Refs #22420 clang-format

Framework/Crystal/inc/MantidCrystal/FindUBUsingIndexedPeaks.h

@@ -8,9 +8,9 @@
 #define MANTID_CRYSTAL_FIND_UB_USING_INDEXED_PEAKS_H_
 
 #include "MantidAPI/Algorithm.h"
+#include "MantidDataObjects/Peak.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
 #include "MantidKernel/System.h"
-#include "MantidDataObjects/Peak.h"
 
 namespace Mantid {
 namespace Crystal {

Framework/Crystal/inc/MantidCrystal/LoadIsawUB.h

@@ -8,8 +8,8 @@
 #define MANTID_CRYSTAL_LOADISAWUB_H_
 
 #include "MantidAPI/Algorithm.h"
-#include "MantidKernel/System.h"
 #include "MantidKernel/Matrix.h"
+#include "MantidKernel/System.h"
 
 namespace Mantid {
 namespace Crystal {

Framework/Crystal/inc/MantidCrystal/PredictSatellitePeaks.h

@@ -70,8 +70,7 @@ private:
   void exec() override;
   void exec_peaks();
   Kernel::V3D getOffsetVector(const std::string &label);
-  void predictOffsets(
-                      int iVector, Kernel::V3D offsets, int &maxOrder,
+  void predictOffsets(int iVector, Kernel::V3D offsets, int &maxOrder,
                       Kernel::V3D &hkl,
                       Geometry::HKLFilterWavelength &lambdaFilter,
                       bool &includePeaksInRange, bool &includeOrderZero,

Framework/Crystal/src/FindUBUsingIndexedPeaks.cpp

@@ -82,8 +82,7 @@ void FindUBUsingIndexedPeaks::exec() {
     if (mnp[0] * mnp[1] != 0 || mnp[1] * mnp[2] != 0 || mnp[2] * mnp[0] != 0)
       CrossTerm = true;
 
-    if (isPeakIndexed(peak))
-    {
+    if (isPeakIndexed(peak)) {
       q_vectors.push_back(peak.getQSampleFrame());
       hkl_vectors.push_back(hkl);
       mnp_vectors.push_back(mnp);
@@ -91,7 +90,7 @@ void FindUBUsingIndexedPeaks::exec() {
     }
   }
 
-  //too few indexed peaks to work with
+  // too few indexed peaks to work with
   if (indexed_count < MIN_INDEXED_PEAKS) {
     throw std::runtime_error(
         "At least three linearly independent indexed peaks are needed.");
@@ -114,7 +113,7 @@ void FindUBUsingIndexedPeaks::exec() {
   {                    // from the full list of peaks, and
     q_vectors.clear(); // save the UB in the sample
     q_vectors.reserve(n_peaks);
-    for (auto & peak : peaks) {
+    for (auto &peak : peaks) {
       q_vectors.push_back(peak.getQSampleFrame());
     }
 
@@ -170,14 +169,14 @@ void FindUBUsingIndexedPeaks::exec() {
                              rsigabc[4], rsigabc[5]);
         g_log.notice() << run_lattice << "\n";
 
-          double average_error = 0.;
-          IndexingUtils::CalculateMillerIndices(
-              UB, run_q_vectors, 1.0, run_fhkl_vectors, average_error);
-          for (size_t i = 0; i < run_indexed; i++) {
-            if (IndexingUtils::ValidIndex(run_fhkl_vectors[i], tolerance))
-              continue;
+        double average_error = 0.;
+        IndexingUtils::CalculateMillerIndices(UB, run_q_vectors, 1.0,
+                                              run_fhkl_vectors, average_error);
+        for (size_t i = 0; i < run_indexed; i++) {
+          if (IndexingUtils::ValidIndex(run_fhkl_vectors[i], tolerance))
+            continue;
 
