From 6e30071492b3c7fab39f29b04eb1f659ce905b30 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 16 Jan 2009 10:27:45 +0000
Subject: [PATCH] removed volumeinfo
---
fsl_glm.cc | 7 +++----
fsl_mvlm.cc | 7 +++----
fsl_regfilt.cc | 7 +++----
fsl_sbca.cc | 9 ++++-----
ggmix.cc | 3 +--
ggmix.h | 3 +--
meldata.cc | 2 +-
meldata.h | 3 +--
melgmix.cc | 3 +--
melgmix.h | 3 +--
melodic.cc | 6 ++----
melreport.cc | 23 +++++++----------------
test.cc | 5 -----
13 files changed, 28 insertions(+), 53 deletions(-)
diff --git a/fsl_glm.cc b/fsl_glm.cc
index bc5ff31..4782dce 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -109,8 +109,7 @@ using namespace std;
Matrix fcontrasts;
Matrix meanR;
RowVector vnscales;
- volume<float> mask;
- volumeinfo volinf; /*
+ volume<float> mask; /*
}
*/
////////////////////////////////////////////////////////////////////////////
@@ -123,7 +122,7 @@ void save4D(Matrix what, string fname){
tempVol.setmatrix(what.t(),mask);
else
tempVol.setmatrix(what,mask);
- save_volume4D(tempVol,fname,volinf);
+ save_volume4D(tempVol,fname);
}
}
@@ -147,7 +146,7 @@ int setup(){
if(fsl_imageexists(fnin.value())){//read data
//input is 3D/4D vol
volume4D<float> tmpdata;
- read_volume4D(tmpdata,fnin.value(),volinf);
+ read_volume4D(tmpdata,fnin.value());
// create mask
if(fnmask.value()>""){
diff --git a/fsl_mvlm.cc b/fsl_mvlm.cc
index cafe3e8..f988a1b 100644
--- a/fsl_mvlm.cc
+++ b/fsl_mvlm.cc
@@ -116,8 +116,7 @@ using namespace std;
Matrix svd_X_U, svd_X_V, svd_Y_U, svd_Y_V;
DiagonalMatrix svd_X_D, svd_Y_D;
RowVector vnscales;
- volume<float> mask;
- volumeinfo volinf;
+ volume<float> mask;
////////////////////////////////////////////////////////////////////////////
@@ -129,7 +128,7 @@ void save4D(Matrix what, string fname){
tempVol.setmatrix(what.t(),mask);
else
tempVol.setmatrix(what,mask);
- save_volume4D(tempVol,fname,volinf);
+ save_volume4D(tempVol,fname);
}
}
@@ -156,7 +155,7 @@ int setup(){
if(fsl_imageexists(fnin.value())){//read data
//input is 3D/4D vol
volume4D<float> tmpdata;
- read_volume4D(tmpdata,fnin.value(),volinf);
+ read_volume4D(tmpdata,fnin.value());
// create mask
if(fnmask.value()>""){
diff --git a/fsl_regfilt.cc b/fsl_regfilt.cc
index 98f39de..310b2ac 100644
--- a/fsl_regfilt.cc
+++ b/fsl_regfilt.cc
@@ -70,8 +70,7 @@ using namespace std;
Matrix meanR;
RowVector vnscales;
volume<float> mask;
- volume<float> Mean;
- volumeinfo volinf; /*
+ volume<float> Mean; /*
}
*/
////////////////////////////////////////////////////////////////////////////
@@ -84,7 +83,7 @@ void save4D(Matrix what, string fname){
tempVol.setmatrix(what.t(),mask);
else
tempVol.setmatrix(what,mask);
- save_volume4D(tempVol,fname,volinf);
+ save_volume4D(tempVol,fname);
}
}
@@ -152,7 +151,7 @@ int setup(){
if(fsl_imageexists(fnin.value())){//read data
//input is 3D/4D vol
volume4D<float> tmpdata;
- read_volume4D(tmpdata,fnin.value(),volinf);
+ read_volume4D(tmpdata,fnin.value());
// create mask
if(fnmask.value()>""){
diff --git a/fsl_sbca.cc b/fsl_sbca.cc
index b1108e2..23a02c6 100644
--- a/fsl_sbca.cc
+++ b/fsl_sbca.cc
@@ -93,8 +93,7 @@ using namespace std;
//Globals {
Matrix data, confounds;
volume4D<float> orig_data;
- volume<float> maskS, maskT;
- volumeinfo volinf;
+ volume<float> maskS, maskT;
int voxels = 0;
Matrix seeds, coords;
vector<Matrix> ttcs;
@@ -111,7 +110,7 @@ void save4D(Matrix what, volume<float>& msk, string fname){
cerr << "DBG: in save4D" << endl;
volume4D<float> tempVol;
tempVol.setmatrix(what,msk);
- save_volume4D(tempVol,fname,volinf);
