From 472315217d7e43cc3c0d13bb781e03e4b8f830b3 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 13 Jun 2024 07:23:35 +0200
Subject: [PATCH 01/14] generic source dir relative to volume for iso + angle

---
 core/CMakeLists.txt                           |  2 +-
 .../opengate_lib/GateGenericSource.cpp        | 16 ++++++----
 .../opengate_lib/GateSPSAngDistribution.cpp   | 19 ++++++++++++
 .../opengate_lib/GateSPSAngDistribution.h     | 30 +++++++++++++++++++
 .../opengate_lib/GateSingleParticleSource.cpp |  6 ++--
 .../opengate_lib/GateSingleParticleSource.h   |  9 +++---
 opengate/tests/src/test067_stl_volume.py      |  0
 7 files changed, 68 insertions(+), 14 deletions(-)
 create mode 100644 core/opengate_core/opengate_lib/GateSPSAngDistribution.cpp
 create mode 100644 core/opengate_core/opengate_lib/GateSPSAngDistribution.h
 mode change 100644 => 100755 opengate/tests/src/test067_stl_volume.py

diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
index 9625df51e..bd30553d6 100644
--- a/core/CMakeLists.txt
+++ b/core/CMakeLists.txt
@@ -24,7 +24,7 @@ if (Geant4_multithreaded_FOUND)
 ENDIF ()
 find_package(Threads REQUIRED)
 
-#GDML
+# GDML
 IF (Geant4_gdml_FOUND)
     message(STATUS "OPENGATE - Geant4 is compiled with GDML")
     add_definitions(-DUSE_GDML=1)
diff --git a/core/opengate_core/opengate_lib/GateGenericSource.cpp b/core/opengate_core/opengate_lib/GateGenericSource.cpp
index 3491c00ff..230db67c9 100644
--- a/core/opengate_core/opengate_lib/GateGenericSource.cpp
+++ b/core/opengate_core/opengate_lib/GateGenericSource.cpp
@@ -30,6 +30,8 @@ GateGenericSource::GateGenericSource() : GateVSource() {
   fEffectiveEventTime = -1;
   fEffectiveEventTime = -1;
   fDirectionRelativeToAttachedVolume = false;
+  fUserParticleLifeTime = -1;
+  fBackToBackMode = false;
 }
 
 GateGenericSource::~GateGenericSource() {
@@ -90,7 +92,6 @@ void GateGenericSource::InitializeUserInfo(py::dict &user_info) {
   fCurrentSkippedEvents = 0;
   fTotalSkippedEvents = 0;
   fEffectiveEventTime = -1;
-
   fDirectionRelativeToAttachedVolume =
       DictGetBool(user_info, "direction_relative_to_attached_volume");
 }
@@ -162,14 +163,13 @@ double GateGenericSource::PrepareNextTime(double current_simulation_time) {
 }
 
 void GateGenericSource::PrepareNextRun() {
-  // The following compute the global transformation from
+  // The following function computes the global transformation from
   // the local volume (mother) to the world
   GateVSource::PrepareNextRun();
+
   // This global transformation is given to the SPS that will
   // generate particles in the correct coordinate system
   auto &l = fThreadLocalData.Get();
-  // auto user_info_pos = py::dict(puser_info["position"]);
-  // auto pos_init = DictGetG4ThreeVector(user_info_pos, "translation");
   auto *pos = fSPS->GetPosDist();
   pos->SetCentreCoords(l.fGlobalTranslation);
 
@@ -180,17 +180,23 @@ void GateGenericSource::PrepareNextRun() {
   pos->SetPosRot1(r1);
   pos->SetPosRot2(r2);
 
+  // For the direction, the orientation may or may not be
+  // relative to the volume according to user option
   auto *ang = fSPS->GetAngDist();
-
+  ang->fDirectionRelativeToAttachedVolume = fDirectionRelativeToAttachedVolume;
+  ang->fGlobalRotation = l.fGlobalRotation;
+  ang->fGlobalTranslation = l.fGlobalTranslation;
   if (fangType == "momentum" && fDirectionRelativeToAttachedVolume) {
     auto new_d = rotation * fInitializeMomentum;
     ang->SetParticleMomentumDirection(new_d);
+    ang->fDirectionRelativeToAttachedVolume = false;
   }
   if (fangType == "focused" && fDirectionRelativeToAttachedVolume) {
     auto vec_f = fInitiliazeFocusPoint - fInitTranslation;
     auto rot_f = rotation * vec_f;
     auto new_f = rot_f + l.fGlobalTranslation;
     ang->SetFocusPoint(new_f);
+    ang->fDirectionRelativeToAttachedVolume = false;
   }
 }
 
diff --git a/core/opengate_core/opengate_lib/GateSPSAngDistribution.cpp b/core/opengate_core/opengate_lib/GateSPSAngDistribution.cpp
new file mode 100644
index 000000000..fb12b1307
--- /dev/null
+++ b/core/opengate_core/opengate_lib/GateSPSAngDistribution.cpp
@@ -0,0 +1,19 @@
+/* --------------------------------------------------
+   Copyright (C): OpenGate Collaboration
+   This software is distributed under the terms
+   of the GNU Lesser General  Public Licence (LGPL)
+   See LICENSE.md for further details
+   -------------------------------------------------- */
+
+#include "GateSPSAngDistribution.h"
+#include "GateHelpers.h"
+
+G4ThreeVector GateSPSAngDistribution::VGenerateOne() {
+  // return GenerateOne();
+  auto direction = GenerateOne();
+  if (fDirectionRelativeToAttachedVolume) {
+    direction = direction / direction.mag();
+    direction = fGlobalRotation * direction;
+  }
+  return direction;
+}
diff --git a/core/opengate_core/opengate_lib/GateSPSAngDistribution.h b/core/opengate_core/opengate_lib/GateSPSAngDistribution.h
new file mode 100644
index 000000000..9bdde37f5
--- /dev/null
+++ b/core/opengate_core/opengate_lib/GateSPSAngDistribution.h
@@ -0,0 +1,30 @@
+/* --------------------------------------------------
+   Copyright (C): OpenGATE Collaboration
+   This software is distributed under the terms
+   of the GNU Lesser General  Public Licence (LGPL)
+   See LICENSE.md for further details
+   -------------------------------------------------- */
+
+#ifndef GateSPSAngDistribution_h
+#define GateSPSAngDistribution_h
+
+#include "G4ParticleDefinition.hh"
+#include "G4SPSAngDistribution.hh"
+
+class GateSPSAngDistribution : public G4SPSAngDistribution {
+
+public:
+  virtual ~GateSPSAngDistribution() = default;
+
+  // Cannot inherit from GenerateOne, so we consider VGenerateOne instead
+  virtual G4ThreeVector VGenerateOne();
+
+  // Store the global orientation that may be applied to the direction
+  // in the GenerateOne function.
+  // (Must be updated each run)
+  bool fDirectionRelativeToAttachedVolume;
+  G4ThreeVector fGlobalTranslation;
+  G4RotationMatrix fGlobalRotation;
+};
+
+#endif // GateSPSAngDistribution_h
diff --git a/core/opengate_core/opengate_lib/GateSingleParticleSource.cpp b/core/opengate_core/opengate_lib/GateSingleParticleSource.cpp
index 2473bbfab..cf3fdd577 100644
--- a/core/opengate_core/opengate_lib/GateSingleParticleSource.cpp
+++ b/core/opengate_core/opengate_lib/GateSingleParticleSource.cpp
@@ -10,13 +10,12 @@
 #include "G4PrimaryVertex.hh"
 #include "G4RunManager.hh"
 #include "GateHelpers.h"
-
 #include "GateRandomMultiGauss.h"
 
 GateSingleParticleSource::GateSingleParticleSource(
     std::string /*mother_volume*/) {
   fPositionGenerator = new GateSPSPosDistribution();
-  fDirectionGenerator = new G4SPSAngDistribution();
+  fDirectionGenerator = new GateSPSAngDistribution();
   fEnergyGenerator = new GateSPSEneDistribution();
 
   // needed
@@ -64,7 +63,8 @@ GateSingleParticleSource::GenerateDirectionWithAA(const G4ThreeVector &position,
   fAAManager->StartAcceptLoop();
   while (!accept_angle) {
     // direction
-    direction = fDirectionGenerator->GenerateOne();
+    direction = fDirectionGenerator->VGenerateOne();
+
     // accept ?
     accept_angle = fAAManager->TestIfAccept(position, direction);
     if (!accept_angle && fAAManager->GetPolicy() ==
diff --git a/core/opengate_core/opengate_lib/GateSingleParticleSource.h b/core/opengate_core/opengate_lib/GateSingleParticleSource.h
index ad75d6863..a68f29ccd 100644
--- a/core/opengate_core/opengate_lib/GateSingleParticleSource.h
+++ b/core/opengate_core/opengate_lib/GateSingleParticleSource.h
@@ -10,16 +10,15 @@
 
 #include "G4AffineTransform.hh"
 #include "G4ParticleDefinition.hh"
-#include "G4SPSAngDistribution.hh"
 #include "G4VPrimaryGenerator.hh"
 #include "GateAcceptanceAngleTester.h"
 #include "GateAcceptanceAngleTesterManager.h"
 #include "GateHelpers.h"
+#include "GateRandomMultiGauss.h"
+#include "GateSPSAngDistribution.h"
 #include "GateSPSEneDistribution.h"
 #include "GateSPSPosDistribution.h"
 
-#include "GateRandomMultiGauss.h"
-
 /*
     Single Particle Source generator.
     We need to re-implement the one from G4 in order to
@@ -37,7 +36,7 @@ class GateSingleParticleSource : public G4VPrimaryGenerator {
 
   GateSPSPosDistribution *GetPosDist() { return fPositionGenerator; }
 
-  G4SPSAngDistribution *GetAngDist() { return fDirectionGenerator; }
+  GateSPSAngDistribution *GetAngDist() { return fDirectionGenerator; }
 