-            V3D fhkl(run_fhkl_vectors[i]);
+          V3D fhkl(run_fhkl_vectors[i]);
           for (int j = 0; j < 3; j++) {
             if (run_mnp_vectors[i][j] != 0) {
               fhkl -= run_lattice.getModVec(j) * run_mnp_vectors[i][j];
@@ -185,9 +184,10 @@ void FindUBUsingIndexedPeaks::exec() {
                 sate_indexed++;
                 V3D errhkl = fhkl - run_hkl_vectors[i];
                 errhkl = errhkl.absoluteValue();
-          for (int k = 0; k < 3; k++)  errorHKL[k][j] += errhkl[k];
+                for (int k = 0; k < 3; k++)
+                  errorHKL[k][j] += errhkl[k];
               }
-            } 
+            }
           }
         }
       }
@@ -224,17 +224,17 @@ void FindUBUsingIndexedPeaks::logLattice(OrientedLattice &o_lattice,
   g_log.notice() << o_lattice << "\n";
   g_log.notice() << "Modulation Dimension is: " << ModDim << "\n";
   for (int i = 0; i < ModDim; i++) {
-    g_log.notice() << "Modulation Vector " << i+1 << ": "
+    g_log.notice() << "Modulation Vector " << i + 1 << ": "
                    << o_lattice.getModVec(i) << "\n";
-    g_log.notice() << "Modulation Vector " << i+1
+    g_log.notice() << "Modulation Vector " << i + 1
                    << " error: " << o_lattice.getVecErr(i) << "\n";
   }
 }
 bool FindUBUsingIndexedPeaks::isPeakIndexed(Peak &peak) {
-            V3D hkl(peak.getIntHKL()); // ##### KEEP
-            V3D mnp(peak.getIntMNP());
-            return (IndexingUtils::ValidIndex(hkl, 1.0) ||
-                IndexingUtils::ValidIndex(mnp, 1.0));
+  V3D hkl(peak.getIntHKL()); // ##### KEEP
+  V3D mnp(peak.getIntMNP());
+  return (IndexingUtils::ValidIndex(hkl, 1.0) ||
+          IndexingUtils::ValidIndex(mnp, 1.0));
 }
 } // namespace Crystal
 } // namespace Mantid

Framework/Crystal/src/IndexPeaks.cpp

@@ -112,7 +112,7 @@ void IndexPeaks::exec() {
     std::vector<V3D> q_vectors;
 
     q_vectors.reserve(n_peaks);
-    for (auto& peak : peaks) {
+    for (auto &peak : peaks) {
       q_vectors.push_back(peak.getQSampleFrame());
     }
 
@@ -132,7 +132,7 @@ void IndexPeaks::exec() {
 
     // get list of run numbers in this peaks workspace
     std::vector<int> run_numbers;
-    for (auto& peak : peaks) {
+    for (auto &peak : peaks) {
       int run = peak.getRunNumber();
       bool found = false;
       size_t k = 0;
@@ -154,7 +154,7 @@ void IndexPeaks::exec() {
       std::vector<V3D> q_vectors;
 
       int run = run_numbers[run_index];
-      for (auto& peak : peaks) {
+      for (auto &peak : peaks) {
         if (peak.getRunNumber() == run)
           q_vectors.push_back(peak.getQSampleFrame());
       }
@@ -228,7 +228,7 @@ void IndexPeaks::exec() {
         }
 
         size_t miller_index_counter = 0;
-        for (auto& peak : peaks) {
+        for (auto &peak : peaks) {
           if (peak.getRunNumber() == run) {
             peak.setHKL(miller_indices[miller_index_counter]);
             peak.setIntHKL(miller_indices[miller_index_counter]);
@@ -262,7 +262,7 @@ void IndexPeaks::exec() {
 
