void
Extractor::Go()
{
double val;
for (int i=0; i<newcube.dimx; i++) {
for (int j=0; j<newcube.dimy; j++) {
for (int k=0; k<newcube.dimz; k++) {
val=regioncode(i,j,k);
if (xvflag==0 || val==xval)
newcube.SetValue(i,j,k,val);
}
}
}
newcube.WriteFile();
return;
}
int receive_3d (char *fifo, char *path, int dimx, int dimy, int dimz, int datatype)
{
char fifo_from_idl [PATH_MAX];
char fifo_to_idl [PATH_MAX];
char line[200];
int i;
strcpy (fifo_from_idl, fifo );
strcpy (fifo_to_idl, fifo );
strcat (fifo_from_idl, "-");
readfifopath = fifo_from_idl;
return_path = fifo_to_idl;
FILE *f = fopen (fifo_from_idl, "rb");
if (!f)
complain(BADPATH);
read_fifo = f;
#ifdef DEBUG
fprintf (stderr, "Entered receive_3d\n");
fflush (stderr);
#endif
//----------------------------------------------
// Check params
//
if (dimx <= 0 || dimy <= 0 || dimz <= 0)
complain(ERROR_BADDIMS);
if (datatype < 0)
complain(ERROR_BADTYPE);
//----------------------------------------------
// Get data type & size.
//
VB_datatype dt2;
int datasize=0;
switch (datatype) {
case 1: dt2 = vb_byte; datasize=1; break;
case 2: dt2 = vb_short; datasize=2; break;
case 3: dt2 = vb_long; datasize=4; break;
case 4: dt2 = vb_float; datasize=sizeof(float); break;
case 5: dt2 = vb_double; datasize=sizeof(double); break;
default:
return ERROR_BADTYPE;
}
//----------------------------------------------
// Get the user-header info.
//
vector<string> user_header;
if (0 > readline(f, line, 199))
complain(ERROR_EOF);
int total_header_items = atoi(line);
if (total_header_items < 0)
complain(ERROR_BADHEADER);
for (i=0; i < total_header_items; i++) {
if (0 > readline(f, line, 199))
complain(ERROR_EOF);
user_header.push_back (string(line));
}
//----------------------------------------------
// Create the Cube object & put the data in it.
//
Cube *c = new Cube(dimx,dimy,dimz,dt2);
if (!c)
complain(ERROR_NOMEM);
//----------------------------------------------
// Store the user header into the Cube object.
//
for (i=0; i < total_header_items; i++) {
c->header.push_back (user_header[i]);
}
//----------------------------------------------
// Now we process specific user header data
// that we know have equivalents in the Tes object.
//
for (i=0; i < total_header_items; i++) {
const char *s = user_header[i].c_str();
char *s2 = s ? strchr(s, ':') : NULL;
if (s2 && '*' == *s2)
continue;
#ifdef DEBUG
fprintf(stderr, "putdata got user header line: %s\n", s);
#endif
if (!s2) s2 = s ? strchr (s, '=') : NULL;
if (s2) {
*s2++ = 0;
if (!strcasecmp (s, "VoxSizes(xyz)")) {
double x,y,z;
if (3 == sscanf (s2, "%lg %lg %lg", &x,&y,&z)) {
c->voxsize[0] = x;
c->voxsize[1] = y;
c->voxsize[2] = z;
} else {
WARNING("invalid voxsizes from user header.");
}
}
else
if (!strcasecmp (s, "Origin(xyz)")) {
int x,y,z;
if (3 == sscanf (s2, "%d %d %d", &x,&y,&z)) {
c->origin[0] = x;
c->origin[1] = y;
c->origin[2] = z;
} else {
WARNING("invalid origin from user header.");
}
}
else
if (!strcasecmp (s, "Orientation")) {
c->orient = s2;
}
else
if (!strcasecmp (s, "Scale")) {
// float f = atof(s2);
// c->scalefactor = f ? f : 1.0;
}
else
if (!strcasecmp (s, "ByteOrder")) {
c->filebyteorder = atoi(s2)? ENDIAN_BIG : ENDIAN_LITTLE;
}
}
}
//----------------------------------------------
// Get the data
//
ulong chunk_size = dimx * dimy * dimz * datasize;
unsigned char *chunk = (unsigned char*) malloc (chunk_size);
if (!chunk)
complain(ERROR_NOMEM);
if (chunk_size != fread (chunk,1,chunk_size,f))
complain(ERROR_READFAIL);
fclose (f);
read_completed = true;
c->data = chunk;
//----------------------------------------------
// Write the Cube to a file.
