diff --git a/fslcpgeom.cc b/fslcpgeom.cc
index 41595b03b4dfd2ffd3375322cf59e73c7836049d..3779c7437649608b577ebe7886d5887648362e43 100755
--- a/fslcpgeom.cc
+++ b/fslcpgeom.cc
@@ -17,12 +17,11 @@ void print_usage(const string& progname)
int avwcpgeom_main(int argc, char *argv[])
{
- 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);
+ headerSrc=loadHeader(return_validimagefilename(string(argv[1])));
+ headerDest=loadHeader(fullDestinationName);
} catch (...) {
perror("Error opening files");
return EXIT_FAILURE;
@@ -38,7 +37,7 @@ int avwcpgeom_main(int argc, char *argv[])
}
vector<NiftiExtension> extensions;
- reader.loadImage(fullDestinationName,buffer,extensions,false);
+ loadImage(fullDestinationName,buffer,extensions,false);
headerDest.sformCode = headerSrc.sformCode;
headerDest.setSForm(headerSrc.getSForm());
@@ -49,7 +48,7 @@ int avwcpgeom_main(int argc, char *argv[])
if (copydim)
headerDest.dim=headerSrc.dim;
- reader.saveImage(fullDestinationName,buffer,extensions,headerDest,FslIsCompressedFileType(fslFileType(fullDestinationName)));
+ saveImage(fullDestinationName,buffer,extensions,headerDest,FslIsCompressedFileType(fslFileType(fullDestinationName)));
return 0;
}
diff --git a/fslcreatehd.cc b/fslcreatehd.cc
index ce97d36dd85c7279829b67e1e47152b2988dcf9a..c102f89847f11ec6152e56ac88ea784a68d9d459 100755
--- a/fslcreatehd.cc
+++ b/fslcreatehd.cc
@@ -23,10 +23,136 @@ void print_usage(const string& progname)
}
+NiftiHeader headerFromXML(vector<string> XMLreport)
+ {
+ NiftiHeader header;
+ int xyzUnits(0);
+ int tUnits(0);
+ int freqDim(0);
+ int phaseDim(0);
+ int sliceDim(0);
+ for(unsigned int setting=1;setting<XMLreport.size()-1;setting++) {
+ //Tokenise
+ size_t pos1=XMLreport[setting].find_first_of(" ")+2;
+ size_t pos2=XMLreport[setting].find_first_of(" ",pos1);
+ size_t pos3=XMLreport[setting].find_first_of('\'')+1;
+ size_t pos4=XMLreport[setting].find_last_of('\'');
+ string field(XMLreport[setting].substr(pos1,pos2-pos1));
+ string value(XMLreport[setting].substr(pos3,pos4-pos3));
+ istringstream values(value);
+ if ( field == "datatype" ) {
+ values >> header.datatype;
+ } else if ( field == "image_offset" ) {
+ values >> header.vox_offset;
+ } else if ( field == "sto_xyz_matrix" ) {
+ mat44 sForm;
+ for ( int i=0;i<4;i++ )
+ for ( int j=0;j<4;j++ )
+ values >> sForm.m[i][j];
+ header.setSForm(sForm);
+ } else if ( field == "ndim" ) {
+ values >> header.dim[0];
+ } else if ( field == "nx" ) {
+ values >> header.dim[1];
+ } else if ( field == "ny" ) {
+ values >> header.dim[2];
+ } else if ( field == "nz" ) {
+ values >> header.dim[3];
+ } else if ( field == "nt" ) {
+ values >> header.dim[4];
+ } else if ( field == "nu" ) {
+ values >> header.dim[5];
+ } else if ( field == "nv" ) {
+ values >> header.dim[6];
+ } else if ( field == "nw" ) {
+ values >> header.dim[7];
+ }else if ( field == "qfac" ) {
+ values >> header.pixdim[0];
+ } else if ( field == "dx" ) {
+ values >> header.pixdim[1];
+ } else if ( field == "dy" ) {
+ values >> header.pixdim[2];
+ } else if ( field == "dz" ) {
+ values >> header.pixdim[3];
+ } else if ( field == "dt" ) {
+ values >> header.pixdim[4];
+ } else if ( field == "du" ) {
+ values >> header.pixdim[5];
+ } else if ( field == "dv" ) {
+ values >> header.pixdim[6];
+ } else if ( field == "dw" ) {
+ values >> header.pixdim[7];
+ } else if ( field == "cal_min" ) {
+ values >> header.cal_min;
+ } else if ( field == "cal_max" ) {
+ values >> header.cal_max;
+ } else if ( field == "scl_slope" ) {
+ values >> header.sclSlope;
+ } else if ( field == "scl_inter" ) {
