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

Update all files to point at include subdir

parent 9abec804
#pragma once
#include "ExperimentSettings.h"
#include <pinkIndexer/ExperimentSettings.h>
#include <Eigen/Dense>
namespace pinkIndexer
......@@ -17,4 +17,4 @@ namespace pinkIndexer
ExperimentSettings experimentSettings;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
......@@ -8,7 +8,7 @@
#ifndef BADINPUTEXCEPTION_H_
#define BADINPUTEXCEPTION_H_
#include <CustomException.h>
#include <pinkIndexer/CustomException.h>
namespace pinkIndexer
{
......
......@@ -8,8 +8,8 @@
#ifndef EXPERIMENTSETTINGS_H_
#define EXPERIMENTSETTINGS_H_
#include "Lattice.h"
#include "WrongUsageException.h"
#include <pinkIndexer/Lattice.h>
#include <pinkIndexer/WrongUsageException.h>
namespace pinkIndexer
{
......
#pragma once
#include "Backprojection.h"
#include "ExperimentSettings.h"
#include "Lattice.h"
#include "Refinement.h"
#include "SimpleDiffractionPatternPrediction.h"
#include "SimpleProjection.h"
#include "Sinogram.h"
#include <pinkIndexer/Backprojection.h>
#include <pinkIndexer/ExperimentSettings.h>
#include <pinkIndexer/Lattice.h>
#include <pinkIndexer/Refinement.h>
#include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
#include <pinkIndexer/SimpleProjection.h>
#include <pinkIndexer/Sinogram.h>
#include <Eigen/Dense>
#include <stdint.h>
......@@ -78,4 +78,4 @@ namespace pinkIndexer
float maxResolutionForIndexing_1_per_A;
float finalRefinementTolerance; //from command line in crystfel
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#pragma once
#include "ExperimentSettings.h"
#include <pinkIndexer/ExperimentSettings.h>
#include <Eigen/Dense>
namespace pinkIndexer
......@@ -16,4 +16,4 @@ namespace pinkIndexer
protected:
ExperimentSettings experimentSettings;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#pragma once
#include "Backprojection.h"
#include "Lattice.h"
#include "ReciprocalToRealProjection.h"
#include <pinkIndexer/Backprojection.h>
#include <pinkIndexer/Lattice.h>
#include <pinkIndexer/ReciprocalToRealProjection.h>
#include <Eigen/Dense>
#include <vector>
......@@ -66,4 +66,4 @@ namespace pinkIndexer
Eigen::Matrix3Xf ulsDirections;
Eigen::Array2Xf ulsBorderNorms;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#pragma once
#include "BadInputException.h"
#include "ExperimentSettings.h"
#include "eigenSTLContainers.h"
#include <pinkIndexer/BadInputException.h>
#include <pinkIndexer/ExperimentSettings.h>
#include <pinkIndexer/eigenSTLContainers.h>
namespace pinkIndexer
{
......@@ -18,4 +18,4 @@ namespace pinkIndexer
std::vector<float> norms_sorted;
float maxRadius;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#pragma once
#include "SimpleProjection.h"
#include <pinkIndexer/SimpleProjection.h>
#include <Eigen/Dense>
namespace pinkIndexer
......@@ -23,4 +23,4 @@ namespace pinkIndexer
float reciprocalLambdaShort_extended_squared, reciprocalLambdaLong_extended_squared;
float detectorDistance;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#pragma once
#include "ReciprocalToRealProjection.h"
#include <pinkIndexer/ReciprocalToRealProjection.h>
#include <Eigen/Dense>
namespace pinkIndexer
......@@ -12,4 +12,4 @@ namespace pinkIndexer
void project(Eigen::Matrix2Xf& projectedPeaks, const Eigen::Matrix3Xf& reciprocalPeaks) const;
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
......@@ -2,9 +2,9 @@
#define EIGEN_DONT_PARALLELIZE
#include "Lattice.h"
#include "ReflectionsInRangeFinder.h"
#include "eigenSTLContainers.h"
#include <pinkIndexer/Lattice.h>
#include <pinkIndexer/ReflectionsInRangeFinder.h>
#include <pinkIndexer/eigenSTLContainers.h>
#include <Eigen/Dense>
#include <string>
#include <vector>
......@@ -45,4 +45,4 @@ namespace pinkIndexer
public:
EIGEN_MAKE_ALIGNED_OPERATOR_NEW
};
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
......@@ -8,7 +8,7 @@
#ifndef WRONGUSAGEEXCEPTION_H_
#define WRONGUSAGEEXCEPTION_H_
#include <CustomException.h>
#include <pinkIndexer/CustomException.h>
namespace pinkIndexer
{
......
......@@ -8,7 +8,7 @@
#ifndef EIGENDISKIMPORT_H_
#define EIGENDISKIMPORT_H_
#include "BadInputException.h"
#include <pinkIndexer/BadInputException.h>
#include <Eigen/Dense>
#include <algorithm>
#include <fstream>
......
#include "Backprojection.h"
#include <pinkIndexer/Backprojection.h>
using namespace std;
......@@ -33,4 +33,4 @@ namespace pinkIndexer
ulsDirections = backprojectedPointsFar.colwise().normalized();
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#include "Chronometer.h"
#include <pinkIndexer/Chronometer.h>
#include <iostream>
#include <string>
......@@ -16,4 +16,4 @@ namespace pinkIndexer
auto duration = std::chrono::system_clock::now() - startTime_;
std::cout << key_ << " elapsed: " << std::chrono::duration_cast<std::chrono::milliseconds>(duration).count() << "\n";
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
......@@ -5,7 +5,7 @@
* Author: Yaro
*/
#include <ExperimentSettings.h>
#include <pinkIndexer/ExperimentSettings.h>
#include <assert.h>
#include <sstream>
......@@ -431,4 +431,4 @@ namespace pinkIndexer
return latticeParametersTolerance;
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
......@@ -5,7 +5,7 @@
* Author: Yaro
*/
#include <Lattice.h>
#include <pinkIndexer/Lattice.h>
#include <algorithm>
#include <assert.h>
#include <inttypes.h>
......@@ -347,4 +347,4 @@ namespace pinkIndexer
}
}
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#include "PinkIndexer.h"
#include <pinkIndexer/PinkIndexer.h>
#include <algorithm>
#include <fstream>
......@@ -364,4 +364,4 @@ namespace pinkIndexer
throw BadInputException("Unknown considered peaks count selected");
}
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#include "ReciprocalToRealProjection.h"
#include <pinkIndexer/ReciprocalToRealProjection.h>
namespace pinkIndexer
{
......
#define _USE_MATH_DEFINES
#include <cmath>
#include "Refinement.h"
#include "WrongUsageException.h"
#include "eigenSTLContainers.h"
#include <pinkIndexer/Refinement.h>
#include <pinkIndexer/WrongUsageException.h>
#include <pinkIndexer/eigenSTLContainers.h>
#include <iostream>
#include <limits>
......@@ -397,4 +397,4 @@ namespace pinkIndexer
{
x = x.array().abs().ceil() * x.array().sign();
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
#include "ReflectionsInRangeFinder.h"
#include <pinkIndexer/ReflectionsInRangeFinder.h>
#include <algorithm>
#include <numeric>
......@@ -76,4 +76,4 @@ namespace pinkIndexer
}
}
}
} // namespace pinkIndexer
\ No newline at end of file
} // namespace pinkIndexer
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