From 9b3a18b53f2013c442db9ccef92ec054daa16604 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Jan 2015 16:00:19 +0000
Subject: [PATCH] Current Version Jan 15
---
fslhd.cc | 268 +++++++++++++++++--------------------------------------
1 file changed, 80 insertions(+), 188 deletions(-)
diff --git a/fslhd.cc b/fslhd.cc
index 17088f8..1bf97ba 100755
--- a/fslhd.cc
+++ b/fslhd.cc
@@ -8,204 +8,96 @@
#include <iostream>
using namespace NEWIMAGE;
-void print_usage(const string& progname)
+void reportXMLHeader(const NiftiHeader& header)
{
- cout << endl;
- cout << "Usage: fslhd [-x] <input>" << endl;
- cout << " -x : instead print an XML-style NIFTI header" << endl;
-}
-
-void ShowNifti(FSLIO* fslio)
-{
- if (fslio == NULL) {
- cerr << "ERROR: Could not open file" << endl;
- return;
- }
- if (fslio->niftiptr!=NULL) {
- cout << nifti_image_to_ascii(fslio->niftiptr) << endl;
- return;
- }
- return;
-}
-
-void ShowHdr(char *fileName, FSLIO* fslio)
-{
- int i, ft, isanalyze=0;
- struct dsr *hdr;
- mat44 mat;
- int icode, jcode, kcode;
-
- if (fslio == NULL)
- {
- cerr << "ERROR: Could not open file" << endl;;
- return;
+ cout << "<nifti_image" << endl;
+ cout << " image_offset = '" << header.vox_offset << "'" << endl;
+ cout << " ndim = '" << header.dim[0] << "'" << endl;
+ cout << " nx = '" << header.dim[1] << "'" << endl;
+ cout << " ny = '" << header.dim[2] << "'" << endl;
+ cout << " nz = '" << header.dim[3] << "'" << endl;
+ cout << " nt = '" << header.dim[4] << "'" << endl;
+ if ( header.dim[0] > 4 ) {
+ cout << " nu = '" << header.dim[5] << "'" << endl;
+ cout << " nv = '" << header.dim[6] << "'" << endl;
+ cout << " nw = '" << header.dim[7] << "'" << endl;
}
-
- ft = FslGetFileType(fslio);
-
- if (fslio->niftiptr == NULL)
- {
- cerr << "ERROR: Not an Analyze or Nifti file" << endl;
- return;
+ cout << " dx = '" << header.pixdim[1] << "'" << endl;
+ cout << " dy = '" << header.pixdim[2] << "'" << endl;
+ cout << " dz = '" << header.pixdim[3] << "'" << endl;
+ cout << " dt = '" << header.pixdim[4] << "'" << endl;
+ if ( header.dim[0] > 4 ) {
+ cout << " du = '" << header.pixdim[5] << "'" << endl;
+ cout << " dv = '" << header.pixdim[6] << "'" << endl;
+ cout << " dw = '" << header.pixdim[7] << "'" << endl;
}
- //-------------------- ANALYZE CASE -----------------------
- if (FslBaseFileType(ft)==FSL_TYPE_ANALYZE)
- {
- isanalyze=1;
- //load raw hdr structure
- hdr = (struct dsr *)calloc(1,sizeof(struct dsr));
- FslReadRawHeader(hdr,fslio->niftiptr->fname);
- if (fslio->niftiptr->byteorder != nifti_short_order())
- {
- cout << "Byte swapping" << endl;
- AvwSwapHeader(hdr);
+ cout << " datatype = '" << header.datatype << "'" << endl;
+ cout << " nvox = '" << header.nElements() << "'" << endl;
+ cout << " nbyper = '" << header.bitsPerVoxel/8 << "'" << endl;
+ cout << " scl_slope = '" << header.sclSlope << "'" << endl;
+ cout << " scl_inter = '" << header.sclInter << "'" << endl;
+ cout << " intent_code = '" << header.intentCode << "'" << endl;
+ cout << " intent_p1 = '" << header.intent_p1 << "'" << endl;
+ cout << " intent_p2 = '" << header.intent_p2 << "'" << endl;
+ cout << " intent_p3 = '" << header.intent_p3 << "'" << endl;
+ cout << " intent_name = '" << header.intentName << "'" << endl;
+ cout << " toffset = '" << header.toffset << "'" << endl;
+ cout << " xyz_units = '" << XYZT_TO_SPACE(header.units) << "'" << endl;
+ cout << " time_units = '" << XYZT_TO_TIME(header.units) << "'" << endl;
+ cout << " freq_dim = '" << (int)header.freqDim() << "'" << endl;
+ cout << " phase_dim = '" << (int)header.phaseDim() << "'" << endl;
+ 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;
+ cout << " sform_code = '" << header.sformCode << "'" << endl;
+ 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];
+ if ( j==3 && i==3 )
+ cout << "'" << endl;
+ else
+ cout << " ";
}
- cout << "filename " << fileName << endl << endl;
-
- //Header Key
- cout << "sizeof_hdr " << hdr->hk.sizeof_hdr<< endl;
- cout << "data_type " << hdr->hk.data_type << endl;
- cout << "db_name " << hdr->hk.db_name << endl;