   GateSPSEneDistribution *GetEneDist() { return fEnergyGenerator; }
 
@@ -62,7 +61,7 @@ class GateSingleParticleSource : public G4VPrimaryGenerator {
   double fCharge;
   double fMass;
   GateSPSPosDistribution *fPositionGenerator;
-  G4SPSAngDistribution *fDirectionGenerator;
+  GateSPSAngDistribution *fDirectionGenerator;
   GateSPSEneDistribution *fEnergyGenerator;
   G4SPSRandomGenerator *fBiasRndm;
   bool fAccolinearityFlag;
diff --git a/opengate/tests/src/test067_stl_volume.py b/opengate/tests/src/test067_stl_volume.py
old mode 100644
new mode 100755

From 529db79b27b3187e4e7e6b6347ac8389ab99c406 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 13 Jun 2024 07:33:00 +0200
Subject: [PATCH 02/14] starting test

---
 .../src/test075_generic_source_rotation.py    | 74 +++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100755 opengate/tests/src/test075_generic_source_rotation.py

diff --git a/opengate/tests/src/test075_generic_source_rotation.py b/opengate/tests/src/test075_generic_source_rotation.py
new file mode 100755
index 000000000..064e0e896
--- /dev/null
+++ b/opengate/tests/src/test075_generic_source_rotation.py
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import opengate as gate
+from opengate.tests import utility
+from scipy.spatial.transform import Rotation
+
+if __name__ == "__main__":
+    # paths = utility.get_default_test_paths(__file__, "gate_test010_generic_source")
+
+    # create the simulation
+    sim = gate.Simulation()
+
+    # main options
+    sim.g4_verbose = False
+    sim.g4_verbose_level = 1
+    sim.visu = True
+    sim.visu_type = "vrml"
+    sim.number_of_threads = 1
+
+    # useful units
+    MeV = gate.g4_units.MeV
+    keV = gate.g4_units.keV
+    Bq = gate.g4_units.Bq
+    deg = gate.g4_units.deg
+    mm = gate.g4_units.mm
+    m = gate.g4_units.m
+    cm = gate.g4_units.cm
+
+    # set the world size like in the Gate macro
+    world = sim.world
+    world.size = [2 * m, 2 * m, 2 * m]
+
+    # add a simple volume
+    waterbox = sim.add_volume("Box", "waterbox")
+    waterbox.size = [40 * cm, 40 * cm, 40 * cm]
+    waterbox.translation = [0 * cm, 0 * cm, 0 * cm]
+    waterbox.material = "G4_AIR"
+
+    # source box
+    b = sim.add_volume("Box", "sourcebox")
+    b.size = [5 * cm, 5 * cm, 5 * cm]
+    b.translation = [0 * cm, 50 * cm, 0 * cm]
+    r = Rotation.from_euler("y", -25, degrees=True)
+    r = r * Rotation.from_euler("x", -35, degrees=True)
+    b.rotation = r.as_matrix()
+
+    # source
+    source = sim.add_source("GenericSource", "source1")
+    source.mother = "sourcebox"
+    source.particle = "gamma"
+    source.n = 50
+    source.position.type = "disc"
+    source.position.radius = 0 * mm
+    source.direction_relative_to_volume = True
+    source.direction.type = "iso"
+    source.direction.focus_point = [1 * cm, 2 * cm, 3 * cm]
+    source.direction.theta = [0 * deg, 10 * deg]
+    source.direction.phi = [0 * deg, 360 * deg]
+
+    source.energy.type = "mono"
+    source.energy.mono = 100 * MeV
+
+    # actors
+    stats_actor = sim.add_actor("SimulationStatisticsActor", "Stats")
+
+    # start simulation
+    sim.run()
+
+    # get results
+    stats = sim.output.get_actor("Stats")
+    print(stats)
+
+    utility.test_ok(False)

From fe67ccdac17d16a6c9b68cdcfa05ff8b494d48de Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Fri, 14 Jun 2024 09:37:40 +0200
Subject: [PATCH 03/14] update test068, no need for test075

---
 opengate/tests/src/test068_rotation_source.py | 21 +++++-
 .../src/test075_generic_source_rotation.py    | 74 -------------------
 2 files changed, 18 insertions(+), 77 deletions(-)
 delete mode 100755 opengate/tests/src/test075_generic_source_rotation.py

diff --git a/opengate/tests/src/test068_rotation_source.py b/opengate/tests/src/test068_rotation_source.py
index c1c214cc9..96d9d40b7 100755
--- a/opengate/tests/src/test068_rotation_source.py
+++ b/opengate/tests/src/test068_rotation_source.py
@@ -8,7 +8,7 @@
 import uproot
 
 
-# The test generates two different generic sources, momentum and focused, which is attached to a plan.
+# The test generates three differents generic sources, momentum, focused and iso, which are attached to a plan.
 # The plan is randomly rotated and we verify that the generated particles have a direction which is in accordance
 # with the applied rotations and the transmissions.
 
@@ -50,6 +50,7 @@ def test068(tab, nb_run, nb_part, nb_source):
     keV = gate.g4_units.keV
     sec = gate.g4_units.s
     gcm3 = gate.g4_units["g/cm3"]
+    deg = gate.g4_units.deg
 
     #  adapt world size
     world = sim.world
@@ -60,7 +61,7 @@ def test068(tab, nb_run, nb_part, nb_source):
     n = 100
 
     # Plan to attach the source
-    nb_source = 2
+    nb_source = 3
     plan = sim.add_volume("Box", "source_plan")
     plan.mother = world.name
     plan.material = "G4_Galactic"
@@ -93,6 +94,20 @@ def test068(tab, nb_run, nb_part, nb_source):
     source2.energy.mono = 1 * MeV
     source2.activity = n * Bq / sim.number_of_threads
 
+    source3 = sim.add_source("GenericSource", "photon_source_3")
+    source3.particle = "gamma"
+    source3.position.type = "disc"
+    source3.position.radius = 0 * mm
+    source3.mother = plan.name
+    source3.position.size = [10 * cm, 10 * cm, 1 * nm]
+    source3.direction.type = "iso"
+    source3.direction.theta = [0 * deg, 10 * deg]
+    source3.direction.phi = [0 * deg, 360 * deg]
+    source3.direction_relative_to_volume = True
+    source3.energy.type = "mono"
+    source3.energy.mono = 1 * MeV
+    source3.activity = n * Bq / sim.number_of_threads
+
     # Phase Space
 
     phsp_plan = sim.add_volume("Box", "phsp_plan")
@@ -171,5 +186,5 @@ def test068(tab, nb_run, nb_part, nb_source):
         + str(int(+3 * err + nb_run * nb_part * nb_source))
         + "]"
     )
-    is_ok = test068(arr, len(sim.run_timing_intervals), nb_part, 2)
+    is_ok = test068(arr, len(sim.run_timing_intervals), nb_part, nb_source)
     utility.test_ok(is_ok)
diff --git a/opengate/tests/src/test075_generic_source_rotation.py b/opengate/tests/src/test075_generic_source_rotation.py
deleted file mode 100755
index 064e0e896..000000000
--- a/opengate/tests/src/test075_generic_source_rotation.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import opengate as gate
-from opengate.tests import utility
-from scipy.spatial.transform import Rotation
-
-if __name__ == "__main__":
-    # paths = utility.get_default_test_paths(__file__, "gate_test010_generic_source")
-
-    # create the simulation
-    sim = gate.Simulation()
-
-    # main options
-    sim.g4_verbose = False
-    sim.g4_verbose_level = 1
-    sim.visu = True
-    sim.visu_type = "vrml"
-    sim.number_of_threads = 1
-
-    # useful units
-    MeV = gate.g4_units.MeV
-    keV = gate.g4_units.keV
-    Bq = gate.g4_units.Bq
-    deg = gate.g4_units.deg
-    mm = gate.g4_units.mm
-    m = gate.g4_units.m
-    cm = gate.g4_units.cm
-
-    # set the world size like in the Gate macro
-    world = sim.world
-    world.size = [2 * m, 2 * m, 2 * m]
-
-    # add a simple volume
-    waterbox = sim.add_volume("Box", "waterbox")
-    waterbox.size = [40 * cm, 40 * cm, 40 * cm]
-    waterbox.translation = [0 * cm, 0 * cm, 0 * cm]
-    waterbox.material = "G4_AIR"
-
-    # source box
-    b = sim.add_volume("Box", "sourcebox")
-    b.size = [5 * cm, 5 * cm, 5 * cm]
-    b.translation = [0 * cm, 50 * cm, 0 * cm]
-    r = Rotation.from_euler("y", -25, degrees=True)
-    r = r * Rotation.from_euler("x", -35, degrees=True)
-    b.rotation = r.as_matrix()
-
-    # source
-    source = sim.add_source("GenericSource", "source1")
-    source.mother = "sourcebox"
-    source.particle = "gamma"
-    source.n = 50
-    source.position.type = "disc"
-    source.position.radius = 0 * mm
-    source.direction_relative_to_volume = True
-    source.direction.type = "iso"
-    source.direction.focus_point = [1 * cm, 2 * cm, 3 * cm]
-    source.direction.theta = [0 * deg, 10 * deg]
-    source.direction.phi = [0 * deg, 360 * deg]
-
-    source.energy.type = "mono"
-    source.energy.mono = 100 * MeV
-
-    # actors
-    stats_actor = sim.add_actor("SimulationStatisticsActor", "Stats")
-
-    # start simulation
-    sim.run()
-
-    # get results
-    stats = sim.output.get_actor("Stats")
-    print(stats)
-
-    utility.test_ok(False)

From 370e67b631c3ab53594f1d82ae1ea5bf847ac309 Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Wed, 26 Jun 2024 13:48:52 +0200
Subject: [PATCH 04/14] Add simulation of a c-arm : siemens cios alpha

---
 opengate/contrib/carm/siemensciosalpha.py     | 160 ++++++++++++++++++
 .../tests/src/test075_siemens_cios_alpha.py   |  65 +++++++
 2 files changed, 225 insertions(+)
 create mode 100644 opengate/contrib/carm/siemensciosalpha.py
 create mode 100644 opengate/tests/src/test075_siemens_cios_alpha.py

