diff --git a/fslchfiletype b/fslchfiletype
index b2d1a5dc37c6917c5ded25f0a0227a54ea5303e6..fe812a3628305ccc287747fa8257165651500c35 100755
--- a/fslchfiletype
+++ b/fslchfiletype
@@ -10,11 +10,7 @@
# SHCOPYRIGHT
if [ $# -lt 2 ] ; then
- echo "Usage: $0 <filetype> <filename> [filename2]" ;
- echo " "
- echo " Changes the file type of the image file, or copies to new file"
- echo " Valid values of filetype are ANALYZE, NIFTI, NIFTI_PAIR,"
- echo " ANALYZE_GZ, NIFTI_GZ, NIFTI_PAIR_GZ"
+ ${FSLDIR}/bin/fslchfiletype_exe
exit 1 ;
fi
@@ -35,12 +31,11 @@ $FSLDIR/bin/fslchfiletype_exe $1 $oldfile $newfile
# for inplace stuff remove and copy old one
# exact mechanism is to be careful not to remove old IF a new one isn't writable in this place (eg over quota)
if [ $inplace = 1 ] ; then
- if [ `$FSLDIR/bin/imtest $newfile` = 1 ] ; then
+ if [ `$FSLDIR/bin/imtest $newfile` = 1 ] ; then
$FSLDIR/bin/immv $newfile ${oldfile}TMP
- if [ `$FSLDIR/bin/imtest ${oldfile}TMP` = 1 ] ; then
- $FSLDIR/bin/imrm $oldfile
+ if [ `$FSLDIR/bin/imtest ${oldfile}TMP` = 1 ] ; then
+ $FSLDIR/bin/imrm $oldfile
$FSLDIR/bin/immv ${oldfile}TMP $oldfile
fi
fi
fi
-
diff --git a/fslchfiletype.cc b/fslchfiletype.cc
index f70b8365f6aa9f493d59315a9863015565bbc505..b64810a91ef57b7c00ce9caa695676314f56477d 100644
--- a/fslchfiletype.cc
+++ b/fslchfiletype.cc
@@ -1,7 +1,7 @@
-// fslchfiletype.cc Conversion program for different volume types
+// fslchfiletype.cc Conversion program for different image types
// Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2008 University of Oxford
-// CCOPYRIGHT
+// Copyright (C) 2008-2019 University of Oxford
+// CCOPYRIGHT
#include "newimage/newimageall.h"
#include "newimage/fmribmain.h"
@@ -9,57 +9,51 @@
using namespace NEWIMAGE;
-int printUsage(const string& progname)
+
+int printUsage(const string& progname)
{
- cout << "Usage: " << progname << " <filetype> <filename> [filename2]" << endl << endl;
- cout << " Changes the file type of the image file, or copies to new file" << endl;
- cout << " Valid values of filetype are ANALYZE, NIFTI, NIFTI_PAIR," << endl;
- cout << " ANALYZE_GZ, NIFTI_GZ, NIFTI_PAIR_GZ" << endl;
+ const vector<pair<string,int> > formats=NEWIMAGE::fileFormats::allFormats();
+ cout << "Usage: fslchfiletype[_exe] <filetype> <filename> [filename2]" << endl << endl;
+ cout << "Changes the file type of the image file [ or copies to new file ]." << endl;
+ cout << "Valid values for filetype are:" << endl;
+ for ( std::vector<const pair<string,int> >::iterator it=formats.begin(); it != formats.end(); it++ )
+ cout << "\t" << it->first << endl;
return 1;
}
+
template <class T>
int fmrib_main(int argc, char *argv[])
{
volume<T> input;
- read_volume(input,string(argv[0]));
- save_volume_dtype(input,string(argv[1]),dtype(string(argv[0])));
+ read_volume(input,string(argv[2]));
+ int format(-1);
+ const vector<pair<string,int> > formats=NEWIMAGE::fileFormats::allFormats();
+ for ( std::vector<const pair<string,int> >::iterator it=formats.begin(); it != formats.end(); it++ )
+ if ( string(argv[1]) == it->first ) format = it->second;
+ if ( format == -1 )
+ return printUsage(string(argv[0]));
+ string outputFile( argc == 4 ? string(argv[3]) : string(argv[2]) );
+ save_volume_dtype(input,outputFile,dtype(string(argv[2])),format);
return 0;
}
+
int main(int argc,char *argv[])
{
if (argc < 3 || argc > 4)
return printUsage(string(argv[0]));
string inputFile(argv[2]);
- string outputFile(argv[2]);
- if (argc==4) outputFile=string(argv[3]);
-
- int outputType(-1);
- if (string(argv[1])=="ANALYZE") outputType=FSL_TYPE_ANALYZE;
- else if (string(argv[1])=="NIFTI") outputType=FSL_TYPE_NIFTI;
- else if (string(argv[1])=="NIFTI_PAIR") outputType=FSL_TYPE_NIFTI_PAIR;
- else if (string(argv[1])=="ANALYZE_GZ") outputType=FSL_TYPE_ANALYZE_GZ;
- else if (string(argv[1])=="NIFTI_GZ") outputType=FSL_TYPE_NIFTI_GZ;
- else if (string(argv[1])=="NIFTI_PAIR_GZ") outputType=FSL_TYPE_NIFTI_PAIR_GZ;
- else return printUsage(string(argv[0]));
+ string outputFile( argc == 4 ? string(argv[3]) : string(argv[2]) );
- //argv[1] has a valid outtype at this point
- setenv("FSLOUTPUTTYPE",argv[1], true);
-
- if (dtype(inputFile)==DT_COMPLEX)
+ if (dtype(inputFile)==DT_COMPLEX)
