From ebe13b9d0add773af437802dd83ead9886412c8b Mon Sep 17 00:00:00 2001
From: kochebina <kochebina@gmail.com>
Date: Thu, 6 Mar 2025 16:13:25 +0100
Subject: [PATCH 1/2] 1st version of test for castor

---
 opengate/tests/src/test0XX_castor.py | 224 +++++++++++++++++++++++++++
 1 file changed, 224 insertions(+)
 create mode 100755 opengate/tests/src/test0XX_castor.py

diff --git a/opengate/tests/src/test0XX_castor.py b/opengate/tests/src/test0XX_castor.py
new file mode 100755
index 000000000..e893539b5
--- /dev/null
+++ b/opengate/tests/src/test0XX_castor.py
@@ -0,0 +1,224 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# config 1 is used for tests of "keepAll", "keepHighestEnergyPair", "removeAll" and "keepCoincidenceIfOnlyOneGood" policies
+
+import opengate as gate
+from pathlib import Path
+import os
+from opengate.tests import utility
+import uproot
+from opengate.actors.coincidences import (
+    coincidences_sorter,
+    #copy_tree_for_dump,
+)
+
+# colors (similar to the ones of Gate)
+red = [1, 0, 0, 1]
+blue = [0, 0, 1, 1]
+green = [0, 1, 0, 1]
+yellow = [0.9, 0.9, 0.3, 1]
+gray = [0.5, 0.5, 0.5, 1]
+white = [1, 1, 1, 0.8]
+
+if __name__ == "__main__":
+    paths = utility.get_default_test_paths(__file__, "gate_test0XX", "test0XX")
+
+    sim = gate.Simulation()
+
+    # options
+    # warning the visualisation is slow !
+    sim.visu = False #True
+    sim.visu_type = "vrml"
+    sim.random_seed = "auto"
+    sim.number_of_threads = 1
+    
+    sim.store_json_archive = True
+    sim.json_archive_filename = paths.output /"simulation_test0XX_castor.json"
+    # units
+    m = gate.g4_units.m
+    mm = gate.g4_units.mm
+    cm = gate.g4_units.cm
+    sec = gate.g4_units.s
+    ps = gate.g4_units.ps
+    keV = gate.g4_units.keV
+    Bq = gate.g4_units.Bq
+    gcm3 = gate.g4_units.g_cm3
+    deg = gate.g4_units.deg
+
+    # folders
+    data_path = paths.data
+    output_path = paths.output
+
+    # world
+    world = sim.world
+    world.size = [200 * mm, 200 * mm, 70 * mm]
+    world.material = "G4_AIR"
+
+    # add the Philips Vereos PET
+    # pet = pet_vereos.add_pet(sim, "pet")
+    # if create_mat:
+    #    create_material(sim)
+
+    # create the material 
+    sim.volume_manager.material_database.add_material_weights(
+        "LYSO",
+        ["Lu", "Y", "Si", "O"],
+        [0.31101534, 0.368765605, 0.083209699, 0.237009356],
+        5.37 * gcm3,
+    )
+
+    # ring volume
+    pet = sim.add_volume("Tubs", "pet")
+    pet.rmax = 95 * mm
+    pet.rmin = 65 * mm
+    pet.dz = 20 * mm 
+    pet.color = gray
+    pet.material = "G4_AIR"
+
+    # block
+    block = sim.add_volume("Box", "block")
+    block.mother = pet.name
+    block.size = [20 * mm, 10 * mm, 40 * mm]
+    translations_ring, rotations_ring = gate.geometry.utility.get_circular_repetition(
+        40, [80 * mm, 0.0 * mm, 0], start_angle_deg=180, axis=[0, 0, 1]
+    )
+    block.translation = translations_ring
+    block.rotation = rotations_ring
+
+    block.material = "G4_AIR"
+    block.color = white
+    
+    # Unit
+    unit = sim.add_volume("Box", "unit")
+    unit.mother = block.name
+    unit.size = [20 * mm, 10 * mm, 10 * mm]
+    unit.material = "G4_AIR"
+    # 2x2 crystals
+    unit.translation = gate.geometry.utility.get_grid_repetition([1, 1, 4], [0 * mm ,0 * mm, 10 * mm]) 
+    unit.color = blue
+
+    
+    #Crystal
+    crystal = sim.add_volume("Box", "crystal")
+    crystal.mother = unit.name
+    crystal.size = [20 * mm, 5 * mm, 5 * mm]
+    crystal.material = "LYSO"
+    # 4rings 
+    crystal.translation = gate.geometry.utility.get_grid_repetition([1, 2, 2], [0 * mm ,5 * mm, 5 * mm]) 