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
new file mode 100644
index 000000000..b3fc22ec2
--- /dev/null
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -0,0 +1,160 @@
+import opengate as gate
+from opengate.utility import g4_units, get_contrib_path
+from scipy.spatial.transform import Rotation
+import numpy as np
+import spekpy as sp
+
+def add_carm(sim, machine_name):
+    # carm
+    carm = add_carm_box(sim, machine_name)
+    add_xray_tank(sim, machine_name)
+    add_collimators(sim, machine_name)
+
+    return carm
+
+def add_carm_box(sim, machine_name):
+    carmbox = sim.volume_manager.create_volume("Box", "carmbox")
+    carmbox.material = "G4_AIR"
+    carmbox.size = [200 * cm,  30* cm, 200 * cm]
+    carmbox.translation = [0 * cm,  0* cm, 0 * cm]
+    carmbox.color = [1, 1, 1, 0.8]
+
+    # create a t_shape to subtract from carmbox
+    hole1 = sim.volume_manager.create_volume("Box", "hole")
+    hole1.size = [191 * cm,  31* cm, 160 * cm]
+    hole1.color = [1, 1, 1, 0.8]
+    hole2 = sim.volume_manager.create_volume("Box", "hole2")
+    hole2.size = [80 * cm,  31* cm, 31 * cm]
+    hole2.color = [1, 1, 1, 0.8]
+    hole3 = sim.volume_manager.create_volume("Box", "hole3")
+    hole3.size = [80 * cm,  31* cm, 31 * cm]
+    hole3.color = [1, 1, 1, 0.8]
+
+    # unite hole 1 and 2
+    hole1and2= gate.geometry.volumes.unite_volumes(
+        hole1, hole2, translation = [-55.5 * cm, 0 * cm, 95 * cm]
+    )
+
+    # t_shape
+    t_shape= gate.geometry.volumes.unite_volumes(
+        hole1and2, hole3, translation = [-55.5 * cm, 0 * cm, -95 * cm]
+    )
+    #sim.add_volume(t_shape)
+
+    # create c-arm
+    carm = gate.geometry.volumes.subtract_volumes(
+        carmbox, t_shape, new_name = machine_name, translation = [-5 * cm, 0 * cm, -10 * cm]
+    )
+    sim.add_volume(carm)
+
+    return carm
+
+def add_xray_tank(sim, machine_name):
+    xray_tank = sim.add_volume("Box", f"{machine_name}_xray_tank")
+    xray_tank.mother = machine_name
+    xray_tank.material = "G4_AIR"
+    xray_tank.size = [40 * cm, 20 * cm, 30 * cm]
+    xray_tank.translation = [0 * cm, 0, 85 * cm]
+    xray_tank.color = [1, 1, 1, 0.8]
+
+def add_carm_source(sim, machine_name, kvp):
+    # Generate spectrum
+    s = sp.Spek(kvp, th=10, physics= 'kqp')
+    s.filter('Al', 3.0).filter('Cu', 0.1)
+
+    # Get the spectrum
+    energy_bins, weights = s.get_spectrum()
+
+    # source box
+    b = sim.add_volume("Box", f"{machine_name}_sourcebox")
+    b.mother = f"{machine_name}_xray_tank"
+    b.translation = [0* cm,0 * cm, 10 * cm]
+    b.size = [1 * cm, 1 * cm, 1 * cm]
+
+    # source
+    source = sim.add_source("GenericSource", f"{machine_name}_source")
+    source.mother = f"{machine_name}_sourcebox"
+    source.particle = "gamma"
+    source.position.type = "disc"
+    source.position.radius = 0 * mm
+
+    source.direction_relative_to_volume = True
+    source.direction.type = "iso"
+    source.direction.theta = [0 * deg, 10 * deg]
+    source.direction.phi = [0 * deg, 360 * deg]
+
+    source.energy.type = "histogram"
+    source.energy.histogram_weight = weights
+    source.energy.histogram_energy = energy_bins
+
+    return source
+
+def add_collimators(sim, machine_name):
+    xray_tank = sim.volume_manager.get_volume(f"{machine_name}_xray_tank")
+    z_xray_tank = xray_tank.size[2]
+
+    collimator1 = sim.add_volume("Box", f"{machine_name}_collimator1")
+    collimator1.mother = f"{machine_name}_xray_tank"
+    collimator1.color = red
+    collimator1.translation = [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+    collimator1.size = [5* cm, 10 * cm, 1 * mm]
+
+    collimator2 = sim.add_volume("Box", f"{machine_name}_collimator2")
+    collimator2.mother = f"{machine_name}_xray_tank"
+    collimator2.color = red
+    collimator2.translation = [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+    collimator2.size = [5* cm, 10 * cm, 1 * mm]
+
+    collimator3 = sim.add_volume("Box", f"{machine_name}_collimator3")
+    collimator3.mother = f"{machine_name}_xray_tank"
+    collimator3.color = red
+    collimator3.translation = [0* cm, 75 * mm , -z_xray_tank / 2 * mm + 3 * mm]
+    collimator3.size = [10* cm, 5 * cm, 1 * mm]
+
+    collimator4 = sim.add_volume("Box", f"{machine_name}_collimator4")
+    collimator4.mother = f"{machine_name}_xray_tank"
+    collimator4.color = red
+    collimator4.translation = [0* cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
+    collimator4.size = [10* cm, 5 * cm, 1 * mm]
+
+    # psycho killer
+    killer = sim.add_actor("KillActor", f"target_kill")
+    killer.mother = [collimator1.name, collimator2.name,collimator3.name,collimator4.name]
+
+
+def update_collimation(sim, machine_name, num, num2):
+    if not 0 <= num <= 50 or not 0 <= num2 <= 50:
+        raise ValueError("Wrong values for collimation")
+
+    num = 50 - num
+    num2 = 50 - num2
+
+    xray_tank = sim.volume_manager.get_volume(f"{machine_name}_xray_tank")
+    z_xray_tank = xray_tank.size[2]
+
+    collimator1 = sim.volume_manager.get_volume(f"{machine_name}_collimator1")
+    collimator1.translation = [75 * mm - num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+
+    collimator2 = sim.volume_manager.get_volume(f"{machine_name}_collimator2")
+    collimator2.translation = [-75 * mm + num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+
+    collimator3 = sim.volume_manager.get_volume(f"{machine_name}_collimator3")
+    collimator3.translation = [0 * cm, 75 * mm - num2, -z_xray_tank / 2 * mm + 3 * mm]
+
+    collimator4 = sim.volume_manager.get_volume(f"{machine_name}_collimator4")
+    collimator4.translation = [0 * cm, -75 * mm + num2, -z_xray_tank / 2 * mm + 3 * mm]
+
+# useful units
+MeV = gate.g4_units.MeV
+keV = gate.g4_units.keV
+Bq = gate.g4_units.Bq
+deg = gate.g4_units.deg
+nm = gate.g4_units.nm
+mm = gate.g4_units.mm
+m = gate.g4_units.m
+cm = gate.g4_units.cm
+
+# colors
+red = [1, 0.7, 0.7, 0.8]
+blue = [0.5, 0.5, 1, 0.8]
+green = [0, 1, 0, 1]
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
new file mode 100644
index 000000000..7a943411e
--- /dev/null
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import opengate as gate
+import opengate.contrib.carm.siemensciosalpha as ciosalpha
+from opengate.tests import utility
+from scipy.spatial.transform import Rotation
+import numpy as np
+import uproot
+import matplotlib.pyplot as plt
+
+if __name__ == "__main__":
+    # paths
+    paths = utility.get_default_test_paths(__file__, output_folder="test075_siemens_cios_alpha")
+
+    # create the simulation
+    sim = gate.Simulation()
+
+    # main options
+    sim.g4_verbose = False
+    sim.visu = True
+    sim.visu_type = "vrml"
+    sim.check_volumes_overlap = False
+    sim.number_of_threads = 1
+    sim.random_seed = 12345678
+    sim.check_volumes_overlap = True
+
+    # units
+    m = gate.g4_units.m
+    cm = gate.g4_units.cm
+    mm = gate.g4_units.mm
+    deg = gate.g4_units.deg
+
+    # world
+    world = sim.world
+    world.size = [5* m, 5 * m, 5 * m]
+    world.material = "G4_AIR"
+
+    # add a carm
+    carm = ciosalpha.add_carm(sim, "cios_alpha")
+    carm.rotation = Rotation.from_euler("ZYX", [0,20,180], degrees=True).as_matrix()
+
+    # xray tube spectrum parameters
+    # tube potential [kV]
+    kvp = 100
+
+    # add carm source
+    source = ciosalpha.add_carm_source(sim, carm.name, kvp)
+    source.n = 1e6
+    if sim.visu:
+        source.n = 1
+
+    # opening of the collimators [0, 50 *mm]
+    ciosalpha.update_collimation(sim, carm.name, 20 * mm, 20 * mm)
+
+    # aluminum table
+    table = sim.add_volume("Box", "aluminum_table")
+    table.size = [60 * cm, 2 * m, 0.9 * mm ]
+    table.material = "G4_Al"
+    table.translation = [0 * m, 0 * cm, 0 * cm]
+    table.color = [0.8, 0.8, 0.8, 1]
+
+    # start simulation
+    sim.run()
+

From 47950fcc3c169616657a35dc335ace1ab6e947d1 Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Thu, 27 Jun 2024 14:15:14 +0200
Subject: [PATCH 05/14] create Ciosalpha class

---
 opengate/contrib/carm/siemensciosalpha.py     | 296 +++++++++---------
 .../tests/src/test075_siemens_cios_alpha.py   |  23 +-
 2 files changed, 166 insertions(+), 153 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index b3fc22ec2..dda021f89 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -4,145 +4,161 @@
 import numpy as np
 import spekpy as sp
 
