diff --git a/Framework/Crystal/src/FindUBUsingLatticeParameters.cpp b/Framework/Crystal/src/FindUBUsingLatticeParameters.cpp
index c1c2f8ea137657d2d3a63e45c8760b0ee22ce9d2..ecc9e59e12b6cfaa61b772e495cb611793d71254 100644
--- a/Framework/Crystal/src/FindUBUsingLatticeParameters.cpp
+++ b/Framework/Crystal/src/FindUBUsingLatticeParameters.cpp
@@ -80,9 +80,10 @@ void FindUBUsingLatticeParameters::exec() {
q_vectors.push_back(peaks[i].getQSampleFrame());
Matrix<double> UB(3, 3, false);
- double error = IndexingUtils::Find_UB(UB, q_vectors, a, b, c, alpha, beta,
- gamma, tolerance, base_index,
- num_initial, degrees_per_step, fixAll);
+ OrientedLattice lattice(a, b, c, alpha, beta, gamma);
+ double error = IndexingUtils::Find_UB(UB, q_vectors, lattice, tolerance,
+ base_index, num_initial,
+ degrees_per_step, fixAll);
g_log.notice() << "Error = " << error << '\n';
g_log.notice() << "UB = " << UB << '\n';
@@ -94,20 +95,6 @@ void FindUBUsingLatticeParameters::exec() {
g_log.notice(std::string("UB NOT SAVED."));
} else // tell user how many would be indexed
{ // and save the UB in the sample
-
- std::vector<double> sigabc(7);
-// std::vector<V3D> miller_ind;
-// std::vector<V3D> indexed_qs;
-// double fit_error;
-// miller_ind.reserve(q_vectors.size());
-// indexed_qs.reserve(q_vectors.size());
-// IndexingUtils::GetIndexedPeaks(UB, q_vectors, tolerance, miller_ind,
-// indexed_qs, fit_error);
-
-//// if(!fixAll) {
-//// IndexingUtils::Optimize_UB(UB, miller_ind, indexed_qs, sigabc, fixAngles);
-//// }
-
char logInfo[200];
int num_indexed = IndexingUtils::NumberIndexed(UB, q_vectors, tolerance);
sprintf(logInfo,
@@ -117,27 +104,21 @@ void FindUBUsingLatticeParameters::exec() {
num_indexed, n_peaks, tolerance);
g_log.notice(std::string(logInfo));
- OrientedLattice o_lattice;
- o_lattice.setUB(UB);
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], sigabc[4],
- sigabc[5]);
-
- o_lattice.setUB(UB);
- double calc_a = o_lattice.a();
- double calc_b = o_lattice.b();
- double calc_c = o_lattice.c();
- double calc_alpha = o_lattice.alpha();
- double calc_beta = o_lattice.beta();
- double calc_gamma = o_lattice.gamma();
+ double calc_a = lattice.a();
+ double calc_b = lattice.b();
+ double calc_c = lattice.c();
+ double calc_alpha = lattice.alpha();
+ double calc_beta = lattice.beta();
+ double calc_gamma = lattice.gamma();
// Show the modified lattice parameters
- g_log.notice() << o_lattice << "\n";
+ g_log.notice() << lattice << "\n";
sprintf(logInfo, std::string("Lattice Parameters (Refined - Input): %11.6f "
"%11.6f %11.6f %11.6f %11.6f %11.6f").c_str(),
calc_a - a, calc_b - b, calc_c - c, calc_alpha - alpha,
calc_beta - beta, calc_gamma - gamma);
g_log.notice(std::string(logInfo));
- ws->mutableSample().setOrientedLattice(&o_lattice);
+ ws->mutableSample().setOrientedLattice(&lattice);
}
}
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/IndexingUtils.h b/Framework/Geometry/inc/MantidGeometry/Crystal/IndexingUtils.h
index 67cecfc0fabdf6b00798c97808e2cd3cb7c2bf0e..c280430d48bdf78885dad17a502811b76e4baf3b 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/IndexingUtils.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/IndexingUtils.h
@@ -7,6 +7,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidKernel/V3D.h"
#include "MantidKernel/Matrix.h"
#include "MantidKernel/Logger.h"
@@ -51,11 +52,10 @@ public:
/// Find the UB matrix that most nearly indexes the specified qxyz values
/// given the lattice parameters
static double Find_UB(Kernel::DblMatrix &UB,
- const std::vector<Kernel::V3D> &q_vectors, double a,
- double b, double c, double alpha, double beta,
- double gamma, double required_tolerance, int base_index,
- size_t num_initial, double degrees_per_step,
- bool fixAll = false);
+ const std::vector<Kernel::V3D> &q_vectors,
+ OrientedLattice& lattice, double required_tolerance,
+ int base_index, size_t num_initial,
+ double degrees_per_step, bool fixAll = false);
/// Find the UB matrix that most nearly indexes the specified qxyz values
/// given the range of possible real space unit cell edge lengths.
