int
init_sr(sr_data* sr_p,
double *sasa,
const coord_t *xyz,
const double *r,
double probe_radius,
int n_points)
{
int n_atoms = freesasa_coord_n(xyz);
coord_t *srp = test_points(n_points);
if (srp == NULL) return fail_msg("Failed to initialize test points.");
//store parameters and reference arrays
sr_data sr = {.n_atoms = n_atoms, .n_points = n_points,
.probe_radius = probe_radius,
.xyz = xyz, .srp = srp,
.sasa = sasa};
sr.r = malloc(sizeof(double)*n_atoms);
sr.r2 = malloc(sizeof(double)*n_atoms);
if (sr.r == NULL || sr.r2 == NULL) {
freesasa_coord_free(srp);
free(sr.r);
free(sr.r2);
return mem_fail();
}
for (int i = 0; i < n_atoms; ++i) {
sr.r[i] = r[i] + probe_radius;
sr.r2[i] = sr.r[i]*sr.r[i];
}
//calculate distances
sr.nb = freesasa_nb_new(xyz,sr.r);
if (sr.nb == NULL) {
freesasa_coord_free(srp);
free(sr.r);
free(sr.r2);
return mem_fail();
}
*sr_p = sr;
return FREESASA_SUCCESS;
}
int
init_sr(sr_data *sr,
double *sasa,
const coord_t *xyz,
const double *r,
double probe_radius,
int n_points)
{
int n_atoms = freesasa_coord_n(xyz);
coord_t *srp = test_points(n_points);
if (srp == NULL) return fail_msg("Failed to initialize test points.");
//store parameters and reference arrays
sr->n_atoms = n_atoms;
sr->n_points = n_points;
sr->probe_radius = probe_radius;
sr->xyz = xyz;
sr->srp = srp;
sr->sasa = sasa;
sr->nb = NULL;
sr->r = malloc(sizeof(double)*n_atoms);
sr->r2 = malloc(sizeof(double)*n_atoms);
if (sr->r == NULL || sr->r2 == NULL) goto cleanup;
for (int i = 0; i < n_atoms; ++i) {
double ri = r[i] + probe_radius;
sr->r[i] = ri;
sr->r2[i] = ri * ri;
}
//calculate distances
sr->nb = freesasa_nb_new(xyz, sr->r);
if (sr->nb == NULL) goto cleanup;
return FREESASA_SUCCESS;
cleanup:
release_sr(sr);
return mem_fail();
}
//============================================================================
// main
//============================================================================
int main() {
//*******************************************************
cout << "---------[Program start]----------" << endl;
/* if (argc < 3) {
fprintf(stderr, "Usage: mnist <k> <mnist path> [<nr train images> <nr test images>]\n");
return EXIT_FAILURE;
}
*/
int k = 5; // TODO atoi(argv[1]);
#ifdef PRINT
cout << "k = " << k << endl;
#endif
string base = "/tmp/images/"; // TODO string base(argv[2]);
LabelIterator *trainLabels = openLabels(base + "train-labels-idx1-ubyte");
ImageIterator *trainImages = openImages(base + "train-images-idx3-ubyte");
LabelIterator *testLabels = openLabels(base + "t10k-labels-idx1-ubyte");
ImageIterator *testImages = openImages(base + "t10k-images-idx3-ubyte");
if (trainLabels == 0 || trainImages == 0 || testLabels == 0 || testImages
== 0) {
cout
<< "One or more files couldn't be found! Make sure that following files are in the directory given as argument:\n"
<< "\ttrain-labels-idx1-ubyte\n"
<< "\ttrain-images-idx3-ubyte\n"
<< "\tt10k-labels-idx1-ubyte\n" << "\tt10k-images-idx3-ubyte\n"
<< endl;
exit(-1);
}
/*
trainLabels->count = 1000;
trainImages->count = 1000;
testLabels->count = 1000;
testImages->count = 1000;
*/
unsigned char label;
unsigned char *image;
Points<unsigned char, unsigned char> training_points(trainImages->count, trainImages->rows
* trainImages->columns);
Points<unsigned char, unsigned char> test_points(testImages->count, testImages->rows
* testImages->columns);
#ifdef PRINT
cout << trainImages->count << " " << trainImages->rows*trainImages->columns << endl;
cout << "size: " << trainImages->rows*trainImages->columns << "\tcount: " << trainImages->count << endl;
#endif
int i = 0;
Point<unsigned char, unsigned char> *trainPoint;
while (hasNextLabel(trainLabels) && hasNextImage(trainImages)) {
image = nextImage(trainImages);
label = nextLabel(trainLabels);
trainPoint = training_points.getPoint(i++);
imageToPoint(trainPoint, label, image, (trainImages->columns
*trainImages->rows));
#ifdef PRINT
if ((i % 1000) == 0)
cout << i << " training images loaded." << endl;
#endif
delete trainPoint;
free(image);
}
i = 0;
Point<unsigned char, unsigned char> *testPoint;
while (hasNextLabel(testLabels) && hasNextImage(testImages)) {
image = nextImage(testImages);
label = nextLabel(testLabels);
testPoint = test_points.getPoint(i++);
imageToPoint(testPoint, label, image, (testImages->columns
* testImages->rows));
#ifdef PRINT
if ((i % 1000) == 0)
cout << i << " test images loaded." << endl;
#endif
delete testPoint;
free(image);
}
//********************************************************
unsigned char *result = classify(k, test_points, training_points);
if (result != 0) {
int errors = 0;
for (int i = 0; i < test_points.getCount(); i++) {
if (result[i] != test_points.getLabel(i)[0]) {
errors++;
}
}
float error_rate = (float) errors / (float) test_points.getCount();
printf("PPE:\t %d out of %d inaccurate classifications\n", errors, test_points.getCount());
printf("PPE:\t Error rate is %f\n", error_rate);
free(result);
}
printf("PPE:\t Program finished\n");
return (0);
}