-def add_carm(sim, machine_name):
-    # carm
-    carm = add_carm_box(sim, machine_name)
-    add_xray_tank(sim, machine_name)
-    add_collimators(sim, machine_name)
-
-    return carm
-
-def add_carm_box(sim, machine_name):
-    carmbox = sim.volume_manager.create_volume("Box", "carmbox")
-    carmbox.material = "G4_AIR"
-    carmbox.size = [200 * cm,  30* cm, 200 * cm]
-    carmbox.translation = [0 * cm,  0* cm, 0 * cm]
-    carmbox.color = [1, 1, 1, 0.8]
-
-    # create a t_shape to subtract from carmbox
-    hole1 = sim.volume_manager.create_volume("Box", "hole")
-    hole1.size = [191 * cm,  31* cm, 160 * cm]
-    hole1.color = [1, 1, 1, 0.8]
-    hole2 = sim.volume_manager.create_volume("Box", "hole2")
-    hole2.size = [80 * cm,  31* cm, 31 * cm]
-    hole2.color = [1, 1, 1, 0.8]
-    hole3 = sim.volume_manager.create_volume("Box", "hole3")
-    hole3.size = [80 * cm,  31* cm, 31 * cm]
-    hole3.color = [1, 1, 1, 0.8]
-
-    # unite hole 1 and 2
-    hole1and2= gate.geometry.volumes.unite_volumes(
-        hole1, hole2, translation = [-55.5 * cm, 0 * cm, 95 * cm]
-    )
-
-    # t_shape
-    t_shape= gate.geometry.volumes.unite_volumes(
-        hole1and2, hole3, translation = [-55.5 * cm, 0 * cm, -95 * cm]
-    )
-    #sim.add_volume(t_shape)
-
-    # create c-arm
-    carm = gate.geometry.volumes.subtract_volumes(
-        carmbox, t_shape, new_name = machine_name, translation = [-5 * cm, 0 * cm, -10 * cm]
-    )
-    sim.add_volume(carm)
-
-    return carm
-
-def add_xray_tank(sim, machine_name):
-    xray_tank = sim.add_volume("Box", f"{machine_name}_xray_tank")
-    xray_tank.mother = machine_name
-    xray_tank.material = "G4_AIR"
-    xray_tank.size = [40 * cm, 20 * cm, 30 * cm]
-    xray_tank.translation = [0 * cm, 0, 85 * cm]
-    xray_tank.color = [1, 1, 1, 0.8]
-
-def add_carm_source(sim, machine_name, kvp):
-    # Generate spectrum
-    s = sp.Spek(kvp, th=10, physics= 'kqp')
-    s.filter('Al', 3.0).filter('Cu', 0.1)
-
-    # Get the spectrum
-    energy_bins, weights = s.get_spectrum()
-
-    # source box
-    b = sim.add_volume("Box", f"{machine_name}_sourcebox")
-    b.mother = f"{machine_name}_xray_tank"
-    b.translation = [0* cm,0 * cm, 10 * cm]
-    b.size = [1 * cm, 1 * cm, 1 * cm]
-
-    # source
-    source = sim.add_source("GenericSource", f"{machine_name}_source")
-    source.mother = f"{machine_name}_sourcebox"
-    source.particle = "gamma"
-    source.position.type = "disc"
-    source.position.radius = 0 * mm
-
-    source.direction_relative_to_volume = True
-    source.direction.type = "iso"
-    source.direction.theta = [0 * deg, 10 * deg]
-    source.direction.phi = [0 * deg, 360 * deg]
-
-    source.energy.type = "histogram"
-    source.energy.histogram_weight = weights
-    source.energy.histogram_energy = energy_bins
-
-    return source
-
-def add_collimators(sim, machine_name):
-    xray_tank = sim.volume_manager.get_volume(f"{machine_name}_xray_tank")
-    z_xray_tank = xray_tank.size[2]
-
-    collimator1 = sim.add_volume("Box", f"{machine_name}_collimator1")
-    collimator1.mother = f"{machine_name}_xray_tank"
-    collimator1.color = red
-    collimator1.translation = [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-    collimator1.size = [5* cm, 10 * cm, 1 * mm]
-
-    collimator2 = sim.add_volume("Box", f"{machine_name}_collimator2")
-    collimator2.mother = f"{machine_name}_xray_tank"
-    collimator2.color = red
-    collimator2.translation = [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-    collimator2.size = [5* cm, 10 * cm, 1 * mm]
-
-    collimator3 = sim.add_volume("Box", f"{machine_name}_collimator3")
-    collimator3.mother = f"{machine_name}_xray_tank"
-    collimator3.color = red
-    collimator3.translation = [0* cm, 75 * mm , -z_xray_tank / 2 * mm + 3 * mm]
-    collimator3.size = [10* cm, 5 * cm, 1 * mm]
-
-    collimator4 = sim.add_volume("Box", f"{machine_name}_collimator4")
-    collimator4.mother = f"{machine_name}_xray_tank"
-    collimator4.color = red
-    collimator4.translation = [0* cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
-    collimator4.size = [10* cm, 5 * cm, 1 * mm]
-
-    # psycho killer
-    killer = sim.add_actor("KillActor", f"target_kill")
-    killer.mother = [collimator1.name, collimator2.name,collimator3.name,collimator4.name]
-
-
-def update_collimation(sim, machine_name, num, num2):
-    if not 0 <= num <= 50 or not 0 <= num2 <= 50:
-        raise ValueError("Wrong values for collimation")
-
-    num = 50 - num
-    num2 = 50 - num2
-
-    xray_tank = sim.volume_manager.get_volume(f"{machine_name}_xray_tank")
-    z_xray_tank = xray_tank.size[2]
-
-    collimator1 = sim.volume_manager.get_volume(f"{machine_name}_collimator1")
-    collimator1.translation = [75 * mm - num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-
-    collimator2 = sim.volume_manager.get_volume(f"{machine_name}_collimator2")
-    collimator2.translation = [-75 * mm + num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-
-    collimator3 = sim.volume_manager.get_volume(f"{machine_name}_collimator3")
-    collimator3.translation = [0 * cm, 75 * mm - num2, -z_xray_tank / 2 * mm + 3 * mm]
-
-    collimator4 = sim.volume_manager.get_volume(f"{machine_name}_collimator4")
-    collimator4.translation = [0 * cm, -75 * mm + num2, -z_xray_tank / 2 * mm + 3 * mm]
+class Ciosalpha:
+    def __init__(self, sim, kvp):
+        self.sim = sim
+        self.machine_name = "ciosalpha"
+        self.volume = self.add_carm_box()
+        self.add_xray_tank()
+        self.add_collimators()
+        self.source = self.add_carm_source(kvp)
+
+    def add_carm_box(self):
+        carmbox = self.sim.volume_manager.create_volume("Box", "carmbox")
+        carmbox.material = "G4_AIR"
+        carmbox.size = [200 * cm, 30 * cm, 200 * cm]
+        carmbox.translation = [0 * cm, 0 * cm, 0 * cm]
+        carmbox.color = [1, 1, 1, 0.8]
+
+        hole1 = self.sim.volume_manager.create_volume("Box", "hole")
+        hole1.size = [191 * cm, 31 * cm, 160 * cm]
+        hole1.color = [1, 1, 1, 0.8]
+        hole2 = self.sim.volume_manager.create_volume("Box", "hole2")
+        hole2.size = [80 * cm, 31 * cm, 31 * cm]
+        hole2.color = [1, 1, 1, 0.8]
+        hole3 = self.sim.volume_manager.create_volume("Box", "hole3")
+        hole3.size = [80 * cm, 31 * cm, 31 * cm]
+        hole3.color = [1, 1, 1, 0.8]
+
+        hole1and2 = gate.geometry.volumes.unite_volumes(
+            hole1, hole2, translation=[-55.5 * cm, 0 * cm, 95 * cm]
+        )
+
+        t_shape = gate.geometry.volumes.unite_volumes(
+            hole1and2, hole3, translation=[-55.5 * cm, 0 * cm, -95 * cm]
+        )
+
+        carm = gate.geometry.volumes.subtract_volumes(
+            carmbox, t_shape, new_name=self.machine_name, translation=[-5 * cm, 0 * cm, -10 * cm]
+        )
+        self.sim.add_volume(carm)
+
+        return carm
+
+    def add_xray_tank(self):
+        xray_tank = self.sim.add_volume("Box", f"{self.machine_name}_xray_tank")
+        xray_tank.mother = self.machine_name
+        xray_tank.material = "G4_AIR"
+        xray_tank.size = [40 * cm, 20 * cm, 30 * cm]
+        xray_tank.translation = [0 * cm, 0, 85 * cm]
+        xray_tank.color = [1, 1, 1, 0.8]
+
+    def add_carm_source(self, kvp):
+        s = sp.Spek(kvp, th=10, physics='kqp')
+        s.filter('Al', 3.0).filter('Cu', 0.1)
+
+        energy_bins, weights = s.get_spectrum()
+
+        b = self.sim.add_volume("Box", f"{self.machine_name}_sourcebox")
+        b.mother = f"{self.machine_name}_xray_tank"
+        b.translation = [0 * cm, 0 * cm, 10 * cm]
+        b.size = [1 * cm, 1 * cm, 1 * cm]
+
+        source = self.sim.add_source("GenericSource", f"{self.machine_name}_source")
+        source.mother = f"{self.machine_name}_sourcebox"
+        source.particle = "gamma"
+        source.position.type = "disc"
+        source.position.radius = 0 * mm
+
+        source.direction_relative_to_volume = True
+        source.direction.type = "iso"
+        source.direction.theta = [0 * deg, 10 * deg]
+        source.direction.phi = [0 * deg, 360 * deg]
+
+        source.energy.type = "histogram"
+        source.energy.histogram_weight = weights
+        source.energy.histogram_energy = energy_bins
+
+        return source
+
+    def add_collimators(self):
+        xray_tank = self.sim.volume_manager.get_volume(f"{self.machine_name}_xray_tank")
+        z_xray_tank = xray_tank.size[2]
+
+        collimator1 = self.sim.add_volume("Box", f"{self.machine_name}_collimator1")
+        collimator1.mother = f"{self.machine_name}_xray_tank"
+        collimator1.color = red
+        collimator1.translation = [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+        collimator1.size = [5 * cm, 10 * cm, 1 * mm]
+
+        collimator2 = self.sim.add_volume("Box", f"{self.machine_name}_collimator2")
+        collimator2.mother = f"{self.machine_name}_xray_tank"
+        collimator2.color = red
+        collimator2.translation = [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+        collimator2.size = [5 * cm, 10 * cm, 1 * mm]
+
+        collimator3 = self.sim.add_volume("Box", f"{self.machine_name}_collimator3")
+        collimator3.mother = f"{self.machine_name}_xray_tank"
+        collimator3.color = red
+        collimator3.translation = [0 * cm, 75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
+        collimator3.size = [10 * cm, 5 * cm, 1 * mm]
+
+        collimator4 = self.sim.add_volume("Box", f"{self.machine_name}_collimator4")
+        collimator4.mother = f"{self.machine_name}_xray_tank"
+        collimator4.color = red
+        collimator4.translation = [0 * cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
+        collimator4.size = [10 * cm, 5 * cm, 1 * mm]
+
+        killer = self.sim.add_actor("KillActor", f"target_kill")
+        killer.mother = [collimator1.name, collimator2.name, collimator3.name, collimator4.name]
+
+    def update_collimation(self, num, num2):
+        if not 0 <= num <= 50 or not 0 <= num2 <= 50:
+            raise ValueError("Wrong values for collimation")
+
+        num = 50 - num
+        num2 = 50 - num2
+
+        xray_tank = self.sim.volume_manager.get_volume(f"{self.machine_name}_xray_tank")
+        z_xray_tank = xray_tank.size[2]
+
+        collimator1 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator1")
+        collimator1.translation = [75 * mm - num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+
+        collimator2 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator2")
+        collimator2.translation = [-75 * mm + num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
+
+        collimator3 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator3")
+        collimator3.translation = [0 * cm, 75 * mm - num2, -z_xray_tank / 2 * mm + 3 * mm]
+
+        collimator4 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator4")
+        collimator4.translation = [0 * cm, -75 * mm + num2, -z_xray_tank / 2 * mm + 3 * mm]
+
+    @property
+    def collimation(self):
+        return self._collimation
+
+    @collimation.setter
+    def collimation(self, value):
+        self._collimation = value
+        self.update_collimation(value[0] / mm, value[1] / mm)
+
+    @property
+    def rotation(self):
+        return self.volume.rotation
+
+    @rotation.setter
+    def rotation(self, value):
+        self.volume.rotation = value
+
+    @property
+    def translation(self):
+        return self.volume.translation
+
+    @translation.setter
+    def translation(self, value):
+        self.volume.translation = value
+
 
