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#ifndef MANTID_GEOMETRY_INDEXING_UTILS_TEST_H_
#define MANTID_GEOMETRY_INDEXING_UTILS_TEST_H_
#include <cxxtest/TestSuite.h>
#include <MantidKernel/Timer.h>
#include <MantidKernel/System.h>
#include <iostream>
#include <iomanip>
#include <algorithm>
Gigg, Martyn Anthony
committed
#include <MantidKernel/V3D.h>
#include <MantidKernel/Matrix.h>
#include <MantidGeometry/Crystal/IndexingUtils.h>
using namespace Mantid::Geometry;
Gigg, Martyn Anthony
committed
using Mantid::Kernel::V3D;
using Mantid::Kernel::Matrix;
class IndexingUtilsTest : public CxxTest::TestSuite
{
public:
#define PI 3.141592653589793238
static std::vector<V3D> getNatroliteQs()
{
std::vector<V3D> q_vectors;
q_vectors.push_back( V3D(-0.57582, -0.35322, -0.19974 ));
q_vectors.push_back( V3D(-1.41754, -0.78704, -0.75974 ));
q_vectors.push_back( V3D(-1.12030, -0.53578, -0.27559 ));
q_vectors.push_back( V3D(-0.68911, -0.59397, -0.12716 ));
q_vectors.push_back( V3D(-1.06863, -0.43255, 0.01688 ));
q_vectors.push_back( V3D(-1.82007, -0.49671, -0.06266 ));
q_vectors.push_back( V3D(-1.10465, -0.73708, -0.01939 ));
q_vectors.push_back( V3D(-0.12747, -0.32380, 0.00821 ));
q_vectors.push_back( V3D(-0.84210, -0.37038, 0.15403 ));
q_vectors.push_back( V3D(-0.54099, -0.46900, 0.11535 ));
q_vectors.push_back( V3D(-0.90478, -0.50667, 0.51072 ));
q_vectors.push_back( V3D(-0.50387, -0.58561, 0.43502 ));
return q_vectors;
}
static std::vector<V3D> getNatroliteIndices()
{
std::vector<V3D> correct_indices;
correct_indices.push_back( V3D( 1, 9, -9) );
correct_indices.push_back( V3D( 4, 20,-24) );
correct_indices.push_back( V3D( 2, 18,-14) );
correct_indices.push_back( V3D( 0, 12,-12) );
correct_indices.push_back( V3D( 1, 19, -9) );
correct_indices.push_back( V3D( 3, 31,-13) );
correct_indices.push_back( V3D( 0, 20,-14) );
correct_indices.push_back( V3D(-1, 3, -5) );
correct_indices.push_back( V3D( 0, 16, -6) );
correct_indices.push_back( V3D(-1, 11, -7) );
correct_indices.push_back( V3D(-2, 20, -4) );
correct_indices.push_back( V3D(-3, 13, -5) );
return correct_indices;
}
static Matrix<double> getNatroliteUB()
{
Matrix<double> UB(3,3,false);
V3D row_0( -0.059660400, -0.049648200, 0.0077539105 );
V3D row_1( 0.093009956, -0.007510495, 0.0419835400 );
V3D row_2( -0.104643770 , 0.021613428, 0.0322586300 );
UB.setRow( 0, row_0 );
UB.setRow( 1, row_1 );
UB.setRow( 2, row_2 );
return UB;
}
/**
Comparator function for sorting list of 3D vectors based on their magnitude,
*/
static bool CompareMagnitude( const V3D & v1, const V3D & v2 )
{
double mag_sq_1 = v1[0]*v1[0] + v1[1]*v1[1] + v1[2]*v1[2];
double mag_sq_2 = v2[0]*v2[0] + v2[1]*v2[1] + v2[2]*v2[2];
return (mag_sq_1 < mag_sq_2);
}
void test_Find_UB_given_lattice_parameters()
{
Matrix<double> UB(3,3,false);
double correct_UB[] = { -0.1015550, 0.0992964, -0.0155078,
0.1274830, 0.0150210, -0.0839671,
-0.0507717, -0.0432269, -0.0645173 };
