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meshify.c
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#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#ifdef _MSC_VER
#else
#include <unistd.h>
#endif
#include <time.h>
#ifdef HAVE_ZLIB
#include <zlib.h>
#ifdef HAVE_JSON
#include "cJSON.h"
#endif
#endif
#include "meshify.h"
#include "base64.h" //required for GIfTI
#include "bwlabel.h"
#include "radixsort.h"
#include "meshtypes.h"
#ifdef USE_CLASSIC_CUBES
#include "oldcubes.h"
#else
#include "MarchingCubes.h"
#endif
#ifndef MIN
#define MIN(a,b) (((a)<(b))?(a):(b))
#define MAX(a,b) (((a)>(b))?(a):(b))
#endif
double sqr(double x) {
return x * x;
}
double dx(vec3d p0, vec3d p1) {
return sqrt( sqr(p0.x - p1.x) + sqr(p0.y - p1.y) + sqr(p0.z - p1.z));
}
int unify_vertices(vec3d **inpt, vec3i *tris, int npt, int ntri, bool verbose) {
//"vertex welding": reduces the number of vertices, number of faces unchanged
double startTime = clockMsec();
vec3d *pts = *inpt;
int *old2new = (int *)malloc(npt * sizeof(int));
vec3d pt0 = pts[0];
float* dx_in = (float*)malloc(npt*sizeof(float));
float* dx_out = (float*)malloc(npt*sizeof(float));
uint32_t* idx_in = (uint32_t*)malloc(npt*sizeof(uint32_t));
uint32_t* idx_out = (uint32_t*)malloc(npt*sizeof(uint32_t));
for (int i = 0; i < npt; i++) {
//printf("%d %d\n", i, npt);
dx_in[i] = dx(pt0, pts[i]);
idx_in[i] = i;
old2new[i] = -1;//not yet set
}
radix11sort_f32(dx_in, dx_out, idx_in, idx_out, npt);
free(dx_in);
free(idx_in);
int nnew = 0; //number of unique vertices
float tol = 0.00001; //tolerance: accept two vertices as identical if they are nearer
for (int i=0;i<npt;i++) {
if (old2new[idx_out[i]] >= 0)
continue; //already assigned
float dx0 = dx_out[i];
vec3d pt0 = pts[idx_out[i]];
int j = i;
while ((j < npt) && ((dx_out[j] - dx0) < tol)) {
if (dx(pt0, pts[idx_out[j]]) < tol) {
old2new[idx_out[j]] = nnew;
}
j++;
}
nnew++;
}
free(dx_out);
free(idx_out);
if (npt == nnew) {
if (verbose)
printf("Unify vertices found no shared vertices\n");
free(old2new);
return npt;
}
for (int i=0;i<ntri;i++) { //remap face indices
tris[i].x = old2new[tris[i].x];
tris[i].y = old2new[tris[i].y];
tris[i].z = old2new[tris[i].z];
}
vec3d *oldpts = (vec3d *) malloc(npt * sizeof(vec3d));
for (int i=0;i<npt;i++)
oldpts[i] = pts[i];
free(*inpt);
*inpt = (vec3d *) malloc(nnew * sizeof(vec3d));
pts = *inpt;
for (int i=0;i<npt;i++)
pts[old2new[i]] = oldpts[i];
free(oldpts);
free(old2new);
if (verbose)
printf("vertex welding %d -> %d: %ld ms\n", npt, nnew, timediff(startTime, clockMsec()));
return nnew;
}
#ifndef FLT_EPSILON
#define FLT_EPSILON 1.19209290e-07F // float
//#define DBL_EPSILON 2.2204460492503131e-16 // double
#endif
int remove_degenerate_triangles(vec3d *pts, vec3i **intris, int ntri, bool verbose) {
//reduces the number of triangles, number of vertices unchanged
double startTime = clockMsec();
vec3i *tris = *intris;
int *isdegenerate = (int *) malloc(ntri * sizeof(int));
int ndegenerate = 0;
for (int i=0;i<ntri;i++) {
//sorted lengths a ≥ b ≥ c
isdegenerate[i] = 0;
double l = dx(pts[tris[i].x], pts[tris[i].y]);
