From f5d38ffd1de80d4ef0b9c2e1c5b090f2e3c10ff3 Mon Sep 17 00:00:00 2001
From: Wiarda <wiardada@ornl.gov>
Date: Tue, 2 Jun 2020 11:53:28 -0400
Subject: [PATCH] Address review comments.
---
sammy/src/salmon/GridData.h | 35 ++++++++++++---
sammy/src/salmon/SammyGridAccess.h | 57 +++++++++++++++++++++++++
sammy/src/salmon/tests/GridDataTest.cpp | 6 +--
3 files changed, 87 insertions(+), 11 deletions(-)
diff --git a/sammy/src/salmon/GridData.h b/sammy/src/salmon/GridData.h
index 485bda0d1..9fd75f36c 100644
--- a/sammy/src/salmon/GridData.h
+++ b/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.
*/
diff --git a/sammy/src/salmon/SammyGridAccess.h b/sammy/src/salmon/SammyGridAccess.h
index 0341a4982..574b7e5b6 100644
--- a/sammy/src/salmon/SammyGridAccess.h
+++ b/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:
diff --git a/sammy/src/salmon/tests/GridDataTest.cpp b/sammy/src/salmon/tests/GridDataTest.cpp
index fd3cb0511..ffdbbd9d9 100644
--- a/sammy/src/salmon/tests/GridDataTest.cpp
+++ b/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);
}
}
--
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