recon_test_pack: fix run_root_GATE.sh and associated files

- the script itself was a bit garbled
- it failed because the num_tangential_poss in the .hroot was too small compared to the data,
such that counts didn't match
- the hroot and template.hs were inconsistent (max num non-arccorrected)

I've also made the template TOF.

recon_test_pack/root_header.hroot

@@ -8,8 +8,8 @@ Inner ring diameter (cm)                 := 65.6
 Average depth of interaction (cm)        := 0.7
 Distance between rings (cm)              := 0.40625
 Default bin size (cm)                    := 0.208626
-Maximum number of non-arc-corrected bins := 344
-Default number of arc-corrected bins 	 := 344
+Maximum number of non-arc-corrected bins := 501
+Default number of arc-corrected bins 	 := 501
 View offset (degrees)					 := 0
 Number of TOF time bins := 410
 Size of timing bin (ps) := 10.00

recon_test_pack/run_root_GATE.sh

@@ -11,7 +11,7 @@
 #      
 # Author Nikos Efthimiou, Kris Thielemans
 
-echo This script should work with STIR version 5.2. If you have
+echo This script should work with STIR version 6.x. If you have
 echo a later version, you might have to update your test pack.
 echo Please check the web site.
 echo
@@ -73,10 +73,7 @@ echo "GATE support detected!"
 fi
 
 
-echo Executing tests on ROOT files generated by GATE simulations, with cylindrical PET scanners
-
-
-
+echo Executing tests on ROOT files generated by GATE simulations
 
 
 # first delete any files remaining from a previous run
@@ -87,22 +84,12 @@ export INPUT_ROOT_FILE=test_PET_GATE.root
 export INPUT=root_header.hroot
 export TEMPLATE=template_for_ROOT_scanner.hs
 
-#
-# Get the number of events unlisted. 
-#
-echo
-echo ------------- Converting ROOT files to ProjData file -------------
-echo
-echo Making ProjData for all events
+echo "------------------------------"
 echo Running lm_to_projdata for all events
 
 export OUT_PROJDATA_FILE=my_proj_from_lm_all_events
 export EXCLUDE_SCATTERED=0
 export EXCLUDE_RANDOM=0
-lm_to_projdata ./lm_to_projdata.par 2>"./my_root_log_all.log"
-all_events=`awk -F ":" '/Number of prompts/ {print $2}' my_root_log_all.log`
-echo "Number of prompts stored in this time period:" ${all_events}
-
 log=lm_to_projdata_from_ROOT_all_events.log
 lm_to_projdata ./lm_to_projdata.par > ${log} 2>&1 
 if [ $? -ne 0 ]; then
@@ -114,17 +101,11 @@ else
   all_events=$(cat ${log}|grep "Number of prompts stored in this time period" | grep -o -E '[0-9]+')
 
   echo Number of prompts stored in this time period: ${all_events}
-  echo
 fi
-echo Reading all values from ROOT file
 
-#
-# Get the number of events directly from the ROOT file
-#
-echo
-echo ------------- Reading values directly from ROOT file -------------
-echo
-cat << EOF > my_root.input
+echo Reading values directly from ROOT file
+log=root_output_all_events.log
+${ROOT} -b -l ${INPUT_ROOT_FILE} << EOF >& ${log}
 Coincidences->Draw(">>eventlist","","goff");
 Int_t N = eventlist->GetN();
 cout<<endl<<"Number of prompts stored in this time period:"<< N<<endl;
@@ -139,10 +120,10 @@ else
   echo All events in ROOT file : ${all_root_num}
 fi
 if [ "$all_events" != "$all_root_num" ];then
+  echo "Mismatched number of events!"
   ThereWereErrors=1
 fi
-echo
-echo Making ProjData for true events only
+echo "------------------------------"
 echo Running lm_to_projdata *ONLY* for true events
 
 export OUT_PROJDATA_FILE=my_proj_from_lm_true_events
@@ -160,11 +141,10 @@ else
   true_events=$(cat ${log}| grep "Number of prompts stored in this time period" | grep -o -E '[0-9]+')
   echo Number of prompts stored in this time period: ${true_events}
 fi
-echo
 echo Reading true values from ROOT file ...
 
 log=root_output_true_events.log
-${ROOT} -b -l ${INPUT_ROOT_FILE} << EOF >& ${log} 
+${ROOT} -b -l ${INPUT_ROOT_FILE} << EOF >& ${log}
 Coincidences->Draw(">>eventlist","eventID1 == eventID2 && comptonPhantom1 == 0 && comptonPhantom2 == 0","goff");
 Int_t N = eventlist->GetN();
 cout<<endl<<"Number of trues stored in this time period:"<< N<<endl;
@@ -179,6 +159,7 @@ else
   echo True events in ROOT file : ${true_root_num}
 fi
 if [ "$true_events" != "$true_root_num" ]; then
+  echo "Mismatched number of events!"
   ThereWereErrors=1
 fi
 

recon_test_pack/template_for_ROOT_scanner.hs

@@ -14,15 +14,17 @@ imagedata byte order := LITTLEENDIAN
 applied corrections := {None}
 !number format := float
 !number of bytes per pixel := 4
-number of dimensions := 4
+number of dimensions := 5
+matrix axis label [5] := timing positions
+!matrix size [5] := 5
 matrix axis label [4] := segment
 !matrix size [4] := 7
 matrix axis label [3] := view
 !matrix size [3] := 252
 matrix axis label [2] := axial coordinate
 !matrix size [2] := { 1,2,3,4,3,2,1}
 matrix axis label [1] := tangential coordinate
-!matrix size [1] := 344
+!matrix size [1] := 501
 minimum ring difference per segment := { -3,-2,-1,0,1,2,3}
 maximum ring difference per segment := { -3,-2,-1,0,1,2,3}
 %TOF mashing factor:= 82
@@ -35,8 +37,8 @@ Average depth of interaction (cm)        := 0.7
 Distance between rings (cm)              := 0.40625
 Default bin size (cm)                    := 0.208626
 View offset (degrees)                    := 0
-Maximum number of non-arc-corrected bins := 344
-Default number of arc-corrected bins     := 344
+Maximum number of non-arc-corrected bins := 501
+Default number of arc-corrected bins     := 501
 Energy resolution := 0
 Reference energy (in keV) := 511
 Number of TOF time bins :=410