+ save_volume4D(tempVol,fname);
}
void save4D(volume<float>& in, string fname){
@@ -119,7 +118,7 @@ void save4D(volume<float>& in, string fname){
cerr << "DBG: in save4D" << endl;
volume4D<float> tempVol;
tempVol.addvolume(in);
- save_volume4D(tempVol,fname,volinf);
+ save_volume4D(tempVol,fname);
}
ReturnMatrix create_coords(string what){
@@ -340,7 +339,7 @@ int setup(){
if(fsl_imageexists(fnin.value())){ //read data
if(verbose.value())
cout << " Reading input file " << fnin.value() << endl;
- read_volume4D(orig_data,fnin.value(),volinf);
+ read_volume4D(orig_data,fnin.value());
}
else{
cerr << "ERROR: Invalid input file " << fnin.value() << endl;
diff --git a/ggmix.cc b/ggmix.cc
index 3648396..4b77a6f 100644
--- a/ggmix.cc
+++ b/ggmix.cc
@@ -34,13 +34,12 @@ string float2str(float f,int width, int prec, bool scientif)
namespace GGMIX{
- void ggmix::setup(const RowVector& dat, volumeinfo inf,
+ void ggmix::setup(const RowVector& dat,
const string dirname,
int cnum, volume<float> themask,
volume<float> themean,
int num_mix, float eps, bool fixit)
{
- bginfo = inf;
cnumber = cnum;
Mask = themask;
Mean = themean;
diff --git a/ggmix.h b/ggmix.h
index 8126e20..e97a4e1 100644
--- a/ggmix.h
+++ b/ggmix.h
@@ -40,7 +40,7 @@ namespace GGMIX{
void save();
- void setup(const RowVector& dat, volumeinfo inf, const string dirname,
+ void setup(const RowVector& dat, const string dirname,
int here, volume<float> themask,
volume<float> themean, int num_mix = 3,
float eps = 0.0, bool fixdim = false);
@@ -194,7 +194,6 @@ namespace GGMIX{
string mmtype;
string dirname;
- volumeinfo bginfo;
vector<string> threshinfo;
};
diff --git a/meldata.cc b/meldata.cc
index 20cf19c..a00f698 100644
--- a/meldata.cc
+++ b/meldata.cc
@@ -337,7 +337,7 @@ namespace Melodic{
{
//initialize Mean
- read_volume(Mean,opts.inputfname.value().at(0),tempInfo);
+ read_volume(Mean,opts.inputfname.value().at(0));
//create mask
create_mask(Mask);
diff --git a/meldata.h b/meldata.h
index c4b911b..8d579bb 100644
--- a/meldata.h
+++ b/meldata.h
@@ -41,7 +41,7 @@ namespace Melodic{
inline void save4D(Matrix what, string fname){
volume4D<float> tempVol;
tempVol.setmatrix(what,Mask);
- save_volume4D(tempVol,logger.appendDir(fname),tempInfo);
+ save_volume4D(tempVol,logger.appendDir(fname));
message(" " << logger.appendDir(fname) << endl);
}
@@ -197,7 +197,6 @@ namespace Melodic{
void sort();
void reregress();
- volumeinfo tempInfo;
vector<Matrix> DWM, WM;
basicGLM glmT, glmS;
Matrix Tdes, Tcon, TconF, Sdes, Scon, SconF, param, paramS;
diff --git a/melgmix.cc b/melgmix.cc
index 9b715bf..b7ff1e9 100644
--- a/melgmix.cc
+++ b/melgmix.cc
@@ -39,12 +39,11 @@ string float2str(float f,int width, int prec, bool scientif){
namespace Melodic{
- void MelGMix::setup(const RowVector& dat, volumeinfo inf,
+ void MelGMix::setup(const RowVector& dat,
const string dirname,
int cnum, volume<float> themask,
volume<float> themean,
int num_mix, float eps, bool fixit){
- bginfo = inf;
cnumber = cnum;
Mask = themask;
Mean = themean;
diff --git a/melgmix.h b/melgmix.h
index 0cf5792..918cb46 100644
--- a/melgmix.h
+++ b/melgmix.h
@@ -37,7 +37,7 @@ namespace Melodic{
void save();
- void setup(const RowVector& dat, volumeinfo inf, const string dirname,
+ void setup(const RowVector& dat, const string dirname,
int here, volume<float> themask,
volume<float> themean, int num_mix = 3,
float eps = 0.0, bool fixdim = false);
@@ -191,7 +191,6 @@ namespace Melodic{
string mmtype;
string dirname;
- volumeinfo bginfo;
vector<string> threshinfo;
};
