void LNLP::prepare_forecast()
{
if(remake_vectors)
{
make_vectors();
init_distances();
}
if(remake_targets)
make_targets();
if(remake_ranges)
{
set_indices_from_range(lib_indices, lib_ranges, (E-1)*tau, -std::max(0, tp), true);
set_indices_from_range(pred_indices, pred_ranges, (E-1)*tau, -std::max(0, tp), false);
check_cross_validation();
which_lib = which_indices_true(lib_indices);
which_pred = which_indices_true(pred_indices);
remake_ranges = false;
}
compute_distances();
return;
}
void classifyDatasetLOO(dataset *current, distances *distanceSet, criteria *criterias)
{
int t1, t2, i;
float **distSet, *scores;
int classFound;
series *ts1, *ts2;
distSet = malloc(current->cardinality * sizeof(float *));
scores = calloc(criterias->nb_criteria, sizeof(float));
for (t1 = 0; t1 < current->cardinality; t1++)
{
for (t2 = 0; t2 < current->cardinality; t2++)
{
ts1 = current->data[t1];
ts2 = current->data[t2];
distSet[t2] = compute_distances(ts1, ts2, distanceSet);
}
normalize_distance(distSet, distanceSet->nb_compute, current->cardinality);
for (i = 0; i < criterias->nb_criteria; i++)
if (criterias->compute[i])
{
classFound = criterias->functions[i](distSet, current->classes, current->cardinality, distanceSet->nb_compute, t1, current->nb_classes);
if (classFound != current->classes[t1])
scores[i]++;
}
}
printf("Global results :\n");
for (i = 0; i < criterias->nb_criteria; i++)
printf("%s \t : %f\n", criterias->name[i], (scores[i] / (float)current->cardinality));
free(scores);
free(distSet);
return;
}
/*}}}*/
void tcs(struct node *top, struct tower_table *table, int all)/*{{{*/
{
struct tower_data *data;
data = malloc(table->n_towers * sizeof(struct tower_data));
make_charts(top, table, data);
compute_distances(table, data);
}
void
WorkerStemFit::run()
{
Stem_fit fit(_cloud,_min_height, _bin_width, _epsilon);
std::vector<pcl::ModelCoefficients> cylinders = fit.getCylinders();
std::vector<float> distances = compute_distances(cylinders);
std::vector<float> distances_only_fitted_points = reduce_distances(distances,cylinders);
float dist = squared_mean(distances_only_fitted_points);
get_optimization()->updateCoeff(dist, _bin_width, _epsilon);
}
int main (int argc, char *argv[])
{
if (argc < 2) usage();
char *root = argv[1];
char vecfn[255];
sprintf (vecfn, "vectors/%s.ds", root);
printf ("vector file '%s'\n", vecfn);
load_vectors (vecfn);
compute_distances ();
char outfn[255];
sprintf (outfn, "results-gonzalez/%s.rank", root);
cluster (outfn, 0);
int index = 2;
while (index < argc) {
char subsetfn[255];
sprintf (subsetfn, "vectors/%s", argv[index]);
printf ("subset file '%s'\n", subsetfn);
char subsetfn2[255];
sprintf (subsetfn2, "vectors/%s.all", argv[index]);
printf ("subset file '%s'\n", subsetfn2);
load_subsets (subsetfn, subsetfn2);
char outfn2[255];
sprintf (outfn2, "results-gonzalez/%s.%s.rank", root, argv[index]);
cluster (outfn2, 0);
sprintf (outfn2, "results-gonzalez/%s.%s.baseline.rank", root, argv[index]);
cluster (outfn2, 1);
sprintf (outfn2, "results-gonzalez/%s.%s.best.rank", root, argv[index]);
cluster (outfn2, 2);
index++;
}
return 0;
}
int main(int argc, char *argv[])
{
t_file_info *files_info; /* Tableau contenant la liste des fichiers */
int nbr;
int i;
nbr = argc - 1;
files_info = malloc(nbr*sizeof(*files_info));
for(i = 0;i < nbr;i++) {
files_info[i].filepath = malloc(strlen(argv[i+1])*sizeof(char)+1);
files_info[i].compressed_size = -1;
strcpy(files_info[i].filepath, argv[i+1]);
}
compute_distances(files_info, nbr, distance_compression);
/*compute_distances(files_info, nbr, distance_lancaster);*/
for(i = 0;i < nbr; i++) {
free(files_info[i].filepath);
}
free(files_info);
return 0;
}
int main(int argc, Char *argv[])
{
pattern_elm ***pattern_array;
long tip_count = 0;
double ln_maxgrp;
double ln_maxgrp1;
double ln_maxgrp2;
node * p;
#ifdef MAC
argc = 1; /* macsetup("Treedist", ""); */
argv[0] = "Treedist";
#endif
init(argc, argv);
emboss_getoptions("ftreedist",argc,argv);
/* Initialize option-based variables, then ask for changes regarding
their values. */
ntrees = 0.0;
lasti = -1;
/* read files to determine size of structures we'll be working with */
countcomma(ajStrGetuniquePtr(&phylotrees[0]->Tree),&tip_count);
tip_count++; /* countcomma does a raw comma count, tips is one greater */
/*
* EWFIX.BUG.756 -- this section may be killed if a good solution
* to bug 756 is found
*
* inside cons.c there are several arrays which are allocated
* to size "maxgrp", the maximum number of groups (sets of
* tips more closely connected than the rest of the tree) we
* can see as the code executes.