//
c->SetFileName (path);
#ifdef DEBUG
fprintf(stderr, "Calling write cube to file %s\n", path);
#endif
c->WriteFile ();
//----------------------------------------------
// Return the success code
//
f = fopen (fifo_to_idl, "wb");
if (!f)
return 0;
fprintf (f, "0\n");
fflush(f);
fclose(f);
delete c;
return 0;
}
int
main(int argc,char *argv[])
{
if (argc==1) {
vbconv_help();
exit(0);
}
tokenlist args;
string outfile;
int floatflag=0,nanflag=0,extractflag=0;
set<int> includeset,excludeset;
list<string> filelist;
VBFF nullff;
args.Transfer(argc-1,argv+1);
for (size_t i=0; i<args.size(); i++) {
if (args[i]=="-f")
floatflag=1;
else if (args[i]=="-n")
nanflag=1;
else if (args[i]=="-i" && i<args.size()-1) {
includeset=numberset(args[++i]);
if (includeset.empty()) {
cout << "[E] vbconv: invalid inclusion range specified with -i\n";
exit(111);
}
}
else if (args[i]=="-e" && i<args.size()-1) {
excludeset=numberset(args[++i]);
if (excludeset.empty()) {
cout << "[E] vbconv: invalid exclusion range specified with -e\n";
exit(111);
}
}
else if (args[i]=="-x" && i<args.size()-1)
extractflag=1;
else if (args[i]=="-v") {
vbconv_version();
exit(0);
}
else if (args[i]=="-h") {
vbconv_help();
exit(0);
}
else if (args[i]=="-o" && i<args.size()-1)
outfile=args[++i];
else {
filelist.push_back(args[i]);
}
}
if (filelist.size()<1) {
printf("[E] vbconv: requires at least one input file\n");
exit(10);
}
// if there's no -o flag and exactly two files specified, convert
// the first to the second
if (filelist.size()==2 && outfile.size()==0) {
outfile=filelist.back();
filelist.pop_back();
}
if (outfile.size()==0) {
printf("[E] vbconv: requires an output filename be provided\n");
exit(11);
}
// multiple files, must be 3D/4D combination
if (filelist.size()>1) {
Tes newtes;
ConvertMultiple(filelist,nanflag,floatflag,newtes);
if (WriteTes(newtes,outfile,extractflag,floatflag,nanflag,includeset,excludeset))
exit(223);
exit(0); // just in case
}
int err;
// just one file, see what kind
Cube cb;
if (cb.ReadFile(filelist.front())==0) {
cb.fileformat=nullff;
if (floatflag && cb.datatype!=vb_float)
cb.convert_type(vb_float);
if (nanflag)
cb.removenans();
if ((err=cb.WriteFile(outfile))) {
printf("[E] vbconv: error %d writing %s\n",err,outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote cube %s\n",outfile.c_str());
exit(0);
}
}
Tes ts;
if (ts.ReadFile(filelist.front())==0) {
ts.fileformat=nullff;
if ((err=WriteTes(ts,outfile,extractflag,floatflag,nanflag,includeset,excludeset))) {
printf("[E] vbconv: error %d writing %s\n",err,outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote 4D volume %s\n",outfile.c_str());
exit(0);
}
}
VB_Vector vv;
if (vv.ReadFile(*filelist.begin())==0) {
// vv.fileformat=nullff; // FIXME -- can we set 1d fileformat?
if (vv.WriteFile(outfile)) {
printf("[E] vbconv: error writing %s\n",outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote vector %s\n",outfile.c_str());
exit(0);
}
}
printf("[E] vbconv: couldn't make sense of file %s\n",filelist.front().c_str());
exit(100);
}
int
main(int argc,char *argv[])
{
tokenlist args;
Tes *tes;
Cube *cub;
int ind=0;
stringstream tmps;
args.Transfer(argc-1,argv+1);
if (args.size() == 0) {
tes2cub_help();
exit(0);
}
if (args.size() != 2 && args.size() != 3) {
tes2cub_help();
exit(5);
}
if (args.size() == 3)
ind = strtol(args[2]);
tes = new Tes();
if (tes->ReadFile(args[0])) {
tmps.str("");
tmps << "tes2cub: couldn't read tes file " << args[0];
printErrorMsg(VB_ERROR,tmps.str());
exit(5);
}
if (!tes->data_valid) {
tmps.str("");
tmps << "tes2cub: tes file " << args[0] << "isn't valid.";
printErrorMsg(VB_ERROR,tmps.str());
exit(5);
}
if (ind > tes->dimt) {
tmps.str("");
tmps << "tes2cub: index (" << ind << ") is beyond the last image (" << tes->dimt << ").";
printErrorMsg(VB_ERROR,tmps.str());
exit(5);
}
cub = new Cube((*tes)[ind]);
if (!cub->data_valid) {
tmps.str("");
tmps << "tes2cub: error extracting the cube from the 4D file (shouldn't happen!).";
printErrorMsg(VB_ERROR,tmps.str());
exit(5);
}
if (!cub->WriteFile(args[1])) {
tmps.str("");
tmps << "tes2cub: wrote cube " << ind << " to file " << args[1] << ".";
printErrorMsg(VB_INFO,tmps.str());
exit(0);
}
else {
tmps.str("");
tmps << "tes2cub: failed to write extracted cube to file " << args[1] << ".";
printErrorMsg(VB_INFO,tmps.str());
exit(5);
}
exit(0);
}