Commit cbcbde5d authored by Thomas White's avatar Thomas White
Browse files

Update all files to point at include subdir

parent 9abec804
#include "SimpleDiffractionPatternPrediction.h" #include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
#include "eigenSTLContainers.h" #include <pinkIndexer/eigenSTLContainers.h>
#include <cmath> #include <cmath>
...@@ -103,4 +103,4 @@ namespace pinkIndexer ...@@ -103,4 +103,4 @@ namespace pinkIndexer
peaksOnEwaldSphere = Map<Matrix3Xf>((float*)peaks.data(), 3, peaks.size()); peaksOnEwaldSphere = Map<Matrix3Xf>((float*)peaks.data(), 3, peaks.size());
millerIndices = Map<Matrix3Xi>((int*)millers.data(), 3, millers.size()); millerIndices = Map<Matrix3Xi>((int*)millers.data(), 3, millers.size());
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "SimpleProjection.h" #include <pinkIndexer/SimpleProjection.h>
using namespace std; using namespace std;
using namespace Eigen; using namespace Eigen;
...@@ -19,4 +19,4 @@ namespace pinkIndexer ...@@ -19,4 +19,4 @@ namespace pinkIndexer
projectedPeaks = projectedPeaks =
reciprocalPeaks.bottomRows(2).array().rowwise() / (reciprocalPeaks.row(0) - rayOriginsX).array() * experimentSettings.getDetectorDistance_m(); reciprocalPeaks.bottomRows(2).array().rowwise() / (reciprocalPeaks.row(0) - rayOriginsX).array() * experimentSettings.getDetectorDistance_m();
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#define _USE_MATH_DEFINES #define _USE_MATH_DEFINES
#include <cmath> #include <cmath>
#include "Sinogram.h" #include <pinkIndexer/Sinogram.h>
#include <algorithm> #include <algorithm>
#include <fstream> #include <fstream>
...@@ -373,4 +373,4 @@ namespace pinkIndexer ...@@ -373,4 +373,4 @@ namespace pinkIndexer
myfile.write((const char*)sinogram.data(), sinogram.size()); myfile.write((const char*)sinogram.data(), sinogram.size());
myfile.close(); myfile.close();
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "adaptions/crystfel/ExperimentSettings.h" #include <pinkIndexer/adaptions/crystfel/ExperimentSettings.h>
#include "ExperimentSettings.h" #include <pinkIndexer/ExperimentSettings.h>
#include <Eigen/Dense> #include <Eigen/Dense>
...@@ -30,4 +30,4 @@ namespace pinkIndexer ...@@ -30,4 +30,4 @@ namespace pinkIndexer
{ {
delete experimentSettings; delete experimentSettings;
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "PinkIndexer.h" #include <pinkIndexer/PinkIndexer.h>
#include "adaptions/crystfel/PinkIndexer.h" #include <pinkIndexer/adaptions/crystfel/PinkIndexer.h>
namespace pinkIndexer namespace pinkIndexer
{ {
...@@ -213,4 +213,4 @@ namespace pinkIndexer ...@@ -213,4 +213,4 @@ namespace pinkIndexer
float disbalance = 1.0f - std::abs(fittedMeanDist / totalMeanDist); float disbalance = 1.0f - std::abs(fittedMeanDist / totalMeanDist);
return disbalance; return disbalance;
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "adaptions/crystfel/SimpleDiffractionPatternPrediction.h" #include <pinkIndexer/adaptions/crystfel/SimpleDiffractionPatternPrediction.h>
#include "SimpleDiffractionPatternPrediction.h" #include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
namespace pinkIndexer namespace pinkIndexer
{ {
...@@ -64,4 +64,4 @@ namespace pinkIndexer ...@@ -64,4 +64,4 @@ namespace pinkIndexer
projectionDirections->coordinates_z[i] = projectionDirections_matrix(2, i); projectionDirections->coordinates_z[i] = projectionDirections_matrix(2, i);
} }
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "adaptions/crystfel/SimpleProjection.h" #include <pinkIndexer/adaptions/crystfel/SimpleProjection.h>
#include "SimpleProjection.h" #include <pinkIndexer/SimpleProjection.h>
namespace pinkIndexer namespace pinkIndexer
{ {
...@@ -34,4 +34,4 @@ namespace pinkIndexer ...@@ -34,4 +34,4 @@ namespace pinkIndexer