std::vector<V3D> q_vectors = getNatroliteQs();
double a = 6.6;
double b = 9.7;
double c = 9.9;
double alpha = 84;
double beta = 71;
double gamma = 70;
// test both default case(-1) and
// case with specified base index(4)
for ( int base_index = -1; base_index < 5 ; base_index += 5 )
double required_tolerance = 0.2;
size_t num_initial = 3;
double degrees_per_step = 3;
double error = IndexingUtils::Find_UB( UB,
q_vectors,
a, b, c,
alpha, beta, gamma,
required_tolerance,
base_index,
num_initial,
degrees_per_step );
TS_ASSERT_DELTA( error, 0.00671575, 1e-5 );
std::vector<double> UB_returned = UB.get_vector();
for ( size_t i = 0; i < 9; i++ )
{
TS_ASSERT_DELTA( UB_returned[i], correct_UB[i], 1e-5 );
}
int num_indexed = IndexingUtils::NumberIndexed( UB,
q_vectors,
required_tolerance );
TS_ASSERT_EQUALS( num_indexed, 12 );
void test_Find_UB_given_d_min_d_max()
{
Matrix<double> UB(3,3,false);
double correct_UB[] = { -0.1015550, 0.0992964, -0.0155078,
0.1274830, 0.0150210, -0.0839671,
-0.0507717, -0.0432269, -0.0645173 };
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std::vector<V3D> q_vectors = getNatroliteQs();
double d_min = 6;
double d_max = 10;
double required_tolerance = 0.08;
int num_initial = 12;
double degrees_per_step = 1;
// test both default case(-1) and
// case with specified base index(4)
for ( int base_index = -1; base_index < 5 ; base_index += 5 )
{
double error = IndexingUtils::Find_UB( UB,
q_vectors,
d_min,
d_max,
required_tolerance,
base_index,
num_initial,
degrees_per_step );
int num_indexed = IndexingUtils::NumberIndexed( UB,
q_vectors,
required_tolerance );
TS_ASSERT_EQUALS( num_indexed, 12 );
TS_ASSERT_DELTA( error, 0.000111616, 1e-5 );
std::vector<double> UB_returned = UB.get_vector();
for ( size_t i = 0; i < 9; i++ )
{
TS_ASSERT_DELTA( UB_returned[i], correct_UB[i], 1e-5 );
}
}
}
void test_Optimize_UB_given_indexing()
std::vector<V3D> q_list = getNatroliteQs();
std::vector<V3D> hkl_list = getNatroliteIndices();
Matrix<double> correct_UB = getNatroliteUB();
Matrix<double> UB(3,3,false);
double sum_sq_error = IndexingUtils::Optimize_UB( UB, hkl_list, q_list );
for ( int i = 0; i < 3; i++ )
for ( int j = 0; j < 3; j++ )
TS_ASSERT_DELTA( UB[i][j], correct_UB[i][j], 1.e-5 );
TS_ASSERT_DELTA( sum_sq_error, 0.000111616, 1e-5 );
void test_Optimize_Direction()
{
std::vector<int> index_values;
int correct_indices[] = { 1, 4, 2, 0, 1, 3, 0, -1, 0, -1, -2, -3 };
for ( size_t i = 0; i < 12; i++ )
{
index_values.push_back( correct_indices[i] );
}
std::vector<V3D> q_vectors = getNatroliteQs();
V3D best_vec;
double error = IndexingUtils::Optimize_Direction( best_vec,
index_values,
q_vectors );
TS_ASSERT_DELTA( error, 0.00218606, 1e-5 );
TS_ASSERT_DELTA( best_vec[0], -2.58222, 1e-4 );
TS_ASSERT_DELTA( best_vec[1], 3.97345, 1e-4 );
TS_ASSERT_DELTA( best_vec[2], -4.55145, 1e-4 );
}
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void test_ScanFor_UB()
{