- cout << "extents " << hdr->hk.extents << endl;
- cout << "session_error " << hdr->hk.session_error << endl;
- cout << "regular " << hdr->hk.regular << endl;
- cout << "hkey_un0 " << hdr->hk.hkey_un0 << endl;
- //Image Dimension
- for(i=0;i<8;i++) cout << "dim" << i << " " << hdr->dime.dim[i] << endl;
- cout << "vox_units " << hdr->dime.vox_units << endl;
- cout << "cal_units " << hdr->dime.cal_units << endl;
- cout << "unused1 " << hdr->dime.unused1 << endl;
- cout << "datatype " << hdr->dime.datatype << endl;
- cout << "bitpix " << hdr->dime.bitpix << endl;
- cout.setf(ios::fixed); //need cout.setf(ios::fixed) instead of << fixed in stream for tru64 comp
- for(i=0;i<8;i++) cout << "pixdim" << i << " " << setprecision(10) << hdr->dime.pixdim[i] << endl;
- cout.precision(4);
- cout << "vox_offset " << setw(6) << hdr->dime.vox_offset << endl;
- cout << "funused1 " << setw(6) << hdr->dime.funused1 << endl;
- cout << "funused2 " << setw(6) << hdr->dime.funused2 << endl;
- cout << "funused3 " << setw(6) << hdr->dime.funused3 << endl;
- cout << "cal_max " << setw(6) << hdr->dime.cal_max << endl;
- cout << "cal_min " << setw(6) << hdr->dime.cal_min << endl;
- cout << "compressed " << hdr->dime.compressed << endl;
- cout << "verified " << hdr->dime.verified << endl;
- cout << "glmax " << hdr->dime.glmax << endl;
- cout << "glmin " << hdr->dime.glmin << endl ;
- //Data History
- cout << "descrip " << hdr->hist.descrip << endl;
- cout << "aux_file " << hdr->hist.aux_file << endl;
- cout << "orient " << (int)hdr->hist.orient << endl; //need cast else blank
- cout << "originator " << hdr->hist.originator << endl;
- /*{
- short blah[5];
- memcpy(blah,hdr->hist.originator,5*sizeof(short));
- cout << "origin1 " << blah[0] << endl;
- cout << "origin2 " <<blah[1] << endl;
- cout << "origin3 " << blah[2] << endl;
- }*/
- cout << "origin1 " << (short)hdr->hist.originator[0] << endl; //These lines don't work on
- cout << "origin2 " << (short)hdr->hist.originator[2] << endl; //all platforms... but WHICH
- cout << "origin3 " << (short)hdr->hist.originator[4] << endl; //ones - that is the question
- cout << "generated " << hdr->hist.generated << endl;
- cout << "scannum " << hdr->hist.scannum << endl;
- cout << "patient_id " << hdr->hist.patient_id << endl;
- cout << "exp_date " << hdr->hist.exp_date << endl;
- cout << "exp_time " << hdr->hist.exp_time << endl;
- cout << "hist_un0 " << hdr->hist.hist_un0 <<endl;
- cout << "views " << hdr->hist.views << endl;
- cout << "vols_added " << hdr->hist.vols_added << endl;
- cout << "start_field " << hdr->hist.start_field << endl;
- cout << "field_skip " << hdr->hist.field_skip << endl;
- cout << "omax " << hdr->hist.omax << endl;
- cout << "omin " << hdr->hist.omin << endl;
- cout << "smin " << hdr->hist.smax << endl;
- cout << "smin " << hdr->hist.smin << endl;
- cout << "file_type " << FslFileTypeString(0) << endl;
- cout << "file_code 0" << endl;
- return;
- }
- /* -------------------- NIFTI CASE ----------------------- */
- if (fslio->niftiptr->byteorder != nifti_short_order())
- {
- cout << "Byte swapping" << endl;
- }
-
- cout << "filename " << fslio->niftiptr->fname << endl << endl;
- cout << "sizeof_hdr " << "348" << endl;
- cout << "data_type " << nifti_datatype_string(fslio->niftiptr->datatype) << endl;
- for(i=0;i<8;i++) cout << "dim" << i << " " << fslio->niftiptr->dim[i] << endl;
- cout << "vox_units " << nifti_units_string(fslio->niftiptr->xyz_units) << endl;
- cout << "time_units " << nifti_units_string(fslio->niftiptr->time_units) << endl;
- cout << "datatype " << fslio->niftiptr->datatype << endl;
- cout << "nbyper " << fslio->niftiptr->nbyper << endl;
- cout << "bitpix " << fslio->niftiptr->nbyper * 8 << endl;
- cout.setf(ios::fixed); //need cout.setf(ios::fixed) instead of << fixed in stream for tru64 comp
- for(i=0;i<8;i++) cout << "pixdim" << i << " " << setprecision(10) << fslio->niftiptr->pixdim[i] << endl;
- cout << "vox_offset " << fslio->niftiptr->iname_offset << endl;
- cout.precision(4);
- cout << "cal_max " << setw(6) << fslio->niftiptr->cal_max << endl;