 # useful units
 MeV = gate.g4_units.MeV
@@ -157,4 +173,4 @@ def update_collimation(sim, machine_name, num, num2):
 # colors
 red = [1, 0.7, 0.7, 0.8]
 blue = [0.5, 0.5, 1, 0.8]
-green = [0, 1, 0, 1]
+green = [0, 1, 0, 1]
\ No newline at end of file
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index 7a943411e..19904a430 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import opengate as gate
-import opengate.contrib.carm.siemensciosalpha as ciosalpha
+from opengate.contrib.carm.siemensciosalpha import Ciosalpha
 from opengate.tests import utility
 from scipy.spatial.transform import Rotation
 import numpy as np
@@ -11,7 +11,7 @@
 
 if __name__ == "__main__":
     # paths
-    paths = utility.get_default_test_paths(__file__, output_folder="test075_siemens_cios_alpha")
+    #paths = utility.get_default_test_paths(__file__, output_folder="test075_siemens_cios_alpha")
 
     # create the simulation
     sim = gate.Simulation()
@@ -36,22 +36,19 @@
     world.size = [5* m, 5 * m, 5 * m]
     world.material = "G4_AIR"
 
-    # add a carm
-    carm = ciosalpha.add_carm(sim, "cios_alpha")
-    carm.rotation = Rotation.from_euler("ZYX", [0,20,180], degrees=True).as_matrix()
-
     # xray tube spectrum parameters
     # tube potential [kV]
     kvp = 100
 
-    # add carm source
-    source = ciosalpha.add_carm_source(sim, carm.name, kvp)
-    source.n = 1e6
-    if sim.visu:
-        source.n = 1
+    # add a carm
+    carm = Ciosalpha(sim, kvp)
+    carm.rotation = Rotation.from_euler("ZYX", [0,20,0], degrees=True).as_matrix()
+    carm.translation = [0 * cm, 0 * cm, 0 * cm]
+    carm.collimation = [30 * mm, 10 * mm]
 
-    # opening of the collimators [0, 50 *mm]
-    ciosalpha.update_collimation(sim, carm.name, 20 * mm, 20 * mm)
+    carm.source.n = 1e6
+    if sim.visu:
+        carm.source.n = 1000
 
     # aluminum table
     table = sim.add_volume("Box", "aluminum_table")

From 5afc3bb440e06a5a6ec7e580ec013068a7933ddf Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Fri, 28 Jun 2024 09:53:26 +0200
Subject: [PATCH 06/14] enhanced code

---
 opengate/contrib/carm/siemensciosalpha.py     | 112 +++++++++---------
 .../tests/src/test075_siemens_cios_alpha.py   |   1 +
 2 files changed, 54 insertions(+), 59 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index dda021f89..3c491c345 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -1,9 +1,18 @@
 import opengate as gate
-from opengate.utility import g4_units, get_contrib_path
-from scipy.spatial.transform import Rotation
+from opengate.utility import g4_units
 import numpy as np
 import spekpy as sp
 
+# useful units
+MeV = gate.g4_units.MeV
+keV = gate.g4_units.keV
+Bq = gate.g4_units.Bq
+deg = gate.g4_units.deg
+nm = gate.g4_units.nm
+mm = gate.g4_units.mm
+m = gate.g4_units.m
+cm = gate.g4_units.cm
+
 class Ciosalpha:
     def __init__(self, sim, kvp):
         self.sim = sim
@@ -85,54 +94,55 @@ def add_collimators(self):
         xray_tank = self.sim.volume_manager.get_volume(f"{self.machine_name}_xray_tank")
         z_xray_tank = xray_tank.size[2]
 
-        collimator1 = self.sim.add_volume("Box", f"{self.machine_name}_collimator1")
-        collimator1.mother = f"{self.machine_name}_xray_tank"
-        collimator1.color = red
-        collimator1.translation = [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-        collimator1.size = [5 * cm, 10 * cm, 1 * mm]
-
-        collimator2 = self.sim.add_volume("Box", f"{self.machine_name}_collimator2")
-        collimator2.mother = f"{self.machine_name}_xray_tank"
-        collimator2.color = red
-        collimator2.translation = [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-        collimator2.size = [5 * cm, 10 * cm, 1 * mm]
-
-        collimator3 = self.sim.add_volume("Box", f"{self.machine_name}_collimator3")
-        collimator3.mother = f"{self.machine_name}_xray_tank"
-        collimator3.color = red
-        collimator3.translation = [0 * cm, 75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
-        collimator3.size = [10 * cm, 5 * cm, 1 * mm]
-
-        collimator4 = self.sim.add_volume("Box", f"{self.machine_name}_collimator4")
-        collimator4.mother = f"{self.machine_name}_xray_tank"
-        collimator4.color = red
-        collimator4.translation = [0 * cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm]
-        collimator4.size = [10 * cm, 5 * cm, 1 * mm]
+        collimators = [
+            {
+                "translation": [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+                "size": [5 * cm, 10 * cm, 1 * mm]
+            },
+            {
+                "translation": [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+                "size": [5 * cm, 10 * cm, 1 * mm]
+            },
+            {
+                "translation": [0 * cm, 75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
+                "size": [10 * cm, 5 * cm, 1 * mm]
+            },
+            {
+                "translation": [0 * cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
+                "size": [10 * cm, 5 * cm, 1 * mm]
+            }
+        ]
+
+        for i, colli in enumerate(collimators):
+            collimator = self.sim.add_volume("Box", f"{self.machine_name}_collimator{i+1}")
+            collimator.mother = f"{self.machine_name}_xray_tank"
+            collimator.color = [1, 0.7, 0.7, 0.8]
+            collimator.translation = colli["translation"]
+            collimator.size = colli["size"]
 
         killer = self.sim.add_actor("KillActor", f"target_kill")
-        killer.mother = [collimator1.name, collimator2.name, collimator3.name, collimator4.name]
+        killer.mother = [f"{self.machine_name}_collimator{i+1}" for i in range(4)]
 
-    def update_collimation(self, num, num2):
-        if not 0 <= num <= 50 or not 0 <= num2 <= 50:
-            raise ValueError("Wrong values for collimation")
+    def set_collimation(self, collimation1, collimation2):
+        if not 0 <= collimation1 <= 50 or not 0 <= collimation2 <= 50:
+            raise ValueError("Collimation values must be between 0 and 50 mm")
 
-        num = 50 - num
-        num2 = 50 - num2
+        collimation1 = 50 - collimation1
+        collimation2 = 50 - collimation2
 
         xray_tank = self.sim.volume_manager.get_volume(f"{self.machine_name}_xray_tank")
         z_xray_tank = xray_tank.size[2]
 
-        collimator1 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator1")
-        collimator1.translation = [75 * mm - num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-
-        collimator2 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator2")
-        collimator2.translation = [-75 * mm + num, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm]
-
-        collimator3 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator3")
-        collimator3.translation = [0 * cm, 75 * mm - num2, -z_xray_tank / 2 * mm + 3 * mm]
+        translations = [
+            [75 * mm - collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+            [-75 * mm + collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+            [0 * cm, 75 * mm - collimation2, -z_xray_tank / 2 * mm + 3 * mm],
+            [0 * cm, -75 * mm + collimation2, -z_xray_tank / 2 * mm + 3 * mm]
+        ]
 
-        collimator4 = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator4")
-        collimator4.translation = [0 * cm, -75 * mm + num2, -z_xray_tank / 2 * mm + 3 * mm]
+        for i, translation in enumerate(translations):
+            collimator = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator{i+1}")
+            collimator.translation = translation
 
     @property
     def collimation(self):
@@ -141,7 +151,7 @@ def collimation(self):
     @collimation.setter
     def collimation(self, value):
         self._collimation = value
-        self.update_collimation(value[0] / mm, value[1] / mm)
+        self.set_collimation(value[0], value[1])
 
     @property
     def rotation(self):
@@ -157,20 +167,4 @@ def translation(self):
 
     @translation.setter
     def translation(self, value):
-        self.volume.translation = value
-
-
-# useful units
-MeV = gate.g4_units.MeV
-keV = gate.g4_units.keV
-Bq = gate.g4_units.Bq
-deg = gate.g4_units.deg
-nm = gate.g4_units.nm
-mm = gate.g4_units.mm
-m = gate.g4_units.m
-cm = gate.g4_units.cm
-
-# colors
-red = [1, 0.7, 0.7, 0.8]
-blue = [0.5, 0.5, 1, 0.8]
-green = [0, 1, 0, 1]
\ No newline at end of file
+        self.volume.translation = value
\ No newline at end of file
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index 19904a430..cde0c9d09 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -60,3 +60,4 @@
     # start simulation
     sim.run()
 
