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MatrixDecompTest.cxx
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...@@ -5,50 +5,117 @@ ...@@ -5,50 +5,117 @@
#include "TMatrix.h" #include "TMatrix.h"
#include "TDecompQRH.h" #include "TDecompQRH.h"
#include "iostream" #include "iostream"
#include "gsl/gsl_linalg.h" #include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_bspline.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_statistics.h>
using namespace std; using namespace std;
int main(){ int main(){
int m = 10; /*int m = 3;
int n = 15; int n = 2;
gsl_matrix *A = gsl_matrix_alloc(m, n); TMatrixD A(3, 2);
for(int i = 0; i < m; i++){ for(int i = 0; i < A.GetNrows(); i++){
for(int j = 0; j < n; j++){ for(int j = 0; j < A.GetNcols(); j++){
gsl_matrix_set(A,i,j,1.0-2.0*rand() / RAND_MAX); A[i][j] = 1.0-2.0*rand() / RAND_MAX;
}
}
std::cout << "Original matrix A:" << std::endl;
for (size_t i = 0; i < m; ++i) {
for (size_t j = 0; j < n; ++j) {
std::cout << gsl_matrix_get(A, i, j) << " ";
} }
std::cout << std::endl;
} }
gsl_vector *tau = gsl_vector_alloc(n); cout << "A: " << endl;
gsl_linalg_QR_decomp(A, tau); A.Print();
gsl_matrix *Q = gsl_matrix_alloc(m, m); TDecompQRH decomp(A);
gsl_matrix *R = gsl_matrix_alloc(m, n); bool succes = decomp.Decompose();
cout << succes << endl;
// Compute R (the upper triangular matrix) auto R = decomp.GetTriangularMatrix();
for (size_t i = 0; i < m; ++i) { auto Q = decomp.GetOrthogonalMatrix();
for (size_t j = 0; j < n; ++j) { cout << "A: " << endl;
if (i <= j) { A.Print();
gsl_matrix_set(R, i, j, gsl_matrix_get(A, i, j)); cout << "QR: " << endl;
} else { (Q*R).Print();*/
gsl_matrix_set(R, i, j, 0.0); const size_t n = 500; /* number of data points to fit */
} const size_t k = 4; /* spline order */
} const double a = 0.0; /* data interval [a,b] */
const double b = 15.0;
const double sigma = 0.2; /* noise */
cout << "workspaces " << endl;
size_t nbreak = 10;
gsl_bspline_workspace *work1 = gsl_bspline_alloc(k, nbreak); /* 40 breakpoints */
gsl_bspline_workspace *work2 = gsl_bspline_alloc(k, nbreak); /* 10 breakpoints */
cout << "workspaces done" << endl;
const size_t p1 = gsl_bspline_ncontrol(work1); /* number of control points */
const size_t p2 = gsl_bspline_ncontrol(work2); /* number of control points */
const size_t dof1 = n - p1; /* degrees of freedom */
const size_t dof2 = n - p2; /* degrees of freedom */
gsl_vector *c1 = gsl_vector_alloc(p1);
gsl_vector *c2 = gsl_vector_alloc(p2);
gsl_vector *x = gsl_vector_alloc(n);
gsl_vector *y = gsl_vector_alloc(n);
gsl_vector *w = gsl_vector_alloc(n);
size_t i;
gsl_rng *r;
double chisq1, chisq2;
gsl_rng_env_setup();
r = gsl_rng_alloc(gsl_rng_default);
/* this is the data to be fitted */
for (i = 0; i < n; ++i)
{
double xi = (b - a) / (n - 1.0) * i + a;
double yi = cos(xi) * exp(-0.1 * xi);
double dyi = gsl_ran_gaussian(r, sigma);
yi += dyi;
gsl_vector_set(x, i, xi);
gsl_vector_set(y, i, yi);
gsl_vector_set(w, i, 1.0 / (sigma * sigma));
printf("%f %f\n", xi, yi);
} }
// Compute Q using gsl_linalg_QR_unpack
gsl_linalg_QR_unpack(A, tau, Q, R); /* use uniform breakpoints on [a, b] */
gsl_matrix *res = gsl_matrix_alloc(m, n); cout << "init " << endl;
gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, Q, R, 0.0, res); gsl_bspline_init_uniform(a, b, work1);
std::cout << "Decomposed matrix A:" << std::endl; gsl_bspline_init_uniform(a, b, work2);
for (size_t i = 0; i < m; ++i) { cout << "init done" << endl;
for (size_t j = 0; j < n; ++j) {
std::cout << gsl_matrix_get(res, i, j) << " "; /* solve least squares problem */
gsl_bspline_wlssolve(x, y, w, c1, &chisq1, work1);
gsl_bspline_wlssolve(x, y, w, c2, &chisq2, work2);
fprintf(stderr, "40 breakpoints: chisq/dof = %e\n", chisq1 / dof1);
fprintf(stderr, "10 breakpoints: chisq/dof = %e\n", chisq2 / dof2);
printf("\n\n");
/* output the spline curves */
{
double xi;
for (xi = a; xi <= b; xi += 0.1)
{
double result1, result2;
gsl_bspline_calc(xi, c1, &result1, work1);
gsl_bspline_calc(xi, c2, &result2, work2);
printf("%f %f %f\n", xi, result1, result2);
} }
std::cout << std::endl;
} }
gsl_rng_free(r);
gsl_vector_free(x);
gsl_vector_free(y);
gsl_vector_free(w);
gsl_vector_free(c1);
gsl_vector_free(c2);
gsl_bspline_free(work1);
gsl_bspline_free(work2);
return 0;
} }
\ No newline at end of file
README.md
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Note: this program uses features which did not come with gsl installed with `apt-get libgsl-dev`. Instead I removed my old version of gsl, installed gsl from [here](https://www.gnu.org/software/gsl/), and recompiled and reinstalled ROOT and AUSAlib.