double m = dx(pts[tris[i].x], pts[tris[i].z]);
double n = dx(pts[tris[i].y], pts[tris[i].z]);
double c = fmin(fmin(l, m), n);
double a = fmax(fmax(l, m), n);
double b = l+m+n-a-c;
if ((c-(a-b)) <= 0.0) {
isdegenerate[i] = 1;
ndegenerate ++;
continue;
}
#define REQUIRE_SIGNIFICANT_AREA
#ifdef REQUIRE_SIGNIFICANT_AREA
//use Heron’s Formula to eliminate triangles of tiny area
// see Kahan: Miscalculating Area and Angles of a Needle-like Triangle
// https://people.eecs.berkeley.edu/~wkahan/Triangle.pdf
double area4 = 0.25 * sqrt( (a+(b+c)) * (c-(a-b)) * (c+(a-b)) * (a+(b-c)) );
if (area4 < FLT_EPSILON) {
isdegenerate[i] = 1;
ndegenerate ++;
}
#endif //REQUIRE_SIGNIFICANT_AREA
}
if (ndegenerate == 0) {
free(isdegenerate);
return ntri;
}
int newtri = ntri - ndegenerate;
vec3i *oldtris = (vec3i *) malloc(ntri * sizeof(vec3i));
for (int i=0;i<ntri;i++)
oldtris[i] = tris[i];
free(*intris);
*intris = (vec3i *) malloc(newtri * sizeof(vec3i));
tris = *intris;
int j = 0;
for (int i=0;i<ntri;i++) {
if (isdegenerate[i])
continue;
tris[j] = oldtris[i];
j++;
}
free(oldtris);
free(isdegenerate);
if (verbose)
printf("remove degenerate triangles %d -> %d: %ld ms\n", ntri, newtri, timediff(startTime, clockMsec()));
return newtri;
}
int quick_smooth(float * img, int nx, int ny, int nz) {
if ((nx < 5) || (ny < 5) || (nz < 5))
return EXIT_FAILURE;
int nvox = nx * ny * nz;
float *tmp = (float *) malloc(nvox * sizeof(float));
#define kwid 2
#define k0 0.45
#define k1 0.225
#define k2 0.05
int nxy = nx * ny;
int nxy2 = nxy * 2;
int nx2 = nx * 2;
//smooth column direction
memcpy(tmp, img, nvox * sizeof(float)); //dst,src,n
for (int z = 0; z < nz; z++) {
for (int y = 0; y < ny; y++) {
int zy = (y * nx) + (z * nxy);
for (int x = kwid; x < (nx-kwid); x++) {
int v = zy + x;
tmp[v] = (img[v-2]*k2)+(img[v-1]*k1)+(img[v]*k0)+(img[v+1]*k1)+(img[v+2]*k2);
}
}
}
//smooth row direction:
memcpy(img, tmp, nvox * sizeof(float)); //dst,src,n
for (int z = 0; z < nz; z++) {
for (int x = 0; x < nx; x++) {
int xz = x + (z * nxy);
for (int y = kwid; y < (ny - kwid); y++) {
int v = xz + (y * nx);
tmp[v] = (img[v-nx2]*k2)+(img[v-nx]*k1)+(img[v]*k0)+(img[v+nx]*k1)+(img[v+nx2]*k2);
}
}
}
memcpy(img, tmp, nvox * sizeof(float)); //dst,src,n
for (int y = 0; y < ny; y++) {
for (int x = 0; x < nx; x++) {
int yx = (y * nx) + x;
for (int z = kwid; z < (nz-kwid); z++) {
int v = yx + (z * nxy);
img[v] = (tmp[v-nxy2]*k2)+(tmp[v-nxy]*k1)+(tmp[v]*k0)+(tmp[v+nxy]*k1)+(tmp[v+nxy2]*k2);
}
}
}
free(tmp);
return EXIT_SUCCESS;
}
void dilate(float * img, size_t dim[3], bool is26) {
int nx = dim[0];
int ny = dim[1];
int nz = dim[2];
int nxy = nx * ny;
int nvox = nx * ny * nz;
uint8_t* mask = (uint8_t *) malloc(nvox * sizeof(uint8_t));
memset(mask, 0, nvox * sizeof(uint8_t));
int numk = 6;
if (is26)
numk = 26;
int32_t *k = (int32_t *)malloc(numk * sizeof(int32_t)); //queue with untested seed
if (is26) {
int j = 0;
for (int z = -1; z <= 1; z++)
for (int y = -1; y <= 1; y++)
for (int x = -1; x <= 1; x++) {
if ((x == 0) && (y == 0) && (z == 0)) continue;
k[j] = x + (y * nx) + (z * nx * ny);
j++;
} //for x
} else { //if 26 neighbors else 6..