double correct_UB[] = { -0.102577, 0.0999725, -0.0136353,
0.123290, 0.0146148, -0.0851386,
-0.055154, -0.0427632, -0.0630785 };
Matrix<double> UB(3,3,false);
int degrees_per_step = 3;
double required_tolerance = 0.2;
double a = 6.6f;
double b = 9.7f;
double c = 9.9f;
double alpha = 84;
double beta = 71;
double gamma = 70;
std::vector<V3D> q_vectors = getNatroliteQs();
double error = IndexingUtils::ScanFor_UB( UB,
q_vectors,
a, b, c, alpha, beta, gamma,
degrees_per_step,
required_tolerance );
TS_ASSERT_DELTA( error, 0.147397, 1.e-5 );
std::vector<double> UB_returned = UB.get_vector();
for ( size_t i = 0; i < 9; i++ )
{
TS_ASSERT_DELTA( UB_returned[i], correct_UB[i], 1e-5 );
}
}
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void test_ScanFor_Directions()
{
double vectors[5][3] = { { 0.08445961, 9.26951000, 3.4138980 },
{ -2.58222370, 3.97345330, -4.5514464 },
{ 2.66668320, 5.29605670, 7.9653444 },
{ 7.01297300, 3.23755380, -5.8988633 },
{ -9.59519700, 0.73589927, 1.3474168 } };
std::vector<V3D> directions;
std::vector<V3D> q_vectors = getNatroliteQs();
double d_min = 6;
double d_max = 10;
double degrees_per_step = 1.0;
double required_tolerance = 0.12;
IndexingUtils::ScanFor_Directions( directions,
q_vectors,
d_min, d_max,
required_tolerance,
degrees_per_step );
TS_ASSERT_EQUALS( 5, directions.size() );
for ( size_t i = 0; i < 3; i++ )
{
V3D vec = directions[i];
for ( int j = 0; j < 3; j++ )
{
TS_ASSERT_DELTA( vectors[i][j], vec[j], 1.e-5 );
}
}
}
void test_GetMagFFT()
{
#define N_FFT_STEPS 256
#define HALF_FFT_STEPS 128
double projections[ N_FFT_STEPS ];
double magnitude_fft[ HALF_FFT_STEPS ];
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V3D current_dir( 1, 2, -3 );
std::vector<V3D> q_vectors;
current_dir.normalize();
for ( size_t i = 0; i < 16; i++ )
{
V3D vec( current_dir );
vec *= ( (double)i + 0.6 );
q_vectors.push_back( vec );
}
double max_q_magnitude = 16.0;
double index_factor = ((double)N_FFT_STEPS) / max_q_magnitude;
double max_mag_fft = IndexingUtils::GetMagFFT( q_vectors, current_dir,
N_FFT_STEPS, projections, index_factor, magnitude_fft );
TS_ASSERT_DELTA( max_mag_fft, 16.0, 1e-5 );
for ( size_t i = 0; i < N_FFT_STEPS/2; i++ )
{
if ( i % 16 == 0 )
{
TS_ASSERT_DELTA( magnitude_fft[i], 16.0, 1e-5 );
}
else
{
TS_ASSERT_DELTA( magnitude_fft[i], 0.0, 1e-5 );
}
}
}
void test_Make_c_dir()
{
V3D a_dir( 1, 2, 3 );
V3D b_dir( -3, 2, 1 );
double gamma = a_dir.angle( b_dir ) * 180.0 / PI;
double alpha = 123;
double beta = 74;
double c_length = 10;
V3D result = IndexingUtils::Make_c_dir( a_dir, b_dir, c_length,
alpha, beta, gamma );
double alpha_calc = result.angle( b_dir ) * 180 / PI;
double beta_calc = result.angle( a_dir ) * 180 / PI;
TS_ASSERT_DELTA( result.norm(), c_length, 1e-5 );
TS_ASSERT_DELTA( alpha_calc, alpha, 1e-5 );
TS_ASSERT_DELTA( beta_calc, beta, 1e-5 );
}
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void test_DiscardDuplicates()
{
std::vector<V3D> new_list;
