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Commit 10f37e0c authored by Matthew Webster's avatar Matthew Webster
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Current Version Jan 15

parent 9b3a18b5
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with 57 additions and 94 deletions
fslcreatehd.cc
+ 57
− 94
View file @ 10f37e0c
......@@ -23,75 +23,57 @@ void print_usage(const string& progname)
int fslcreatehd_main(int argc, char *argv[])
{
FSLIO* fslio;
void *buffer=NULL;
char *hdrxml, *filename;
int fileread=1, filetype=-1, existingimage=0;
size_t bufsize=0;
short x,y,z,v, dt=-1;
NiftiIO reader;
vector <NiftiExtension> extensions;
NiftiHeader header,originalHeader;
char *buffer(NULL);
string filename;
int fileread(1);
bool existingImage(false);
if (argc==3) {
/* use the XML form of header specification */
filename = argv[2];
} else {
filename = argv[13];
}
if (argc==3) /* use the XML form of header specification */
filename = string(argv[2]);
else
filename = string(argv[13]);
/* check if file already exists and if so, read the image contents */
/* also store the size of this buffer for later in case it is wrong */
if (FslFileExists(filename)) {
/* buffer = FslReadAllVolumes(fslio,filename); */
existingimage = 1;
fslio = FslOpen(filename,"rb");
FslGetDim(fslio,&x,&y,&z,&v);
filetype = FslGetFileType(fslio);
bufsize = x * y * z * v * (FslGetDataType(fslio,&dt) / 8);
buffer = (void *) calloc(bufsize,1);
FslReadVolumes(fslio,buffer,v);
FslClose(fslio);
existingImage = true;
filename=return_validimagefilename(filename);
header=reader.loadImage(filename,buffer,extensions);
originalHeader=header;
}
if (existingimage) {
fslio = FslXOpen(filename,"wb",filetype);
} else {
fslio = FslOpen(filename,"wb");
filetype = FslGetFileType(fslio);
}
if (argc>3) {
/* set uninteresting defaults */
if (existingimage) {
FslSetDataType(fslio,dt);
} else {
FslSetDataType(fslio,atoi(argv[12]));
}
FslSetDim(fslio,atoi(argv[1]),atoi(argv[2]),atoi(argv[3]),atoi(argv[4]));
FslSetVoxDim(fslio,atof(argv[5]),atof(argv[6]),atof(argv[7]),atof(argv[8]));
{
short short_array[100];
short_array[0]=atoi(argv[9]);
short_array[1]=atoi(argv[10]);
short_array[2]=atoi(argv[11]);
if ( (short_array[0]!=0) || (short_array[1]!=0) || (short_array[2]!=0) )
{
FslSetAnalyzeSform(fslio,short_array,
atof(argv[5]),atof(argv[6]),atof(argv[7]));
}
if (!existingImage)
header.datatype=atoi(argv[12]);
header.dim[0]=4;
for (int i=1;i<=4;i++)
header.dim[i]=atoi(argv[i]);
for (int i=1;i<=4;i++)
header.pixdim[i]=atoi(argv[i+4]);
if ( atoi(argv[9]) != 0 || atoi(argv[10]) != 0 || atoi(argv[11]) != 0 ) {
header.sX[3]=atoi(argv[9]);
header.sY[3]=atoi(argv[10]);
header.sZ[3]=atoi(argv[11]);
header.sX[0]=atoi(argv[5]);
header.sY[1]=atoi(argv[6]);
header.sZ[2]=atoi(argv[7]);
}
} else {
/* read XML form */
char *newstr, *oldfname, *oldiname;
ifstream inputfile;
vector<string> settings;
if (strcmp(argv[1],"-")==0) {fileread=0;}
newstr = (char *)calloc(10000,1);
oldfname = (char *)calloc(10000,1);
oldiname = (char *)calloc(10000,1);
//hdrxml = (char *)calloc(65534,1); /* too long, to be safe */
hdrxml = new char[65534];
if (fileread)
{
inputfile.open (argv[1], ifstream::in | ifstream::binary);
......@@ -112,60 +94,41 @@ int fslcreatehd_main(int argc, char *argv[])
{
if (fgets(newstr,9999,stdin)==NULL) break;
}
strcat(hdrxml,newstr);
} while (strcmp(newstr + strlen(newstr) - 2,"/>")!=0);
settings.push_back(string(newstr));
} while (settings[settings.size()-1]!="/>");
strcpy(oldfname,fslio->niftiptr->fname);
strcpy(oldiname,fslio->niftiptr->iname);
int bytes_read=1; //dummy for function call
fslio->niftiptr = nifti_image_from_ascii(hdrxml, &bytes_read);
header=NiftiHeader(settings);
if (fslio->niftiptr == NULL)
{
cerr << "Incomplete or incorrect text: could not form header info" << endl;
return EXIT_FAILURE;
}
fslio->niftiptr->fname = oldfname;
fslio->niftiptr->iname = oldiname;
if (fileread)
inputfile.close();
}
//free(hdrxml);
delete [] hdrxml;
if (fileread) inputfile.close();
/* reset datatype in case it has been overwritten */
if (existingImage) {
header.datatype=originalHeader.datatype;
header.bitsPerVoxel=header.bpvOfDatatype();
}
/* reset filetype and datatype in case it has been overwritten */
FslSetFileType(fslio,filetype);
if (existingimage) {
/* dt is only set if an image was previously read */
FslSetDataType(fslio,dt);
/* if previously read buffer is wrong size then make a zero image here */
if ( header.nElements() != originalHeader.nElements() ) {
if(buffer!=NULL)
delete buffer;
buffer = new char[header.nElements()*(header.bpvOfDatatype()/8)];
fill(buffer,buffer+header.nElements(),0);
}
fslio->niftiptr->byteorder = nifti_short_order();
// if (strcmp(argv[argc-1],"-r")==0) {
// /* swap */
// if (nifit_short_order()==MSB_FIRST) fslio->niftiptr->byteorder = LSB_FIRST;
// else fslio->niftiptr->byteorder = MSB_FIRST;
// }
/* write header */
FslWriteHeader(fslio);
int filetype=FslGetEnvOutputType();
if(!existingImage) {
filename=make_basename(filename)+outputExtension(filetype);
}
/* if previously read buffer is wrong size then make a zero image here */
FslGetDim(fslio,&x,&y,&z,&v);
if ( bufsize != ( x * y * z * v * (FslGetDataType(fslio,&dt)/8)) ) {
if (bufsize>0) free(buffer); /* only if previously read */
buffer = (void *) calloc(x * y * z * v,FslGetDataType(fslio,&dt)/8);
}
//header.report();
header.bitsPerVoxel=header.bpvOfDatatype();
header.setNiftiVersion(FslNiftiVersionFileType(filetype),FslIsSingleFileType(filetype));
reader.saveImage(filename,buffer,extensions,header, FslIsCompressedFileType(filetype));
/* write the data out - either from previous read or zeros */
FslWriteVolumes(fslio,buffer,fslio->niftiptr->dim[4]);
FslClose(fslio);
return 0;
}
}
int main(int argc,char *argv[])
......
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