From 10f37e0c82d75a55322247b69b4ac5fa8509abc1 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Jan 2015 16:41:17 +0000
Subject: [PATCH] Current Version Jan 15
---
fslcreatehd.cc | 151 +++++++++++++++++++------------------------------
1 file changed, 57 insertions(+), 94 deletions(-)
diff --git a/fslcreatehd.cc b/fslcreatehd.cc
index 1faf1eb..947e991 100755
--- a/fslcreatehd.cc
+++ b/fslcreatehd.cc
@@ -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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