         // Index satellite peaks
         size_t miller_index_counter = 0;
-        for (auto& peak : peaks) {
+        for (auto &peak : peaks) {
           if (peak.getRunNumber() == run) {
             peak.setHKL(miller_indices[miller_index_counter]);
             miller_index_counter++;
@@ -297,7 +297,7 @@ void IndexPeaks::exec() {
                   if (order == 0)
                     continue; // exclude order 0
                   V3D hkl1(hkl);
-                  hkl1 -= offsets2* order;
+                  hkl1 -= offsets2 * order;
                   if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
                     peak.setIntHKL(hkl1);
                     peak.setIntMNP(V3D(0, order, 0));
@@ -328,7 +328,7 @@ void IndexPeaks::exec() {
                   if (order == 0)
                     continue; // exclude order 0
                   V3D hkl1(hkl);
-                  hkl1 -= offsets1  * order;
+                  hkl1 -= offsets1 * order;
                   if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
                     peak.setIntHKL(hkl1);
                     peak.setIntMNP(V3D(order, 0, 0));
@@ -344,7 +344,7 @@ void IndexPeaks::exec() {
                     if (m == 0 && n == 0)
                       continue; // exclude 0,0
                     V3D hkl1(hkl);
-                    hkl1 -= offsets1 * m +  offsets2 * n;
+                    hkl1 -= offsets1 * m + offsets2 * n;
                     if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
                       peak.setIntHKL(hkl1);
                       peak.setIntMNP(V3D(m, n, 0));
@@ -361,8 +361,7 @@ void IndexPeaks::exec() {
                       if (m == 0 && n == 0 && p == 0)
                         continue; // exclude 0,0,0
                       V3D hkl1(hkl);
-                      hkl1 -=
-                           offsets1 * m + offsets2 * n + offsets3 * p;
+                      hkl1 -= offsets1 * m + offsets2 * n + offsets3 * p;
                       if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
                         peak.setIntHKL(hkl1);
                         peak.setIntMNP(V3D(m, n, p));

Framework/Crystal/src/IndexPeaksWithSatellites.cpp

@@ -178,8 +178,9 @@ void IndexPeaksWithSatellites::exec() {
 
     // get list of run numbers in this peaks workspace
     std::unordered_set<int> run_numbers;
-    transform(peaks.begin(), peaks.end(), std::inserter(run_numbers, run_numbers.begin()), 
-            [] (const auto& peak) { return peak.getRunNumber(); });
+    transform(peaks.begin(), peaks.end(),
+              std::inserter(run_numbers, run_numbers.begin()),
+              [](const auto &peak) { return peak.getRunNumber(); });
 
     // index the peaks for each run separately, using a UB matrix optimized for
     // that run

Framework/Crystal/src/PredictSatellitePeaks.cpp

@@ -212,10 +212,9 @@ void PredictSatellitePeaks::exec() {
   for (auto it = possibleHKLs.begin(); it != possibleHKLs.end(); ++it) {
     V3D hkl = *it;
     if (crossTerms) {
-      predictOffsetsWithCrossTerms(offsets1, offsets2,
-                                   offsets3, maxOrder, hkl, lambdaFilter,
-                                   includePeaksInRange, includeOrderZero,
-                                   AlreadyDonePeaks);
+      predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, hkl,
+                                   lambdaFilter, includePeaksInRange,
+                                   includeOrderZero, AlreadyDonePeaks);
     } else {
       predictOffsets(0, offsets1, maxOrder, hkl, lambdaFilter,
                      includePeaksInRange, includeOrderZero, AlreadyDonePeaks);
@@ -291,10 +290,9 @@ void PredictSatellitePeaks::exec_peaks() {
     auto peak = *it;
     V3D hkl = peak.getHKL();
     if (crossTerms) {
-      predictOffsetsWithCrossTerms(offsets1, offsets2,
-                                   offsets3, maxOrder, hkl, lambdaFilter,
-                                   includePeaksInRange, includeOrderZero,
-                                   AlreadyDonePeaks);
+      predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, hkl,
+                                   lambdaFilter, includePeaksInRange,
+                                   includeOrderZero, AlreadyDonePeaks);
     } else {
       predictOffsets(0, offsets1, maxOrder, hkl, lambdaFilter,
                      includePeaksInRange, includeOrderZero, AlreadyDonePeaks);
@@ -322,10 +320,9 @@ void PredictSatellitePeaks::exec_peaks() {
 }
 
 void PredictSatellitePeaks::predictOffsets(
-    int indexModulatedVector,
-    V3D offsets, int &maxOrder, V3D &hkl, HKLFilterWavelength &lambdaFilter,
-    bool &includePeaksInRange, bool &includeOrderZero,
-    vector<vector<int>> &AlreadyDonePeaks) {
+    int indexModulatedVector, V3D offsets, int &maxOrder, V3D &hkl,
+    HKLFilterWavelength &lambdaFilter, bool &includePeaksInRange,
+    bool &includeOrderZero, vector<vector<int>> &AlreadyDonePeaks) {
   if (offsets == V3D(0, 0, 0))
     return;
   const Kernel::DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
@@ -379,8 +376,7 @@ void PredictSatellitePeaks::predictOffsets(
 }
 
