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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>
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;
}
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()
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double h_vals[] = { 1, 0, 0, -1, 0, 0, 1, 1 };
double k_vals[] = { .1, 1, 0, 0, -1, 0, 1, 2 };
double l_vals[] = {-.1, 0, 1, 0, 0, -1, 1, 3 };
double qx_vals[] = { 2, 0, 0, -2, 0, 0, 2, 2 };
double qy_vals[] = { 1, 3, 0, 0, -3, 0, 3, 6 };
double qz_vals[] = { 0, 0, 4, 0, 0, -4, 4, 12 };
double correct_UB[] = { 2.000000e+00, 0.000000e+00, -0.000000e+00,
2.766704e-01, 2.959570e+00, -7.214043e-02,
1.580974e-01, -2.310306e-02, 3.958777e+00 };
size_t N_INDEXED_PEAKS = 8;
Matrix<double> UB(3,3,false);
std::vector<V3D> q_list( N_INDEXED_PEAKS );
for ( size_t row = 0; row < N_INDEXED_PEAKS; row++ )
{
V3D qxyz( qx_vals[row], qy_vals[row], qz_vals[row] );
q_list[row] = qxyz;
}
std::vector<V3D> hkl_list( N_INDEXED_PEAKS );
for ( size_t row = 0; row < N_INDEXED_PEAKS; row++ )
{
V3D hkl( h_vals[row], k_vals[row], l_vals[row] );
hkl_list[row] = hkl;
}
double sum_sq_error = IndexingUtils::Optimize_UB( UB, hkl_list, q_list );
std::vector<double> UB_returned = UB.get_vector();
for ( int i = 0; i < 3; i++ )
TS_ASSERT_DELTA( UB_returned[i], correct_UB[i], 1.e-5 );
TS_ASSERT_DELTA( sum_sq_error, 0.390147, 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_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 );
}
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 );
}
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void test_NumberIndexed()
{
Matrix<double> UB(3,3,false);
V3D row_values( -0.141251, 0.3042650, -0.147160 );
UB.setRow( 0, row_values );
row_values( 0.120633, 0.0907082, 0.106323 );
UB.setRow( 1, row_values );
row_values( 0.258332, -0.0062807, -0.261151 );
UB.setRow( 2, row_values );
std::vector<V3D> q_list( 5 );
V3D qxyz( -1.02753, 0.47106, -0.25957 );
q_list[0] = qxyz;
qxyz( -2.05753, 0.93893, -0.51988 );
q_list[1] = qxyz;
qxyz( -2.19878, 1.05926, -0.27486 );
q_list[2] = qxyz;
qxyz( -2.63576, 1.39119, -0.53007 );
q_list[3] = qxyz;
qxyz( -1.75324, 1.02999, -0.52537 );
q_list[4] = qxyz;
TS_ASSERT_EQUALS( IndexingUtils::NumberIndexed( UB, q_list, 0.017 ), 4 );
}
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void test_CalculateMillerIndices()
{
Matrix<double> UB(3,3,false);
UB.setRow( 0, V3D( -0.1015550, 0.0992964, -0.0155078 ) );
UB.setRow( 1, V3D( 0.1274830, 0.0150210, -0.0839671 ) );
UB.setRow( 2, V3D( -0.0507717, -0.0432269, -0.0645173 ) );
std::vector<V3D> q_vectors = getNatroliteQs();
double tolerance = 0.08;
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, 0.0103505, 1e-5 );
V3D mi_0 = V3D( 0.992465, -4.00351, 4.997260 );
V3D mi_1 = V3D( 3.991040, -8.00753, 14.00010 );
V3D mi_2 = V3D( 2.018340, -7.96556, 8.020210 );
V3D mi_11 = V3D( -3.006000, -7.99572, 0.980049 );
double diff;
// spot check a few indices
diff = (mi_0 - miller_indices[0] ).norm();
TS_ASSERT_DELTA( diff, 0, 1e-5 );
diff = (mi_1 - miller_indices[1] ).norm();
TS_ASSERT_DELTA( diff, 0, 1e-5 );
diff = (mi_2 - miller_indices[2] ).norm();
TS_ASSERT_DELTA( diff, 0, 1e-5 );
diff = (mi_11 - miller_indices[11]).norm();
TS_ASSERT_DELTA( diff, 0, 1e-5 );
}
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> 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) );
std::vector<V3D> q_vectors = getNatroliteQs();
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 );
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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> 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) );
std::vector<V3D> q_vectors = getNatroliteQs();
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 );
Matrix<double> UB(3,3,false);
UB.setRow( 0, row_0 );
UB.setRow( 1, row_1 );
UB.setRow( 2, row_2 );
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_ */