+    # TODO: Test

From 60da033976b5605a79fe5fb449636ab424fea354 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 08:05:03 +0000
Subject: [PATCH 07/14] [pre-commit.ci] Automatic python and c++ formatting

---
 opengate/contrib/carm/siemensciosalpha.py     | 32 ++++++++++++-------
 .../tests/src/test075_siemens_cios_alpha.py   |  8 ++---
 2 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 3c491c345..73309aaa3 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -13,6 +13,7 @@
 m = gate.g4_units.m
 cm = gate.g4_units.cm
 
+
 class Ciosalpha:
     def __init__(self, sim, kvp):
         self.sim = sim
@@ -48,7 +49,10 @@ def add_carm_box(self):
         )
 
         carm = gate.geometry.volumes.subtract_volumes(
-            carmbox, t_shape, new_name=self.machine_name, translation=[-5 * cm, 0 * cm, -10 * cm]
+            carmbox,
+            t_shape,
+            new_name=self.machine_name,
+            translation=[-5 * cm, 0 * cm, -10 * cm],
         )
         self.sim.add_volume(carm)
 
@@ -63,8 +67,8 @@ def add_xray_tank(self):
         xray_tank.color = [1, 1, 1, 0.8]
 
     def add_carm_source(self, kvp):
-        s = sp.Spek(kvp, th=10, physics='kqp')
-        s.filter('Al', 3.0).filter('Cu', 0.1)
+        s = sp.Spek(kvp, th=10, physics="kqp")
+        s.filter("Al", 3.0).filter("Cu", 0.1)
 
         energy_bins, weights = s.get_spectrum()
 
@@ -97,24 +101,26 @@ def add_collimators(self):
         collimators = [
             {
                 "translation": [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-                "size": [5 * cm, 10 * cm, 1 * mm]
+                "size": [5 * cm, 10 * cm, 1 * mm],
             },
             {
                 "translation": [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-                "size": [5 * cm, 10 * cm, 1 * mm]
+                "size": [5 * cm, 10 * cm, 1 * mm],
             },
             {
                 "translation": [0 * cm, 75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
-                "size": [10 * cm, 5 * cm, 1 * mm]
+                "size": [10 * cm, 5 * cm, 1 * mm],
             },
             {
                 "translation": [0 * cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
-                "size": [10 * cm, 5 * cm, 1 * mm]
-            }
+                "size": [10 * cm, 5 * cm, 1 * mm],
+            },
         ]
 
         for i, colli in enumerate(collimators):
-            collimator = self.sim.add_volume("Box", f"{self.machine_name}_collimator{i+1}")
+            collimator = self.sim.add_volume(
+                "Box", f"{self.machine_name}_collimator{i+1}"
+            )
             collimator.mother = f"{self.machine_name}_xray_tank"
             collimator.color = [1, 0.7, 0.7, 0.8]
             collimator.translation = colli["translation"]
@@ -137,11 +143,13 @@ def set_collimation(self, collimation1, collimation2):
             [75 * mm - collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
             [-75 * mm + collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
             [0 * cm, 75 * mm - collimation2, -z_xray_tank / 2 * mm + 3 * mm],
-            [0 * cm, -75 * mm + collimation2, -z_xray_tank / 2 * mm + 3 * mm]
+            [0 * cm, -75 * mm + collimation2, -z_xray_tank / 2 * mm + 3 * mm],
         ]
 
         for i, translation in enumerate(translations):
-            collimator = self.sim.volume_manager.get_volume(f"{self.machine_name}_collimator{i+1}")
+            collimator = self.sim.volume_manager.get_volume(
+                f"{self.machine_name}_collimator{i+1}"
+            )
             collimator.translation = translation
 
     @property
@@ -167,4 +175,4 @@ def translation(self):
 
     @translation.setter
     def translation(self, value):
-        self.volume.translation = value
\ No newline at end of file
+        self.volume.translation = value
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index cde0c9d09..e720cd7fd 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -11,7 +11,7 @@
 
 if __name__ == "__main__":
     # paths
-    #paths = utility.get_default_test_paths(__file__, output_folder="test075_siemens_cios_alpha")
+    # paths = utility.get_default_test_paths(__file__, output_folder="test075_siemens_cios_alpha")
 
     # create the simulation
     sim = gate.Simulation()
@@ -33,7 +33,7 @@
 
     # world
     world = sim.world
-    world.size = [5* m, 5 * m, 5 * m]
+    world.size = [5 * m, 5 * m, 5 * m]
     world.material = "G4_AIR"
 
     # xray tube spectrum parameters
@@ -42,7 +42,7 @@
 
     # add a carm
     carm = Ciosalpha(sim, kvp)
-    carm.rotation = Rotation.from_euler("ZYX", [0,20,0], degrees=True).as_matrix()
+    carm.rotation = Rotation.from_euler("ZYX", [0, 20, 0], degrees=True).as_matrix()
     carm.translation = [0 * cm, 0 * cm, 0 * cm]
     carm.collimation = [30 * mm, 10 * mm]
 
@@ -52,7 +52,7 @@
 
     # aluminum table
     table = sim.add_volume("Box", "aluminum_table")
-    table.size = [60 * cm, 2 * m, 0.9 * mm ]
+    table.size = [60 * cm, 2 * m, 0.9 * mm]
     table.material = "G4_Al"
     table.translation = [0 * m, 0 * cm, 0 * cm]
     table.color = [0.8, 0.8, 0.8, 1]

From 80f742035d874dc6579acc9865fea8962b48b673 Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Fri, 28 Jun 2024 14:01:39 +0200
Subject: [PATCH 08/14] change some carm measures

---
 opengate/contrib/carm/siemensciosalpha.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 73309aaa3..11a8c0ad1 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -26,26 +26,26 @@ def __init__(self, sim, kvp):
     def add_carm_box(self):
         carmbox = self.sim.volume_manager.create_volume("Box", "carmbox")
         carmbox.material = "G4_AIR"
-        carmbox.size = [200 * cm, 30 * cm, 200 * cm]
+        carmbox.size = [200 * cm, 30 * cm, 120 * cm]
         carmbox.translation = [0 * cm, 0 * cm, 0 * cm]
         carmbox.color = [1, 1, 1, 0.8]
 
         hole1 = self.sim.volume_manager.create_volume("Box", "hole")
-        hole1.size = [191 * cm, 31 * cm, 160 * cm]
+        hole1.size = [191 * cm, 31 * cm, 80 * cm]
         hole1.color = [1, 1, 1, 0.8]
         hole2 = self.sim.volume_manager.create_volume("Box", "hole2")
-        hole2.size = [80 * cm, 31 * cm, 31 * cm]
+        hole2.size = [100 * cm, 31 * cm, 31 * cm]
         hole2.color = [1, 1, 1, 0.8]
         hole3 = self.sim.volume_manager.create_volume("Box", "hole3")
-        hole3.size = [80 * cm, 31 * cm, 31 * cm]
+        hole3.size = [100 * cm, 31 * cm, 31 * cm]
         hole3.color = [1, 1, 1, 0.8]
 
         hole1and2 = gate.geometry.volumes.unite_volumes(
-            hole1, hole2, translation=[-55.5 * cm, 0 * cm, 95 * cm]
+            hole1, hole2, translation=[-55.5 * cm, 0 * cm, 55 * cm]
         )
 
         t_shape = gate.geometry.volumes.unite_volumes(
-            hole1and2, hole3, translation=[-55.5 * cm, 0 * cm, -95 * cm]
+            hole1and2, hole3, translation=[-55.5 * cm, 0 * cm, -55 * cm]
         )
 
         carm = gate.geometry.volumes.subtract_volumes(
@@ -62,8 +62,8 @@ def add_xray_tank(self):
         xray_tank = self.sim.add_volume("Box", f"{self.machine_name}_xray_tank")
         xray_tank.mother = self.machine_name
         xray_tank.material = "G4_AIR"
-        xray_tank.size = [40 * cm, 20 * cm, 30 * cm]
-        xray_tank.translation = [0 * cm, 0, 85 * cm]
+        xray_tank.size = [20 * cm, 20 * cm, 30 * cm]
+        xray_tank.translation = [0 * cm, 0, 45 * cm]
         xray_tank.color = [1, 1, 1, 0.8]
 
     def add_carm_source(self, kvp):

From be05da7f93f7a9f3036ea69064815b478e670935 Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Fri, 28 Jun 2024 16:24:40 +0200
Subject: [PATCH 09/14] add option to only have source box geometry

---
 opengate/contrib/carm/siemensciosalpha.py     | 34 +++++++++++++++----
 .../tests/src/test075_siemens_cios_alpha.py   |  3 +-
 2 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 11a8c0ad1..6b3f68896 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -15,9 +15,10 @@
 
 
 class Ciosalpha:
-    def __init__(self, sim, kvp):
+    def __init__(self, sim, kvp, source_only=False):
         self.sim = sim
         self.machine_name = "ciosalpha"
+        self.source_only = source_only
         self.volume = self.add_carm_box()
         self.add_xray_tank()
         self.add_collimators()
@@ -34,23 +35,42 @@ def add_carm_box(self):
         hole1.size = [191 * cm, 31 * cm, 80 * cm]
         hole1.color = [1, 1, 1, 0.8]
         hole2 = self.sim.volume_manager.create_volume("Box", "hole2")
-        hole2.size = [100 * cm, 31 * cm, 31 * cm]
+        hole2.size = [90 * cm, 31 * cm, 31 * cm]
         hole2.color = [1, 1, 1, 0.8]
         hole3 = self.sim.volume_manager.create_volume("Box", "hole3")
-        hole3.size = [100 * cm, 31 * cm, 31 * cm]
+        hole3.size = [90 * cm, 31 * cm, 31 * cm]
         hole3.color = [1, 1, 1, 0.8]
 
         hole1and2 = gate.geometry.volumes.unite_volumes(
-            hole1, hole2, translation=[-55.5 * cm, 0 * cm, 55 * cm]
+            hole1, hole2, translation=[-50.5 * cm, 0 * cm, 55 * cm]
         )
 
