hiding things behind the pinkIndexer namespace

include/Backprojection.h

 #pragma once
 
-#include <Eigen/Dense>
 #include "ExperimentSettings.h"
+#include <Eigen/Dense>
 
-class Backprojection
+namespace pinkIndexer
 {
+
+    class Backprojection
+    {
       public:
         Backprojection(const ExperimentSettings& experimentSettings);
 
-    void backProject(const Eigen::Matrix2Xf& detectorPeaks_m, Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms ) const;
+        void backProject(const Eigen::Matrix2Xf& detectorPeaks_m, Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms) const;
 
       private:
         ExperimentSettings experimentSettings;
-};
+    };
\ No newline at end of file
+
+} // namespace pinkIndexer
\ No newline at end of file

include/BadInputException.h

@@ -10,20 +10,19 @@
 
 #include <CustomException.h>
 
-//! A specialization of MyException.
-/*!
- * This exception is thrown whenever the input to a method/function is not as expected
- */
-class BadInputException: public CustomException {
-public:
-    BadInputException(const std::string& msg) :
-            CustomException(msg)
-    {
-    }
+namespace pinkIndexer
+{
 
-    virtual ~BadInputException() throw ()
+    class BadInputException : public CustomException
+    {
+      public:
+        BadInputException(const std::string& msg)
+            : CustomException(msg)
         {
         }
-};
+
+        virtual ~BadInputException() throw() {}
+    };
+} // namespace pinkIndexer
 
 #endif /* BADINPUTEXCEPTION_H_ */

include/Chronometer.h

@@ -4,9 +4,11 @@
 #include <cstdint>
 #include <string>
 
-class Chronometer
+namespace pinkIndexer
 {
-public:
+    class Chronometer
+    {
+      public:
         /**
          * @brief Chronometer constructor - saves the current time
          * @param key the key for the debug protocol value
@@ -18,9 +20,10 @@ public:
          */
         ~Chronometer();
 
-private:
+      private:
         /// the key for the time value
         const std::string key_;
         /// the timestamp at object construction
         std::chrono::time_point<std::chrono::system_clock> startTime_;
-};
+    };
+} // namespace pinkIndexer
\ No newline at end of file

include/CustomException.h

@@ -11,40 +11,43 @@
 #include <exception>
 #include <string>
 
-//! The Exception class from which every exception type in this project inherits from.
-/*!
+namespace pinkIndexer
+{
+    //! The Exception class from which every exception type in this project inherits from.
+    /*!
      * This is the superclass for all the custom exception types used in this project.
      * This class itself inherits from std::exception.
      */
-class CustomException: public std::exception {
-public:
+    class CustomException : public std::exception
+    {
+      public:
         /*!
          * The constructor taking a message as parameter.
          * @param msg The message of the exception.
          */
-    CustomException(const std::string& msg) :
-            msg(msg)
+        CustomException(const std::string& msg)
+            : msg(msg)
         {
         }
 
         /*!
          * The virtual destructor.
          */
-    virtual ~CustomException() throw ()
-    {
-    }
+        virtual ~CustomException() throw() {}
 
         /*!
          * Returns the message of the exception.
          * @return
          */
-    virtual const char* what() const throw ()
+        virtual const char* what() const throw()
         {
             return msg.c_str();
         }
 
-private:
+      private:
         std::string msg;
-};
+    };
+
+} // namespace pinkIndexer
 
 #endif /* CUSTOMEXCEPTION_H_ */

include/ExperimentSettings.h

@@ -11,8 +11,11 @@
 #include "Lattice.h"
 #include "WrongUsageException.h"
 
-class ExperimentSettings
+namespace pinkIndexer
 {
+
+    class ExperimentSettings
+    {
       public:
         ExperimentSettings(float coffset_m, float clen_mm, float beamEenergy_eV, float divergenceAngle_deg, float nonMonochromaticity, float pixelLength_m,
                            float detectorRadius_pixel, float minRealLatticeVectorLength_A, float maxRealLatticeVectorLength_A, float reflectionRadius_1_per_A);
@@ -107,6 +110,6 @@ class ExperimentSettings
 
       public:
         EIGEN_MAKE_ALIGNED_OPERATOR_NEW
-};
-
+    };
+} // namespace pinkIndexer
 #endif /* EXPERIMENTSETTINGS_H_ */

include/Lattice.h

@@ -11,8 +11,11 @@
 #include <Eigen/Dense>
 #include <iostream>
 
-class Lattice
+namespace pinkIndexer
 {
+
+    class Lattice
+    {
       public:
         Lattice();
         Lattice(const Eigen::Matrix3f& basis);
@@ -54,6 +57,6 @@ class Lattice
 
       public:
         EIGEN_MAKE_ALIGNED_OPERATOR_NEW
-};
-
+    };
+} // namespace pinkIndexer
 #endif /* LATTICE_H_ */

include/PinkIndexer.h

@@ -11,9 +11,11 @@
 #include <Eigen/Dense>
 #include <stdint.h>
 
-
-class PinkIndexer
+namespace pinkIndexer
 {
+
+    class PinkIndexer
+    {
       public:
         enum class ConsideredPeaksCount
         {
@@ -47,10 +49,10 @@ class PinkIndexer
         PinkIndexer(const ExperimentSettings& experimentSettings, ConsideredPeaksCount consideredPeaksCount, AngleResolution angleResolution,
                     RefinementType refinementType, float maxResolutionForIndexing_1_per_A);
 