std::vector<V3D> directions;
std::vector<V3D> q_vectors = getNatroliteQs();
double required_tolerance = 0.12;
double length_tol = 0.05;
double angle_tol = 3;
V3D v1 ( -2.5822200, 3.97345, -4.55145 );
V3D v1b( -2.6000000, 3.98000, -4.56000 );
V3D v1c( -2.8000000, 3.90000, -4.60000 );
V3D v2 ( -9.5952000, 0.73590, 1.34742 );
V3D v3 ( 7.0129700, 3.23755, -5.89886 );
V3D v3b( 7.1129700, 3.53755, -5.99886 );
V3D v4 ( 0.0844598, 9.26951, 3.41390 );
V3D v5 ( 2.6666800, 5.29606, 7.96534 );
V3D v5b( 2.7666800, 5.29606, 7.96534 );
V3D v5c( 2.8666800, 5.39606, 8.06534 );
V3D v5d( 2.9666800, 5.49606, 8.16534 );
directions.push_back( v1 );
directions.push_back( v1b);
directions.push_back( v1c);
directions.push_back( v2 );
directions.push_back( v3 );
directions.push_back( v3b);
directions.push_back( v4 );
directions.push_back( v5 );
directions.push_back( v5b);
directions.push_back( v5c);
directions.push_back( v5d);
IndexingUtils::DiscardDuplicates( new_list,
directions,
q_vectors,
required_tolerance,
length_tol,
angle_tol );
TS_ASSERT_EQUALS( new_list.size(), 5 );
TS_ASSERT_DELTA ( new_list[0].norm(), 6.57053, 1e-4 );
TS_ASSERT_DELTA ( new_list[1].norm(), 9.71725, 1e-4 );
TS_ASSERT_DELTA ( new_list[2].norm(), 9.71905, 1e-4 );
TS_ASSERT_DELTA ( new_list[3].norm(), 9.87855, 1e-4 );
TS_ASSERT_DELTA ( new_list[4].norm(), 9.93006, 1e-4 );
}
void test_ValidIndex()
{
V3D hkl(0,0,0);
TS_ASSERT_EQUALS( IndexingUtils::ValidIndex(hkl,0.1), false );
hkl( 2.09, -3.09, -2.91 );
TS_ASSERT_EQUALS( IndexingUtils::ValidIndex(hkl,0.1), true );
hkl( 2.11, -3.09, -2.91 );
TS_ASSERT_EQUALS( IndexingUtils::ValidIndex(hkl,0.1), false );
hkl( 2.09, -3.11, -2.91 );
TS_ASSERT_EQUALS( IndexingUtils::ValidIndex(hkl,0.1), false );
hkl( 2.09, -3.09, -2.89 );
TS_ASSERT_EQUALS( IndexingUtils::ValidIndex(hkl,0.1), false );
}
void test_CheckUB()
{
Matrix<double> UB(3,3,false);
for ( int i = 0; i < 3; i++ ) // check for matrix and det OK
for ( int j = 0; j < 3; j++ )
if ( i == j )
UB[i][j] = .1;
else
UB[i][j] = 0;
TS_ASSERT_EQUALS( IndexingUtils::CheckUB(UB), true );
for ( int i = 0; i < 3; i++ ) // check for det too small
TS_ASSERT_EQUALS( IndexingUtils::CheckUB(UB), false );
for ( int i = 0; i < 3; i++ ) // check for det too large
UB[i][i] = 3;
TS_ASSERT_EQUALS( IndexingUtils::CheckUB(UB), false );
for ( int i = 0; i < 2; i++ ) // check for NaN
UB[i][i] = 0.1;
TS_ASSERT_EQUALS( IndexingUtils::CheckUB(UB), false );
Matrix<double> UB_4(4,4,false); // check wrong size
for ( int i = 0; i < 4; i++ )
for ( int j = 0; j < 4; j++ )
if ( i == j )
UB_4[i][j] = .1;
else
UB_4[i][j] = 0;
TS_ASSERT_EQUALS( IndexingUtils::CheckUB(UB_4), false );
}
void test_NumberIndexed()
{
std::vector<V3D> q_list = getNatroliteQs();
Matrix<double> UB = getNatroliteUB();
num_indexed = IndexingUtils::NumberIndexed( UB, q_list, 0.05 );
TS_ASSERT_EQUALS( num_indexed, 10 )
}
void test_NumberIndexed_1D()
{
std::vector<V3D> q_list = getNatroliteQs();
