Commit 12b23628 authored by Tobias Weber's avatar Tobias Weber

Merge branch 'indexing_random_sphere' into 'develop'

Indexing random sphere

See merge request !123
parents 3c4c071f 36189a65
Pipeline #23025 passed with stage
in 28 minutes and 14 seconds
......@@ -52,6 +52,11 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID MATCHES "Cla
" (older than 7.0) is not tested,"
" and not expected to work because of insufficient support for C++17")
endif()
if(CMAKE_BUILD_TYPE MATCHES Debug)
add_compile_options(-ggdb -rdynamic)
endif()
if(BUILD_OPTIMIZED_DEBUG)
add_compile_options(-Og)
endif()
......
......@@ -75,14 +75,19 @@ const std::string ProgressHandler::getStatus()
void ProgressHandler::log(const std::string& message)
{
std::lock_guard<std::mutex> lock(_mutex);
_log.push_back(message);
{
std::lock_guard<std::mutex> lock(_mutex);
_log.push_back(message);
}
// without this the logs are not shown unless setProgress is called
if (_callback)
_callback();
}
void ProgressHandler::log(const char* message)
{
std::lock_guard<std::mutex> lock(_mutex);
_log.push_back(message);
log(std::string{message});
}
std::vector<std::string> ProgressHandler::getLog()
......
......@@ -110,8 +110,8 @@ void AutoIndexer::computeFFTSolutions(const std::vector<Peak3D*>& peaks)
}
if (_handler)
_handler->log(
"Searching direct lattice vectors using" + std::to_string(qvects.size())
+ "peaks defined on numors:");
"Searching direct lattice vectors using " + std::to_string(qvects.size())
+ " peaks defined on numors.");
// Find the best vectors via FFT
std::vector<Eigen::RowVector3d> tvects = algo::findOnSphere(
......
......@@ -13,8 +13,11 @@
// ***********************************************************************************************
#include <algorithm>
#include <chrono>
#include <cmath>
#include <complex>
#include <fstream>
#include <iomanip>
#include <random>
#include <vector>
......@@ -24,6 +27,10 @@
#include "base/utils/Units.h"
#include "core/algo/FFTIndexing.h"
//#define RANDOMISE_FFTINDEXING_SPHERE
//#define DEBUG_HISTOGRAMS
namespace nsx {
//! Returns a list of approximately equal distributed points on the unit sphere.
......@@ -35,11 +42,22 @@ std::vector<Eigen::RowVector3d> algo::pointsOnSphere(unsigned int n_vertices)
std::vector<Eigen::RowVector3d> result;
result.reserve(n_vertices);
// We use the Fibonacci sphere algorithm, which is simple, and just good enough.
// See https://stackoverflow.com/questions/9600801/evenly-distributing-n-points-on-a-sphere.
std::default_random_engine generator;
#ifdef RANDOMISE_FFTINDEXING_SPHERE
// random number generator, seeded with ms since epoch
static auto epoch = std::chrono::system_clock::now().time_since_epoch();
static std::mt19937 generator(
std::chrono::duration_cast<std::chrono::milliseconds>(epoch).count());
std::uniform_real_distribution<double> distribution(0.0, 1.0);
const double rnd(distribution(generator));
#else
// TODO: TestAutoIndexer.py only works with this special number, something is wrong...
const double rnd(0.131538);
#endif
// We use the Fibonacci sphere algorithm, which is simple, and just good enough.
// See https://stackoverflow.com/questions/9600801/evenly-distributing-n-points-on-a-sphere.
const double offset = 2.0 / n_vertices;
const double increment = M_PI * (3. - sqrt(5.));
......@@ -56,6 +74,41 @@ std::vector<Eigen::RowVector3d> algo::pointsOnSphere(unsigned int n_vertices)
return result;
}
#ifdef DEBUG_HISTOGRAMS
// Output a histogram and its trafo for debugging.