- cout << "cal_min " << setw(6) << fslio->niftiptr->cal_min << endl;
- cout.precision(6);
- cout << "scl_slope " << fslio->niftiptr->scl_slope << endl;
- cout << "scl_inter " << fslio->niftiptr->scl_inter << endl;
- cout << "phase_dim " << fslio->niftiptr->phase_dim << endl;
- cout << "freq_dim " << fslio->niftiptr->freq_dim << endl;
- cout << "slice_dim " << fslio->niftiptr->slice_dim << endl;
- cout << "slice_name " << nifti_slice_string(fslio->niftiptr->slice_code) << endl;
- cout << "slice_code " << fslio->niftiptr->slice_code << endl;
- cout << "slice_start " << fslio->niftiptr->slice_start << endl;
- cout << "slice_end " << fslio->niftiptr->slice_end << endl;
- cout << "slice_duration " << fslio->niftiptr->slice_duration << endl;
- cout << "time_offset " << fslio->niftiptr->toffset << endl;
- cout << "intent " << nifti_intent_string(fslio->niftiptr->intent_code) << endl;
- cout << "intent_code " << fslio->niftiptr->intent_code << endl;
- cout << "intent_name " << fslio->niftiptr->intent_name << endl;
- cout << "intent_p1 " << fslio->niftiptr->intent_p1 << endl;
- cout << "intent_p2 " << fslio->niftiptr->intent_p2 << endl;
- cout << "intent_p3 " << fslio->niftiptr->intent_p3 << endl;
- cout << "qform_name " << nifti_xform_string(fslio->niftiptr->qform_code) << endl;
- cout << "qform_code " << fslio->niftiptr->qform_code << endl;
- mat = fslio->niftiptr->qto_xyz;
- for(i=1;i<=4;i++) cout << "qto_xyz:" << i << " " << mat.m[i-1][0] << " " << mat.m[i-1][1] << " " << mat.m[i-1][2] << " " << mat.m[i-1][3] << endl;
- nifti_mat44_to_orientation(mat,&icode,&jcode,&kcode);
- cout << "qform_xorient " << nifti_orientation_string(icode) << endl;
- cout << "qform_yorient " << nifti_orientation_string(jcode) << endl;
- cout << "qform_zorient " << nifti_orientation_string(kcode) << endl;
- cout << "sform_name " << nifti_xform_string(fslio->niftiptr->sform_code) << endl;
- cout << "sform_code " << fslio->niftiptr->sform_code << endl;
- mat = fslio->niftiptr->sto_xyz;
- for(i=1;i<=4;i++) cout << "sto_xyz:" << i << " " << mat.m[i-1][0] << " " << mat.m[i-1][1] << " " << mat.m[i-1][2] << " " << mat.m[i-1][3] << endl;
- nifti_mat44_to_orientation(mat,&icode,&jcode,&kcode);
- cout << "sform_xorient " << nifti_orientation_string(icode) << endl;
- cout << "sform_yorient " << nifti_orientation_string(jcode) << endl;
- cout << "sform_zorient " << nifti_orientation_string(kcode) << endl;
- cout << "file_type " << FslFileTypeString(fslio->niftiptr->nifti_type) << endl;
- cout << "file_code " << fslio->niftiptr->nifti_type << endl;
- //Data History
- cout << "descrip " << fslio->niftiptr->descrip << endl;
- cout << "aux_file " << fslio->niftiptr->aux_file << endl;
- /*cout << "orient %d\n", hdr->hist.orient); */
- return;
+ cout << " slice_code = '" << header.sliceCode << "'" << endl;
+ cout << " slice_start = '" << header.sliceStart << "'" << endl;
+ cout << " scl_end = '" << header.sliceEnd << "'" << endl;
+ cout << " scl_duration = '" << header.sliceDuration << "'" << endl;
+ cout << "/>" << endl;
}
+int print_usage(const string& progname)
+{
+ cout << endl;
+ cout << "Usage: fslhd [-x] <input>" << endl;
+ cout << " -x : instead print an XML-style NIFTI header" << endl;
+ return 1;
+}
int main(int argc,char *argv[])
{
if (argc < 2)
- {
- print_usage(string(argv[0]));
- return 1;
- }
- FSLIO* fslio=NULL;
- int argval=1, niftiform=0;
- if (strcmp(argv[1],"-x")==0)
- {
- niftiform=1;
- argval=2;
- }
- fslio = FslOpen(FslMakeBaseName(argv[argval]),"rb");
- FslClose(fslio);
- if (niftiform==0) ShowHdr(argv[argval], fslio);
- else ShowNifti(fslio);
+ return print_usage(string(argv[0]));
+ NiftiIO reader;
+ try {
+ string filename(return_validimagefilename(argv[argc-1]));
+ NiftiHeader header(reader.loadHeader(filename));
+ if ( argc==3 && strcmp(argv[1],"-x")==0 )
+ reportXMLHeader(header);
+ else {
+ cout << "filename\t" << filename << endl;
+ header.report();
+ }
+ } catch ( exception& e ) { cerr << e.what() << endl; return 1;}
return 0;
}
--
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