From 9ced373966b75bd99a2537ff9d36ad944ae7c619 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Wed, 8 Feb 2006 20:10:01 +0000
Subject: [PATCH] CVS:
----------------------------------------------------------------------
---
volumeseries.cc | 135 ++++++++++++++++++++++++++----------------------
volumeseries.h | 1 +
2 files changed, 75 insertions(+), 61 deletions(-)
diff --git a/volumeseries.cc b/volumeseries.cc
index 1638665..9bb49a3 100644
--- a/volumeseries.cc
+++ b/volumeseries.cc
@@ -154,76 +154,54 @@ namespace MISCMATHS {
volinfo.miscinfo = FslInit();
FslCloneHeader(volinfo.miscinfo,IP);
- size_t imagesize=x*y*z*v;
+ size_t imagesize=x*y*z;
FslGetDataType(IP,&type);
output.ReSize(v,x*y*z);
- switch(type)
+ for(size_t i=1; i<=(size_t)v; i++)
{
- case DT_SIGNED_SHORT:
- {
- short* sbuffer=new short[imagesize];
-
- FslReadVolumes(IP, sbuffer,v);
-
- size_t volsize = volinfo.x*volinfo.y*volinfo.z;
- size_t volstart = 1;
-
- for(size_t i=1; i<=(size_t)v; i++)
+ switch(type)
+ {
+ case DT_SIGNED_SHORT:
{
- volstart = (i-1)*volsize;
- for(size_t j = 1; j<=(size_t)x*y*z; j++)
+ short* sbuffer=new short[imagesize];
+ FslReadVolumes(IP, sbuffer,1);
+ for(size_t j = 1; j<=imagesize; j++)
{
- if (doscaling==0) { output(i,j)=sbuffer[volstart+j-1]; }
- else { output(i,j)=(slope * sbuffer[volstart+j-1]) + intercept;}
+ if (doscaling==0) { output(i,j)=sbuffer[j-1]; }
+ else { output(i,j)=(slope * sbuffer[j-1]) + intercept;}
}
+ delete[] sbuffer;
}
-
- delete[] sbuffer;
- }
- break;
- case DT_FLOAT:
- {
- float* fbuffer=new float[imagesize];
- FslReadVolumes(IP,fbuffer,v);
-
- size_t volsize = volinfo.x*volinfo.y*volinfo.z;
- size_t volstart = 1;
- for(size_t i=1; i<=(size_t)v; i++)
+ break;
+ case DT_FLOAT:
{
- volstart = (i-1)*volsize;
- for(size_t j = 1; j<=(size_t)x*y*z; j++)
+ float* fbuffer=new float[imagesize];
+ FslReadVolumes(IP,fbuffer,1);
+ for(size_t j = 1; j<=imagesize; j++)
{
- if (doscaling==0) { output(i,j)=fbuffer[volstart+j-1]; }
- else { output(i,j)=(slope * fbuffer[volstart+j-1]) + intercept;}
-
+ if (doscaling==0) { output(i,j)=fbuffer[j-1]; }
+ else { output(i,j)=(slope * fbuffer[j-1]) + intercept;}
}
+ delete[] fbuffer;
}
- delete[] fbuffer;
- }
- break;
- case DT_UNSIGNED_CHAR:
- {
- unsigned char* cbuffer=new unsigned char[imagesize];
- FslReadVolumes(IP,cbuffer,v);
-
- size_t volsize = volinfo.x*volinfo.y*volinfo.z;
- size_t volstart = 1;
- for(size_t i=1; i<=(size_t)v; i++)
+ break;
+ case DT_UNSIGNED_CHAR:
{
- volstart = (i-1)*volsize;
- for(size_t j = 1; j<=(size_t)x*y*z; j++)
+ unsigned char* cbuffer=new unsigned char[imagesize];
+ FslReadVolumes(IP,cbuffer,1);
+ for(size_t j = 1; j<=imagesize; j++)
{
- if (doscaling==0) { output(i,j)=cbuffer[volstart+j-1]; }
- else { output(i,j)=(slope * cbuffer[volstart+j-1]) + intercept;}
+ if (doscaling==0) { output(i,j)=cbuffer[j-1]; }
+ else { output(i,j)=(slope * cbuffer[j-1]) + intercept;}
}
+ delete[] cbuffer;
}
- delete[] cbuffer;
- }
- break;
- default:
- perror("FslRead: DT not supported");
+ break;
+ default:
+ perror("FslRead: DT not supported");
+ }
}
FslClose(IP);
@@ -252,23 +230,58 @@ namespace MISCMATHS {
FslSetIntent(OP, volinfo.intent_code, volinfo.intent_p1, volinfo.intent_p2,
volinfo.intent_p3);
- int volStart = 1;
int volSize = getNumSeries();
int volNum = getNumVolumes();
- float *qv = new float[volSize*volNum];
+ FslWriteHeader(OP);
+
+ float *qv = new float[volSize];
for(int i = 1; i<= volNum; i++)
{
- volStart = (i-1)*volSize;
for(int j = 1; j <= volSize; j++)
- {
- qv[volStart+j-1] = (*this)(i,j);
- }
+ qv[j-1] = (*this)(i,j);
+ FslWriteVolumes(OP, qv, 1);
}
-
+
+ delete [] qv;
+
+ FslClose(OP);
+
+ }
+
+ void VolumeSeries::writeThresholdedSeriesAsFloat(const VolumeInfo& pvolinfo,const ColumnVector& in,const string& fname)
+ {
+ volinfo = pvolinfo;
+ preThresholdPositions = in;
+
+ Time_Tracer ts(string("VolumeSeries::writeThresholdedSeriesAsFloat" + fname).c_str());
+
+ FSLIO* OP = FslOpen(fname.c_str(), "wb");
+
+ FslCloneHeader(OP,volinfo.miscinfo);
+
+ FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, volinfo.v);
+ FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr);
+ FslSetDataType(OP, DT_FLOAT);
+ FslSetIntent(OP, volinfo.intent_code, volinfo.intent_p1, volinfo.intent_p2, volinfo.intent_p3);
+
+ int volSize = getUnthresholdNumSeries();
+ int numThresholdedSeries = getNumSeries();
+ int volNum = getNumVolumes();
+
FslWriteHeader(OP);
- FslWriteVolumes(OP, qv, volNum);
+
+ float *qv = new float[volSize];
+
+ for(int i = 1; i<= volNum; i++)
+ {
+ for(int j = 1; j <= volSize; j++)
+ qv[j-1]=0;
+ for(int j = 1; j <= numThresholdedSeries; j++)
+ qv[int(preThresholdPositions(j))-1] = (*this)(i,j);
+ FslWriteVolumes(OP, qv, 1);
+ }
delete [] qv;
diff --git a/volumeseries.h b/volumeseries.h
index 855fd83..bde1d7d 100644
--- a/volumeseries.h
+++ b/volumeseries.h
@@ -98,6 +98,7 @@ namespace MISCMATHS {
void read(const string& fname);
void writeAsInt(const string& fname);
void writeAsFloat(const string& fname);
+ void writeThresholdedSeriesAsFloat(const VolumeInfo& pvolinfo,const ColumnVector& in,const string& fname);
void replaceMeans();
--
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