Matrix<double> UB = getNatroliteUB();
UB.Invert();
V3D direction( UB[0][0], UB[0][1], UB[0][2] );
int num_indexed;
num_indexed = IndexingUtils::NumberIndexed_1D( direction, q_list, 0.10 );
TS_ASSERT_EQUALS( num_indexed, 12 );
num_indexed = IndexingUtils::NumberIndexed_1D( direction, q_list, 0.05 );
TS_ASSERT_EQUALS( num_indexed, 12 );
num_indexed = IndexingUtils::NumberIndexed_1D( direction, q_list, 0.01 );
TS_ASSERT_EQUALS( num_indexed, 8 );
void test_CalculateMillerIndices()
{
std::vector<V3D> q_vectors = getNatroliteQs();
std::vector<V3D> indices = getNatroliteIndices();
Matrix<double> UB = getNatroliteUB();
double tolerance = 0.1;
std::vector<V3D> miller_indices;
double average_error;
int num_indexed = IndexingUtils::CalculateMillerIndices( UB,
q_vectors,
tolerance,
miller_indices,
average_error );
TS_ASSERT_EQUALS( num_indexed, 12 );
TS_ASSERT_DELTA( average_error, 0.0185, 1e-3 );
double diff;
for ( size_t i = 0; i < indices.size(); i++ )
{
diff = ( indices[i] - miller_indices[i] ).norm();
TS_ASSERT_DELTA( diff, 0, 0.1 );
}
void test_GetIndexedPeaks_1D()
int correct_indices[] = { 1, 4, 2, 0, 1, 3, 0, -1, 0, -1, -2, -3 };
std::vector<V3D> q_vectors = getNatroliteQs();
V3D direction( -2.5825930, 3.9741700, -4.5514810 );
double required_tolerance = 0.1;
double fit_error = 0;
std::vector<int> index_vals;
std::vector<V3D> indexed_qs;
int num_indexed = IndexingUtils::GetIndexedPeaks_1D( direction,
q_vectors,
required_tolerance,
index_vals,
indexed_qs,
fit_error );
TS_ASSERT_EQUALS( num_indexed, 12 );
TS_ASSERT_EQUALS( index_vals.size(), 12 );
TS_ASSERT_EQUALS( indexed_qs.size(), 12 );
TS_ASSERT_DELTA( fit_error, 0.00218634, 1e-5 );
for ( size_t i = 0; i < index_vals.size(); i++ )
{
TS_ASSERT_EQUALS( index_vals[i], correct_indices[i] );
}
}
void test_GetIndexedPeaks_3D()
{
std::vector<V3D> q_vectors = getNatroliteQs();
std::vector<V3D> correct_indices = getNatroliteIndices();
V3D direction_1( -2.5825930, 3.9741700, -4.5514810 );
V3D direction_2( -16.6087800, -2.5005515, 7.2465878 );
V3D direction_3( 2.7502847, 14.5671910, 11.3796620 );
double required_tolerance = 0.1;
double fit_error = 0;
std::vector<V3D> index_vals;
std::vector<V3D> indexed_qs;
int num_indexed = IndexingUtils::GetIndexedPeaks_3D( direction_1,
direction_2,
direction_3,
required_tolerance,
index_vals,
indexed_qs,
fit_error );
TS_ASSERT_EQUALS( num_indexed, 12 );
TS_ASSERT_EQUALS( index_vals.size(), 12 );
TS_ASSERT_EQUALS( indexed_qs.size(), 12 );
TS_ASSERT_DELTA( fit_error, 0.023007052, 1e-5 );
for ( size_t i = 0; i < index_vals.size(); i++ )
{
for ( size_t j = 0; j < 3; j++ )
{
TS_ASSERT_EQUALS( (index_vals[i])[j], (correct_indices[i])[j] );
}
}
}
void test_GetIndexedPeaks()
{
std::vector<V3D> q_vectors = getNatroliteQs();
std::vector<V3D> correct_indices = getNatroliteIndices();
Matrix<double> UB = getNatroliteUB();
double required_tolerance = 0.1;
double fit_error = 0;
std::vector<V3D> index_vals;
std::vector<V3D> indexed_qs;