*
* We have two measures we use to determine how much space to
* allot:
* (1) based on the tip count of the trees in the infile
* (2) based on total number of trees in infile, and
*
* (1) -- Tip Count Method
* Since each group is a subset of the set of tips we must
* represent at most pow(2,tips) different groups. (Technically
* two fewer since we don't store the empty or complete subsets,
* but let's keep this simple.
*
* (2) -- Total Tree Size Method
* Each tree we read results in
* singleton groups for each tip, plus
* a group for each interior node except the root
* Since the singleton tips are identical for each tree, this gives
* a bound of #tips + ( #trees * (# tips - 2 ) )
*
*
* Ignoring small terms where expedient, either of the following should
* result in an adequate allocation:
* pow(2,#tips)
* (#trees + 1) * #tips
*
* Since "maxgrp" is a limit on the number of items we'll need to put
* in a hash, we double it to make space for quick hashing
*
* BUT -- all of this has the possibility for overflow, so -- let's
* make the initial calculations with doubles and then convert
*
*/
/* limit chosen to make hash arithmetic work */
maxgrp = LONG_MAX / 2;
ln_maxgrp = log((double)maxgrp);
/* 2 * (#trees + 1) * #tips */
ln_maxgrp1 = log(2.0 * (double)tip_count *
((double)trees_in_1 + (double)trees_in_2));
/* ln only for 2 * pow(2,#tips) */
ln_maxgrp2 = (double)(1 + tip_count) * log(2.0);
/* now -- find the smallest of the three */
if(ln_maxgrp1 < ln_maxgrp)
{
maxgrp = 2 * (trees_in_1 + trees_in_2 + 1) * tip_count;
ln_maxgrp = ln_maxgrp1;
}
if(ln_maxgrp2 < ln_maxgrp)
{
maxgrp = pow(2,tip_count+1);
}
/* Read the (first) tree file and put together grouping, order, and
timesseen */
read_groups (&pattern_array, trees_in_1 + trees_in_2, tip_count, phylotrees);
if ((tree_pairing == ADJACENT_PAIRS) ||
(tree_pairing == ALL_IN_FIRST)) {
/* Here deal with the adjacent or all-in-first pairing
difference computation */
compute_distances (pattern_array, trees_in_1, 0);
} else if (tree_pairing == NO_PAIRING) {
/* Compute the consensus tree. */
putc('\n', outfile);
/* consensus(); Reserved for future development */
}
if (progress)
printf("\nOutput written to file \"%s\"\n\n", outfilename);
FClose(outtree);
FClose(intree);
FClose(outfile);
if ((tree_pairing == ALL_IN_1_AND_2) ||
(tree_pairing == CORR_IN_1_AND_2))
FClose(intree2);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
free_patterns (pattern_array, trees_in_1 + trees_in_2);
clean_up_final();
/* clean up grbg */
p = grbg;
while (p != NULL) {
node * r = p;
p = p->next;
free(r->nodeset);
free(r->view);
free(r);
}
printf("Done.\n\n");
embExit();
return 0;
} /* main */