-    int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
-                     const Eigen::Matrix2Xf& detectorPeaks_m, int threadCount);
-    int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
-                     const Eigen::Matrix3Xf& meanReciprocalPeaks_1_per_A, int threadCount);
+        int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks,
+                         Eigen::RowVectorXf& intensities, const Eigen::Matrix2Xf& detectorPeaks_m, int threadCount);
+        int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks,
+                         Eigen::RowVectorXf& intensities, const Eigen::Matrix3Xf& meanReciprocalPeaks_1_per_A, int threadCount);
 
       private:
         void reducePeakCount(Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms, Eigen::RowVectorXf& intensities,
@@ -72,4 +74,5 @@ class PinkIndexer
         RefinementType refinementType;
         float maxResolutionForIndexing_1_per_A;
         float finalRefinementTolerance;
-};
+    };
\ No newline at end of file
+} // namespace pinkIndexer
\ No newline at end of file

include/ReciprocalToRealProjection.h

@@ -3,9 +3,10 @@
 #include "ExperimentSettings.h"
 #include <Eigen/Dense>
 
-
-class ReciprocalToRealProjection
+namespace pinkIndexer
 {
+    class ReciprocalToRealProjection
+    {
       public:
         ReciprocalToRealProjection(const ExperimentSettings& experimentSettings);
         virtual ~ReciprocalToRealProjection() = default;
@@ -14,4 +15,5 @@ class ReciprocalToRealProjection
 
       protected:
         ExperimentSettings experimentSettings;
-};
+    };
+} // namespace pinkIndexer
\ No newline at end of file

include/Refinement.h

@@ -7,8 +7,10 @@
 #include <Eigen/Dense>
 #include <vector>
 
-class Refinement
+namespace pinkIndexer
 {
+    class Refinement
+    {
       public:
         Refinement(float tolerance);
         Refinement(float tolerance, const Backprojection& backprojection);
@@ -63,4 +65,5 @@ class Refinement
         Eigen::Matrix2Xf detectorPeaks_m_shifted;
         Eigen::Matrix3Xf ucsDirections;
         Eigen::Array2Xf ucsBorderNorms;
-};
+    };
+} // namespace pinkIndexer
\ No newline at end of file

include/ReflectionsInRangeFinder.h

 #pragma once
 
+#include "BadInputException.h"
 #include "ExperimentSettings.h"
 #include "eigenSTLContainers.h"
-#include "BadInputException.h"
 
-class ReflectionsInRangeFinder
+namespace pinkIndexer
 {
+    class ReflectionsInRangeFinder
+    {
       public:
         ReflectionsInRangeFinder(const Lattice& lattice);
 
@@ -15,4 +17,5 @@ class ReflectionsInRangeFinder
         Eigen::Matrix3Xf reflectionsDirections_sorted;
         std::vector<float> norms_sorted;
         float maxRadius;
-};
+    };
\ No newline at end of file
+} // namespace pinkIndexer
\ No newline at end of file

include/SimpleDiffractionPatternPrediction.h

@@ -4,8 +4,10 @@
 #include "SimpleProjection.h"
 #include <Eigen/Dense>
 
-class SimpleDiffractionPatternPrediction
+namespace pinkIndexer
 {
+    class SimpleDiffractionPatternPrediction
+    {
       public:
         SimpleDiffractionPatternPrediction(const ExperimentSettings& experimentSettings);
 
@@ -20,4 +22,5 @@ class SimpleDiffractionPatternPrediction
         float reciprocalLambdaShort, reciprocalLambdaLong;
         float reciprocalLambdaShort_extended_squared, reciprocalLambdaLong_extended_squared;
         float detectorDistance;
-};
+    };
+} // namespace pinkIndexer
\ No newline at end of file

include/SimpleProjection.h

@@ -3,10 +3,13 @@
 #include "ReciprocalToRealProjection.h"
 #include <Eigen/Dense>
 
-class SimpleProjection : public ReciprocalToRealProjection
+namespace pinkIndexer
 {
+    class SimpleProjection : public ReciprocalToRealProjection
+    {
       public:
         SimpleProjection(const ExperimentSettings& experimentSettings);
 
         void project(Eigen::Matrix2Xf& projectedPeaks, const Eigen::Matrix3Xf& reciprocalPeaks) const;
-};
+    };
+} // namespace pinkIndexer
\ No newline at end of file

include/Sinogram.h

@@ -9,8 +9,10 @@
 #include <string>
 #include <vector>
 
-class Sinogram
+namespace pinkIndexer
 {
+    class Sinogram
+    {
       public:
         Sinogram(const Lattice& lattice);
 