-        t_shape = gate.geometry.volumes.unite_volumes(
-            hole1and2, hole3, translation=[-55.5 * cm, 0 * cm, -55 * cm]
+        subtract_to_carm = gate.geometry.volumes.unite_volumes(
+            hole1and2, hole3, translation=[-50.5 * cm, 0 * cm, -55 * cm]
         )
 
+        if self.source_only:
+            hole4 = self.sim.volume_manager.create_volume("Box", "hole4")
+            hole4.size = [45 * cm, 31 * cm, 31 * cm]
+            hole4.color = [1, 1, 1, 0.8]
+            # hole4 = self.sim.volume_manager.create_volume("Box", "hole4")
+            # hole4.size = [90 * cm, 31 * cm, 31 * cm]
+            # hole4.color = [1, 1, 1, 0.8]
+            hole5 = self.sim.volume_manager.create_volume("Box", "hole5")
+            hole5.size = [90 * cm, 31 * cm, 121* cm]
+            hole5.color = [1, 1, 1, 0.8]
+
+            hole4and5 = gate.geometry.volumes.unite_volumes(
+                hole4, hole5, translation=[55 * cm, 0 * cm, 45 * cm]
+            )
+
+            subtract_to_carm = gate.geometry.volumes.unite_volumes(
+                subtract_to_carm, hole4and5, translation=[5 * cm, 0 * cm, -35* cm]
+            )
+
         carm = gate.geometry.volumes.subtract_volumes(
             carmbox,
-            t_shape,
+            subtract_to_carm,
             new_name=self.machine_name,
             translation=[-5 * cm, 0 * cm, -10 * cm],
         )
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index e720cd7fd..369c8793a 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -20,7 +20,6 @@
     sim.g4_verbose = False
     sim.visu = True
     sim.visu_type = "vrml"
-    sim.check_volumes_overlap = False
     sim.number_of_threads = 1
     sim.random_seed = 12345678
     sim.check_volumes_overlap = True
@@ -41,7 +40,7 @@
     kvp = 100
 
     # add a carm
-    carm = Ciosalpha(sim, kvp)
+    carm = Ciosalpha(sim, kvp, source_only=True)
     carm.rotation = Rotation.from_euler("ZYX", [0, 20, 0], degrees=True).as_matrix()
     carm.translation = [0 * cm, 0 * cm, 0 * cm]
     carm.collimation = [30 * mm, 10 * mm]

From 2afcca38d7cff442c8f27553ae981a4575db1907 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 14:24:47 +0000
Subject: [PATCH 10/14] [pre-commit.ci] Automatic python and c++ formatting

---
 opengate/contrib/carm/siemensciosalpha.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 6b3f68896..09ee371ff 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -57,7 +57,7 @@ def add_carm_box(self):
             # hole4.size = [90 * cm, 31 * cm, 31 * cm]
             # hole4.color = [1, 1, 1, 0.8]
             hole5 = self.sim.volume_manager.create_volume("Box", "hole5")
-            hole5.size = [90 * cm, 31 * cm, 121* cm]
+            hole5.size = [90 * cm, 31 * cm, 121 * cm]
             hole5.color = [1, 1, 1, 0.8]
 
             hole4and5 = gate.geometry.volumes.unite_volumes(
@@ -65,7 +65,7 @@ def add_carm_box(self):
             )
 
             subtract_to_carm = gate.geometry.volumes.unite_volumes(
-                subtract_to_carm, hole4and5, translation=[5 * cm, 0 * cm, -35* cm]
+                subtract_to_carm, hole4and5, translation=[5 * cm, 0 * cm, -35 * cm]
             )
 
         carm = gate.geometry.volumes.subtract_volumes(

From 0ab8cc4b237897d7bb7b6b3381840ceb35984569 Mon Sep 17 00:00:00 2001
From: axelrannou <axeranno29@gmail.com>
Date: Wed, 10 Jul 2024 11:44:39 +0200
Subject: [PATCH 11/14] Use histogram direction type instead of iso to simulate
 anode heel effect

---
 .../GateAcceptanceAngleTesterManager.cpp      |   8 +-
 .../opengate_lib/GateGenericSource.cpp        |   4 +-
 opengate/contrib/carm/anodeheeleffect.npz     | Bin 0 -> 1108 bytes
 opengate/contrib/carm/siemensciosalpha.py     |  75 ++++++++++--------
 .../tests/src/test075_siemens_cios_alpha.py   |   4 +-
 5 files changed, 51 insertions(+), 40 deletions(-)
 create mode 100644 opengate/contrib/carm/anodeheeleffect.npz

diff --git a/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp b/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
index 9070fb8e8..d40899b82 100644
--- a/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
+++ b/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
@@ -19,7 +19,7 @@ GateAcceptanceAngleTesterManager::GateAcceptanceAngleTesterManager() {
 }
 
 void GateAcceptanceAngleTesterManager::Initialize(py::dict puser_info,
-                                                  bool is_iso) {
+                                                  bool is_valid_type) {
   fAcceptanceAngleVolumeNames = DictGetVecStr(puser_info, "volumes");
   fEnabledFlag = !fAcceptanceAngleVolumeNames.empty();
   if (!fEnabledFlag)
@@ -39,10 +39,10 @@ void GateAcceptanceAngleTesterManager::Initialize(py::dict puser_info,
     Fatal(oss.str());
   }
 
-  // Cannot use SkipEvent with non iso source
-  if (!is_iso && fPolicy == AASkipEvent) {
+  // Cannot use SkipEvent with not a valid type of source
+  if (!is_valid_type && fPolicy == AASkipEvent) {
     std::ostringstream oss;
-    oss << "Cannot use 'SkipEvent' mode without 'iso' direction type";
+    oss << "Cannot use 'SkipEvent' mode without 'iso' or 'histogram' direction type";
     Fatal(oss.str());
   }
 }
diff --git a/core/opengate_core/opengate_lib/GateGenericSource.cpp b/core/opengate_core/opengate_lib/GateGenericSource.cpp
index 230db67c9..0f380f933 100644
--- a/core/opengate_core/opengate_lib/GateGenericSource.cpp
+++ b/core/opengate_core/opengate_lib/GateGenericSource.cpp
@@ -449,10 +449,10 @@ void GateGenericSource::InitializeDirection(py::dict puser_info) {
   // set the angle acceptance volume if needed
   auto d = py::dict(puser_info["direction"]);
   auto dd = py::dict(d["acceptance_angle"]);
-  auto is_iso = ang->GetDistType() == "iso";
+  auto is_valid_type = ang->GetDistType() == "iso" || ang->GetDistType() == "user";
   auto &l = fThreadLocalDataAA.Get();
   l.fAAManager = new GateAcceptanceAngleTesterManager;
-  l.fAAManager->Initialize(dd, is_iso);
+  l.fAAManager->Initialize(dd, is_valid_type);
   fSPS->SetAAManager(l.fAAManager);
 }
 
diff --git a/opengate/contrib/carm/anodeheeleffect.npz b/opengate/contrib/carm/anodeheeleffect.npz
new file mode 100644
index 0000000000000000000000000000000000000000..cc60bb367413b310c678ad8065fb4bca182276d9
GIT binary patch
literal 1108
zcmWIWW@Zs#fB;2?)_DQ{H!w0VfG{V62t#6CdQPfdUO^=zg8*0%q!1(t0+anheFGvH
z8Oj){)l*W7lZ(`?6x40fEYx)r)YI~dN{SNm;`57AQbFQwi8;loK=I;?#DY{HU&Gi!
zM^i_kR)KuL_2tu>iB9<(4(pHVZ+u<B;gB_>=)#mH4hOaDt?zAnI2<0@{@{B)mBV3<
zfVJL)`5X=rk86D`S8_OrY&($iXcLFS`3~lu?mZk1UD0l<O^$ImxaxJDx_h3(fsygd
z%eI>w4tp;1aT+}4a426EsB!ZRhl5e&6!)fY91iciucv7<a5}7%lWM!d$?1^#F=lD4
zFsFmUk@-i|WH}uKroDK4UX9b?bcQx_r2(fyhjpHkk`<?eGv7wX)6Sd@{~ml!DDmZV
z*tyxPK{lMzp`@*H{;>p32ZP8x`|`6m9bRkyzbjF~>9Fjd<KKg|oDPW>TV%4^IUQt|
z9Jdyk$mwvSj4OKYEKY|hp1xISOE?|;WhTtzU&rad{r=L99osn_jvW-ek$8~Pp>ayY
zcdpZ%4mRnt#kO4GbO=C+>T`k4<tu<O3Bp{!s4h><OwTBR#WhG21Yk5}acxd<T+f;b
z0z2)+YV}@xzjMewUUves^4k;kcLY>}8VwHFs~&92UE^@VzS(%{MXr{E_Gce|dt*A~
zxV`7`ZtE%657<vCe;c;{`7wL`=%%Hz+6U|-xSt&Gus&wL;_gQ|zrXwJW#`}0y3}{n
z-h}o3r-UVY?H?OmoD%)$h<&ry{*T4pd+fVI9Yvm+9<k>uT647R(=K~R=zJJ-bbvP_
vlL#}e3=MHLh-?7IFFbprYeP*O$l6{5H6oHqfHx}}NR|l*^MUkvW)Kem$>}^u

literal 0
HcmV?d00001

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 09ee371ff..b62719a25 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -1,7 +1,8 @@
 import opengate as gate
-from opengate.utility import g4_units
+from scipy.spatial.transform import Rotation
 import numpy as np
 import spekpy as sp
+import pathlib
 
 # useful units
 MeV = gate.g4_units.MeV
@@ -13,6 +14,7 @@
 m = gate.g4_units.m
 cm = gate.g4_units.cm
 
+current_path = pathlib.Path(__file__).parent.resolve()
 
 class Ciosalpha:
     def __init__(self, sim, kvp, source_only=False):
@@ -27,7 +29,7 @@ def __init__(self, sim, kvp, source_only=False):
     def add_carm_box(self):
         carmbox = self.sim.volume_manager.create_volume("Box", "carmbox")
         carmbox.material = "G4_AIR"
-        carmbox.size = [200 * cm, 30 * cm, 120 * cm]
+        carmbox.size = [200 * cm, 10 * cm, 120 * cm]
         carmbox.translation = [0 * cm, 0 * cm, 0 * cm]
         carmbox.color = [1, 1, 1, 0.8]
 