k[0] = nx * ny; //up
k[1] = -k[0]; //down
k[2] = nx; //anterior
k[3] = -k[2]; //posterior
k[4] = 1; //left
k[5] = -1;
}
for (int z = 1; z < (nz - 1); z++) {
for (int y = 1; y < (ny - 1); y++) {
size_t iyz = + (z * nxy) + (y * nx);
for (int x = 1; x < (nx - 1); x++) {
size_t vx = iyz + x;
for (int n = 1; n < numk; n++) {
if (img[vx + k[n]] > 0)
mask[vx] = 1;
} //check all neighbors
} //x
} //y
} //z
for (int v = 1; v < nvox; v++)
if (mask[v] > 0)
img[v] = 1;
free(mask);
free(k);
}
double clockMsec() { //return milliseconds since midnight
#ifdef _MSC_VER
clock_t t = clock();
return (double)((double)t) / (CLOCKS_PER_SEC / 1000.0);
#else
struct timespec _t;
clock_gettime(CLOCK_MONOTONIC, &_t);
return _t.tv_sec*1000.0 + (_t.tv_nsec/1.0e6);
#endif
}
long timediff(double startTimeMsec, double endTimeMsec) {
return round(endTimeMsec - startTimeMsec);
}
int meshify(float * img, size_t dim[3], int originalMC, float isolevel, vec3i **t, vec3d **p, int *nt, int *np, int preSmooth, bool onlyLargest, bool fillBubbles, bool verbose) {
// img: input volume
// hdr: nifti header
// isolevel: air/surface threshold
// t: triangle indices e.g. [0,1,3] indicates triangle composed of vertices 0,1,3
// p: 3D points, aka vertices
// nt: number of triangles, aka faces
// np: number of points
int NX = dim[0];
int NY = dim[1];
int NZ = dim[2];
int nvox = NX*NY*NZ;
// preSmooth: Gaussian blur to soften image
if (preSmooth) {
double startTime = clockMsec();
quick_smooth(img, NX, NY, NZ);
if (verbose)
printf("pre-smooth: %ld ms\n", timediff(startTime, clockMsec()));
}
//determine image intensity range - ensure isolvel will detect edge
float mx = img[0];
float mn = mx;
for (int i=0; i< nvox; i++) {
mx = fmaxf(mx, img[i]);
mn = fminf(mn, img[i]);
}
if (mn == mx) {
printf("Error: No variability in image intensity.\n");
return EXIT_FAILURE;
}
if ((isolevel <= mn) || (isolevel > mx)) {
isolevel = 0.5 * (mn + mx);
printf("Suggested isolevel out of range. Intensity range %g..%g, setting isolevel to %g\n", mn, mx, isolevel);
}
if (verbose)
printf("intensity range %g..%g, isolevel %g\n", mn, mx, isolevel);
//(optional) fill bubbles and only extract largest contiguous object
if ((onlyLargest) || (fillBubbles)) {
double startTime = clockMsec();
float* mask = (float *) malloc(nvox * sizeof(float));
size_t dim[3] = {(size_t)NX, (size_t)NY, (size_t)NZ};
memset(mask, 0, nvox * sizeof(float));
for (int i=0;i<nvox;i++)
if (img[i] >= isolevel)
mask[i] = 1;
bwlabel(mask, 18, dim, onlyLargest, fillBubbles);
if (fillBubbles) {
for (int i=0;i<nvox;i++)
if (mask[i] != 0)
img[i] = fmax(img[i], isolevel);
}
if (onlyLargest) {
dilate(mask, dim, true); //expand by one voxel to preserve subvoxel edges
for (int i=0;i<nvox;i++)
if (mask[i] == 0)
img[i] = mn;
}
free(mask);
if (verbose)
printf("voxel clustering (largest cluster, bubbles): %ld ms\n", timediff(startTime, clockMsec()));
}
//edge darken
float edgeMax = 0.75 * (mn + isolevel);
int vx = 0;
int lo[3] = {NX,NY,NZ};
int hi[3] = {0,0,0};
for (int z=0;z<NZ;z++) //darken edges
for (int y=0;y<NY;y++)
for (int x=0;x<NX;x++) {
if (img[vx] >= isolevel) {
lo[0] = MIN(x, lo[0]);
lo[1] = MIN(y, lo[1]);
lo[2] = MIN(z, lo[2]);
hi[0] = MAX(x, hi[0]);
hi[1] = MAX(y, hi[1]);
hi[2] = MAX(z, hi[2]);
}
if ((x == 0) || (y == 0) || (z == 0) || (x == (NX-1)) || (y == (NY-1)) || (z == (NZ-1)) )
img[vx] = fminf(edgeMax, img[vx]);
vx++;
}
//printf("Bounding box for bright voxels: %d..%d %d..%d %d..%d\n", lo[0], hi[0], lo[1], hi[1], lo[2], hi[2]);
for (int i=0;i<3;i++) {
lo[i] = MAX(lo[i] - 1, 0);
hi[i] = MIN(hi[i] + 2, dim[i]);
}
double startTimeMC = clockMsec();
vec3d *pts = NULL;
vec3i *tris = NULL;
int ntri;
int npt;
if (marchingCubes(img, dim, lo, hi, originalMC, isolevel, &pts, &tris, &npt, &ntri) != EXIT_SUCCESS)
