T25 offline

t25_offline_digit/mac/main1.mac

@@ -168,9 +168,9 @@
 #/gate/digitizer/Singles/insert                        readout
 #/gate/digitizer/Singles/readout/setDepth              1
 
-#/gate/digitizer/Singles/insert                        blurring
-#/gate/digitizer/Singles/blurring/setResolution        0.26
-#/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
+/gate/digitizer/Singles/insert                        blurring
+/gate/digitizer/Singles/blurring/setResolution        0.26
+/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
 
 /gate/digitizer/Singles/insert                        thresholder
 /gate/digitizer/Singles/thresholder/setThreshold      350. keV
@@ -182,6 +182,8 @@
 #===================================================== 
 
 /gate/digitizer/Coincidences/setWindow          10. ns
+/gate/digitizer/Coincidences/minSectorDifference 1
+/gate/digitizer/Coincidences/MultiplesPolicy killAll
 
 #=====================================================
 #  P A R T I C L E   S O U R C E

t25_offline_digit/mac/main1_offline_digitizer.mac

@@ -7,12 +7,6 @@
 
 /gate/digitizer/layers/insert adder
 
-#/gate/digitizer/layers/insert                        readout
-#/gate/digitizer/layers/readout/setDepth              1
-
-#/gate/digitizer/Singles/insert                        adder
-#/gate/digitizer/Singles/insert                        readout
-#/gate/digitizer/Singles/readout/setDepth              1
 
 /gate/digitizer/layers/insert                        blurring
 /gate/digitizer/layers/blurring/setResolution        0.26
@@ -26,9 +20,6 @@
 # INITIALIZE is needed to recover volumeID from hits using DetectorConstruction
 /gate/run/initialize
 
-#=======================================================================
-#   how to include a R A N D O M   E N G I N E  A N D  S E E D for offline digitizer ???
-#=============================================================================================
 
 
 

t25_offline_digit/mac/main1_offline_geom.mac

@@ -0,0 +1,9 @@
+
+
+# Geometry is needed to identify layer with volumeID of hits and to perform operations with pulses
+/gate/geometry/setMaterialDatabase data/GateMaterials_pet.db
+/control/execute mac/PET_CylindricalPET_geom.mac
+
+
+# INITIALIZE is needed to recover volumeID from hits using DetectorConstruction
+/gate/run/initialize

t25_offline_digit/mac/main1_offline_sorter.mac

@@ -5,6 +5,10 @@
 
 
 /gate/digitizer/Coincidences/setWindow 10. ns
+#/gate/digitizer/Coincidences/setAcceptancePolicy4CC keepIfMultipleVolumeIDsInvolved
+/gate/digitizer/Coincidences/setAcceptancePolicy4CC keepAll
+#why there are more coincidences in keepAll than in keepIfMultipleVolumeIDsInvolved ? Is it possible that in the semi head BGo and LSO same volume ID ?? To be checked,
+
 
 # There may be problems since by default in PET there is this minSectorDifference.
 # I do not know how this is read offline.

t25_offline_digit/readme.md

@@ -10,21 +10,43 @@ Simple Cylindrical PET with 20 x 20 block, 5x5 crystal, LSO and BGO layer, 4 rin
 - Source: back to back 511 keV, half-life of 1223 sec (C11)
 
 ```shell
-Gate mac/main2.mac
+Gate mac/main1.mac
 ```
-This will generate ```output/output1.root``` with all hits only.
+This will generate ```output/output1.root``` with hits, singles and coincidences
 
-
-```shell
+Offline digitizer
+```shell 
 GateDigit_hits_digitizer output/output1.root output/output1-singles.root mac/main1_offline_digitizer.mac
 ```
-This will generate ```output/output1-singles.root``` with the singles.
+This will generate ```output/output1-singles.root``` with the singles. There is an error message since there are branches not found since it is designed for CCMod data and those branches are missing here 
+
+Offline sorter
+```shell 
+GateDigit_singles_sorter output/output1-singles.root output/output1-coincCCMod.root mac/main1_offline_sorter.mac abs
+GateDigit_singles_sorter output/output1.root    output/output1-coincCCMod.root  mac/main1_offline_sorter.mac abs
+```
+We can generate the coincidences either from the  singles of simulation stored in   ```output/output1.root``` or from the offline generated singles  ```output/output1-singles.root```
+This will generate ```output/output1-coincCCMod.root``` with the coincidences
+
+Convert CCMod coincidences into PET/SPECT coincidences format  ( On branch anetxe offlineDigitizer, not yet in OpenGate)
+```shell 
+ Convert_CCMod2PETCoinc output/output1-coincCCMod.root output/output1-coinc.root  mac/main1_offline_geom.mac
+ ```
 
+ test with gam_gate. test_main.py
+
+ ## Example 1.b
+
+Simple Cylindrical PET with 20 x 20 block, 5x5 crystal, LSO and BGO layer, 4 rings. 
+- No phantom.
+- Physics list: emstandard_opt4
+- Digitizer: adder, readout (depth 1 or head), threshold, coinc 10 ns
+- Source: back to back 511 keV, half-life of 1223 sec (C11)
 
 ```shell
-GateDigit_singles_sorter output/output1-singles.root output/output1-coinc.root mac/main1_offline_sorter.mac abs
+Gate mac/main1b.mac
 ```
-This will generate ```output/output1-coinc.root``` with the singles.
+This will generate ```output/output1b.root``` with hits, singles and coincidences
 
 
 

t25_offline_digit/test_main1.py

@@ -20,33 +20,38 @@
 is_ok = gam.compare_root3(root_ref, root_offline,
                           "Singles", "Singles",
                           checked_keys, checked_keys,
-                          tols, scalings, scalings,
+                          tols, scalings,
                           'output/main1_root_singles.png')
 print(is_ok)
 
 
 # ------------------------------------------------------
 # not yet possible to compare
 
-'''print()
+print()
 gam.warning('Compare root coinc')
 root_ref = 'output/output1.root'
 root_offline = 'output/output1-coinc.root'
 
-checked_keys = ['time', 'energy',
-                'globalPosX', 'globalPosY', 'globalPosZ']
+checked_keys = ['time1','time2', 'energy1','energy2',
+                'globalPosX1','globalPosX2', 'globalPosY1','globalPosY2', 'globalPosZ1','globalPosZ2']
 scalings = [1] * len(checked_keys)
 tols = [0.01] * len(checked_keys)
-tols[0] = 0.02  # time
-tols[1] = 0.001  # energy
-tols[2] = 0.8  # globalPosX
-tols[3] = 0.4  # globalPosY
-tols[4] = 0.2  # globalPosZ
+tols[0] = 0.02  # time1
+tols[1] = 0.02
+tols[2] = 0.001  # energy1
+tols[3] = 0.001  # energy2
+tols[4] = 0.8  # globalPosX1
+tols[5] = 0.8  # globalPosX2
+tols[6] = 0.8  # globalPosY1
+tols[7] = 0.8  # globalPosY2
+tols[8] = 0.2  # globalPosZ1
+tols[9] = 0.2  # globalPosZ2
 
 print(scalings, tols)
 is_ok = gam.compare_root3(root_ref, root_offline,
                           "Coincidences", "Coincidences",
                           checked_keys, checked_keys,
-                          tols, scalings, scalings,
-                          'output/main1_root_singles.png')
-print(is_ok)'''
+                          tols, scalings,
+                          'output/main1_root_coincidences.png')
+print(is_ok)