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Adds new nurbs format #107

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10 changes: 7 additions & 3 deletions gecatsim/clib_build/src/ct_nurbs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -101,16 +101,20 @@ typedef struct qnet
POINT **Qw;
} QNET;

typedef struct surface
{
typedef struct material {
int MU_ID;
float FRACTION;
} MATERIAL;

typedef struct surface {
CNET net;
DEGREE p,
q;
KNOTVECTOR knu,
knv;
float min_x, max_x, min_y, max_y, min_z, max_z;
float centerx, centery, centerz;
int MU_ID;
MATERIAL MU[10];
} SURFACE;

typedef struct xpoint
Expand Down
120 changes: 104 additions & 16 deletions gecatsim/clib_build/src/nCAT_main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3218,7 +3218,27 @@ int isEmptyString(char *line)
return 1;
}

DLLEXPORT void Parse_Phantom(char *filename, int *materials, float *coord_origin_offset, float scale) // JDP
int get_line(char *buffer, int buffer_size, FILE *fp) {
for (;;) {
char *q = fgets(buffer, buffer_size, fp);
if (q == NULL) {
if (feof(fp)) {
return EOF;
}
if (ferror(fp)) {
return -1;
}
}
if (isEmptyString(q)) {
continue;
}
break;
}
return 1;
}

DLLEXPORT void Parse_Phantom(char *filename, int *materials,
float *coord_origin_offset, float scale) // JDP
/* This routine parses a NURBS phantom file output from the NCAT */
{
FILE *fp;
Expand All @@ -3227,7 +3247,11 @@ DLLEXPORT void Parse_Phantom(char *filename, int *materials, float *coord_origin
float temp, tx, ty, tz;
char line[160];
int tmp = 0;
int ID;
int num_ids = 0;
int num_fractions = 0;
char temp_char = 0;
int ID[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
float fraction[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0};

use_tri_model = 0;
if ((fp = fopen(filename, "r")) == NULL)
Expand Down Expand Up @@ -3329,13 +3353,53 @@ DLLEXPORT void Parse_Phantom(char *filename, int *materials, float *coord_origin
dbug(0, "Error: Maximum number of nurbs models (%d) exceeded.\r\nSee Parse_Phantom routine in nCAT_main.c\r\n", max_num_models);
exit(1);
}
fscanf(fp, "%i", &ID);
nrb_model[k].MU_ID = ID; // Material integer ID for the object, ID's I use are in ct_global_vars.h file
materials[ID] = 1; // Place a 1 in the materials array to let it know material[ID] is included
// reads MU IDs
get_line(line, sizeof(line) - 1, fp);
dbug(1, line);
num_ids =
sscanf(line, "%i,%i,%i,%i,%i,%i,%i,%i,%i,%i", &ID[0], &ID[1], &ID[2],
&ID[3], &ID[4], &ID[5], &ID[6], &ID[7], &ID[8], &ID[9]);

// Tries to read M parameter for old ct format. If not, use new ct format.
get_line(line, sizeof(line) - 1, fp);
dbug(1, line);

sscanf(line, "%i %cM", &m, &temp_char);
fraction[0] = 1.0;
dbug(1, "temp_char: %c\n", temp_char);
if (temp_char != ':') {
num_fractions = sscanf(
line, "%f,%f,%f,%f,%f,%f,%f,%f,%f,%f", &fraction[0], &fraction[1],
&fraction[2], &fraction[3], &fraction[4], &fraction[5], &fraction[6],
&fraction[7], &fraction[8], &fraction[9]);
if (num_fractions == EOF || num_fractions != num_ids) {
dbug(0,
"Error: Number of material fractions doesn't match number of "
"material ids in phantom surface declaration.\r\n num_fractions: "
"%i, num_ids: %i. \r\n See "
"Parse_Phantom routine in nCAT_main.c\r\n",
max_num_models, num_ids, num_fractions);
exit(1);
}
get_line(line, sizeof(line) - 1, fp);
dbug(1, line);
sscanf(line, "%i", &m);
}
for (i = 0; i < 8; i++) {
nrb_model[k].MU[i].MU_ID =
ID[i]; // Material integer ID for the object, ID's I use are in
// ct_global_vars.h file
nrb_model[k].MU[i].FRACTION = fraction[i];
materials[ID[i]] = 1; // Place a 1 in the materials array to let it know
// material[ID] is included
if (ID[i] < 0 | fraction[i] < 0) {
dbug(1, "%s %i %f", k, ID[i], fraction[i]);
}
ID[i] = 0;
fraction[i] = 0;
}

/* Read in M and N parameters */
fscanf(fp, "%i", &m);
fscanf(fp, "%s", line);
fscanf(fp, "%i", &n);
fscanf(fp, "%s", line);