+    crystal.color = red
+    
+
+    source = sim.add_source("GenericSource", "b2b")
+    source.particle = "back_to_back"
+    source.activity =  200000000 * Bq  # 2000000 * Bq
+    source.position.type = "cylinder"
+    source.position.radius = 60 * mm
+    source.position.dz = 40 * mm /2
+    source.position.translation = [0 * cm, 0 * cm, 0 * cm]
+    # source.direction.type = "iso"
+    # source.direction.accolinearity_flag = False
+    source.energy.mono = 511 * keV
+    source.direction.theta = [80 * deg, 110 * deg]
+    source.direction.phi = [0, 360 * deg]
+    #source.color = red
+ 
+    # physics
+    sim.physics_manager.physics_list_name = "G4EmStandardPhysics_option3"
+    # sim.physics_manager.enable_decay = True
+    # sim.physics_manager.set_production_cut("world", "all", 1 * m)
+    # sim.physics_manager.set_production_cut("waterbox", "all", 1 * mm)
+
+    # add the PET digitizer
+
+    # Hits
+    hc = sim.add_actor("DigitizerHitsCollectionActor", f"Hits_{crystal.name}")
+    hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
+    hc.output_filename = output_path / "output_singles.root"
+    # hc.output = "output_config1.root"
+    hc.attributes = [
+        "EventID",
+        "PostPosition",
+        "TotalEnergyDeposit",
+        "PreStepUniqueVolumeID",
+        "GlobalTime",
+    ]
+
+    # Singles
+    sc = sim.add_actor("DigitizerAdderActor", f"Singles_{crystal.name}")
+    sc.attached_to = hc.attached_to
+    sc.authorize_repeated_volumes = True
+    sc.input_digi_collection = hc.name
+    sc.policy = "EnergyWinnerPosition"
+    sc.output_filename = hc.output_filename
+
+    # timing
+    sim.run_timing_intervals = [[0, 0.0002 * sec]]
+    # go
+    sim.run()
+
+
+    # open root file
+    root_filename = sc.output_filename
+    
+    # this test need output/test072/output_singles.root
+    if not os.path.exists(root_filename):
+        # ignore on windows
+        if os.name == "nt":
+            utility.test_ok(True)
+            sys.exit(0)
+        cmd = "python " + str(paths.current / dependency)
+        r = os.system(cmd)
+
+    # open root file
+    print(f"Opening {root_filename} ...")
+    root_file = uproot.open(root_filename)
+
+    # consider the tree of "singles"
+    singles_tree = root_file["Singles_crystal"]
+    n = int(singles_tree.num_entries)
+    print(f"There are {n} singles")
+
+    # time windows
+    ns = gate.g4_units.nanosecond
+    time_window = 3 * ns
+    policy = "takeAllGoods"
+
+    mm = gate.g4_units.mm
+    min_trans_dist = 0 * mm
+    transaxial_plane = "xy"
+    max_trans_dist = 190 * mm
+    # apply coincidences sorter
+    # (chunk size can be much larger, keep a low value to check it is ok)
+    coincidences = coincidences_sorter(
+        singles_tree,
+        time_window,
+        policy,
+        min_trans_dist,
+        transaxial_plane,
+        max_trans_dist,
+        chunk_size=1000000,
+    )
+    nc = len(coincidences["GlobalTime1"])
+    print(f"There are {nc} coincidences for policy", policy)
+
+    # save to file
+    # WARNING root version >= 5.2.2 needed
+    output_file = uproot.recreate(paths.output / f"output_coincidences.root")
+    output_file["coincidences"] = coincidences
+    #output_file["singles"] = copy_tree_for_dump(singles_tree)
+    
+
+    # end
+    """print(f"Output statistics are in {stats.output}")
+    print(f"Output edep map is in {dose.output}")
+    print(f"vv {ct.image} --fusion {dose.output}")
+    stats = sim.output.get_actor("Stats")
+    print(stats)"""
+    
+    is_ok = True #(
+    # test here 
+    #)
+
+    utility.test_ok(is_ok)