 void PredictSatellitePeaks::predictOffsetsWithCrossTerms(
-    V3D offsets1,
-    V3D offsets2, V3D offsets3, int &maxOrder, V3D &hkl,
+    V3D offsets1, V3D offsets2, V3D offsets3, int &maxOrder, V3D &hkl,
     HKLFilterWavelength &lambdaFilter, bool &includePeaksInRange,
     bool &includeOrderZero, vector<vector<int>> &AlreadyDonePeaks) {
   if (offsets1 == V3D(0, 0, 0) && offsets2 == V3D(0, 0, 0) &&

Framework/Crystal/test/FindUBUsingIndexedPeaksTest.h

@@ -14,11 +14,11 @@
 #include <cxxtest/TestSuite.h>
 
 #include "MantidCrystal/FindUBUsingIndexedPeaks.h"
+#include "MantidCrystal/LoadIsawPeaks.h"
 #include "MantidCrystal/LoadIsawUB.h"
 #include "MantidDataHandling/LoadNexusProcessed.h"
 #include "MantidDataObjects/PeaksWorkspace.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
-#include "MantidCrystal/LoadIsawPeaks.h"
 
 using namespace Mantid::Crystal;
 using Mantid::Geometry::OrientedLattice;
@@ -102,7 +102,8 @@ public:
       const V3D mnp = peak.getIntMNP();
       V3D mnpNew = mnp;
       srand(0);
-      if(std::abs(mnp[0]) == 1) mnpNew[1] = rand() % 2;
+      if (std::abs(mnp[0]) == 1)
+        mnpNew[1] = rand() % 2;
       peak.setIntMNP(mnpNew);
     }
     FindUBUsingIndexedPeaks alg2;
@@ -123,8 +124,8 @@ public:
     // Check that the UB matrix is the same as in TOPAZ_3007.mat
     OrientedLattice latt = ws->mutableSample().getOrientedLattice();
 
-    double correct_err1[] = {0.003723,0.002231,0.002820};
-    double correct_err2[] = {0.000796,0.002043,0.002671};
+    double correct_err1[] = {0.003723, 0.002231, 0.002820};
+    double correct_err2[] = {0.000796, 0.002043, 0.002671};
 
     std::vector<double> err_calculated1 = latt.getVecErr(0);
     std::vector<double> err_calculated2 = latt.getVecErr(1);

Framework/Kernel/src/V3D.cpp

@@ -574,29 +574,28 @@ V3D V3D::directionAngles(bool inDegrees) const {
 */
 int V3D::maxCoeff() {
   int MaxOrder = 0;
-    if (abs(static_cast<int>(x)) > MaxOrder)
-      MaxOrder = abs(static_cast<int>(x));
-    if (abs(static_cast<int>(y)) > MaxOrder)
-      MaxOrder = abs(static_cast<int>(y));
-    if (abs(static_cast<int>(z)) > MaxOrder)
-      MaxOrder = abs(static_cast<int>(z));
-    return MaxOrder;
+  if (abs(static_cast<int>(x)) > MaxOrder)
+    MaxOrder = abs(static_cast<int>(x));
+  if (abs(static_cast<int>(y)) > MaxOrder)
+    MaxOrder = abs(static_cast<int>(y));
+  if (abs(static_cast<int>(z)) > MaxOrder)
+    MaxOrder = abs(static_cast<int>(z));
+  return MaxOrder;
 }
 
 /**
-  Calculates the absolute value. 
+  Calculates the absolute value.
   @return The absolute value
 */
-V3D V3D::absoluteValue() const {
-  return V3D(fabs(x), fabs(y), fabs(z));
-}
+V3D V3D::absoluteValue() const { return V3D(fabs(x), fabs(y), fabs(z)); }
 