return EXIT_FAILURE;
if (verbose)
printf("marching cubes (%dx%dx%d): %ld ms\n", NX, NY, NZ, timediff(startTimeMC, clockMsec()));
npt = unify_vertices(&pts, tris, npt, ntri, verbose);
if (npt < 3) return EXIT_FAILURE;
ntri = remove_degenerate_triangles(pts, &tris, ntri, verbose);
*t = tris;
*p = pts;
*nt = ntri;
*np = npt;
return EXIT_SUCCESS;
}
bool littleEndianPlatform () {
uint32_t value = 1;
return (*((char *) &value) == 1);
}
void swap_4bytes( size_t n , void *ar ) { // 4 bytes at a time
size_t ii ;
unsigned char * cp0 = (unsigned char *)ar, * cp1, * cp2 ;
unsigned char tval ;
for( ii=0 ; ii < n ; ii++ ){
cp1 = cp0; cp2 = cp0+3;
tval = *cp1; *cp1 = *cp2; *cp2 = tval;
cp1++; cp2--;
tval = *cp1; *cp1 = *cp2; *cp2 = tval;
cp0 += 4;
}
return ;
}
typedef struct {
float x,y,z;
} vec3s; //single precision (float32)
vec3s vec3d2vec4s(vec3d v) {
return (vec3s){.x = (float)v.x, .y = (float)v.y, .z = (float)v.z};
} // convert float64 to float32
int save_freesurfer(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt) {
//FreeSurfer Triangle Surface Binary Format http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm
uint8_t magic[3] = {0xFF, 0xFF, 0xFE};
FILE *fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
fwrite(magic, 3, 1, fp);
time_t t = time(NULL);
char s[128] = "";
struct tm *tm = localtime(&t);
strftime(s, sizeof(s), "created by niimath on %c\n\n", tm);
fwrite(s, strlen(s), 1, fp);
int32_t VertexCount = npt;
int32_t FaceCount = ntri;
if ( &littleEndianPlatform) {
swap_4bytes(1, &VertexCount);
swap_4bytes(1, &FaceCount);
}
fwrite(&VertexCount, sizeof(int32_t), 1, fp);
fwrite(&FaceCount, sizeof(int32_t), 1, fp);
vec3s *pts32 = (vec3s *) malloc(npt * sizeof(vec3s));
for (int i = 0; i < npt; i++) //double->single precision
pts32[i] = vec3d2vec4s(pts[i]);
if (&littleEndianPlatform)
swap_4bytes(npt * 3, pts32);
fwrite(pts32, npt * sizeof(vec3s), 1, fp);
free(pts32);
if (&littleEndianPlatform) {
vec3i *trisSwap = (vec3i *) malloc(ntri * sizeof(vec3i));
for (int i = 0; i < ntri; i++)
trisSwap[i] = tris[i];
swap_4bytes(ntri * 3, trisSwap);
fwrite(trisSwap, ntri * sizeof(vec3i), 1, fp);
free(trisSwap);
} else
fwrite(tris, ntri * sizeof(vec3i), 1, fp);
fclose(fp);
return EXIT_SUCCESS;
}
#ifdef HAVE_ZLIB
#ifdef HAVE_JSON
enum TZipMethod {zmZlib, zmGzip, zmBase64, zmLzip, zmLzma, zmLz4, zmLz4hc};
int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize, unsigned char **outputbuf, const int zipid, int *ret, const int iscompress){
z_stream zs;
size_t buflen[2]={0};
*outputbuf=NULL;
zs.zalloc = Z_NULL;
zs.zfree = Z_NULL;
zs.opaque = Z_NULL;
if(inputsize==0)
return -1;
if(iscompress){
/** perform compression or encoding */
if(zipid==zmBase64){
/** base64 encoding */
*outputbuf=base64_encode((const unsigned char*)inputstr, inputsize, outputsize);
}else if(zipid==zmZlib){
/** zlib (.zip) or gzip (.gz) compression */
if(deflateInit(&zs, (iscompress>0) ? Z_DEFAULT_COMPRESSION : (-iscompress)) != Z_OK)
return -2;
buflen[0] =deflateBound(&zs,inputsize);
*outputbuf=(unsigned char *)malloc(buflen[0]);
zs.avail_in = inputsize; /* size of input, string + terminator*/
zs.next_in = (Bytef *)inputstr; /* input char array*/
zs.avail_out = buflen[0]; /* size of output*/
zs.next_out = (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/
*ret=deflate(&zs, Z_FINISH);
*outputsize=zs.total_out;
if(*ret!=Z_STREAM_END && *ret!=Z_OK)
return -3;
deflateEnd(&zs);
}else{
return -7;
}
}else{
/** perform decompression or decoding */
if(zipid==zmBase64){
/** base64 decoding */
*outputbuf=base64_decode((const unsigned char*)inputstr, inputsize, outputsize);
}else if(zipid==zmZlib){
/** zlib (.zip) or gzip (.gz) decompression */
int count=1;
if(zipid==zmZlib)
if(inflateInit(&zs) != Z_OK)