diff --git a/melodic.cc b/melodic.cc
index d991c0e..ce7133e 100644
--- a/melodic.cc
+++ b/melodic.cc
@@ -189,14 +189,13 @@ void mmonly(Log& logger, MelodicOptions& opts,
Matrix ICs;
Matrix mixMatrix;
Matrix fmixMatrix;
- volumeinfo ICvolInfo;
volume<float> Mask;
volume<float> Mean;
{
volume4D<float> RawData;
message("Reading data file " << opts.inputfname.value().at(0) << " ... ");
- read_volume4D(RawData,opts.inputfname.value().at(0),ICvolInfo);
+ read_volume4D(RawData,opts.inputfname.value().at(0));
message(" done" << endl);
Mean = meanvol(RawData);
}
@@ -261,7 +260,6 @@ void mmonly(Log& logger, MelodicOptions& opts,
}
}
- melodat.tempInfo = ICvolInfo;
melodat.set_mask(Mask);
melodat.set_mean(Mean);
melodat.set_IC(ICs);
@@ -316,7 +314,7 @@ Matrix mmall(Log& logger, MelodicOptions& opts,MelodicData& melodat, MelodicRepo
wherelog = logger.getDir();
dbgmsg(" ICmap max : "<< mean(ICmap,2).AsScalar() << endl);
- mixmod.setup( ICmap, melodat.tempInfo,
+ mixmod.setup( ICmap,
wherelog,ctr,
melodat.get_mask(),
melodat.get_mean(),3);
diff --git a/melreport.cc b/melreport.cc
index bf1fc2d..abe803a 100644
--- a/melreport.cc
+++ b/melreport.cc
@@ -86,11 +86,9 @@ namespace Melodic{
melodat.get_bg().percentile(0.02),
melodat.get_bg().percentile(0.98),
map1min, map1max, map2max, map2min,
- 0, 0, &melodat.tempInfo);
+ 0, 0);
char instr[10000];
- //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
- // melodat.tempInfo);
sprintf(instr," ");
strcat(instr,axials_instr.c_str());
strcat(instr,string(report.appendDir(mmodel.get_prefix()+
@@ -362,8 +360,7 @@ namespace Melodic{
volume<float> map2;
map1 = threshold(tempVol[0],float(0.0), tempVol[0].max());
map2 = threshold(tempVol[0],tempVol[0].min(), float(0.0));
- // save_volume(map,report.appendDir(mmodel.get_prefix()+"_thresh")
- // ,melodat.tempInfo);
+
volume<float> newvol;
miscpic newpic;
@@ -382,12 +379,10 @@ namespace Melodic{
melodat.get_bg().percentile(0.02),
melodat.get_bg().percentile(0.98),
map1min, map1max, map2max, map2min,
- 0, 0, &melodat.tempInfo);
+ 0, 0);
char instr[10000];
- //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
- // melodat.tempInfo);
sprintf(instr," ");
strcat(instr,axials_instr.c_str());
strcat(instr,string(report.appendDir(mmodel.get_prefix()+"_thresh"+
@@ -478,12 +473,10 @@ namespace Melodic{
float(0.0),
float(0.0),
float(0.01), map1max, float(-0.01), map2min,
- 0, 0, &melodat.tempInfo);
+ 0, 0);
char instr[10000];
-
- //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
- // melodat.tempInfo);
+
sprintf(instr," ");
strcat(instr,axials_instr.c_str());
strcat(instr,string(report.appendDir(mmodel.get_prefix()+
@@ -514,7 +507,7 @@ namespace Melodic{
melodat.get_bg().percentile(0.02),
melodat.get_bg().percentile(0.98),
float(0.1), float(1.0), float(0.0), float(0.0),
- 0, 0, &melodat.tempInfo);
+ 0, 0);
char instr[10000];
@@ -650,12 +643,10 @@ namespace Melodic{
float(0.0),
float(0.0),
float(0.01), map1max, float(-0.01), map2min,
- 0, 0, &melodat.tempInfo);
+ 0, 0);
char instr[10000];
- //save_volume(newvol,report.appendDir(prefix+"rendered"),
- // melodat.tempInfo);
sprintf(instr," ");
strcat(instr,axials_instr.c_str());
strcat(instr,string(report.appendDir(prefix+
diff --git a/test.cc b/test.cc
index 549caf2..8994048 100644
--- a/test.cc
+++ b/test.cc
@@ -37,11 +37,6 @@ using namespace std;
/*
}
*/
-//Globals {
-
- volumeinfo volinf; /*
-}
-*/
////////////////////////////////////////////////////////////////////////////
// Local functions
--
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