From 254ec932d3fb350b6af499cf143613e4a6c26e16 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Fri, 17 Sep 2004 16:55:44 +0000
Subject: [PATCH] *** empty log message ***
---
cs.mat | 12 ----
cspline.h | 1 +
deb | 144 -----------------------------------------------
design.con | 7 ---
design.fts | 7 ---
dm.mat | 12 ----
kertest.cc | 8 +++
miscprob.ccbak | 119 ---------------------------------------
miscprob.hbak | 73 ------------------------
quick.cc | 8 +++
sparse_matrix.cc | 9 +++
sparsefn.cc | 8 +++
12 files changed, 34 insertions(+), 374 deletions(-)
delete mode 100644 cs.mat
delete mode 100755 deb
delete mode 100644 design.con
delete mode 100755 design.fts
delete mode 100644 dm.mat
delete mode 100755 miscprob.ccbak
delete mode 100755 miscprob.hbak
diff --git a/cs.mat b/cs.mat
deleted file mode 100644
index 45f73fc..0000000
--- a/cs.mat
+++ /dev/null
@@ -1,12 +0,0 @@
-! VEST-Waveform File
-/NumWaves 1
-/NumPoints 6
-/Skip
-
-/Matrix
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
diff --git a/cspline.h b/cspline.h
index 9afcc5f..467a4e8 100644
--- a/cspline.h
+++ b/cspline.h
@@ -6,6 +6,7 @@
Copyright (C) 1999-2000 University of Oxford */
/* CCOPYRIGHT */
+
#if !defined(__cspline_h)
#define __cspline_h
diff --git a/deb b/deb
deleted file mode 100755
index aa07200..0000000
--- a/deb
+++ /dev/null
@@ -1,144 +0,0 @@
-Log directory is: /usr/people/woolrich/fsl/nsrc/smmfast/logdir++++
-epibt =1000
-spatialdatafile =/usr/people/woolrich/matlab/smm/data/art_z_checker
-maskfile =/usr/people/woolrich/matlab/smm/data/art_mask_checker
-mrf_precision=0.25
-means=-0.187964 2.466296 -5.830409
-
-vars=0.781579 2.096998 1.603299
-
-props=0.559440 0.127918 0.312642
-
-it=1
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=1988.99
-smmfunc.evaluate_withmrfprec(latest)=-1702.47
-latest(nclasses*num_superthreshold+1)=71.6585
-mrf_precision=71.6585
-it=2
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-1702.47
-smmfunc.evaluate_withmrfprec(latest)=-1969.63
-latest(nclasses*num_superthreshold+1)=114.107
-mrf_precision=114.107
-it=3
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-1969.63
-smmfunc.evaluate_withmrfprec(latest)=-2069.99
-latest(nclasses*num_superthreshold+1)=135.829
-mrf_precision=135.829
-it=4
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2069.99
-smmfunc.evaluate_withmrfprec(latest)=-2119.04
-latest(nclasses*num_superthreshold+1)=147.931
-mrf_precision=147.931
-it=5
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2119.04
-smmfunc.evaluate_withmrfprec(latest)=-2168.2
-latest(nclasses*num_superthreshold+1)=161.158
-mrf_precision=161.158
-it=6
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2168.2
-smmfunc.evaluate_withmrfprec(latest)=-2202.21
-latest(nclasses*num_superthreshold+1)=170.851
-mrf_precision=170.851
-it=7
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2202.21
-smmfunc.evaluate_withmrfprec(latest)=-2257.59
-latest(nclasses*num_superthreshold+1)=187.959
-mrf_precision=187.959
-it=8
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2257.59
-smmfunc.evaluate_withmrfprec(latest)=-2291.83
-latest(nclasses*num_superthreshold+1)=199.568
-mrf_precision=199.568
-it=9
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2291.83
-smmfunc.evaluate_withmrfprec(latest)=-2320.1
-latest(nclasses*num_superthreshold+1)=209.342
-mrf_precision=209.342
-it=10
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2320.1
-smmfunc.evaluate_withmrfprec(latest)=-2339.78
-latest(nclasses*num_superthreshold+1)=216.569
-mrf_precision=216.569
-it=11
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2339.78
-smmfunc.evaluate_withmrfprec(latest)=-2362.63
-latest(nclasses*num_superthreshold+1)=225.299
-mrf_precision=225.299
-it=12
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2362.63