## WalkCharacterization ## WalkCharacterization
This program takes a sorted (time aligned) root tree with INDiE neutron data and creates 2D-histograms with the value This program takes a sorted (time aligned) root tree with INDiE neutron data and creates 2D-histograms with the value
```math ```math
\Omega = \frac{\sqrt{r_0^2+\left(v(t_R-t_L)\right)^2}}{c} + \frac{1}{2}(t_L + t_R) - t_0 \Omega = \frac{\sqrt{r_0^2+\left(v(t_R-t_L)\right)^2}}{c} + \frac{1}{2}(t_L + t_R) - t_0
``` ```
(same is in [IndieAlignment](https://gitlab.au.dk/ausa/Jeppe/ausalibneutrons/indiealignment)), and the measured energy in every SiPM and INDiE PMT used to create the value. Ideally for an aligned tree, this value should be 0, but as signal shapes may vary with larger signals there might be some timing walk. This walk is fitted in the 2d-histograms, and some parametrization is made, which can be used to correct timing walk. The process consists of two executables, `histogramCreator` and `walkFitter`. The first creates the 2d-histograms and saves them to a file, as this is a longer process, and the second reads in the histograms, creates slices for every signal amplitude, fits a reversed crystal ball function to the gamma peak, and makes a plot of the walk as a function of signal amplitude. Finally some parametrization is fitted, and the parameters are outputted to a file. (same is in [IndieAlignment](https://gitlab.au.dk/ausa/Jeppe/ausalibneutrons/indiealignment)), and the measured energy in every SiPM and INDiE PMT used to create the value. Ideally for an aligned tree, this value should be 0, but as signal shapes may vary with larger signals there might be some timing walk. This walk is fitted in the 2d-histograms, and some parametrization is made, which can be used to correct timing walk. That is, we assume that what the histograms are really showing is
```math
0 + W_i(E_i) = \frac{\sqrt{r_0^2+\left(v(t_R-t_L)\right)^2}}{c} + \frac{1}{2}(t_L + t_R) - t_0
```
Where $`W_i`$ is the walk function for the detector from which signal amplitudes is used to create the histogram, and $`E_i`$ is the signal amplitude in that detector. Of course the walk in all detectors couple to each other, which is why this is perhaps best done iteratively until the walk curves converge. From this equation it also clear that in order to correct the walk, we must subtract $`2W_i(E_i)`$ from the timestamp if it is an INDiE detector, or add $`W_i(E_i)`$ if it is a SiPM. To get around this, a factor of $`-2`$ is multiplied to all points in the INDiE walk graphs, so that a walk correction is always an addition.
The process consists of two executables, `histogramCreator` and `walkFitter`. The first creates the 2d-histograms and saves them to a file, as this is a longer process, and the second reads in the histograms, creates slices for every signal amplitude, fits a reversed crystal ball function to the gamma peak, and makes a plot of the walk as a function of signal amplitude. Finally some parametrization is fitted, and the parameters are outputted to a file.
### histogramCreator ### histogramCreator
The usage is The usage is
...@@ -15,9 +22,6 @@ Where `histFile` is the file containing the histogram output, and file1, file2.. ...@@ -15,9 +22,6 @@ Where `histFile` is the file containing the histogram output, and file1, file2..
### walkFitter ### walkFitter
The usage is The usage is
``` ```
./walkFitter [histFile] [outfile] [fitWidth] [betaWalkFunction] [indieWalkFunction] ./walkFitter [histFile] [fitWidth] [betaPol] [indiePol]
``` ```
where [histFile] is the output of histogramCreater, [fitWidth] is the fitting range around the maximum (+-) in picoseconds that will be used to fit the gamma peak, and [betaWalkFunction] and [indieWalkFunction] are the functions that will be used to parametrize the timing walk. The options for these are: where [histFile] is the output of histogramCreater, [fitWidth] is the fitting range around the maximum (+-) in picoseconds that will be used to fit the gamma peak, and [betaPol] and [indiePol] are the degrees of the polynomials that will be used to fit the walk. The weights of the points on the walk graphs used to fit are 1/sqrt(number) of the number entries in the histogram used to create that point. It then outputs a file with "Fitted" appended, where the fits can be inspected, and a file called "walks.txt" where the parameters for each fit are written. The first number written in the file is the 5th last point written on the graph: energies above this point are walk corrected with the value at this point to avoid extrapolating the fit.
