Update all files to point at include subdir

include/pinkIndexer/Backprojection.h

 #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

include/pinkIndexer/BadInputException.h

@@ -8,7 +8,7 @@
 #ifndef BADINPUTEXCEPTION_H_
 #define BADINPUTEXCEPTION_H_
 
-#include <CustomException.h>
+#include <pinkIndexer/CustomException.h>
 
 namespace pinkIndexer
 {

include/pinkIndexer/ExperimentSettings.h

@@ -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
 {

include/pinkIndexer/PinkIndexer.h

 #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

include/pinkIndexer/ReciprocalToRealProjection.h

 #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

include/pinkIndexer/Refinement.h

 #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

include/pinkIndexer/ReflectionsInRangeFinder.h

 #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

include/pinkIndexer/SimpleDiffractionPatternPrediction.h

 #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

include/pinkIndexer/SimpleProjection.h

 #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

include/pinkIndexer/Sinogram.h

@@ -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

include/pinkIndexer/WrongUsageException.h

@@ -8,7 +8,7 @@
 #ifndef WRONGUSAGEEXCEPTION_H_
 #define WRONGUSAGEEXCEPTION_H_
 
-#include <CustomException.h>
+#include <pinkIndexer/CustomException.h>
 
 namespace pinkIndexer
 {

include/pinkIndexer/eigenDiskImport.h

@@ -8,7 +8,7 @@
 #ifndef EIGENDISKIMPORT_H_
 #define EIGENDISKIMPORT_H_
 
-#include "BadInputException.h"
+#include <pinkIndexer/BadInputException.h>
 #include <Eigen/Dense>
 #include <algorithm>
 #include <fstream>

src/Backprojection.cpp

 
-#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

src/Chronometer.cpp

-#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

src/ExperimentSettings.cpp

@@ -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

src/Lattice.cpp

@@ -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

src/PinkIndexer.cpp

-#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

src/ReciprocalToRealProjection.cpp

-#include "ReciprocalToRealProjection.h"
+#include <pinkIndexer/ReciprocalToRealProjection.h>
 
 namespace pinkIndexer
 {

src/Refinement.cpp

 #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

src/ReflectionsInRangeFinder.cpp

-#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