return -2;
buflen[0] =inputsize*20;
*outputbuf=(unsigned char *)malloc(buflen[0]);
zs.avail_in = inputsize; /* size of input, string + terminator*/
zs.next_in =inputstr; /* input char array*/
zs.avail_out = buflen[0]; /* size of output*/
zs.next_out = (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/
while((*ret=inflate(&zs, Z_SYNC_FLUSH))!=Z_STREAM_END && count<=10){
*outputbuf=(unsigned char *)realloc(*outputbuf, (buflen[0]<<count));
zs.next_out = (Bytef *)(*outputbuf+(buflen[0]<<(count-1)));
zs.avail_out = (buflen[0]<<(count-1)); /* size of output*/
count++;
}
*outputsize=zs.total_out;
if(*ret!=Z_STREAM_END && *ret!=Z_OK)
return -3;
inflateEnd(&zs);
}else{
return -7;
}
}
return 0;
}
int save_jmsh(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
FILE *fp;
cJSON *root=NULL, *hdr=NULL, *node=NULL, *face=NULL;
char *jsonstr=NULL;
int dim[2]={0,3}, len[2]={1,0};
size_t compressedbytes, totalbytes;
unsigned char *compressed=NULL, *buf=NULL;
int ret=0, status=0;
root=cJSON_CreateObject();
cJSON_AddItemToObject(root, "_DataInfo_", hdr = cJSON_CreateObject());
cJSON_AddStringToObject(hdr, "JMeshVersion", "0.5");
cJSON_AddStringToObject(hdr, "Comment", "Created by nii2mesh");
cJSON_AddItemToObject(root, "MeshVertex3", node = cJSON_CreateObject());
cJSON_AddStringToObject(node,"_ArrayType_","double");
dim[0]=npt;
cJSON_AddItemToObject(node, "_ArraySize_",cJSON_CreateIntArray(dim,2));
cJSON_AddStringToObject(node,"_ArrayZipType_","zlib");
len[1]=dim[0]*dim[1];
cJSON_AddItemToObject(node, "_ArrayZipSize_",cJSON_CreateIntArray(len,2));
totalbytes=dim[0]*dim[1]*sizeof(pts[0].x);
unsigned int *val=(unsigned int *)malloc(totalbytes);
memcpy(val,&(tris[0].x),totalbytes);
for(int i=0;i<len[1];i++)
val[i]++;
ret=zmat_run(totalbytes, (unsigned char *)val, &compressedbytes, (unsigned char **)&compressed, zmZlib, &status,1);
free(val);
if(!ret){
ret=zmat_run(compressedbytes, compressed, &totalbytes, (unsigned char **)&buf, zmBase64, &status,1);
cJSON_AddStringToObject(node, "_ArrayZipData_",(char *)buf);
}
if(compressed){
free(compressed);
compressed=NULL;
}
if(buf){
free(buf);
buf=NULL;
}
cJSON_AddItemToObject(root, "MeshTri3", face = cJSON_CreateObject());
cJSON_AddStringToObject(face,"_ArrayType_","uint32");
dim[0]=ntri;
cJSON_AddItemToObject(face, "_ArraySize_",cJSON_CreateIntArray(dim,2));
cJSON_AddStringToObject(face,"_ArrayZipType_","zlib");
len[1]=dim[0]*dim[1];
cJSON_AddItemToObject(face, "_ArrayZipSize_",cJSON_CreateIntArray(len,2));
totalbytes=dim[0]*dim[1]*sizeof(tris[0].x);
ret=zmat_run(totalbytes, (unsigned char *)&(tris[0].x), &compressedbytes, (unsigned char **)&compressed, zmZlib, &status,1);
if(!ret){
ret=zmat_run(compressedbytes, compressed, &totalbytes, (unsigned char **)&buf, zmBase64, &status,1);
cJSON_AddStringToObject(face, "_ArrayZipData_",(char *)buf);
}
if(compressed)
free(compressed);
if(buf)
free(buf);
jsonstr=cJSON_Print(root);
if(jsonstr==NULL)
return EXIT_FAILURE;
fp=fopen(fnm,"wt");
if(fp==NULL)
return EXIT_FAILURE;
fprintf(fp,"%s\n",jsonstr);
fclose(fp);
if(jsonstr)
free(jsonstr);
if(root)
cJSON_Delete(root);
return EXIT_SUCCESS;
}
#endif //HAVE_JSON
#endif //HAVE_ZLIB
int save_json(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
FILE *fp = fopen(fnm,"w");
if (fp == NULL)
return EXIT_FAILURE;
fprintf(fp,"{\n");
fprintf(fp,"\t\"_DataInfo_\":{\n\t\t\"JMeshVersion\":\"0.5\",\n\t\t\"Comment\":\"Created by nii2mesh\"\n\t},\n");
fprintf(fp,"\t\"MeshVertex3\":[\n");
for (int i=0;i<npt;i++)
fprintf(fp, "[%g,\t%g,\t%g],\n", pts[i].x, pts[i].y,pts[i].z);
fprintf(fp,"\t],\n\t\"MeshTri3\":[\n");
for (int i=0;i<ntri;i++)
fprintf(fp, "[%d,\t%d,\t%d],\n", tris[i].x+1, tris[i].y+1, tris[i].z+1);
fprintf(fp,"\t]\n}\n");
fclose(fp);
return EXIT_SUCCESS;