 /**
   Calculates the error of the HKL to compare with tolerance
   @return The error
 */
 double V3D::hklError() const {
-  return fabs(x - std::round(x)) + fabs(y - std::round(y)) + fabs(z - std::round(z));
+  return fabs(x - std::round(x)) + fabs(y - std::round(y)) +
+         fabs(z - std::round(z));
 }
 
 } // Namespace Kernel

Framework/MDAlgorithms/test/Integrate3DEventsTest.h

@@ -151,17 +151,15 @@ public:
     UBinv.setRow(1, V3D(0, .2, 0));
     UBinv.setRow(2, V3D(0, 0, .25));
 
-    std::vector<V3D> hkl_list{
-        UBinv * peak_1,  UBinv * peak_2, UBinv * peak_3};
- 
+    std::vector<V3D> hkl_list{UBinv * peak_1, UBinv * peak_2, UBinv * peak_3};
+
     // synthesize a ModHKL
     DblMatrix ModHKL(3, 3, false); // Q to h,k,l
     ModHKL.setRow(0, V3D(0.4, 0, 0));
     ModHKL.setRow(1, V3D(0, 0, 0));
     ModHKL.setRow(2, V3D(0, 0, 0));
 
-    std::vector<V3D> mnp_list{
-        V3D(-1, 0, 0), V3D(0, 0, 0), V3D(0, 0, 0)};
+    std::vector<V3D> mnp_list{V3D(-1, 0, 0), V3D(0, 0, 0), V3D(0, 0, 0)};
 
     // synthesize events around the
     // peaks.  All events with in one
@@ -209,7 +207,8 @@ public:
     double radius_s = 0.1;
     int maxOrder = 1;
     bool crossTerm = false;
-    Integrate3DEvents integrator(peak_q_list, hkl_list, mnp_list, UBinv, ModHKL, radius, radius_s, maxOrder, crossTerm);
+    Integrate3DEvents integrator(peak_q_list, hkl_list, mnp_list, UBinv, ModHKL,
+                                 radius, radius_s, maxOrder, crossTerm);
 
     integrator.addEvents(event_Qs, false);
 

Framework/MDAlgorithms/test/IntegrateEllipsoidsWithSatellitesTest.h

@@ -28,9 +28,9 @@ using Mantid::Types::Event::TofEvent;
 
 namespace {
 // Add A Fake 'Peak' to both the event data and to the peaks workspace
-void addFakeEllipsoid(const V3D &peakHKL, const V3D &peakMNP, const int &totalNPixels,
-                      const int &nEvents, const double tofGap,
-                      EventWorkspace_sptr &eventWS,
+void addFakeEllipsoid(const V3D &peakHKL, const V3D &peakMNP,
+                      const int &totalNPixels, const int &nEvents,
+                      const double tofGap, EventWorkspace_sptr &eventWS,
                       PeaksWorkspace_sptr &peaksWS) {
   // Create the peak and add it to the peaks ws
   Peak *peak = peaksWS->createPeakHKL(peakHKL);
@@ -358,7 +358,8 @@ public:
     TSM_ASSERT_DELTA("Wrong intensity for peak 0",
                      integratedPeaksWS->getPeak(0).getIntensity(), 6, 0.01);
     TSM_ASSERT_DELTA("Wrong intensity for peak 1",
-                     integratedPeaksWS->getPeak(1).getIntensity(), 10.8964, 0.01);
+                     integratedPeaksWS->getPeak(1).getIntensity(), 10.8964,
+                     0.01);
     TSM_ASSERT_DELTA("Wrong intensity for peak 2",
                      integratedPeaksWS->getPeak(2).getIntensity(), 9, 0.01);
     TSM_ASSERT_DELTA("Wrong intensity for peak 3",
@@ -366,7 +367,8 @@ public:
     TSM_ASSERT_DELTA("Wrong intensity for peak 4",
                      integratedPeaksWS->getPeak(4).getIntensity(), 0, 0.01);
     TSM_ASSERT_DELTA("Wrong intensity for peak 5",
-                     integratedPeaksWS->getPeak(5).getIntensity(), 20.9410, 0.01);
+                     integratedPeaksWS->getPeak(5).getIntensity(), 20.9410,
+                     0.01);
   }
 
   void test_execution_histograms_adaptive() {