Expand Down Expand Up @@ -3388,13 +3452,14 @@ DLLEXPORT void Parse_Phantom(char *filename, int *materials, float *coord_origin
dbug(2, "f\n");

k++;
tmp = fscanf(fp, "%s", line);
tmp = get_line(line, sizeof(line), fp);
}
NUM_NRB = k;
fclose(fp);
NUM_MODELS = NUM_NRB;

dbug(0, "Done parsing nCAT phantom.\r\n");
return;
}

int Intersect_segments(LINE_SEG A, LINE_SEG B) /*A = higher priority segment*/
Expand Down Expand Up @@ -3612,8 +3677,28 @@ void Break_segment2(SEG_ARRAY lines, SEG_ARRAY *segments)
}
}

void Calc_line_int(SEG_ARRAY lines, SEG_ARRAY segments, float mu_table[MAXIMUM_NUMBER_OF_MATERIALS][300], int energy_ID, float *line_int)
{
float get_attenuation(SURFACE surface,
float mu_table[MAXIMUM_NUMBER_OF_MATERIALS][300],
int energy_ID

) {
float atten = 0;
int id;
float frac;
int j;

for (j = 0; j < 8; j++) {
id = surface.MU[j].MU_ID;
frac = surface.MU[j].FRACTION;
dbug(1, "id: %i, frac: %f\n", id, frac);
atten = atten + mu_table[id][energy_ID] * frac;
}
return atten;
}

void Calc_line_int(SEG_ARRAY lines, SEG_ARRAY segments,
float mu_table[MAXIMUM_NUMBER_OF_MATERIALS][300],
int energy_ID, float *line_int) {

// THIS FUNCTION IS NOW OBSOLETE

Expand All @@ -3627,14 +3712,16 @@ void Calc_line_int(SEG_ARRAY lines, SEG_ARRAY segments, float mu_table[MAXIMUM_N
for (i = 0; i < segments.length; i++)
{
dist = segments.sp[i].x2 - segments.sp[i].x1;
atten = mu_table[nrb_model[segments.sp[i].organ_id].MU_ID][energy_ID];
atten = get_attenuation(nrb_model[segments.sp[i].organ_id], mu_table,
energy_ID);
*line_int += (atten * dist);
// dbug(1,"dist[%d]: %1.14f atten: %1.14f\r\n",i,dist,atten);
}

dist = lines.sp[lines.length - 1].x2 - lines.sp[lines.length - 1].x1;
dbug(1, "dist[X]: %1.14f\r\n", dist);
atten = mu_table[nrb_model[lines.sp[lines.length - 1].organ_id].MU_ID][energy_ID];
atten = get_attenuation(nrb_model[lines.sp[lines.length - 1].organ_id],
mu_table, energy_ID);
*line_int += (atten * dist);
}
}
Expand Down Expand Up @@ -3678,7 +3765,8 @@ void Calc_line_int2(SEG_ARRAY segments, float mu_table[MAXIMUM_NUMBER_OF_MATERIA
// dbug(0,"%d %d\r\n",i, segments.sp[i].organ_id);
// dbug(0,"%d\r\n",nrb_model[segments.sp[i].organ_id].MU_ID);
dist = segments.sp[i].x2 - segments.sp[i].x1;
atten = mu_table[nrb_model[segments.sp[i].organ_id].MU_ID][energy_ID];
atten = get_attenuation(nrb_model[segments.sp[i].organ_id], mu_table,
energy_ID);
*line_int += (atten * dist);
// dbug(1,"dist[%d]: %1.14f atten: %1.14f\r\n",i,dist,atten);
}
Expand Down Expand Up @@ -5899,14 +5987,14 @@ void intersections_NCAT_all(SEG_ARRAY *segments, float *a, float *alpha, float *
// Update: June 2019: I went ahead and switched this to Break_segment2... seems to work fine
}
}

/*
DLLEXPORT void make_vol_ncat(float *volume, int Nx, double xoff, double dx, int Ny, double yoff, double dy, int Nz, double zoff, double dz, int oversampling, int UNUSED_num_volumes, int material_volumes)

{
int i, j, k, l, m, p, energyBinsToSkip = 0, volume_offset, muid, muidp;
float a[3], alpha[3], alpha_inv[3], *matl_tabl, tmp;
double rayLength, xbrd;
SEG_ARRAY segments; /*Array of line segments*/
SEG_ARRAY segments; /*Array of line segments

other_initializations();
matl_tabl = malloc(sizeof(float) * n_materials);
Expand Down Expand Up @@ -6044,7 +6132,7 @@ DLLEXPORT void make_vol_ncat(float *volume, int Nx, double xoff, double dx, int
}
free(matl_tabl);
}

*/
void intersections_NCAT(double *detCenter, double *right, double *up, double *sampling, int nSubDets, float *sourcePoints, double *thisView, int detIndex, double subviewWeight, double *detWeights)

{
Expand Down