}
int save_mz3(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt, bool isGz) {
//https://github.com/neurolabusc/surf-ice/tree/master/mz3
#ifdef _MSC_VER
#pragma pack(2)
struct mz3hdr {
uint16_t SIGNATURE, ATTR;
uint32_t NFACE, NVERT, NSKIP;
};
#pragma pack()
#else
struct __attribute__((__packed__)) mz3hdr {
uint16_t SIGNATURE, ATTR;
uint32_t NFACE, NVERT, NSKIP;
};
#endif
struct mz3hdr h;
h.SIGNATURE = 0x5A4D;
h.ATTR = 3;//isFACE +1 isVERT +2
h.NFACE = ntri;
h.NVERT = npt;
h.NSKIP = 0;
if (! &littleEndianPlatform)
swap_4bytes(3, &h.NFACE);
FILE *fp;
#ifdef HAVE_ZLIB
gzFile fgz;
if (isGz) {
fgz = gzopen(fnm, "w");
if (! fgz)
return EXIT_FAILURE;
gzwrite(fgz, &h, sizeof(struct mz3hdr));
} else
#endif
{
fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
fwrite(&h, sizeof(struct mz3hdr), 1, fp);
}
if (! &littleEndianPlatform) {
vec3i *trisSwap = (vec3i *) malloc(ntri * sizeof(vec3i));
for (int i = 0; i < ntri; i++)
trisSwap[i] = tris[i];
swap_4bytes(ntri * 3, trisSwap);
#ifdef HAVE_ZLIB
if (isGz)
gzwrite(fgz, trisSwap, ntri * sizeof(vec3i));
else
#else
fwrite(trisSwap, ntri * sizeof(vec3i), 1, fp);
#endif
free(trisSwap);
} else {
#ifdef HAVE_ZLIB
if (isGz)
gzwrite(fgz, tris, ntri * sizeof(vec3i));
else
#endif
fwrite(tris, ntri * sizeof(vec3i), 1, fp);
}
vec3s *pts32 = (vec3s *) malloc(npt * sizeof(vec3s));
for (int i = 0; i < npt; i++) //double->single precision
pts32[i] = vec3d2vec4s(pts[i]);
if (! &littleEndianPlatform)
swap_4bytes(npt * 3, pts32);
#ifdef HAVE_ZLIB
if (isGz) {
gzwrite(fgz, pts32, npt * sizeof(vec3s));
gzclose(fgz);
} else
#endif
{
fwrite(pts32, npt * sizeof(vec3s), 1, fp);
fclose(fp);
}
free(pts32);
return EXIT_SUCCESS;
}
int save_off(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
FILE *fp = fopen(fnm,"w");
if (fp == NULL)
return EXIT_FAILURE;
fprintf(fp,"OFF\n%d\t%d\t0\n",npt,ntri);
for (int i=0;i<npt;i++)
fprintf(fp, "%g %g %g\n", pts[i].x, pts[i].y,pts[i].z);
for (int i=0;i<ntri;i++)
fprintf(fp, "%d %d %d\n", tris[i].x+1, tris[i].y+1, tris[i].z+1);
fclose(fp);
return EXIT_SUCCESS;
}
int save_obj(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
FILE *fp = fopen(fnm,"w");
if (fp == NULL)
return EXIT_FAILURE;
for (int i=0;i<npt;i++)
fprintf(fp, "v %g %g %g\n", pts[i].x, pts[i].y,pts[i].z);
for (int i=0;i<ntri;i++)
fprintf(fp, "f %d %d %d\n", tris[i].x+1, tris[i].y+1, tris[i].z+1);
fclose(fp);
return EXIT_SUCCESS;
}
int save_stl(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
//binary STL http://paulbourke.net/dataformats/stl/
//n.b. like other tools, ignores formal restriction that all adjacent facets must share two common vertices.
//n.b. does not write normal
#ifdef _MSC_VER
#pragma pack(2)
typedef struct {
vec3s norm, pts[3];
uint16_t spacer;
} tfacet;
#pragma pack()
#else
typedef struct __attribute__((__packed__)) {
vec3s norm, pts[3];
uint16_t spacer;
} tfacet;
#endif
FILE *fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
uint8_t hdr[80] = { 0 };
fwrite(hdr, 80, 1, fp);
int32_t nf = ntri;
fwrite(&nf, sizeof(int32_t), 1, fp);
tfacet *facets = (tfacet *) malloc(ntri * sizeof(tfacet));
vec3s n0 = (vec3s){.x = 0.0, .y = 0.0, .z = 0.0};
for (int i = 0; i < ntri; i++) { //double->single precision
facets[i].norm = n0;
facets[i].pts[0] = vec3d2vec4s(pts[tris[i].x]);
facets[i].pts[1] = vec3d2vec4s(pts[tris[i].y]);
facets[i].pts[2] = vec3d2vec4s(pts[tris[i].z]);
facets[i].spacer = 0;
}
fwrite(facets, ntri * sizeof(tfacet), 1, fp);
free(facets);
fclose(fp);
return EXIT_SUCCESS;
}
int save_ply(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
#ifdef _MSC_VER
#pragma pack(1)
typedef struct {
uint8_t n;
int32_t x,y,z;
} vec1b3i;
#pragma pack()
#else
typedef struct __attribute__((__packed__)) {
uint8_t n;
int32_t x,y,z;