+ values >> header.sclInter;
+ } else if ( field == "intentCode" ) {
+ values >> header.sclSlope;
+ } else if ( field == "intent_p1" ) {
+ values >> header.sclInter;
+ } else if ( field == "intent_p2" ) {
+ values >> header.cal_min;
+ } else if ( field == "intent_p3" ) {
+ values >> header.cal_max;
+ } else if ( field == "intent_name" ) {
+ values >> header.intentName;
+ } else if ( field == "toffset" ) {
+ values >> header.toffset;
+ } else if ( field == "xyz_units" ) {
+ values >> xyzUnits;
+ } else if ( field == "time_units" ) {
+ values >> tUnits;
+ } else if ( field == "descrip" ) {
+ values >> header.description;
+ } else if ( field == "aux_file" ) {
+ values >> header.auxillaryFile;
+ } else if ( field == "qform_code" ) {
+ values >> header.qformCode;
+ } else if ( field == "sform_code" ) {
+ values >> header.sformCode;
+ } else if ( field == "quatern_b" ) {
+ values >> header.qB;
+ } else if ( field == "quatern_c" ) {
+ values >> header.qC;
+ } else if ( field == "quatern_d" ) {
+ values >> header.qD;
+ } else if ( field == "qoffset_x" ) {
+ values >> header.qX;
+ } else if ( field == "qoffset_y" ) {
+ values >> header.qY;
+ } else if ( field == "qoffset_z" ) {
+ values >> header.qZ;
+ } else if ( field == "freq_dim" ) {
+ values >> freqDim;
+ } else if ( field == "phase_dim" ) {
+ values >> phaseDim;
+ } else if ( field == "slice_dim" ) {
+ values >> sliceDim;
+ } else if ( field == "slice_code" ) {
+ values >> header.sliceCode;
+ } else if ( field == "slice_start" ) {
+ values >> header.sliceStart;
+ } else if ( field == "slice_end" ) {
+ values >> header.sliceEnd;
+ } else if ( field == "slice_duration" ) {
+ values >> header.sliceDuration;
+ } else {
+ //cerr << XMLreport[setting] << endl;
+ //cerr << "Unknown" << endl;
+ }
+ }
+ header.units=xyzUnits+tUnits;
+ header.sliceOrdering=freqDim | ( phaseDim << 2 ) | ( sliceDim << 4 );
+ header.bitsPerVoxel=header.bpvOfDatatype();
+ return header;
+ }
int fslcreatehd_main(int argc, char *argv[])
{
- NiftiIO reader;
vector <NiftiExtension> extensions;
NiftiHeader header,originalHeader;
char *buffer(NULL);
@@ -43,7 +169,7 @@ int fslcreatehd_main(int argc, char *argv[])
if (FslFileExists(filename)) {
existingImage = true;
filename=return_validimagefilename(filename);
- header=reader.loadImage(filename,buffer,extensions);
+ header=loadImage(filename,buffer,extensions);
originalHeader=header;
}
@@ -75,33 +201,27 @@ int fslcreatehd_main(int argc, char *argv[])
if (strcmp(argv[1],"-")==0) {fileread=0;}
newstr = (char *)calloc(10000,1);
- if (fileread)
- {
+ if (fileread) {
inputfile.open (argv[1], ifstream::in | ifstream::binary);
- if (!inputfile.is_open())
- {
- cerr << "Cannot open file " << argv[1] << endl;
- return EXIT_FAILURE;
- }
+ if (!inputfile.is_open()) {
+ cerr << "Cannot open file " << argv[1] << endl;
+ return EXIT_FAILURE;
+ }
}
- do
- {
- if (fileread)
- {
- inputfile.getline(newstr,9999); // maybe use > for delimiting character remove while increase size
- }
- else
- {
- if (fgets(newstr,9999,stdin)==NULL) break;
- }
- settings.push_back(string(newstr));
+ do {
+ if (fileread) {
+ inputfile.getline(newstr,9999); // maybe use > for delimiting character remove while increase size
+ } else {
+ if (fgets(newstr,9999,stdin)==NULL) break;
+ }
+ settings.push_back(string(newstr));
} while (settings[settings.size()-1]!="/>");
- header=NiftiHeader(settings);
+ header=headerFromXML(settings);
if (fileread)
- inputfile.close();
+ inputfile.close();
}
/* reset datatype in case it has been overwritten */
@@ -125,7 +245,7 @@ int fslcreatehd_main(int argc, char *argv[])