// Plot in gnuplot with:
// plot "hist_0.dat" u 4:5 w boxes
// plot "hist_0.dat" u 4:6 w boxes
static void save_histogram(
std::size_t projidx, const Eigen::RowVector3d& proj_dir, double dq, double qMax,
const std::vector<double>& hist, const std::vector<std::complex<double>>& hist_ft)
{
int spacing = 16;
std::ofstream ofHist("hist_" + std::to_string(projidx) + ".dat");
ofHist << std::setw(spacing) << std::left << "# proj_dir_x"
<< " " << std::setw(spacing) << std::left << "proj_dir_y"
<< " " << std::setw(spacing) << std::left << "proj_dir_z"
<< " " << std::setw(spacing) << std::left << "q_proj"
<< " " << std::setw(spacing) << std::left << "hist"
<< " " << std::setw(spacing) << std::left << "hist_ft"
<< "\n";
for (std::size_t idx = 0; idx < std::min(hist.size(), hist_ft.size()); ++idx) {
ofHist << std::setw(spacing) << std::left << proj_dir[0] << " " // proj_dir[0]
<< std::setw(spacing) << std::left << proj_dir[1] << " " // proj_dir[1]
<< std::setw(spacing) << std::left << proj_dir[2] << " " // proj_dir[2]
<< std::setw(spacing) << std::left << double(idx) * dq - qMax << " " // q_proj
<< std::setw(spacing) << std::left << hist[idx] << " " << std::setw(spacing)
<< std::left << std::abs(hist_ft[idx]) << "\n";
}
ofHist.flush();
}
#endif
std::vector<Eigen::RowVector3d> algo::findOnSphere(
const std::vector<ReciprocalVector>& qvects, unsigned int n_vertices, unsigned int nsolutions,
int nSubdiv, double amax, double freq_tol)
......@@ -85,7 +138,10 @@ std::vector<Eigen::RowVector3d> algo::findOnSphere(
std::vector<std::pair<Eigen::RowVector3d, double>> vectorWithQuality;
vectorWithQuality.reserve(n_vertices);
for (const Eigen::RowVector3d q_direction : pointsOnSphere(n_vertices)) {
std::vector<Eigen::RowVector3d> q_directions = pointsOnSphere(n_vertices);
for (std::size_t q_diridx = 0; q_diridx < q_directions.size(); ++q_diridx) {
const Eigen::RowVector3d& q_direction = q_directions[q_diridx];
std::vector<double> hist(nPoints, 0); // reciprocal space histogram
for (const auto& vect : qvects) {
const Eigen::RowVector3d& q_vector = vect.rowVector();
......@@ -98,6 +154,10 @@ std::vector<Eigen::RowVector3d> algo::findOnSphere(
std::vector<std::complex<double>> spectrum;
fft.fwd(spectrum, hist); // Fourier transform the histogram
#ifdef DEBUG_HISTOGRAMS
save_histogram(q_diridx, q_direction, dq, qMax, hist, spectrum);
#endif
const double FZero = std::abs(spectrum[0]); // zero mode
size_t pos_max = 0; // position of maximum mode, other than zero mode
double value = 0; // value of maxmimum mode
......@@ -117,7 +177,7 @@ std::vector<Eigen::RowVector3d> algo::findOnSphere(
if (pos_max > 2)
vectorWithQuality.push_back(
{q_direction * (pos_max)*nSubdiv * amax / double(nPoints), value});
{q_direction * double(pos_max * nSubdiv) * amax / double(nPoints), value});
}
std::sort(
......
......@@ -611,7 +611,17 @@ void PeakFinder::find(const DataList numors)
if (loop_begin == -1)
loop_begin = 0;
if (loop_end == -1)
loop_end = numor->nFrames();
loop_end = nframes;
// keep frame indices in bounds for current numor
if (loop_begin < 0)
loop_begin = 0;
if (loop_begin > nframes)
loop_begin = nframes;
if (loop_end < 0)
loop_end = 0;
if (loop_end > nframes)
loop_end = nframes;
std::map<int, Blob3D> local_blobs = {{}};
nsx::EquivalenceList local_equivalences;
......
......@@ -29,9 +29,15 @@ NexusDataReader::NexusDataReader(const std::string& filename, Diffractometer* in
Eigen::MatrixXi NexusDataReader::data(size_t frame)
{
// std::cout << "NexusDataReader::data, this=" << std::hex << (void*)this << ", frame=" <<
// std::dec << frame << std::endl;
if (!_isOpened)
open();
if (frame >= _nFrames)
throw std::runtime_error("Requested invalid frame " + std::to_string(frame));
Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic, Eigen::ColMajor> m(_nRows, _nCols);
hsize_t count[3] = {1, _nCols, _nRows};
......