} vec1b3i;
#endif
FILE *fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
fputs("ply\n",fp);
if (&littleEndianPlatform)
fputs("format binary_little_endian 1.0\n",fp);
else
fputs("format binary_big_endian 1.0\n",fp);
fputs("comment niimath\n",fp);
char vpts[80];
sprintf(vpts, "element vertex %d\n", npt);
fwrite(vpts, strlen(vpts), 1, fp);
fputs("property float x\n",fp);
fputs("property float y\n",fp);
fputs("property float z\n",fp);
char vfc[80];
sprintf(vfc, "element face %d\n", ntri);
fwrite(vfc, strlen(vfc), 1, fp);
fputs("property list uchar int vertex_indices\n",fp);
fputs("end_header\n",fp);
vec3s *pts32 = (vec3s *) malloc(npt * sizeof(vec3s));
for (int i = 0; i < npt; i++) { //double->single precision
pts32[i].x = pts[i].x;
pts32[i].y = pts[i].y;
pts32[i].z = pts[i].z;
}
fwrite(pts32, npt * sizeof(vec3s), 1, fp);
free(pts32);
vec1b3i *tris4 = (vec1b3i *) malloc(ntri * sizeof(vec1b3i));
for (int i = 0; i < ntri; i++) { //double->single precision
tris4[i].n = 3;
tris4[i].x = tris[i].x;
tris4[i].y = tris[i].y;
tris4[i].z = tris[i].z;
}
fwrite(tris4, ntri * sizeof(vec1b3i), 1, fp);
free(tris4);
fclose(fp);
return EXIT_SUCCESS;
}
int save_gii(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt, bool isGz){
//https://www.nitrc.org/projects/gifti/
//https://stackoverflow.com/questions/342409/how-do-i-base64-encode-decode-in-c
FILE *fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
fputs("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",fp);
fputs("<!DOCTYPE GIFTI SYSTEM \"http://www.nitrc.org/frs/download.php/115/gifti.dtd\">\n",fp);
fputs("<GIFTI Version=\"1.0\" NumberOfDataArrays=\"2\">\n",fp);
fputs(" <MetaData>\n",fp);
fputs(" <MD>\n",fp);
fputs(" <Name><![CDATA[nii2mesh-version]]></Name>\n",fp);
fputs(" <Value><![CDATA[nii2mesh, 1 Jan 2022]]></Value>\n",fp);
fputs(" </MD>\n",fp);
fputs(" </MetaData>\n",fp);
fputs(" <LabelTable/>\n",fp);
fputs(" <DataArray ArrayIndexingOrder=\"RowMajorOrder\"\n",fp);
fputs(" DataType=\"NIFTI_TYPE_INT32\"\n",fp);
char fc[80];
sprintf(fc, " Dim0=\"%d\"\n", ntri);
fwrite(fc, strlen(fc), 1, fp);
fputs(" Dim1=\"3\"\n",fp);
fputs(" Dimensionality=\"2\"\n",fp);
#ifdef HAVE_ZLIB
if (isGz)
fputs(" Encoding=\"GZipBase64Binary\"\n" ,fp);
else
#endif
fputs(" Encoding=\"Base64Binary\"\n" ,fp);
if (&littleEndianPlatform)
fputs(" Endian=\"LittleEndian\"\n",fp);
else
fputs(" Endian=\"BigEndian\"\n",fp);
fputs(" ExternalFileName=\"\"\n",fp);
fputs(" ExternalFileOffset=\"\"\n",fp);
fputs(" Intent=\"NIFTI_INTENT_TRIANGLE\">\n" ,fp);
fputs(" <MetaData>\n",fp);
fputs(" </MetaData>\n",fp);
fputs(" <Data>",fp);
size_t out_len;
unsigned char * fcs;
#ifdef HAVE_ZLIB
if (isGz) {
unsigned long srcLen = ntri * sizeof(vec3i);
unsigned long destLen = compressBound(srcLen);
unsigned char* ostream = (unsigned char*) malloc(destLen);
int res = compress(ostream, &destLen,(const unsigned char *) tris, srcLen);
if (res != Z_OK)
printf("Compression error\n");
fcs = base64_encode(ostream, destLen, &out_len);
free(ostream);
} else
#endif
fcs = base64_encode((const unsigned char *) tris, ntri * sizeof(vec3i), &out_len);
fwrite(fcs, out_len, 1, fp);
free(fcs);
fputs("</Data>\n",fp);
fputs(" </DataArray>\n",fp);
fputs(" <DataArray ArrayIndexingOrder=\"RowMajorOrder\"\n",fp);
fputs(" DataType=\"NIFTI_TYPE_FLOAT32\"\n",fp);
char vpts[80];
sprintf(vpts, " Dim0=\"%d\"\n", npt);
fwrite(vpts, strlen(vpts), 1, fp);
fputs(" Dim1=\"3\"\n",fp);
fputs(" Dimensionality=\"2\"\n",fp);
#ifdef HAVE_ZLIB
if (isGz)
fputs(" Encoding=\"GZipBase64Binary\"\n" ,fp);
else
#endif
fputs(" Encoding=\"Base64Binary\"\n" ,fp);
if (&littleEndianPlatform)
fputs(" Endian=\"LittleEndian\"\n",fp);
else
fputs(" Endian=\"BigEndian\"\n",fp);
fputs(" ExternalFileName=\"\"\n",fp);