int num_indexed = IndexingUtils::GetIndexedPeaks( UB,
q_vectors,
required_tolerance,
index_vals,
indexed_qs,
fit_error );
TS_ASSERT_EQUALS( num_indexed, 12 );
TS_ASSERT_EQUALS( index_vals.size(), 12 );
TS_ASSERT_EQUALS( indexed_qs.size(), 12 );
TS_ASSERT_DELTA( fit_error, 0.023007052, 1e-5 );
for ( size_t i = 0; i < index_vals.size(); i++ )
{
for ( size_t j = 0; j < 3; j++ )
{
TS_ASSERT_EQUALS( (index_vals[i])[j], (correct_indices[i])[j] );
}
}
void test_MakeHemisphereDirections()
{
std::vector<V3D> direction_list=IndexingUtils::MakeHemisphereDirections(5);
TS_ASSERT_EQUALS( direction_list.size(), 64 );
// check some random entries
TS_ASSERT_DELTA( direction_list[0].X(), 0, 1e-5 );
TS_ASSERT_DELTA( direction_list[0].Y(), 1, 1e-5 );
TS_ASSERT_DELTA( direction_list[0].Z(), 0, 1e-5 );
TS_ASSERT_DELTA( direction_list[5].X(), -0.154508, 1e-5 );
TS_ASSERT_DELTA( direction_list[5].Y(), 0.951057, 1e-5 );
TS_ASSERT_DELTA( direction_list[5].Z(), -0.267617, 1e-5 );
TS_ASSERT_DELTA( direction_list[10].X(), 0, 1e-5 );
TS_ASSERT_DELTA( direction_list[10].Y(), 0.809017, 1e-5 );
TS_ASSERT_DELTA( direction_list[10].Z(), 0.587785, 1e-5 );
TS_ASSERT_DELTA( direction_list[63].X(), -0.951057, 1e-5 );
TS_ASSERT_DELTA( direction_list[63].Y(), 0, 1e-5 );
TS_ASSERT_DELTA( direction_list[63].Z(), 0.309017, 1e-5 );
}
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void test_MakeCircleDirections()
{
int num_steps = 8;
V3D axis( 1, 1, 1 );
double angle_degrees = 90;
std::vector<V3D> direction_list
= IndexingUtils::MakeCircleDirections( num_steps, axis, angle_degrees);
TS_ASSERT_EQUALS( direction_list.size(), 8 );
TS_ASSERT_DELTA( direction_list[0].X(), -0.816497, 1e-5 );
TS_ASSERT_DELTA( direction_list[0].Y(), 0.408248, 1e-5 );
TS_ASSERT_DELTA( direction_list[0].Z(), 0.408248, 1e-5 );
TS_ASSERT_DELTA( direction_list[1].X(), -0.577350, 1e-5 );
TS_ASSERT_DELTA( direction_list[1].Y(), -0.211325, 1e-5 );
TS_ASSERT_DELTA( direction_list[1].Z(), 0.788675, 1e-5 );
TS_ASSERT_DELTA( direction_list[7].X(), -0.577350, 1e-5 );
TS_ASSERT_DELTA( direction_list[7].Y(), 0.788675, 1e-5 );
TS_ASSERT_DELTA( direction_list[7].Z(), -0.211325, 1e-5 );
double dot_prod;
for ( size_t i = 0; i < direction_list.size(); i++ )
{
dot_prod = axis.scalar_prod( direction_list[i] );
TS_ASSERT_DELTA( dot_prod, 0, 1e-10 );
}
}
void test_SelectDirection()
{
V3D best_direction;
std::vector<V3D> q_vectors = getNatroliteQs();
std::vector<V3D> directions = IndexingUtils::MakeHemisphereDirections(90);
double plane_spacing = 1.0/6.5781;
double required_tolerance = 0.1;
int num_indexed = IndexingUtils::SelectDirection( best_direction,
q_vectors,
directions,
plane_spacing,
required_tolerance );
TS_ASSERT_DELTA( best_direction[0], -0.399027, 1e-5 );
TS_ASSERT_DELTA( best_direction[1], 0.615661, 1e-5 );
TS_ASSERT_DELTA( best_direction[2], -0.679513, 1e-5 );
TS_ASSERT_EQUALS( num_indexed, 12 );
}
};
#endif /* MANTID_GEOMETRY_INDEXING_UTILS_TEST_H_ */