@@ -42,4 +44,5 @@ class Sinogram
 
       public:
         EIGEN_MAKE_ALIGNED_OPERATOR_NEW
-};
+    };
\ No newline at end of file
+} // namespace pinkIndexer
\ No newline at end of file

include/WrongUsageException.h

@@ -10,20 +10,18 @@
 
 #include <CustomException.h>
 
-//! A specialization of MyException.
-/*!
- * This exception is thrown whenever a function/method is used in a wrong way
- */
-class WrongUsageException: public CustomException {
-public:
-    WrongUsageException(const std::string& msg) :
-            CustomException(msg)
-    {
-    }
+namespace pinkIndexer
+{
 
-    virtual ~WrongUsageException() throw ()
+    class WrongUsageException : public CustomException
+    {
+      public:
+        WrongUsageException(const std::string& msg)
+            : CustomException(msg)
         {
         }
-};
 
+        virtual ~WrongUsageException() throw() {}
+    };
+} // namespace pinkIndexer
 #endif /* WRONGUSAGEEXCEPTION_H_ */

include/adaptions/crystfel/ExperimentSettings.h

@@ -4,22 +4,25 @@
 #include "Lattice.h"
 
 #ifdef __cplusplus
-extern "C" {
+namespace pinkIndexer
+{
+    extern "C" {
 #endif
 
-typedef struct ExperimentSettings ExperimentSettings;
+    typedef struct ExperimentSettings ExperimentSettings;
 
-ExperimentSettings* ExperimentSettings_new_nolatt(float beamEenergy_eV, float detectorDistance_m, float detectorRadius_m, float divergenceAngle_deg,
+    ExperimentSettings* ExperimentSettings_new_nolatt(float beamEenergy_eV, float detectorDistance_m, float detectorRadius_m, float divergenceAngle_deg,
                                                       float nonMonochromaticity, float minRealLatticeVectorLength_A, float maxRealLatticeVectorLength_A,
                                                       float reflectionRadius_1_per_A);
 
-ExperimentSettings* ExperimentSettings_new(float beamEenergy_eV, float detectorDistance_m, float detectorRadius_m, float divergenceAngle_deg,
+    ExperimentSettings* ExperimentSettings_new(float beamEenergy_eV, float detectorDistance_m, float detectorRadius_m, float divergenceAngle_deg,
                                                float nonMonochromaticity, const Lattice_t sampleReciprocalLattice_1A, float tolerance,
                                                float reflectionRadius_1_per_A);
 
-void ExperimentSettings_delete(ExperimentSettings* experimentSettings);
+    void ExperimentSettings_delete(ExperimentSettings* experimentSettings);
 
 #ifdef __cplusplus
+    }
 }
 #endif
 

include/adaptions/crystfel/Lattice.h

@@ -30,14 +30,17 @@ typedef struct
 } LatticeTransform_t;
 
 #ifdef __cplusplus
-extern "C" {
+namespace pinkIndexer
+{
+    extern "C" {
 #endif
 
-void reorderLattice(const Lattice_t* prototype, Lattice_t* lattice);
-void reduceLattice(Lattice_t* lattice, LatticeTransform_t* appliedReductionTransform);
-void restoreLattice(Lattice_t* lattice, LatticeTransform_t* appliedReductionTransform);
+    void reorderLattice(const Lattice_t* prototype, Lattice_t* lattice);
+    void reduceLattice(Lattice_t* lattice, LatticeTransform_t* appliedReductionTransform);
+    void restoreLattice(Lattice_t* lattice, LatticeTransform_t* appliedReductionTransform);
 
 #ifdef __cplusplus
+    }
 }
 #endif
 

include/adaptions/crystfel/PinkIndexer.h

@@ -6,11 +6,13 @@
 #include "indexerData.h"
 
 #ifdef __cplusplus
-extern "C" {
+namespace pinkIndexer
+{
+    extern "C" {
 #endif
 
-typedef enum
-{
+    typedef enum
+    {
         CONSIDERED_PEAKS_COUNT_veryFew = 0,
         CONSIDERED_PEAKS_COUNT_few = 1,
         CONSIDERED_PEAKS_COUNT_standard = 2,
@@ -18,10 +20,10 @@ typedef enum
         CONSIDERED_PEAKS_COUNT_manyMany = 4,
 
         CONSIDERED_PEAKS_COUNT_lastEnum
-} consideredPeaksCount_t;
+    } consideredPeaksCount_t;
 
-typedef enum
-{
+    typedef enum
+    {
         ANGLE_RESOLUTION_extremelyLoose = 0,
         ANGLE_RESOLUTION_loose = 1,
         ANGLE_RESOLUTION_standard = 2,
@@ -29,10 +31,10 @@ typedef enum
         ANGLE_RESOLUTION_extremelyDense = 4,
 
         ANGLE_RESOLUTION_lastEnum
-} angleResolution_t;
+    } angleResolution_t;