updates to analysis flow

NN-Eventdisplay.md

@@ -4,6 +4,8 @@ To differentiate between standard (variable threshold) and next-neighbour cleani
 - *TS* for variable threshold cleaning (default, set to 5/2.5 for image/border thresholds)
 - *NN* for next-neighbour cleaning
 
+*TS* and *NN* are called analysis types in the following documentation and in the run scripts.
+
 ## Installation
 
 ### Code
@@ -34,6 +36,10 @@ git clone https://github.com/VERITAS-Observatory/Eventdisplay_AnalysisFiles_VTS.
 git checkout v500_nncleaning
 ```
 
+Expect that these directories are in `${VERITAS_USER_DATA_DIR}/analysis/Results/${EDVERSION}/<analysis type>/Eventdisplay_AnalysisFiles/`
+(currently, `EDVERSION=v505`).
+
+
 ### Analysis scripts
 
 Same set of analysis scripts as for official science analysis in VERITAS
@@ -42,21 +48,6 @@ git clone https://github.com/VERITAS-Observatory/Eventdisplay_AnalysisScripts_VT
 git checkout v500_nncleaning
 ```
 
-## Running a test analysis
-
-The only difference between running the two analyses is in the usage of different run parameters for the evndisp step. 
-Note that for all following analysis, different lookup tables and IRFs are required.
-
-Running the TS analysis:
-```
-./ANALYSIS.evndisp.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v500/TS EVNDISP.reconstruction.runparameter
-```
-
-Running the NN analysis:
-```
-./ANALYSIS.evndisp.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v500/NN EVNDISP.reconstruction.runparameter.NN
-```
-
 ## Small IRF production
 
 Running a small IRF production for lookup table / effective area generation. 
@@ -72,8 +63,13 @@ Add line 80/after CARE_June2020 in IRF.production.sh:
     WOBBLE_OFFSETS=( 0.5 )
     # (END TEMPORARY)
 ```
-2. Set analysis type in IRF.production to select correct run parameter file (e.g., ACUTS="EVNDISP.reconstruction.runparameter.NN")
-use NN for optimised next-neighbour cleaning, TS for default cleaning.
+2. Set all paths and analysis type
+
+Use NN for optimised next-neighbour cleaning, TS for default cleaning.
+
+This will:
+- select the correct runparameter file for `evndisp` (e.g., ACUTS="EVNDISP.reconstruction.runparameter.NN") 
+- set the correct path for IRF and data products
 
 3. Evndisp analysis
 ```
@@ -87,8 +83,7 @@ use NN for optimised next-neighbour cleaning, TS for default cleaning.
 ```
 ./IRF.production.sh CARE_June2020 COMBINETABLES V6_2012_2013a 61 0
 ```
-Tables should be moved into $VERITAS_EVNDISP_AUX_DIR/Tables and renamed, e.g., 
-`table-v505-auxv01-CARE_June2020-ATM61-V6_2012_2013a-GEO.root` --> `table-v505-auxv01NN-CARE_June2020-ATM61-V6_2012_2013a-GEO.root`
+Tables should be copied from `$VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/Tables` into `$VERITAS_EVNDISP_AUX_DIR/Tables` (same for NN)
 
 6. Analyse lookup tables
 ```
@@ -99,3 +94,38 @@ Tables should be moved into $VERITAS_EVNDISP_AUX_DIR/Tables and renamed, e.g.,
 ```
 ./IRF.production.sh CARE_June2020 EFFECTIVEAREAS  V6_2012_2013a 61 0
 ```
+
+8. Combine effective areas
+```
+./IRF.production.sh CARE_June2020 COMBINEEFFECTIVEAREAS V6_2012_2013a 61 0
+```
+
+Effective area files should be copied from `$VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/CARE_June2020/V6_2012_2013a_ATM61_gamma/EffectiveAreas` to `$VERITAS_EVNDISP_AUX_DIR/EffectiveAreas`
+
+## Running a test analysis
+
+The only difference between running the two analyses is in the usage of different run parameters for the evndisp step. 
+Note that for all following analysis, different lookup tables and IRFs are required.
+
+Running the TS evndisp analysis:
+```
+./ANALYSIS.evndisp.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v500/TS/evndisp/ EVNDISP.reconstruction.runparameter
+```
+
+Running the NN evndisp analysis:
+```
+./ANALYSIS.evndisp.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v500/NN/evndisp/ EVNDISP.reconstruction.runparameter.NN
+```
+
+Table analysis:
+```
+./ANALYSIS.mscw_energy.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/Crab/evndisp $VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/Crab/mscw 0 CARE_June2020 61
+```
+(note that we override the flag for the atmosphere, as we have produced IRFs for atmosphere 61 only)
+
+Anasum analysis:
+```
+./ANALYSIS.anasum_parallel_from_runlist.sh runlist.txt $VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/Crab/anasum_soft/ softbox IGNOREACCEPTANCE $VERITAS_USER_DATA_DIR/analysis/Results/v505/runparameter_crab/runparameter.dat $VERITAS_USER_DATA_DIR/analysis/Results/v505/TS/Crab/mscw CARE_June2020 0 61
+```
+
+