@@ -89,9 +89,9 @@ public:
/// Scan rotations to find UB that indexes peaks given lattice parameters
static double ScanFor_UB(Kernel::DblMatrix &UB,
- const std::vector<Kernel::V3D> &q_vectors, double a,
- double b, double c, double alpha, double beta,
- double gamma, double degrees_per_step,
+ const std::vector<Kernel::V3D> &q_vectors,
+ const UnitCell& lattice,
+ double degrees_per_step,
double required_tolerance);
/// Get list of possible directions and lengths for real space unit cell
diff --git a/Framework/Geometry/src/Crystal/IndexingUtils.cpp b/Framework/Geometry/src/Crystal/IndexingUtils.cpp
index f0e49f6e355502ffa63a200640d0fcbeff4e9dca..e81c586843eecf4f83028dbf2775fef1f8f49a8f 100644
--- a/Framework/Geometry/src/Crystal/IndexingUtils.cpp
+++ b/Framework/Geometry/src/Crystal/IndexingUtils.cpp
@@ -1,6 +1,5 @@
#include "MantidGeometry/Crystal/IndexingUtils.h"
#include "MantidGeometry/Crystal/NiggliCell.h"
-#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidKernel/Quat.h"
#include <algorithm>
#include <cmath>
@@ -53,12 +52,9 @@ const constexpr double RAD_TO_DEG = 180. / M_PI;
@param q_vectors std::vector of V3D objects that contains the
list of q_vectors that are to be indexed
NOTE: There must be at least 2 q_vectors.
- @param a First unit cell edge length in Angstroms.
- @param b Second unit cell edge length in Angstroms.
- @param c Third unit cell edge length in Angstroms.
- @param alpha First unit cell angle in degrees.
- @param beta second unit cell angle in degrees.
- @param gamma third unit cell angle in degrees.
+ @param lattice The orientated lattice with the lattice
+ parameters a,b,c and alpha, beta, gamma. The found
+ UB and errors will be set on this lattice.
@param required_tolerance The maximum allowed deviation of Miller indices
from integer values for a peak to be indexed.
@param base_index The sequence number of the peak that should
@@ -87,8 +83,7 @@ const constexpr double RAD_TO_DEG = 180. / M_PI;
is <= 0.
*/
double IndexingUtils::Find_UB(DblMatrix &UB, const std::vector<V3D> &q_vectors,
- double a, double b, double c, double alpha,
- double beta, double gamma,
+ OrientedLattice& lattice,
double required_tolerance, int base_index,
size_t num_initial, double degrees_per_step,
bool fixAll) {
@@ -157,8 +152,7 @@ double IndexingUtils::Find_UB(DblMatrix &UB, const std::vector<V3D> &q_vectors,
for (size_t i = 0; i < num_initial; i++)
some_qs.push_back(sorted_qs[i]);
- ScanFor_UB(UB, some_qs, a, b, c, alpha, beta, gamma, degrees_per_step,
- required_tolerance);
+ ScanFor_UB(UB, some_qs, lattice, degrees_per_step, required_tolerance);
double fit_error = 0;
@@ -167,19 +161,11 @@ double IndexingUtils::Find_UB(DblMatrix &UB, const std::vector<V3D> &q_vectors,
miller_ind.reserve(q_vectors.size());
indexed_qs.reserve(q_vectors.size());
- // If the user has requested we fix all parameters then return here with the
- // found UB and do not optimise it.