{
volume4D<float> real, imaginary;
read_complexvolume(real, imaginary, inputFile);
save_complexvolume(real, imaginary, outputFile);
+ return 0;
}
- else
- {
- argv[0]= const_cast <char*>(inputFile.c_str());
- argv[1]= const_cast <char*>(outputFile.c_str());
- call_fmrib_main(dtype(inputFile),argc,argv);
- }
+ call_fmrib_main(dtype(inputFile),argc,argv);
return 0;
}
-
diff --git a/fslcpgeom.cc b/fslcpgeom.cc
index 6911ec22f3bb49bbb42b0546175211d7ce42e573..41595b03b4dfd2ffd3375322cf59e73c7836049d 100755
--- a/fslcpgeom.cc
+++ b/fslcpgeom.cc
@@ -28,7 +28,7 @@ int avwcpgeom_main(int argc, char *argv[])
return EXIT_FAILURE;
}
- short copydim=1;
+ short copydim( argc > 3 ? 0 : 1);
char *buffer = NULL;
size_t nbytes(max(headerSrc.nElements(),headerDest.nElements())*headerDest.bitsPerVoxel/8);
@@ -37,9 +37,6 @@ int avwcpgeom_main(int argc, char *argv[])
return EXIT_FAILURE;
}
- if (argc>3)
- copydim=0;
-
vector<NiftiExtension> extensions;
reader.loadImage(fullDestinationName,buffer,extensions,false);
diff --git a/fslcreatehd.cc b/fslcreatehd.cc
index 1e9ca3e98e22ac93706504e6da945e95fac6c34d..ce97d36dd85c7279829b67e1e47152b2988dcf9a 100755
--- a/fslcreatehd.cc
+++ b/fslcreatehd.cc
@@ -61,7 +61,7 @@ int fslcreatehd_main(int argc, char *argv[])
header.sX[0]=-header.pixdim[1];
header.sY[1]=header.pixdim[2];
header.sZ[2]=header.pixdim[3];
- header.sX[3]-=header.pixdim[1]*atoi(argv[9]);
+ header.sX[3]=-header.pixdim[1]*atoi(argv[9]);
header.sY[3]=-header.pixdim[2]*atoi(argv[10]);
header.sZ[3]=-header.pixdim[3]*atoi(argv[11]);
header.qformCode=2;
diff --git a/fslhd.cc b/fslhd.cc
index 1bf97ba90f750f251b57d45c56c87f91d09b00e6..773bac17bcf9e288f87b1aa24bee0c8058c83765 100755
--- a/fslhd.cc
+++ b/fslhd.cc
@@ -1,7 +1,7 @@
// fslhd.cc - show image header
// Steve Smith, Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2000-2012 University of Oxford
-// CCOPYRIGHT
+// Copyright (C) 2000-2012 University of Oxford
+// CCOPYRIGHT
#include "newimage/newimageall.h"
#include <iomanip>
@@ -49,20 +49,22 @@ void reportXMLHeader(const NiftiHeader& header)
cout << " slice_dim = '" << (int)header.sliceDim() << "'" << endl;
cout << " descrip = '" << header.description << "'" << endl;
cout << " aux_file = '" << header.auxillaryFile << "'" << endl;
- cout << " qform_code = '" << header.qformCode << "'" << endl;
- cout << " qfac = '" << header.leftHanded() << "'" << endl;
- cout << " quatern_b = '" << header.qB << "'" << endl;
- cout << " quatern_c = '" << header.qC << "'" << endl;
- cout << " quatern_d = '" << header.qD << "'" << endl;
- cout << " qoffset_x = '" << header.qX << "'" << endl;
- cout << " qoffset_y = '" << header.qY << "'" << endl;
- cout << " qoffset_z = '" << header.qZ << "'" << endl;
+ if ( !header.isAnalyze() ) {
+ cout << " qform_code = '" << header.qformCode << "'" << endl;
+ cout << " qfac = '" << header.leftHanded() << "'" << endl;
+ cout << " quatern_b = '" << header.qB << "'" << endl;
+ cout << " quatern_c = '" << header.qC << "'" << endl;
+ cout << " quatern_d = '" << header.qD << "'" << endl;
+ cout << " qoffset_x = '" << header.qX << "'" << endl;
+ cout << " qoffset_y = '" << header.qY << "'" << endl;
+ cout << " qoffset_z = '" << header.qZ << "'" << endl;
+ }
cout << " sform_code = '" << header.sformCode << "'" << endl;
- cout << " sto_xyz_matrix = '";
+ cout << " sto_xyz_matrix = '";
mat44 output(header.getSForm());
for (int i=0;i<4;i++)
for (int j=0;j<4;j++) {
- cout << output.m[i][j];
+ cout << output.m[i][j];
if ( j==3 && i==3 )
cout << "'" << endl;
else
@@ -75,7 +77,7 @@ void reportXMLHeader(const NiftiHeader& header)
cout << "/>" << endl;
}
-int print_usage(const string& progname)
+int print_usage(const string& progname)
{
cout << endl;
cout << "Usage: fslhd [-x] <input>" << endl;
@@ -85,20 +87,19 @@ int print_usage(const string& progname)
int main(int argc,char *argv[])
{
- if (argc < 2)
+ 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));
- if ( argc==3 && strcmp(argv[1],"-x")==0 )
+ if (reportXML)
reportXMLHeader(header);
else {
- cout << "filename\t" << filename << endl;
+ cout << "filename\t" << filename << endl << endl;
header.report();
}
} catch ( exception& e ) { cerr << e.what() << endl; return 1;}
return 0;
}
-
-