw*ah];
float *schan = &data[4*aw*ah];
double angle_scale = 2.0*M_PI/NUM_ANGLES;
for (int y = 0; y < ah; y++) {
int *ann_row = (int *) ann->line[y];
int *annd_row = (int *) annd_final->line[y];
int *ann_sim_row = ann_sim_final ? (int *) ann_sim_final->line[y]: NULL;
for (int x = 0; x < aw; x++) {
int pp = ann_row[x];
int pos = y + x * ah;
xchan[pos] = INT_TO_X(pp);
ychan[pos] = INT_TO_Y(pp);
dchan[pos] = annd_row[x];
if (ann_sim_final) {
int v = ann_sim_row[x];
int tval = INT_TO_Y(v)&(NUM_ANGLES-1);
int sval = INT_TO_X(v);
tchan[pos] = tval*angle_scale;
schan[pos] = xform_scale_table[sval]*(1.0/65536.0);
}
}
}
} else {
mwSize dims[3] = { ah, aw, 3 };
ans = mxCreateNumericArray(3, dims, mxINT32_CLASS, mxREAL);
int *data = (int *) mxGetData(ans);
int *xchan = &data[0];
int *ychan = &data[aw*ah];
int *dchan = &data[2*aw*ah];
for (int y = 0; y < ah; y++) {
int *ann_row = (int *) ann->line[y];
int *annd_row = (int *) annd_final->line[y];
for (int x = 0; x < aw; x++) {
int pp = ann_row[x];
int pos = y + x * ah;
xchan[pos] = INT_TO_X(pp);
ychan[pos] = INT_TO_Y(pp);
dchan[pos] = annd_row[x];
}
}
}
pout[0] = ans;
}
// clean up
delete vann;
delete vann_sim;
delete vannd;
delete p;
delete rp;
destroy_bitmap(a);
destroy_bitmap(borig);
delete ab;
delete bb;
delete af;
delete bf;
destroy_bitmap(ann);
destroy_bitmap(annd_final);
destroy_bitmap(ann_sim_final);
if (ann_prev) destroy_bitmap(ann_prev);
if (ann_window) destroy_bitmap(ann_window);
if (awinsize) destroy_bitmap(awinsize);
}
int main()
{
FILE *f;
char s1[100],s2[100],al1[300],al2[300];
int i,j,len,max,row,col,ch;
printf("Enter rype of sequence :\n");
printf("1.Protein sequence\n");
printf("2.Nucleotide sequence\n");
scanf("%d",&ch);
if(ch==1)
f=fopen("blosum62.txt","r");
else
f=fopen("iub.txt","r");
//printf("Enter the CharacterSet :\n");
fscanf(f,"%s",charset);
len = strlen(charset);
//printf("Enter Scoring Matrix :\n");
for(i=0;i<len;i++)
for(j=0;j<len;j++)
fscanf(f,"%d",&score[i][j]);
printf("Enter Gap Penalty:\n");
scanf("%d",&gap);
printf("Enter Number of Sequences :\n");
scanf("%d",&num_seq);
printf("Enter sequences :\n");
for(i=0;i<num_seq;i++)
scanf("%s",seq[i]);
num_clust = num_seq;
alive = num_clust;
for(i=0;i<100;i++)
visit[i] = 0;
init_ham();
/*for(i=0;i<num_seq;i++)
{
for(j=0;j<num_seq;j++)
{
printf("%f ",hamdist[i][j]);
}
printf("\n");
}
printf("---------------------------------------------\n");*/
init_dist();
/*for(i=0;i<num_seq;i++)
{
for(j=0;j<num_seq;j++)
{
if(j<=i)
printf(" ");
else
printf("%f ",dismat[i][j]);
}
printf("\n");
}*/
init_clust();
while(alive>2)
{
/*for(i=0;i<num_clust;i++)
{
printf("Cluster : %d\n",i+1);
for(j=0;j<cluster[i].tot_seq;j++)
printf("%s\n",cluster[i].seq_list[j]);
}
printf("\n#######################################\n\n");
getch();*/
init_dist();
matrixmin(num_clust,&row,&col);
clust_align(row,col);
}
matrixmin(num_clust,&row,&col);
clust_align(row,col);
len = strlen(cluster[num_clust-1].seq_list[0]);
printf("\n\nFinal Output :\n\n");
for(j=0;j<cluster[num_clust-1].tot_seq;j++)
{
for(i=0;i<len;i++)
{
if(cluster[num_clust-1].seq_list[j][i]=='X')
printf("-");
else
printf("%c",cluster[num_clust-1].seq_list[j][i]);
}
printf("\n");
}
printf("\n\nFinal SP Score : %d",Make_SP());
getch();
return 0;
}
static void
erl_init(int ncpu,
int proc_tab_sz,
int legacy_proc_tab,
int port_tab_sz,
int port_tab_sz_ignore_files,
int legacy_port_tab)
{
init_benchmarking();
erts_init_monitors();
erts_init_time();
erts_init_sys_common_misc();
erts_init_process(ncpu, proc_tab_sz, legacy_proc_tab);
erts_init_scheduling(no_schedulers,
no_schedulers_online);
erts_init_cpu_topology(); /* Must be after init_scheduling */
erts_init_gc(); /* Must be after init_scheduling */
erts_alloc_late_init();
H_MIN_SIZE = erts_next_heap_size(H_MIN_SIZE, 0);
BIN_VH_MIN_SIZE = erts_next_heap_size(BIN_VH_MIN_SIZE, 0);
erts_init_trace();
erts_init_binary();
erts_init_bits();
erts_code_ix_init();
erts_init_fun_table();
init_atom_table();
init_export_table();
init_module_table();
init_register_table();
init_message();
erts_bif_info_init();
erts_ddll_init();
init_emulator();
erts_ptab_init(); /* Must be after init_emulator() */
erts_bp_init();
init_db(); /* Must be after init_emulator */
erts_bif_timer_init();
erts_init_node_tables();
init_dist();
erl_drv_thr_init();
erts_init_async();
erts_init_io(port_tab_sz, port_tab_sz_ignore_files, legacy_port_tab);
init_load();
erts_init_bif();
erts_init_bif_chksum();
erts_init_bif_binary();
erts_init_bif_re();
erts_init_unicode(); /* after RE to get access to PCRE unicode */
erts_init_external();
erts_delay_trap = erts_export_put(am_erlang, am_delay_trap, 2);
erts_late_init_process();
#if HAVE_ERTS_MSEG
erts_mseg_late_init(); /* Must be after timer (erts_init_time()) and thread
initializations */
#endif
#ifdef HIPE
hipe_mode_switch_init(); /* Must be after init_load/beam_catches/init */
#endif
packet_parser_init();
erl_nif_init();
}