* polX where x is the order of polynomial.
* expDecayPol3 where the fitting function is a polynomial plus an exponential decay.
More can be added directly to the code. For the 8He experiment of IS659, pol4 was used for indie, and expDecayPol3 was used for
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build /home/jeppe/devel/projects/is659/ausalibNeutrons/walkCharacterization/CMakeLists.txt /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeCInformation.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeCXXInformation.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeCommonLanguageInclude.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeFindDependencyMacro.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeGenericSystem.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeInitializeConfigs.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeLanguageInformation.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeParseArguments.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeSystemSpecificInformation.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/CMakeSystemSpecificInitialize.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Compiler/CMakeCommonCompilerMacros.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Compiler/GNU-C.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Compiler/GNU-CXX.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Compiler/GNU.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/FindCURL.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/FindGSL.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/FindPackageMessage.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/FindPkgConfig.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/Linux-GNU-C.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/Linux-GNU-CXX.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/Linux-GNU.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/Linux-Initialize.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/Linux.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/Platform/UnixPaths.cmake /snap/clion/290/bin/cmake/linux/x64/share/cmake-3.29/Modules/SelectLibraryConfigurations.cmake /usr/lib/x86_64-linux-gnu/cmake/fmt/fmt-config-version.cmake /usr/lib/x86_64-linux-gnu/cmake/fmt/fmt-config.cmake /usr/lib/x86_64-linux-gnu/cmake/fmt/fmt-targets-none.cmake /usr/lib/x86_64-linux-gnu/cmake/fmt/fmt-targets.cmake /usr/local/cmake/ROOTConfig-targets-release.cmake /usr/local/cmake/ROOTConfig-targets.cmake /usr/local/cmake/ROOTConfig-version.cmake /usr/local/cmake/ROOTConfig.cmake /usr/local/cmake/RootMacros.cmake /usr/local/lib/AUSALIB/cmake/AUSALIBConfig.cmake /usr/local/lib/AUSALIB/cmake/AUSALIBConfigVersion.cmake /usr/local/lib/AUSALIB/cmake/AUSALIBTargets-relwithdebinfo.cmake /usr/local/lib/AUSALIB/cmake/AUSALIBTargets.cmake /usr/share/cmake/RapidJSON/RapidJSONConfig.cmake /usr/share/cmake/RapidJSON/RapidJSONConfigVersion.cmake /usr/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake /usr/share/cmake/nlohmann_json/nlohmann_jsonConfigVersion.cmake /usr/share/cmake/nlohmann_json/nlohmann_jsonTargets.cmake CMakeCache.txt CMakeFiles/3.29.6/CMakeCCompiler.cmake CMakeFiles/3.29.6/CMakeCXXCompiler.cmake CMakeFiles/3.29.6/CMakeSystem.cmake: phony
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# Clean all the built files.
build clean: CLEAN
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# Print all primary targets available.
build help: HELP
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# Make the all target the default.
default all
cmake-build-debug/cmake_install.cmake deleted 100644 → 0
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# Install script for directory: /home/jeppe/devel/projects/is659/ausalibNeutrons/walkCharacterization
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
set(CMAKE_INSTALL_PREFIX "/usr/local")
endif()
string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
# Set the install configuration name.
if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
if(BUILD_TYPE)
string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
else()
set(CMAKE_INSTALL_CONFIG_NAME "Debug")
endif()
message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
endif()
# Set the component getting installed.
if(NOT CMAKE_INSTALL_COMPONENT)
if(COMPONENT)
message(STATUS "Install component: \"${COMPONENT}\"")
set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
else()
set(CMAKE_INSTALL_COMPONENT)
endif()
endif()
# Install shared libraries without execute permission?
if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
set(CMAKE_INSTALL_SO_NO_EXE "1")
endif()
# Is this installation the result of a crosscompile?
if(NOT DEFINED CMAKE_CROSSCOMPILING)
set(CMAKE_CROSSCOMPILING "FALSE")
endif()
# Set default install directory permissions.
if(NOT DEFINED CMAKE_OBJDUMP)
set(CMAKE_OBJDUMP "/usr/bin/objdump")
endif()
if(CMAKE_INSTALL_COMPONENT)
set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
else()
set(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
endif()
string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
"${CMAKE_INSTALL_MANIFEST_FILES}")
file(WRITE "/home/jeppe/devel/projects/is659/ausalibNeutrons/walkCharacterization/cmake-build-debug/${CMAKE_INSTALL_MANIFEST}"
"${CMAKE_INSTALL_MANIFEST_CONTENT}")
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