fputs(" ExternalFileOffset=\"\"\n",fp);
fputs(" Intent=\"NIFTI_INTENT_POINTSET\">\n",fp);
fputs(" <MetaData>\n",fp);
fputs(" </MetaData>\n",fp);
fputs(" <CoordinateSystemTransformMatrix>\n",fp);
fputs(" <DataSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></DataSpace>\n",fp);
fputs(" <TransformedSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></TransformedSpace>\n",fp);
fputs(" <MatrixData>1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 </MatrixData>\n",fp);
fputs(" </CoordinateSystemTransformMatrix>\n",fp);
fputs(" <Data>",fp);
vec3s *pts32 = (vec3s *) malloc(npt * sizeof(vec3s));
for (int i = 0; i < npt; i++)//double->single precision
pts32[i] = vec3d2vec4s(pts[i]);
unsigned char * vts;
#ifdef HAVE_ZLIB
if (isGz) {
unsigned long srcLen = npt * sizeof(vec3s);
unsigned long destLen = compressBound(srcLen);
unsigned char* ostream = (unsigned char*) malloc(destLen);
int res = compress(ostream, &destLen,(const unsigned char *) pts32, srcLen);
if (res != Z_OK)
printf("Compression error\n");
vts = base64_encode(ostream, destLen, &out_len);
free(ostream);
} else
#endif
vts = base64_encode((const unsigned char *) pts32, npt * sizeof(vec3s), &out_len);
free(pts32);
fwrite(vts, out_len, 1, fp);
free(vts);
fputs("</Data>\n",fp);
fputs(" </DataArray>\n",fp);
fputs("</GIFTI>\n",fp);
fclose(fp);
return EXIT_SUCCESS;
}
int save_vtk(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt){
typedef struct {
uint32_t n, x,y,z;
} vec4i;
FILE *fp = fopen(fnm,"wb");
if (fp == NULL)
return EXIT_FAILURE;
fputs("# vtk DataFile Version 3.0\n",fp);
fputs("this file was written using niimath\n",fp);
fputs("BINARY\n",fp);
fputs("DATASET POLYDATA\n",fp);
char vpts[80];
sprintf(vpts, "POINTS %d float\n", npt);
fwrite(vpts, strlen(vpts), 1, fp);
vec3s *pts32 = (vec3s *) malloc(npt * sizeof(vec3s));
for (int i = 0; i < npt; i++)//double->single precision
pts32[i] = vec3d2vec4s(pts[i]);
if (&littleEndianPlatform)
swap_4bytes(3*npt, pts32);
fwrite(pts32, npt * sizeof(vec3s), 1, fp);
free(pts32);
char vfac[80];
sprintf(vfac, "POLYGONS %d %d\n", ntri, ntri * 4);
fwrite(vfac, strlen(vfac), 1, fp);
vec4i *tris4 = (vec4i *) malloc(ntri * sizeof(vec4i));
for (int i = 0; i < ntri; i++) { //double->single precision
tris4[i].n = 3;
tris4[i].x = tris[i].x;
tris4[i].y = tris[i].y;
tris4[i].z = tris[i].z;
}
if (&littleEndianP
5B57
latform)
swap_4bytes(4*ntri, tris4);
fwrite(tris4, ntri * sizeof(vec4i), 1, fp);
free(tris4);
fclose(fp);
return EXIT_SUCCESS;
}
void strip_ext(char *fname){
char *end = fname + strlen(fname);
while (end > fname && *end != '.' && *end != '\\' && *end != '/') {
--end;
}
if ((end > fname && *end == '.') &&
(*(end - 1) != '\\' && *(end - 1) != '/')) {
*end = '\0';
}
}
int save_mesh(const char *fnm, vec3i *tris, vec3d *pts, int ntri, int npt, bool isGz){
char basenm[768], ext[768] = "";
strcpy(basenm, fnm);
strip_ext(basenm); // ~/file.nii -> ~/file
if (strlen(fnm) > strlen(basenm))
strcpy(ext, fnm + strlen(basenm));
if (strstr(ext, ".gii"))
return save_gii(fnm, tris, pts, ntri, npt, isGz);
else if ((strstr(ext, ".inflated")) || (strstr(ext, ".pial")))
return save_freesurfer(fnm, tris, pts, ntri, npt);
#ifdef HAVE_ZLIB
#ifdef HAVE_JSON
else if (strstr(ext, ".jmsh"))
return save_jmsh(fnm, tris, pts, ntri, npt);
#endif //HAVE_JSON
#endif //HAVE_ZLIB
else if (strstr(ext, ".json"))
return save_json(fnm, tris, pts, ntri, npt);
else if (strstr(ext, ".mz3"))
return save_mz3(fnm, tris, pts, ntri, npt, isGz);
else if (strstr(ext, ".off"))
return save_off(fnm, tris, pts, ntri, npt);
else if (strstr(ext, ".obj"))
return save_obj(fnm, tris, pts, ntri, npt);
else if (strstr(ext, ".ply"))
return save_ply(fnm, tris, pts, ntri, npt);
else if (strstr(ext, ".stl"))
return save_stl(fnm, tris, pts, ntri, npt);