From 9c680c20c4be6bf3bb9a8e828f39b4439c7f7437 Mon Sep 17 00:00:00 2001
From: Mark Woolrich <woolrich@fmrib.ox.ac.uk>
Date: Tue, 17 Jul 2001 16:11:55 +0000
Subject: [PATCH] *** empty log message ***
---
ContrastMgr.cc | 42 ++++++++++++++++++++++++------------------
1 file changed, 24 insertions(+), 18 deletions(-)
diff --git a/ContrastMgr.cc b/ContrastMgr.cc
index 6121170..9703767 100644
--- a/ContrastMgr.cc
+++ b/ContrastMgr.cc
@@ -16,6 +16,7 @@
#include "t2z.h"
#include "f2z.h"
#include "paradigm.h"
+#include "tracer_plus.h"
using namespace Utilities;
@@ -62,14 +63,13 @@ namespace FILM {
void ContrastMgr::run()
{
- Tracer ts("ContrastMgr::run");
+ Tracer_Plus ts("ContrastMgr::run");
Load();
// Loop through tcontrasts:
for(int c = 1; c <= parad.getTContrasts().Nrows(); c++)
{
-
if(ContrastMgrOptions::getInstance().verbose)
{
cerr << "T contrast no. " << c << endl;
@@ -88,7 +88,6 @@ namespace FILM {
// Loop through fcontrasts:
for(int c = 1; c <= parad.getFContrasts().Nrows(); c++)
{
-
SetFContrast(c, c+ContrastMgrOptions::getInstance().copenumber-1);
if(ContrastMgrOptions::getInstance().verbose)
@@ -108,25 +107,26 @@ namespace FILM {
void ContrastMgr::Load()
{
- Tracer ts("ContrastMgr::Load");
+ Tracer_Plus ts("ContrastMgr::Load");
// Need to read in b, sigmaSquareds, corrections and dof
Log& logger = Log::getInstance();
-
+
// Load contrasts:
parad.load("", ContrastMgrOptions::getInstance().contrastfname, ContrastMgrOptions::getInstance().fcontrastfname, false, 0);
numParams = parad.getTContrasts().Ncols();
+
if(ContrastMgrOptions::getInstance().verbose)
{
- logger.str() << "T Contrasts:" << endl << parad.getTContrasts();
- logger.str() << "F Contrasts:" << endl << parad.getFContrasts();
+ cerr << "T Contrasts:" << endl << parad.getTContrasts();
+ cerr << "F Contrasts:" << endl << parad.getFContrasts();
}
// sigmaSquareds:
sigmaSquareds.read(logger.getDir() + "/sigmasquareds");
sigmaSquareds.threshold(0.0);
- numTS = sigmaSquareds.getVolumeSize();
-
+ numTS = sigmaSquareds.getVolumeSize();
+
// b:
Volume peVol;
b.ReSize(numTS, numParams);
@@ -148,7 +148,7 @@ namespace FILM {
// dof:
ColumnVector dofVec = MISCMATHS::read_ascii_matrix(logger.getDir() + "/dof");
- dof = dofVec(1);
+ dof = dofVec(1);
// corrections - maybe ASCII (old version) or avw file:
ifstream in;
@@ -158,6 +158,12 @@ namespace FILM {
// avw format
is_avw_corrections = true;
corrections.read(logger.getDir() + "/corrections");
+ if(corrections.getDims().x == sigmaSquareds.getDims().x)
+ {
+ // unthresholded avw
+ corrections.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
+ corrections.thresholdSeries();
+ }
}
else
{
@@ -172,7 +178,7 @@ namespace FILM {
void ContrastMgr::SaveFContrast(const string& suffix)
{
- Tracer ts("ContrastMgr::SaveFContrast");
+ Tracer_Plus ts("ContrastMgr::SaveFContrast");
Log& logger = Log::getInstance();
// prepare contrast number:
@@ -195,7 +201,7 @@ namespace FILM {
void ContrastMgr::SaveTContrast(const string& suffix)
{
- Tracer ts("ContrastMgr::SaveTContrast");
+ Tracer_Plus ts("ContrastMgr::SaveTContrast");
Log& logger = Log::getInstance();
// prepare contrast number:
@@ -237,7 +243,7 @@ namespace FILM {
void ContrastMgr::GetCorrection(Matrix& corr, const int ind)
{
- Tracer ts("ContrastMgr::GetCorrection");
+ Tracer_Plus ts("ContrastMgr::GetCorrection");
// puts ColumnVector of length p*p from correction
// into Matrix corr which is p*p:
@@ -254,7 +260,7 @@ namespace FILM {
void ContrastMgr::ComputeZStat()
{
- Tracer ts("ContrastMgr::ComputeZStat");
+ Tracer_Plus ts("ContrastMgr::ComputeZStat");
Log& logger = Log::getInstance();
@@ -297,7 +303,7 @@ namespace FILM {
void ContrastMgr::ComputeCope()
{
- Tracer ts("ContrastMgr::ComputeCope");
+ Tracer_Plus ts("ContrastMgr::ComputeCope");
cb.ReSize(numTS);
for(int i = 1; i <= numTS; i++)
@@ -308,7 +314,7 @@ namespace FILM {
void ContrastMgr::ComputeNeff()
{
- Tracer ts("ContrastMgr::ComputeNeff");
+ Tracer_Plus ts("ContrastMgr::ComputeNeff");
Log& logger = Log::getInstance();
Matrix corr;
@@ -344,7 +350,7 @@ namespace FILM {
void ContrastMgr::ComputeFStat()
{
- Tracer ts("ContrastMgr::ComputeFStat");
+ Tracer_Plus ts("ContrastMgr::ComputeFStat");
//Log& logger = Log::getInstance();
Matrix corr;
@@ -377,7 +383,7 @@ namespace FILM {
void ContrastMgr::ComputeVarCope()
{
- Tracer ts("ContrastMgr::ComputeVarCope");
+ Tracer_Plus ts("ContrastMgr::ComputeVarCope");
varcb.ReSize(numTS);
for(int i = 1; i <= numTS; i++)
--
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