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Add find peak-depth option to UVD_FILTER #76

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Apr 26, 2023
Merged

Add find peak-depth option to UVD_FILTER #76

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39 changes: 38 additions & 1 deletion src/LN2_UVD_FILTER.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ int show_help(void) {
" -min : (Optional) Take the minimum within the window.\n"
" -max : (Optional) Take the maximum within the window.\n"
" -columns : (Optional) Take the mode within the window.\n"
" -peak_d : (Optional) Take depth of the maximum value in the window.\n"
" -output : (Optional) Output basename for all outputs.\n"
"\n");
return 0;
Expand All @@ -45,7 +46,7 @@ int main(int argc, char* argv[]) {
char *fin1 = NULL, *fout = NULL, *fin2=NULL, *fin3=NULL, *fin4=NULL;
int ac;
float radius = 3, height = 0.25;
bool mode_median = true, mode_min = false, mode_max = false, mode_cols = false;
bool mode_median = true, mode_min = false, mode_max = false, mode_cols = false, mode_peak = false;

// Process user options
if (argc < 2) return show_help();
Expand Down Expand Up @@ -95,21 +96,31 @@ int main(int argc, char* argv[]) {
mode_max = false;
mode_cols = false;
mode_min = false;
mode_peak = false;
} else if (!strcmp(argv[ac], "-min")) {
mode_median = false;
mode_max = false;
mode_cols = false;
mode_min = true;
mode_peak = false;
} else if (!strcmp(argv[ac], "-max")) {
mode_median = false;
mode_min = false;
mode_cols = false;
mode_max = true;
mode_peak = false;
} else if (!strcmp(argv[ac], "-peak_d")) {
mode_median = false;
mode_min = false;
mode_cols = false;
mode_max = false;
mode_peak = true;
} else if (!strcmp(argv[ac], "-columns")) {
mode_median = false;
mode_min = false;
mode_max = false;
mode_cols = true;
mode_peak = false;
} else if (!strcmp(argv[ac], "-output")) {
if (++ac >= argc) {
fprintf(stderr, "** missing argument for -output\n");
Expand Down Expand Up @@ -235,6 +246,7 @@ int main(int argc, char* argv[]) {
cout << "\r " << i * 100 / nr_voi << " %" << flush;
vector <float> temp_vec;
vector <int> temp_vec_id;
vector <float> temp_vec_d;

// --------------------------------------------------------------------
// Cylinder windowing in UVD space
Expand All @@ -247,6 +259,8 @@ int main(int argc, char* argv[]) {
if (dist_uv < radius_sqr) { // Check Euclidean distance
temp_vec.push_back(vec_val[j]);
temp_vec_id.push_back(vec_voi_id[j]);
temp_vec_d.push_back(vec_d[j]);

}
}
}
Expand Down Expand Up @@ -313,6 +327,26 @@ int main(int argc, char* argv[]) {
*(nii_output_data + vec_voi_id[i]) = temp_max;
*(temp_nii_output_extra_data + vec_voi_id[i]) = static_cast<float>(n);
}

// --------------------------------------------------------------------
// Find peak depth of maximum (Works with binary mask)
// NOTE: temp_mask = 1 or 0
// --------------------------------------------------------------------
if (mode_peak) {
float temp_ref = vec_val[i];
float temp_max = vec_val[i];
float temp_peak = vec_d[i];

for (int j = 0; j != n; ++j) {
if (temp_vec[j] > temp_max) {
temp_max = temp_vec[j];
temp_peak = temp_vec_d[j];
}
}
*(nii_output_data + vec_voi_id[i]) = temp_peak;
*(temp_nii_output_extra_data + vec_voi_id[i]) = static_cast<float>(n);
}

// --------------------------------------------------------------------
// A) Find functional columns: write back to a single voxel
// TODO[Faruk]: Code review this part.
Expand Down Expand Up @@ -383,6 +417,9 @@ int main(int argc, char* argv[]) {
} else if (mode_max) {
save_output_nifti(fout, "UVD_max_filter", nii_output, true);
save_output_nifti(fout, "UVD_max_filter_window_count", temp_nii_output_extra, true);
} else if (mode_peak) {
save_output_nifti(fout, "UVD_peak_filter", nii_output, true);
save_output_nifti(fout, "UVD_peak_filter_window_count", temp_nii_output_extra, true);

} else if (mode_cols) {
save_output_nifti(fout, "UVD_columns_mode_filter", nii_output, true);
Expand Down