-smmfunc.evaluate_withmrfprec(latest)=-2374.07
-latest(nclasses*num_superthreshold+1)=229.721
-mrf_precision=229.721
-it=13
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2374.07
-smmfunc.evaluate_withmrfprec(latest)=-2385.38
-latest(nclasses*num_superthreshold+1)=234.241
-mrf_precision=234.241
-it=14
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2385.38
-smmfunc.evaluate_withmrfprec(latest)=-2397.25
-latest(nclasses*num_superthreshold+1)=239.055
-mrf_precision=239.055
-it=15
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2397.25
-smmfunc.evaluate_withmrfprec(latest)=-2412.04
-latest(nclasses*num_superthreshold+1)=245.244
-mrf_precision=245.244
-it=16
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2412.04
-smmfunc.evaluate_withmrfprec(latest)=-2422.29
-latest(nclasses*num_superthreshold+1)=249.555
-mrf_precision=249.555
-it=17
-sit=1
-"Updating distribution params"=Updating distribution params
-"Updating weights"=Updating weights
-smmfunc.evaluate_withmrfprec(latest)=-2422.29
diff --git a/design.con b/design.con
deleted file mode 100644
index ed55c78..0000000
--- a/design.con
+++ /dev/null
@@ -1,7 +0,0 @@
-! VEST-Waveform File
-/NumWaves 1
-/NumPoints 1
-/Skip
-
-/Matrix
-1.000000e+00
diff --git a/design.fts b/design.fts
deleted file mode 100755
index ed55c78..0000000
--- a/design.fts
+++ /dev/null
@@ -1,7 +0,0 @@
-! VEST-Waveform File
-/NumWaves 1
-/NumPoints 1
-/Skip
-
-/Matrix
-1.000000e+00
diff --git a/dm.mat b/dm.mat
deleted file mode 100644
index 45f73fc..0000000
--- a/dm.mat
+++ /dev/null
@@ -1,12 +0,0 @@
-! VEST-Waveform File
-/NumWaves 1
-/NumPoints 6
-/Skip
-
-/Matrix
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
-1.000000e+00
diff --git a/kertest.cc b/kertest.cc
index 441b4e4..45ac76e 100644
--- a/kertest.cc
+++ b/kertest.cc
@@ -1,3 +1,11 @@
+/* kertest.cc
+
+ Mark Jenkinson, FMRIB Image Analysis Group
+
+ Copyright (C) 2001 University of Oxford */
+
+/* CCOPYRIGHT */
+
#include "kernel.h"
using namespace MISCMATHS;
diff --git a/miscprob.ccbak b/miscprob.ccbak
deleted file mode 100755
index a8e767f..0000000
--- a/miscprob.ccbak
+++ /dev/null
@@ -1,119 +0,0 @@
-/* miscprob.cc
-
- Christian Beckmann & Mark Woolrich, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2000 University of Oxford */
-
-/* CCOPYRIGHT */
-
-// Miscellaneous maths functions that rely on libprob
-
-#include "miscprob.h"
-#include "stdlib.h"
-#include "newmatio.h"
-
-using namespace NEWMAT;
-
-namespace MISCMATHS {
-
-ReturnMatrix unifrnd(const int dim1, const int dim2, const float start, const float end)
-{
- int tdim = dim2;
- double tmpD=1.0;
- if(tdim<0){tdim=dim1;}
- Matrix res(dim1,tdim);
- for (int mc=1; mc<=res.Ncols(); mc++) {
- for (int mr=1; mr<=res.Nrows(); mr++) {
- drand(&tmpD);
- res(mr,mc)=(tmpD-1)*(end-start)+start;
- }
- }
-
- res.Release();
- return res;
-}
-
-ReturnMatrix normrnd(const int dim1, const int dim2, const float mu, const float sigma)
-{
- int tdim = dim2;
- double tmpD=1.0;
- if(tdim<0){tdim=dim1;}
- Matrix res(dim1,tdim);
- for (int mc=1; mc<=res.Ncols(); mc++) {
- for (int mr=1; mr<=res.Nrows(); mr++) {
- drand(&tmpD);
- res(mr,mc)=ndtri(tmpD-1.0)*sigma+mu ;
- }
- }
-
- res.Release();
-
- return res;
-}
-
-ReturnMatrix normpdf(const RowVector& vals, const float mu, const float sigma)
-{
- RowVector res(vals);
- for (int mc=1; mc<=res.Ncols(); mc++){
- res(mc) = std::exp(-0.5*(std::pow(vals(mc)-mu,2)/sigma))*std::pow(2*M_PI*sigma,-0.5);
- }
-
- res.Release();
- return res;
-}
-
-ReturnMatrix normcdf(const RowVector& vals, const float mu, const float sigma)
-{
- RowVector res(vals);
- RowVector tmp;
- tmp = (vals-mu)/std::sqrt(sigma);
- for (int mc=1; mc<=res.Ncols(); mc++){
- res(mc) = ndtr(tmp(mc));
- }
-
- res.Release();
- return res;
-}
-