......@@ -15,6 +15,7 @@
#include "test/cpp/catch.hpp"
#include <Eigen/Dense>
#include <iostream>
#include "core/algo/DataReaderFactory.h"
#include "core/experiment/Experiment.h"
......@@ -22,6 +23,12 @@
TEST_CASE("test/crystal/TestFFTIndexing.cpp", "")
{
auto logger = std::make_shared<nsx::ProgressHandler>();
logger->setCallback([logger]() {
for (const auto& log : logger->getLog())
std::cout << log << std::endl;
});
nsx::IndexerParameters params;
params.maxdim = 70.0;
params.nSolutions = 10;
......@@ -35,17 +42,20 @@ TEST_CASE("test/crystal/TestFFTIndexing.cpp", "")
params.unitCellEquivalenceTolerance = 0.05;
params.solutionCutoff = 10.0;
Eigen::Matrix3d M;
M << 45.0, 1.0, -2.0, -1.5, 36.0, -2.2, 1.25, -3, 50.0;
nsx::UnitCell C(M);
C.reduce(params.niggliReduction, params.niggliTolerance, params.gruberTolerance);
const nsx::UnitCell uc = C.applyNiggliConstraints();
// real basis of unit cell
Eigen::Matrix3d basis;
basis << 45.0, 1.0, -2.0, -1.5, 36.0, -2.2, 1.25, -3, 50.0;
nsx::UnitCell uc(basis);
uc.reduce(params.niggliReduction, params.niggliTolerance, params.gruberTolerance);
uc = uc.applyNiggliConstraints();
std::cout << "Basis:\n" << uc.basis() << std::endl;
std::vector<nsx::ReciprocalVector> qs;
const Eigen::Matrix3d BU = uc.reciprocalBasis();
const auto reflections = uc.generateReflectionsInShell(0.5, 100, 2.67);
for (const nsx::MillerIndex& index : reflections)
qs.emplace_back(index.rowVector().cast<double>() * BU);
for (const nsx::MillerIndex& index : reflections) {
// std::cout << "reflection: " << index << std::endl;
qs.emplace_back(index.rowVector().cast<double>() * uc.reciprocalBasis());
}
nsx::Experiment experiment("test", "BioDiff2500");
const nsx::sptrDataSet data(
......@@ -55,8 +65,12 @@ TEST_CASE("test/crystal/TestFFTIndexing.cpp", "")
nsx::PeakCollection peak_collection;
const auto events = nsx::algo::qs2events(qs, data->instrumentStates(), data->detector());
for (const nsx::DetectorEvent& event : events) {
// std::cout << "event x=" << event._px << " y=" << event._py
// << " frame=" << event._frame << " tof=" << event._tof
// << std::endl;
nsx::Peak3D peak(data);
const Eigen::Vector3d center = {event._px, event._py, event._frame};
// dummy shape
try {
peak.setShape(nsx::Ellipsoid(center, 1.0));
......@@ -69,7 +83,8 @@ TEST_CASE("test/crystal/TestFFTIndexing.cpp", "")
}
CHECK(peak_collection.numberOfPeaks() >= 5900);
nsx::AutoIndexer* const auto_indexer = experiment.autoIndexer();
nsx::AutoIndexer* auto_indexer = experiment.autoIndexer();
auto_indexer->setHandler(logger);
auto_indexer->setParameters(params);
auto_indexer->autoIndex(peak_collection.getPeakList());
......@@ -78,8 +93,10 @@ TEST_CASE("test/crystal/TestFFTIndexing.cpp", "")
CHECK(solutions.front().second > 99.9);
const Eigen::Matrix3d autoBasis = solutions.front().first->basis();
const Eigen::Matrix3d E = autoBasis.inverse() * uc.basis();
std::cout << "Basis:\n" << autoBasis << std::endl;
// check for identity
const Eigen::Matrix3d E = autoBasis.inverse() * uc.basis();
// square because of the orientation issue
CHECK((E * E - Eigen::Matrix3d::Identity()).norm() < 1e-10);
}
// ***********************************************************************************************
//
// NSXTool: data reduction for neutron single-crystal diffraction
//
//! @file test/cpp/crystal/TestFFTIndexingSphere.cpp
//! @brief Test ...
//!