header.bitsPerVoxel=header.bpvOfDatatype();
header.setNiftiVersion(FslNiftiVersionFileType(filetype),FslIsSingleFileType(filetype));
- reader.saveImage(filename,buffer,extensions,header, FslIsCompressedFileType(filetype));
+ saveImage(filename,buffer,extensions,header, FslIsCompressedFileType(filetype));
return 0;
}
diff --git a/fslhd.cc b/fslhd.cc
index 773bac17bcf9e288f87b1aa24bee0c8058c83765..9d2171224a9bb18b2eb3d308b3ee6edbe531996c 100755
--- a/fslhd.cc
+++ b/fslhd.cc
@@ -1,6 +1,6 @@
// fslhd.cc - show image header
// Steve Smith, Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2000-2012 University of Oxford
+// Copyright (C) 2000-2019 University of Oxford
// CCOPYRIGHT
#include "newimage/newimageall.h"
@@ -90,10 +90,9 @@ int main(int argc,char *argv[])
if (argc < 2)
return print_usage(string(argv[0]));
bool reportXML(argc==3 && strcmp(argv[1],"-x")==0 );
- NiftiIO reader;
try {
string filename(return_validimagefilename(argv[argc-1]));
- NiftiHeader header(reader.loadHeader(filename));
+ NiftiHeader header(loadHeader(filename));
if (reportXML)
reportXMLHeader(header);
else {
diff --git a/fslmerge.cc b/fslmerge.cc
index 01e8ea117e958e20ea33024aef4f69f14dc04f8a..4ebf90f76368087bac1fde3ed2be5d8aa920a808 100755
--- a/fslmerge.cc
+++ b/fslmerge.cc
@@ -1,6 +1,6 @@
// fslmerge.cc concatenate AVW files into a single output
// Steve Smith, David Flitney, Stuart Clare and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2000-2010 University of Oxford
+// Copyright (C) 2000-2019 University of Oxford
// CCOPYRIGHT
#define EXPOSE_TREACHEROUS
#include "newimage/newimageall.h"
@@ -25,8 +25,7 @@ int fmrib_main(int argc, char *argv[])
volume4D<T> input_volume;
int direction,dimerror=0,xoffset=0,yoffset=0,zoffset=0,toffset=0;
- NiftiIO reader;
- NiftiHeader header(reader.loadHeader(return_validimagefilename(string(argv[3]))));
+ NiftiHeader header(loadHeader(return_validimagefilename(string(argv[3]))));
float newTR(header.pixdim[4]);
if (!strcmp(argv[1], "-t")) direction=0;
@@ -54,7 +53,7 @@ int fmrib_main(int argc, char *argv[])
for(int vol = 4; vol < argc; vol++)
{
- header=reader.loadHeader(return_validimagefilename(string(argv[vol])));
+ header=loadHeader(return_validimagefilename(string(argv[vol])));
if (direction==0) tdimtot+=std::max(header.dim[4],(int64_t)1);
if (direction==1) xdimtot+=std::max(header.dim[1],(int64_t)1);
if (direction==2) ydimtot+=std::max(header.dim[2],(int64_t)1);
diff --git a/fslnvols.cc b/fslnvols.cc
index 2557dcba18e94bdd1fe11315769e29fe94def26e..47fb2e8962af765d98773c8e701a9cc844d44ebe 100755
--- a/fslnvols.cc
+++ b/fslnvols.cc
@@ -1,13 +1,13 @@
// fslnvols.cc REALLY advanced program for counting the volumes in a 4D file
// Stephen Smith and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 1999-2005 University of Oxford
-// CCOPYRIGHT
+// Copyright (C) 1999-2019 University of Oxford
+// CCOPYRIGHT
#include "newimage/newimageall.h"
using namespace NEWIMAGE;
-void print_usage(const string& progname)
+void print_usage(const string& progname)
{
cout << endl;
cout << "Usage: fslnvols <input>" << endl;
@@ -21,14 +21,12 @@ int main(int argc,char *argv[])
print_usage(progname);
return 1;
}
- if (!FslFileExists(string(argv[1])))
- {
+ if (!FslFileExists(string(argv[1])))
+ {
cout << "0" << endl;
return 0; // the intended usage is to return "0" and not show an error
}
- NiftiIO reader;
- NiftiHeader header(reader.loadHeader(return_validimagefilename(string(argv[1]))));
+ NiftiHeader header(loadHeader(return_validimagefilename(string(argv[1]))));
cout << header.dim[4] << endl;
return 0;
}
-