-ReturnMatrix gammapdf(const RowVector& vals, const float mu, const float sigma)
-{
- RowVector res(vals);
- float a = std::pow(mu,2)/sigma;
- float b = mu/sigma;
- float c = std::pow(b,a)/gamma(a);
- for (int mc=1; mc<=res.Ncols(); mc++){
- res(mc) = c*std::pow(std::abs(vals(mc)),a-1)*std::exp(-b*std::abs(vals(mc)));
- }
-
- res.Release();
- return res;
-}
-
-
-ReturnMatrix normpdf(const RowVector& vals, const RowVector& mu, const RowVector& sigma)
-{
- Matrix res(mu.Ncols(),vals.Ncols());
- for (int mc=1; mc<=res.Ncols(); mc++){
- for (int mr=1; mr<=res.Nrows(); mr++){
- res(mr,mc) = std::exp(-0.5*(std::pow(vals(mc)-mu(mr),2)/sigma(mr)))*std::pow(2*M_PI*sigma(mr),-0.5);
- }
- }
-
- res.Release();
- return res;
-}
-
-
-ReturnMatrix mvnormrandm(const RowVector& mu, const SymmetricMatrix& covar, int nsamp)
-{
-// Matrix eig_vec;
-// DiagonalMatrix eig_val;
-// EigenValues(covar,eig_val,eig_vec);
-
-// Matrix ret = ones(nsamp, 1)*mu + dnormrandm(nsamp,mu.Ncols())*sqrt(eig_val)*eig_vec.t();
- Mvnormrandm mvn(mu, covar);
-
- return mvn.next(nsamp);
-}
-
-}
diff --git a/miscprob.hbak b/miscprob.hbak
deleted file mode 100755
index 8d1125d..0000000
--- a/miscprob.hbak
+++ /dev/null
@@ -1,73 +0,0 @@
-/* miscprob.h
-
- Christian Beckmann & Mark Woolrich, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2000 University of Oxford */
-
-/* CCOPYRIGHT */
-
-// Miscellaneous maths functions that rely on libprob build ontop of miscmaths
-
-
-#if !defined(__miscprob_h)
-#define __miscprob_h
-
-#include "miscmaths.h"
-#include "libprob.h"
-
-using namespace NEWMAT;
-
-namespace MISCMATHS {
-
- ReturnMatrix unifrnd(const int dim1 = 1, const int dim2 = -1, const float start = 0, const float end = 1);
-
- ReturnMatrix normrnd(const int dim1 = 1, const int dim2 = -1, const float mu = 0, const float sigma = 1);
-
- ReturnMatrix normpdf(const RowVector& vals, const float mu = 0, const float sigma = 1);
-
- ReturnMatrix normcdf(const RowVector& vals, const float mu = 0, const float sigma = 1);
-
- ReturnMatrix gammapdf(const RowVector& vals, const float mu, const float sigma);
-
- ReturnMatrix normpdf(const RowVector& vals, const RowVector& mus, const RowVector& sigmas);
-
- ReturnMatrix mvnrnd(const RowVector& mu, const SymmetricMatrix& covar, int nsamp = 1);
-
- class Mvnormrandm
- {
- public:
- Mvnormrandm(){}
-
- Mvnormrandm(const RowVector& pmu, const SymmetricMatrix& pcovar) :
- mu(pmu),
- covar(pcovar)
- {
- Matrix eig_vec;
- DiagonalMatrix eig_val;
- EigenValues(covar,eig_val,eig_vec);
-
- covarw = sqrt(eig_val)*eig_vec.t();
- }
-
- ReturnMatrix next(int nsamp = 1) const
- {
- Matrix ret = ones(nsamp, 1)*mu + normrnd(nsamp,mu.Ncols())*covarw;
- ret.Release();
- return ret;
- }
- private:
-
- RowVector mu;
- SymmetricMatrix covar;
-
- Matrix covarw;
-
- };
-}
-#endif
-
-
-
-
-
-
diff --git a/quick.cc b/quick.cc
index 976093c..940cde6 100644
--- a/quick.cc
+++ b/quick.cc
@@ -1,3 +1,11 @@
+/* quick.cc
+
+ Mark Woolrich, FMRIB Image Analysis Group
+
+ Copyright (C) 1999-2000 University of Oxford */
+
+/* CCOPYRIGHT */
+
#include <iostream>
#include <fstream>
#include <iomanip>
diff --git a/sparse_matrix.cc b/sparse_matrix.cc
index 4f6c6c7..5972be6 100644
--- a/sparse_matrix.cc
+++ b/sparse_matrix.cc
@@ -1,3 +1,12 @@
+/* sparse_matrix.h
+
+ Mark Woolrich, FMRIB Image Analysis Group
+
+ Copyright (C) 1999-2000 University of Oxford */
+
+/* CCOPYRIGHT */
+
+
#include <iostream>
#include <iomanip>
#include <strstream>
diff --git a/sparsefn.cc b/sparsefn.cc
index 4c3539f..5bf5a36 100644
--- a/sparsefn.cc
+++ b/sparsefn.cc
@@ -1,3 +1,11 @@
+/* sparsefn.h
+
+ Mark Woolrich, FMRIB Image Analysis Group
+
+ Copyright (C) 1999-2000 University of Oxford */
+
+/* CCOPYRIGHT */
+
#include <iostream>
#include <iomanip>
#include <strstream>
--
GitLab