//! @homepage ###HOMEPAGE###
//! @license GNU General Public License v3 or higher (see COPYING)
//! @copyright Institut Laue-Langevin and Forschungszentrum Jülich GmbH 2016-
//! @authors see CITATION, MAINTAINER
//
// ***********************************************************************************************
#include "test/cpp/catch.hpp"
#include <fstream>
#include <iostream>
#include "core/algo/FFTIndexing.h"
TEST_CASE("test/crystal/TestFFTIndexingSphere.cpp", "")
{
unsigned int n_vertices = 128;
std::vector<Eigen::RowVector3d> points = nsx::algo::pointsOnSphere(n_vertices);
// plot these points with:
// gnuplot -p -e "set xyplane 0; splot \"sphere.dat\" u 1:2:3 w points pt 7
std::ofstream ofstrdat("sphere.dat");
for (const Eigen::RowVector3d& vec : points) {
ofstrdat << vec[0] << " " << vec[1] << " " << vec[2] << std::endl;
}
CHECK(points.size() == n_vertices);
}
......@@ -28,7 +28,7 @@
#define OUTPUT_INTERMEDIATE
#define ONLY_FIRST_FILE
//#define ONLY_FIRST_FILE
TEST_CASE("test/data/TestNexusData.cpp", "")
......@@ -51,23 +51,25 @@ TEST_CASE("test/data/TestNexusData.cpp", "")
nsx::DataReaderFactory factory;
nsx::DataList numors;
std::string dir = "/users/tw/tmp/nsx-data/dkdp/nexus/";
std::vector<std::string> files = {
"/home/tw/tmp/nsx/internal-192/501168.nxs", "/home/tw/tmp/nsx/internal-192/501169.nxs",
"/home/tw/tmp/nsx/internal-192/501170.nxs", "/home/tw/tmp/nsx/internal-192/501171.nxs",
"/home/tw/tmp/nsx/internal-192/501172.nxs", "/home/tw/tmp/nsx/internal-192/501173.nxs",
"/home/tw/tmp/nsx/internal-192/501174.nxs", "/home/tw/tmp/nsx/internal-192/501175.nxs",
"/home/tw/tmp/nsx/internal-192/501176.nxs", "/home/tw/tmp/nsx/internal-192/501177.nxs",
"/home/tw/tmp/nsx/internal-192/501178.nxs", "/home/tw/tmp/nsx/internal-192/501179.nxs",
"/home/tw/tmp/nsx/internal-192/501180.nxs", "/home/tw/tmp/nsx/internal-192/501181.nxs",
"/home/tw/tmp/nsx/internal-192/501182.nxs", "/home/tw/tmp/nsx/internal-192/501183.nxs",
"/home/tw/tmp/nsx/internal-192/501184.nxs", "/home/tw/tmp/nsx/internal-192/501185.nxs",
"501168.nxs", "501169.nxs",
/* "501170.nxs", "501171.nxs",
"501172.nxs", "501173.nxs",
"501174.nxs", "501175.nxs",
"501176.nxs", "501177.nxs",
"501178.nxs", "501179.nxs",
"501180.nxs", "501181.nxs",
"501182.nxs", "501183.nxs",
"501184.nxs", "501185.nxs", */
};
nsx::Diffractometer* diffractometer = nsx::Diffractometer::create("D19");
nsx::Experiment exp("test", diffractometer->name());
std::size_t numframes = 0;
for (const std::string& file : files) {
for (const std::string& _file : files) {
std::string file = dir + _file;
std::cout << "Loading " << file << "..." << std::endl;
std::ifstream ifstr(file);
......@@ -240,6 +242,13 @@ TEST_CASE("test/data/TestNexusData.cpp", "")
nsx::AutoIndexer* auto_indexer = exp.autoIndexer();
nsx::IndexerParameters parameters;
// parameters for FFTIndexing
parameters.nVertices = 5000; // points on the direction sphere
parameters.subdiv = 50; // number of bins
parameters.frequencyTolerance = 0.5; // peaks to discard
parameters.maxdim = 500.; // unit cell length
parameters.nSolutions = 20;
std::cout << "AutoIndexer parameters: ";
std::cout << "maxdim = " << parameters.maxdim << ", ";
std::cout << "nSolutions = " << parameters.nSolutions << ", ";
......@@ -254,10 +263,6 @@ TEST_CASE("test/data/TestNexusData.cpp", "")
<< ", ";
std::cout << "solutionCutoff = " << parameters.solutionCutoff << std::endl;
// parameters.minUnitCellVolume = 1.;
// parameters.maxdim = 500.;
// parameters.nVertices = 1000;
// parameters.solutionCutoff = 5.;
auto_indexer->setParameters(parameters);
auto peaksToIndex = filtered_collection->getPeakList();
......
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