Address review comments.

sammy/src/salmon/GridData.h

@@ -10,12 +10,21 @@ namespace sammy{
    /**
    * @brief The GridData class contains energy data and potentially data points
    *
-   * The grid can be energy or angle (energy in pos 0 and angle in pos 1) or anything that
-   * The row offset is stored for use by calling programs (for example to indicate that
-   * we want position i in energy the first energy. But because there can be more than
-   * one equal energy in position 0, the use of this parameter is left to the calling program
+   * Ideally, there is going to be one grid with experiental data points for each data set to be
+   * fitted. There may be corresponding auxiallary grid for each data set with additional points
+   * needed for calculation (for exampe extra energy points for doppler broadening)
    *
-   * The start of the data is indicated by the function getDataIndex
+   * Since SAMMY uses one grid and one auxillary grid only, we allowed to have
+   * more than one column to allow to experimental data (for example energy in column 0, angle in column 1)
+   * In this case energy points for each angle are repeated  (as SAMMY requires all angle data to be on the
+   * same energy grid).  But we want to relax that going forward.
+   *
+   * To indicate where the data start, the grid has a function (getDataIndex) to indicate the data column
+   *
+   * Sometimes we may want to store more energy data then are used for the calculation, for example extra data points being read
+   * in or points of the auxillary grid not used, therefore we allow for an offset, that indicates from where counting of
+   * data points start (getRowOffset/setRowOffset()). This does not affect the indexing used by getData to retrieve data from the
+   * grid.
    *
    */
   class GridData {
@@ -140,7 +149,13 @@ namespace sammy{
 
       /**
        * Get the index of the auxillary grid, if using.
-       * By default this is the second grid if present and the first grid otherwise
+       * By default this is the second grid if present and the first grid otherwise.
+       *
+       * Note: In principle this should be in the GridAccess class. However,
+       * only the GridDataList is currently globally available in SAMMY.
+       * Thus, until a correct object of GridAccess can be passed arround,
+       * we opted to have the information in this class.
+       *
        * @brief getAuxGridIndex index of the auxillary grid, if using.
        * @return index of the auxillary grid, if using.
        */
@@ -148,7 +163,13 @@ namespace sammy{
 
       /**
        * Get the index of the experimental grid, if using.
-       * By default this is the first grid
+       * By default this is the first grid.
+       *
+       * Note: In principle this should be in the GridAccess class. However,
+       * only the GridDataList is currently globally available in SAMMY.
+       * Thus, until a correct object of GridAccess can be passed arround,
+       * we opted to have the information in this class.
+       *
        * @brief getExpGridIndex index of the experimental grid, if using.
        * @return index of the experimental grid, if using.
        */

sammy/src/salmon/SammyGridAccess.h

@@ -4,22 +4,79 @@
 #include "GridData.h"
 
 namespace sammy{
+     /**
+     * @brief The SammyGridAccess class enables easier use of the new GridData in SAMMY
+     *
+     * Going forward, we would like to store experimental, theoretical and derivative data in
+     * the new GridData. This class attempts to make the transition within SAMMY easier.
+     *
+     * Currently, SAMMY has two grids: experimental grid and auxiallary grid. If angle data
+     * are given, the angle grid (of length numcro) needs to be the same for each energy at
+     * which angles are given. In addition energies sometimes are used with an additional calibration
+     * applied (ktzero != 0).
+     *
+     * In order to allow for the least amount of changes in SAMMY, this class gives functions to access the
+     * energy just as SAMMY would access its current energy grid, with the function  getEnergy. If a
+     * If the underlying GridData has a row offset applied it is taken into acount in the index passed to getEnergy.
+     * Depending on the value of ktzero, the orignal or the calibrated energy is returned (getOrigEnergy) will always
+     * give the user energy.
+     *
+     * The grid access can be either to the experimental grid or the auxillary grid.
+     */
     class SammyGridAccess
     {
        public:
          SammyGridAccess():numcro(1),ktzero(0),gridIndex(0){}
          virtual ~SammyGridAccess(){}
 
+         /**
+           * Set the values for numcro and ktzero.
+           * See class description for more info.
+           *
+           * @param numcro number of angles on the angle grid for each energy
+           * @param ktzero do we have an energy calibration applied
+           */
           void setParameters(int numcro, int ktzero);
 
+          /**
+           * Indicate that this access is for the experimental grid
+           * @param list the container for the underlying grids
+           */
           void setExpGrid(const GridDataList & list);
 
+          /**
+           * Indicate that this access is for the auxillary grid
+           * @param list the container for the underlying grids
+           */
           void setAuxGrid(const GridDataList & list);
 
+          /**
+           * Get the energy at the desired index.
+           * If a row offset is set on the underlying grid, the index is corrected for the offset before
+           * retrieving the data
+           * @param index the index for the desired energy
+           * @param list the underlying list info
+           * @return  the energy at the indicated index
+           */
           double getEnergy(int index, const GridDataList & list) const;
 
+          /**
+           * Get the original energy at the desired index. Unless ktzero != 0, this is the same as getEnergy.
+           *
+           * If a row offset is set on the underlying grid, the index is corrected for the offset before
+           * retrieving the data
+           * @param index the index for the desired energy
+           * @param list the underlying list info
+           * @return  the energy at the indicated index
+           */
           double getOrigEnergy(int index, const GridDataList & list) const;
 
+          /**
+           * Get the number of energy points on the desired grid.
+           *  If a row offset is set on the underlying grid, the number is adjusted accordingly.
+           * @param list the underlying list info
+           * @return  number of energy points on the desired grid.
+           */
           int getNumEnergies(const GridDataList & list) const;
 
        private:

sammy/src/salmon/tests/GridDataTest.cpp

@@ -78,8 +78,8 @@ TEST(DataInfo,gridData){
 
    // copy constructor
    sammy::GridData gridCopy(grid);
-   gridCopy.setDataIndex(6);
-   gridCopy.setRowOffset(9);
+   ASSERT_EQ(6, gridCopy.getDataIndex());
+   ASSERT_EQ(9, gridCopy.getRowOffset());
    xx = 1.0;
    for (int i = 0; i < 5; i++){
        for( int j = 0; j < 3; j++){
@@ -118,7 +118,6 @@ TEST(GridList, gridDataList){
 
         for( int j = 0; j < 2; j++){
             ASSERT_NEAR(i+1, grid->getData(j,1), 1e-3);
-            \
             ASSERT_NEAR( i+5, list.getExperimentalCov(i*3, j), 1e-3);
         }
     }
@@ -134,7 +133,6 @@ TEST(GridList, gridDataList){
 
         for( int j = 0; j < 2; j++){
             ASSERT_NEAR(i+1, grid->getData(j,1), 1e-3);
-            \
             ASSERT_NEAR( i+5, listCopy.getExperimentalCov(i*3, j), 1e-3);
         }
     }