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

Update all files to point at include subdir

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