projectedPeaks_m->coordinates_y[i] = projectedPeaks_m_matrix(1, i); projectedPeaks_m->coordinates_y[i] = projectedPeaks_m_matrix(1, i);
} }
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "adaptions/crystfel/indexerData.h" #include <pinkIndexer/adaptions/crystfel/indexerData.h>
void allocReciprocalPeaks(reciprocalPeaks_1_per_A_t* reciprocalPeaks_1_per_A) void allocReciprocalPeaks(reciprocalPeaks_1_per_A_t* reciprocalPeaks_1_per_A)
{ {
...@@ -12,4 +12,4 @@ void freeReciprocalPeaks(reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A) ...@@ -12,4 +12,4 @@ void freeReciprocalPeaks(reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A)
delete[] reciprocalPeaks_1_per_A.coordinates_x; delete[] reciprocalPeaks_1_per_A.coordinates_x;
delete[] reciprocalPeaks_1_per_A.coordinates_y; delete[] reciprocalPeaks_1_per_A.coordinates_y;
delete[] reciprocalPeaks_1_per_A.coordinates_z; delete[] reciprocalPeaks_1_per_A.coordinates_z;
} }
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#include "adaptions/crystfel/Lattice.h" #include <pinkIndexer/adaptions/crystfel/Lattice.h>
#include "Lattice.h" #include <pinkIndexer/Lattice.h>
#include <Eigen/Dense> #include <Eigen/Dense>
namespace pinkIndexer namespace pinkIndexer
...@@ -91,4 +91,4 @@ namespace pinkIndexer ...@@ -91,4 +91,4 @@ namespace pinkIndexer
lattice->cz = basis(2, 2); lattice->cz = basis(2, 2);
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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#include "adaptions/crystfel/projectionData.h" #include <pinkIndexer/adaptions/crystfel/projectionData.h>
void allocDetectorPeaks(detectorPeaks_m_t* detectorPeaks_m) void allocDetectorPeaks(detectorPeaks_m_t* detectorPeaks_m)
{ {
...@@ -39,4 +39,4 @@ void freeMillerIndices(millerIndices_t millerIndices) ...@@ -39,4 +39,4 @@ void freeMillerIndices(millerIndices_t millerIndices)
delete[] millerIndices.h; delete[] millerIndices.h;
delete[] millerIndices.k; delete[] millerIndices.k;
delete[] millerIndices.l; delete[] millerIndices.l;
} }
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#define EIGEN_DONT_PARALLELIZE #define EIGEN_DONT_PARALLELIZE
#include "Chronometer.h" #include <pinkIndexer/Chronometer.h>
#include <Eigen/Dense> #include <Eigen/Dense>
#include <iostream> #include <iostream>
......
...@@ -19,16 +19,16 @@ ...@@ -19,16 +19,16 @@
#include <sstream> #include <sstream>
#include <string> #include <string>
#include "Backprojection.h" #include <pinkIndexer/Backprojection.h>
#include "Chronometer.h" #include <pinkIndexer/Chronometer.h>
#include "ExperimentSettings.h" #include <pinkIndexer/ExperimentSettings.h>
#include "PinkIndexer.h" #include <pinkIndexer/PinkIndexer.h>
#include "Refinement.h" #include <pinkIndexer/Refinement.h>
#include "ReflectionsInRangeFinder.h" #include <pinkIndexer/ReflectionsInRangeFinder.h>
#include "SimpleDiffractionPatternPrediction.h" #include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
#include "SimpleProjection.h" #include <pinkIndexer/SimpleProjection.h>
#include "Sinogram.h" #include <pinkIndexer/Sinogram.h>
#include "eigenDiskImport.h" #include <pinkIndexer/eigenDiskImport.h>
using namespace std; using namespace std;
using namespace Eigen; using namespace Eigen;
...@@ -341,4 +341,4 @@ namespace pinkIndexer ...@@ -341,4 +341,4 @@ namespace pinkIndexer
return ExperimentSettings(beamEenergy_eV, detectorDistance_m, detectorRadius_m, divergenceAngle_deg, nonMonochromaticity, sampleReciprocalLattice_1A, return ExperimentSettings(beamEenergy_eV, detectorDistance_m, detectorRadius_m, divergenceAngle_deg, nonMonochromaticity, sampleReciprocalLattice_1A,
tolerance, reflectionRadius_1_per_A); tolerance, reflectionRadius_1_per_A);
} }
} // namespace pinkIndexer } // namespace pinkIndexer
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