From d7553ddc38f77d41741fc483ae78a341f45f9767 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Jan 2015 15:03:25 +0000
Subject: [PATCH] Current Version Jan 15
---
fslcpgeom.cc | 76 +++++++++++++++++-----------------------------------
1 file changed, 24 insertions(+), 52 deletions(-)
diff --git a/fslcpgeom.cc b/fslcpgeom.cc
index ab481b1..9977a84 100755
--- a/fslcpgeom.cc
+++ b/fslcpgeom.cc
@@ -17,70 +17,42 @@ void print_usage(const string& progname)
int avwcpgeom_main(int argc, char *argv[])
{
- FSLIO *src = NULL, *dest = NULL, *destcopy = NULL;
- short x, y, z, v, copydim=1, t, scode, qcode, dt=-1;
- float vx, vy, vz, tr;
- int filetype;
- mat44 smat, qmat;
- void *buffer = NULL;
- char desthdrname[10000];
- size_t nbytes, nsrcbytes, ndestbytes;
-
- if (argc>3)
- copydim=0;
-
- src = FslOpen(argv[1], "r");
-
- dest = FslOpen(argv[2], "r");
- destcopy = (FSLIO *)calloc(sizeof(FSLIO),1);
- FslCloneHeader(destcopy,dest);
-
- if ((src == NULL) || (dest == NULL)) {
+ NiftiIO reader;
+ NiftiHeader headerSrc,headerDest;
+ string fullDestinationName(return_validimagefilename(string(argv[2])));
+ try {
+ headerSrc=reader.loadHeader(return_validimagefilename(string(argv[1])));
+ headerDest=reader.loadHeader(fullDestinationName);
+ } catch (...) {
perror("Error opening files");
return EXIT_FAILURE;
}
- FslGetDim(src, &x, &y, &z, &v);
- nsrcbytes = x * y * z * v * (FslGetDataType(dest, &t) / 8);
- FslGetDim(dest, &x, &y, &z, &v);
- ndestbytes = x * y * z * v * (FslGetDataType(dest, &t) / 8);
- if (nsrcbytes > ndestbytes) nbytes=nsrcbytes; else nbytes=ndestbytes;
- if( (buffer = calloc(nbytes,1)) == NULL ) {
+ short copydim=1;
+ char *buffer = NULL;
+ size_t nbytes(max(headerSrc.nElements(),headerDest.nElements())*headerDest.bitsPerVoxel/8);
+
+ if( (buffer = (char*)calloc(nbytes,1)) == NULL ) {
perror("Unable to allocate memory for copy");
return EXIT_FAILURE;
}
- FslReadVolumes(dest, buffer, v);
+ if (argc>3)
+ copydim=0;
- strcpy(desthdrname,dest->niftiptr->fname);
- filetype = FslGetFileType(dest);
- FslGetDataType(dest,&dt);
- FslClose(dest);
- dest = FslXOpen(desthdrname, "wb", filetype);
- FslCloneHeader(dest,destcopy);
+ vector<NiftiExtension> extensions;
+ reader.loadImage(fullDestinationName,buffer,extensions,false);
- scode = FslGetStdXform(src,&smat);
- FslSetStdXform(dest,scode,smat);
- qcode = FslGetRigidXform(src,&qmat);
- FslSetRigidXform(dest,qcode,qmat);
-
- FslGetVoxDim(src, &vx, &vy, &vz, &tr);
- FslSetVoxDim(dest, vx, vy, vz, tr);
+ headerDest.sformCode = headerSrc.sformCode;
+ headerDest.setSForm(headerSrc.getSForm());
+ headerDest.qformCode = headerSrc.qformCode;
+ headerDest.setSForm(headerSrc.getQForm());
+ headerDest.pixdim=headerSrc.pixdim;
- if (copydim) {
- FslGetDim(src, &x, &y, &z, &v);
- FslSetDim(dest, x, y, z, v);
- }
-
-
- /* Preserve the datatype - probably unneccesary now, but left for safety */
- FslSetDataType(dest,dt);
-
- FslWriteHeader(dest);
- FslWriteVolumes(dest, buffer, v);
- FslClose(dest);
+ if (copydim)
+ headerDest.dim=headerSrc.dim;
- FslClose(src);
+ reader.saveImage(fullDestinationName,buffer,extensions,headerDest,FslIsCompressedFileType(fslFileType(fullDestinationName)));
return 0;
}
--
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