From 1a52d5f74e7962f3124de05fd9da30ae9401afa0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:14:50 +0000
Subject: [PATCH 2/2] [pre-commit.ci] Automatic python and c++ formatting

---
 opengate/tests/src/test0XX_castor.py | 50 ++++++++++++++--------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/opengate/tests/src/test0XX_castor.py b/opengate/tests/src/test0XX_castor.py
index e893539b5..8c8d035d0 100755
--- a/opengate/tests/src/test0XX_castor.py
+++ b/opengate/tests/src/test0XX_castor.py
@@ -10,7 +10,7 @@
 import uproot
 from opengate.actors.coincidences import (
     coincidences_sorter,
-    #copy_tree_for_dump,
+    # copy_tree_for_dump,
 )
 
 # colors (similar to the ones of Gate)
@@ -28,13 +28,13 @@
 
     # options
     # warning the visualisation is slow !
-    sim.visu = False #True
+    sim.visu = False  # True
     sim.visu_type = "vrml"
     sim.random_seed = "auto"
     sim.number_of_threads = 1
-    
+
     sim.store_json_archive = True
-    sim.json_archive_filename = paths.output /"simulation_test0XX_castor.json"
+    sim.json_archive_filename = paths.output / "simulation_test0XX_castor.json"
     # units
     m = gate.g4_units.m
     mm = gate.g4_units.mm
@@ -60,7 +60,7 @@
     # if create_mat:
     #    create_material(sim)
 
-    # create the material 
+    # create the material
     sim.volume_manager.material_database.add_material_weights(
         "LYSO",
         ["Lu", "Y", "Si", "O"],
@@ -72,7 +72,7 @@
     pet = sim.add_volume("Tubs", "pet")
     pet.rmax = 95 * mm
     pet.rmin = 65 * mm
-    pet.dz = 20 * mm 
+    pet.dz = 20 * mm
     pet.color = gray
     pet.material = "G4_AIR"
 
@@ -88,41 +88,43 @@
 
     block.material = "G4_AIR"
     block.color = white
-    
+
     # Unit
     unit = sim.add_volume("Box", "unit")
     unit.mother = block.name
     unit.size = [20 * mm, 10 * mm, 10 * mm]
     unit.material = "G4_AIR"
     # 2x2 crystals
-    unit.translation = gate.geometry.utility.get_grid_repetition([1, 1, 4], [0 * mm ,0 * mm, 10 * mm]) 
+    unit.translation = gate.geometry.utility.get_grid_repetition(
+        [1, 1, 4], [0 * mm, 0 * mm, 10 * mm]
+    )
     unit.color = blue
 
-    
-    #Crystal
+    # Crystal
     crystal = sim.add_volume("Box", "crystal")
     crystal.mother = unit.name
     crystal.size = [20 * mm, 5 * mm, 5 * mm]
     crystal.material = "LYSO"
-    # 4rings 
-    crystal.translation = gate.geometry.utility.get_grid_repetition([1, 2, 2], [0 * mm ,5 * mm, 5 * mm]) 
+    # 4rings
+    crystal.translation = gate.geometry.utility.get_grid_repetition(
+        [1, 2, 2], [0 * mm, 5 * mm, 5 * mm]
+    )
     crystal.color = red
-    
 
     source = sim.add_source("GenericSource", "b2b")
     source.particle = "back_to_back"
-    source.activity =  200000000 * Bq  # 2000000 * Bq
+    source.activity = 200000000 * Bq  # 2000000 * Bq
     source.position.type = "cylinder"
     source.position.radius = 60 * mm
-    source.position.dz = 40 * mm /2
+    source.position.dz = 40 * mm / 2
     source.position.translation = [0 * cm, 0 * cm, 0 * cm]
     # source.direction.type = "iso"
     # source.direction.accolinearity_flag = False
     source.energy.mono = 511 * keV
     source.direction.theta = [80 * deg, 110 * deg]
     source.direction.phi = [0, 360 * deg]
-    #source.color = red
- 
+    # source.color = red
+
     # physics
     sim.physics_manager.physics_list_name = "G4EmStandardPhysics_option3"
     # sim.physics_manager.enable_decay = True
@@ -158,10 +160,9 @@
     # go
     sim.run()
 
-
     # open root file
     root_filename = sc.output_filename
-    
+
     # this test need output/test072/output_singles.root
     if not os.path.exists(root_filename):
         # ignore on windows
@@ -207,8 +208,7 @@
     # WARNING root version >= 5.2.2 needed
     output_file = uproot.recreate(paths.output / f"output_coincidences.root")
     output_file["coincidences"] = coincidences
-    #output_file["singles"] = copy_tree_for_dump(singles_tree)
-    
+    # output_file["singles"] = copy_tree_for_dump(singles_tree)
 
     # end
     """print(f"Output statistics are in {stats.output}")
@@ -216,9 +216,9 @@
     print(f"vv {ct.image} --fusion {dose.output}")
     stats = sim.output.get_actor("Stats")
     print(stats)"""
-    
-    is_ok = True #(
-    # test here 
-    #)
+
+    is_ok = True  # (
+    # test here
+    # )
 
     utility.test_ok(is_ok)