- if (fixAll) {
- GetIndexedPeaks(UB, q_vectors, required_tolerance, miller_ind, indexed_qs,
- fit_error);
- return fit_error;
- }
-
// now gradually bring in the remaining
// peaks and re-optimize the UB to index
// them as well
size_t count = 0;
- while (num_initial < sorted_qs.size()) {
+ while (!fixAll && num_initial < sorted_qs.size()) {
count++;
num_initial = std::lround(1.5 * static_cast<double>(num_initial + 3));
// add 3, in case we started with
@@ -191,25 +177,24 @@ double IndexingUtils::Find_UB(DblMatrix &UB, const std::vector<V3D> &q_vectors,
some_qs.push_back(sorted_qs[i]);
try {
- std::vector<double> sigabc(7);
GetIndexedPeaks(UB, some_qs, required_tolerance, miller_ind, indexed_qs,
fit_error);
Matrix<double> temp_UB(3, 3, false);
- fit_error = Optimize_UB(temp_UB, miller_ind, indexed_qs, sigabc);
+ fit_error = Optimize_UB(temp_UB, miller_ind, indexed_qs);
UB = temp_UB;
} catch (...) {
// failed to fit using these peaks, so add some more and try again
}
}
- if (q_vectors.size() >= 3) // try one last refinement using all peaks
+ std::vector<double> sigabc(7);
+ if (!fixAll && q_vectors.size() >= 3) // try one last refinement using all peaks
{
try {
- std::vector<double> sigabc(7);
GetIndexedPeaks(UB, q_vectors, required_tolerance, miller_ind, indexed_qs,
fit_error);
- Matrix<double> temp_UB(3, 3, false);
- fit_error = Optimize_UB(temp_UB, miller_ind, indexed_qs, sigabc);
+ Matrix<double> temp_UB = UB;
+ fit_error = Optimize_UB(temp_UB, miller_ind, indexed_qs);
UB = temp_UB;
} catch (...) {
// failed to improve UB using these peaks, so just return the current UB
@@ -220,6 +205,10 @@ double IndexingUtils::Find_UB(DblMatrix &UB, const std::vector<V3D> &q_vectors,
// HKL space.
GetIndexedPeaks(UB, q_vectors, required_tolerance, miller_ind, indexed_qs,
fit_error);
+ // set the error on the lattice parameters
+ lattice.setUB(UB);
+ lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], sigabc[4],
+ sigabc[5]);
return fit_error;
}
@@ -894,12 +883,8 @@ double IndexingUtils::Optimize_Direction(V3D &best_vec,
@param UB This will be set to the UB matrix that best
indexes the supplied list of q_vectors.
@param q_vectors List of locations of peaks in "Q".
- @param a Lattice parameter "a".
- @param b Lattice parameter "b".
- @param c Lattice parameter "c".
- @param alpha Lattice parameter alpha.
- @param beta Lattice parameter beta.
- @param gamma Lattice parameter gamma.
+ @param cell Unit cell defining the parameters a,b,c and
+ alpha, beta, gamma.
@param degrees_per_step The number of degrees per step used when
scanning through all possible directions and
orientations for the unit cell. NOTE: The
@@ -920,14 +905,22 @@ double IndexingUtils::Optimize_Direction(V3D &best_vec,
*/
double IndexingUtils::ScanFor_UB(DblMatrix &UB,
- const std::vector<V3D> &q_vectors, double a,
- double b, double c, double alpha, double beta,
- double gamma, double degrees_per_step,
+ const std::vector<V3D> &q_vectors,
+ const UnitCell& cell,
+ double degrees_per_step,
double required_tolerance) {
if (UB.numRows() != 3 || UB.numCols() != 3) {
throw std::invalid_argument("Find_UB(): UB matrix NULL or not 3X3");
}
+ auto a = cell.a();
+ auto b = cell.b();
+ auto c = cell.c();
+
+ auto alpha = cell.alpha();
+ auto beta = cell.beta();
+ auto gamma = cell.gamma();
+
V3D a_dir;
V3D b_dir;
V3D c_dir;
diff --git a/Framework/Geometry/test/IndexingUtilsTest.h b/Framework/Geometry/test/IndexingUtilsTest.h
index b8b66458b2b4b6dfe85472af9af4e42ff788d271..0974588a716466556c90e4c07104ddbaaa7e5740 100644
--- a/Framework/Geometry/test/IndexingUtilsTest.h
+++ b/Framework/Geometry/test/IndexingUtilsTest.h
@@ -111,12 +111,7 @@ public:
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;
+ OrientedLattice lattice(6.6, 9.7, 9.9, 84, 71, 70);
// test both default case(-1) and
// case with specified base index(4)
for (int base_index = -1; base_index < 5; base_index += 5) {
@@ -125,7 +120,7 @@ public:
double degrees_per_step = 3;
double error = IndexingUtils::Find_UB(
- UB, q_vectors, a, b, c, alpha, beta, gamma, required_tolerance,
+ UB, q_vectors, lattice, required_tolerance,
base_index, num_initial, degrees_per_step);
// std::cout << std::endl << "USING LATTICE PARAMETERS\n";
@@ -260,17 +255,12 @@ public:
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;
+ UnitCell cell(6.6f, 9.7f, 9.9f, 84, 71, 70);
std::vector<V3D> q_vectors = getNatroliteQs();
double error =
- IndexingUtils::ScanFor_UB(UB, q_vectors, a, b, c, alpha, beta, gamma,
+ IndexingUtils::ScanFor_UB(UB, q_vectors, cell,
degrees_per_step, required_tolerance);
TS_ASSERT_DELTA(error, 0.147397, 1.e-5);