From 1ab127f03633f04682060226be38dd7568b00ac7 Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Fri, 16 Sep 2005 15:31:13 +0000
Subject: [PATCH] *** empty log message ***
---
Makefile | 5 ++-
fslpspec.cc | 114 ++++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 fslpspec.cc
diff --git a/Makefile b/Makefile
index bd1ce77..3ced221 100644
--- a/Makefile
+++ b/Makefile
@@ -20,7 +20,7 @@ XFILES = avwcpgeom avwmerge avwnvols avwsplit \
avwinterleave_8UI avwinterleave_8SI avwinterleave_16UI avwinterleave_16SI avwinterleave_32UI avwinterleave_32SI avwinterleave_32R avwinterleave_64R \
avwroi_8UI avwroi_8SI avwroi_16UI avwroi_16SI avwroi_32UI avwroi_32SI avwroi_32R avwroi_64R \
avwfill_8UI avwfill_8SI avwfill_16UI avwfill_16SI avwfill_32UI avwfill_32SI avwfill_32R avwfill_64R \
- avwstats avwcomplex avwstats++ avwfft avwmeants avwcheck avwswapdim avwconv avwslice avworient
+ avwstats avwcomplex avwstats++ avwfft avwmeants avwcheck avwswapdim avwconv avwslice avworient avwpspec
SCRIPTS = avwval avwchpixdim avwanimate sliceanimate avwsize avwinfo avwedithd avwchfiletype
FSCRIPTS = fmriborient
@@ -113,3 +113,6 @@ avworient: avworient.o
avwslice: avwslice.cc
${CXX} ${CXXFLAGS} ${LDFLAGS} -o avwslice avwslice.cc ${LIBS}
+
+avwpspec: avwpspec.o
+ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ avwpspec.o ${LIBS}
diff --git a/fslpspec.cc b/fslpspec.cc
new file mode 100644
index 0000000..6e31e19
--- /dev/null
+++ b/fslpspec.cc
@@ -0,0 +1,114 @@
+/* avwswapdim.cc
+
+ Christian F. Beckmann, FMRIB Image Analysis Group
+
+ Copyright (C) 2003-2004 University of Oxford */
+
+/* CCOPYRIGHT */
+
+
+#include "newmatap.h"
+#include "newmatio.h"
+#include "newimage/newimageall.h"
+#include "newimage/fmribmain.h"
+
+using namespace NEWIMAGE;
+
+void print_usage(const string& progname) {
+ cout << "Usage: " << progname << " <input> [options] [output]" << endl;
+ cout << endl;
+ cout << " " << endl;
+ cout << " " << endl;
+ cout << " e.g. " << progname << " " << endl;
+}
+
+ReturnMatrix calcFFT(const Matrix& Mat)
+{
+ Matrix res;
+ for(int ctr=1; ctr <= Mat.Ncols(); ctr++)
+ {
+ ColumnVector tmpCol;
+ tmpCol=Mat.Column(ctr);
+ ColumnVector FtmpCol_real;
+ ColumnVector FtmpCol_imag;
+ ColumnVector tmpPow;
+ if(tmpCol.Nrows()%2 != 0){
+ Matrix empty(1,1); empty=0;
+ tmpCol &= empty;}
+ RealFFT(tmpCol,FtmpCol_real,FtmpCol_imag);
+ tmpPow = pow(FtmpCol_real,2)+pow(FtmpCol_imag,2);
+ tmpPow = tmpPow.Rows(2,tmpPow.Nrows());
+ //if(opts.logPower.value()) tmpPow = log(tmpPow);
+ if(res.Storage()==0){res= tmpPow;}else{res|=tmpPow;}
+ }
+ res.Release();
+ return res;
+} //Matrix calcFFT()
+
+int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin, float& lthr, float& uthr)
+{
+ mask = binarise(vin,lthr,uthr,exclusive);
+ masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
+ return 0;
+}
+
+int generate_masks(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin)
+{
+ masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
+ return 0;
+}
+
+int fmrib_main_float(int argc, char* argv[])
+{
+ string inname=argv[1];
+ string maskname="";
+ string outname="";
+
+ cout << argc << endl;
+ if(argc>2)
+ outname=argv[2];
+ else
+ outname=inname;
+
+ Matrix iMat, oMat;
+ volume4D<float> vout;
+ volume<float> smask, smasknz;
+ volumeinfo volinfo;
+
+ {
+ volume4D<float> vin, mask, masknz;
+ read_volume4D(vin,argv[1],volinfo);
+
+ float lthr=0, uthr=0;
+ generate_masks(mask,masknz,vin,lthr,uthr);
+
+ smask=mask[0];
+ smasknz=masknz[0];
+
+ iMat = vin.matrix(smasknz);
+ }
+
+ oMat = calcFFT(iMat);
+
+ vout.setmatrix(oMat,smasknz);
+
+ int retval=0;
+ retval = save_volume4D(vout,outname,volinfo);
+ return retval;
+}
+
+
+int main(int argc,char *argv[])
+{
+ Tracer tr("main");
+
+ string progname=argv[0];
+ if (argc<3) {
+ print_usage(progname);
+ return 1;
+ }
+
+ return fmrib_main_float(argc,argv);
+
+}
+
--
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