@@ -35,7 +37,7 @@ def add_carm_box(self):
         hole1.size = [191 * cm, 31 * cm, 80 * cm]
         hole1.color = [1, 1, 1, 0.8]
         hole2 = self.sim.volume_manager.create_volume("Box", "hole2")
-        hole2.size = [90 * cm, 31 * cm, 31 * cm]
+        hole2.size = [101 * cm, 31 * cm, 31 * cm]
         hole2.color = [1, 1, 1, 0.8]
         hole3 = self.sim.volume_manager.create_volume("Box", "hole3")
         hole3.size = [90 * cm, 31 * cm, 31 * cm]
@@ -53,11 +55,8 @@ def add_carm_box(self):
             hole4 = self.sim.volume_manager.create_volume("Box", "hole4")
             hole4.size = [45 * cm, 31 * cm, 31 * cm]
             hole4.color = [1, 1, 1, 0.8]
-            # hole4 = self.sim.volume_manager.create_volume("Box", "hole4")
-            # hole4.size = [90 * cm, 31 * cm, 31 * cm]
-            # hole4.color = [1, 1, 1, 0.8]
             hole5 = self.sim.volume_manager.create_volume("Box", "hole5")
-            hole5.size = [90 * cm, 31 * cm, 121 * cm]
+            hole5.size = [100 * cm, 31 * cm, 121 * cm]
             hole5.color = [1, 1, 1, 0.8]
 
             hole4and5 = gate.geometry.volumes.unite_volumes(
@@ -82,7 +81,7 @@ def add_xray_tank(self):
         xray_tank = self.sim.add_volume("Box", f"{self.machine_name}_xray_tank")
         xray_tank.mother = self.machine_name
         xray_tank.material = "G4_AIR"
-        xray_tank.size = [20 * cm, 20 * cm, 30 * cm]
+        xray_tank.size = [10 * cm, 10 * cm, 30 * cm]
         xray_tank.translation = [0 * cm, 0, 45 * cm]
         xray_tank.color = [1, 1, 1, 0.8]
 
@@ -92,26 +91,38 @@ def add_carm_source(self, kvp):
 
         energy_bins, weights = s.get_spectrum()
 
-        b = self.sim.add_volume("Box", f"{self.machine_name}_sourcebox")
-        b.mother = f"{self.machine_name}_xray_tank"
-        b.translation = [0 * cm, 0 * cm, 10 * cm]
-        b.size = [1 * cm, 1 * cm, 1 * cm]
+        sourcebox = self.sim.add_volume("Box", f"{self.machine_name}_sourcebox")
+        sourcebox.mother = f"{self.machine_name}_xray_tank"
+        sourcebox.translation = [0 * cm, 0 * cm, 10 * cm]
+        sourcebox.size = [1 * cm, 1 * cm, 1 * cm]
+        sourcebox.rotation = Rotation.from_euler("ZYX", [0, 90, 90], degrees=True).as_matrix()
 
         source = self.sim.add_source("GenericSource", f"{self.machine_name}_source")
-        source.mother = f"{self.machine_name}_sourcebox"
+        source.mother = sourcebox.name
         source.particle = "gamma"
         source.position.type = "disc"
         source.position.radius = 0 * mm
 
         source.direction_relative_to_volume = True
-        source.direction.type = "iso"
-        source.direction.theta = [0 * deg, 10 * deg]
-        source.direction.phi = [0 * deg, 360 * deg]
+        source.direction.type = "histogram"
+        source.direction.histogram_theta_weight = [0, 1]
+        source.direction.histogram_theta_angle = [85 * deg, 95 * deg]
+
+        # TODO: Need real values for the anode heel effect
+        data = np.load(current_path / 'anodeheeleffect.npz')
+        source.direction.histogram_phi_weight = data['weight']
+        source.direction.histogram_phi_angle = data['angle']
 
         source.energy.type = "histogram"
         source.energy.histogram_weight = weights
         source.energy.histogram_energy = energy_bins
 
+        source.direction.acceptance_angle.volumes = [sourcebox.name]
+        source.direction.acceptance_angle.normal_flag = True
+        source.direction.acceptance_angle.normal_vector = [1, 0, 0]
+        source.direction.acceptance_angle.normal_tolerance = 5 * deg
+        source.direction.acceptance_angle.skip_policy = "SkipEvents"
+
         return source
 
     def add_collimators(self):
@@ -120,20 +131,20 @@ def add_collimators(self):
 
         collimators = [
             {
-                "translation": [75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-                "size": [5 * cm, 10 * cm, 1 * mm],
+                "translation": [37.5 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+                "size": [2.5 * cm, 5 * cm, 1 * mm],
             },
             {
-                "translation": [-75 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-                "size": [5 * cm, 10 * cm, 1 * mm],
+                "translation": [-37.5 * mm, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+                "size": [2.5 * cm, 5 * cm, 1 * mm],
             },
             {
-                "translation": [0 * cm, 75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
-                "size": [10 * cm, 5 * cm, 1 * mm],
+                "translation": [0 * cm, 37.5 * mm, -z_xray_tank / 2 * mm + 3 * mm],
+                "size": [5 * cm, 2.5 * cm, 1 * mm],
             },
             {
-                "translation": [0 * cm, -75 * mm, -z_xray_tank / 2 * mm + 3 * mm],
-                "size": [10 * cm, 5 * cm, 1 * mm],
+                "translation": [0 * cm, -37.5 * mm, -z_xray_tank / 2 * mm + 3 * mm],
+                "size": [5 * cm, 2.5 * cm, 1 * mm],
             },
         ]
 
@@ -150,20 +161,20 @@ def add_collimators(self):
         killer.mother = [f"{self.machine_name}_collimator{i+1}" for i in range(4)]
 
     def set_collimation(self, collimation1, collimation2):
-        if not 0 <= collimation1 <= 50 or not 0 <= collimation2 <= 50:
-            raise ValueError("Collimation values must be between 0 and 50 mm")
+        if not 0 <= collimation1 <= 25 or not 0 <= collimation2 <= 25:
+            raise ValueError("Collimation values must be between 0 and 25 mm")
 
-        collimation1 = 50 - collimation1
-        collimation2 = 50 - collimation2
+        collimation1 = 25 - collimation1
+        collimation2 = 25 - collimation2
 
         xray_tank = self.sim.volume_manager.get_volume(f"{self.machine_name}_xray_tank")
         z_xray_tank = xray_tank.size[2]
 
         translations = [
-            [75 * mm - collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-            [-75 * mm + collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
-            [0 * cm, 75 * mm - collimation2, -z_xray_tank / 2 * mm + 3 * mm],
-            [0 * cm, -75 * mm + collimation2, -z_xray_tank / 2 * mm + 3 * mm],
+            [37.5 * mm - collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+            [-37.5 * mm + collimation1, 0 * cm, -z_xray_tank / 2 * mm + 1 * mm],
+            [0 * cm, 37.5 * mm - collimation2, -z_xray_tank / 2 * mm + 3 * mm],
+            [0 * cm, -37.5 * mm + collimation2, -z_xray_tank / 2 * mm + 3 * mm],
         ]
 
         for i, translation in enumerate(translations):
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index 369c8793a..6d4bc0ab4 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -40,10 +40,10 @@
     kvp = 100
 
     # add a carm
-    carm = Ciosalpha(sim, kvp, source_only=True)
+    carm = Ciosalpha(sim, kvp, source_only=False)
     carm.rotation = Rotation.from_euler("ZYX", [0, 20, 0], degrees=True).as_matrix()
     carm.translation = [0 * cm, 0 * cm, 0 * cm]
-    carm.collimation = [30 * mm, 10 * mm]
+    carm.collimation = [25* mm, 25 * mm]
 
     carm.source.n = 1e6
     if sim.visu:

From d611881f5e08cf5a999891b50ea6b49f95183ce3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 09:46:48 +0000
Subject: [PATCH 12/14] [pre-commit.ci] Automatic python and c++ formatting

---
 .../opengate_lib/GateAcceptanceAngleTesterManager.cpp |  3 ++-
 core/opengate_core/opengate_lib/GateGenericSource.cpp |  3 ++-
 opengate/contrib/carm/siemensciosalpha.py             | 11 +++++++----
 opengate/tests/src/test075_siemens_cios_alpha.py      |  2 +-
 4 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp b/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
index d40899b82..1b2532043 100644
--- a/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
+++ b/core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp
@@ -42,7 +42,8 @@ void GateAcceptanceAngleTesterManager::Initialize(py::dict puser_info,
   // Cannot use SkipEvent with not a valid type of source
   if (!is_valid_type && fPolicy == AASkipEvent) {
     std::ostringstream oss;
-    oss << "Cannot use 'SkipEvent' mode without 'iso' or 'histogram' direction type";
+    oss << "Cannot use 'SkipEvent' mode without 'iso' or 'histogram' direction "
+           "type";
     Fatal(oss.str());
   }
 }
diff --git a/core/opengate_core/opengate_lib/GateGenericSource.cpp b/core/opengate_core/opengate_lib/GateGenericSource.cpp
index 0f380f933..88748a25d 100644
--- a/core/opengate_core/opengate_lib/GateGenericSource.cpp
+++ b/core/opengate_core/opengate_lib/GateGenericSource.cpp
@@ -449,7 +449,8 @@ void GateGenericSource::InitializeDirection(py::dict puser_info) {
   // set the angle acceptance volume if needed
   auto d = py::dict(puser_info["direction"]);
   auto dd = py::dict(d["acceptance_angle"]);
-  auto is_valid_type = ang->GetDistType() == "iso" || ang->GetDistType() == "user";
+  auto is_valid_type =
+      ang->GetDistType() == "iso" || ang->GetDistType() == "user";
   auto &l = fThreadLocalDataAA.Get();
   l.fAAManager = new GateAcceptanceAngleTesterManager;
   l.fAAManager->Initialize(dd, is_valid_type);
diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index b62719a25..362f1c14f 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -16,6 +16,7 @@
 
 current_path = pathlib.Path(__file__).parent.resolve()
 
+
 class Ciosalpha:
     def __init__(self, sim, kvp, source_only=False):
         self.sim = sim
@@ -95,7 +96,9 @@ def add_carm_source(self, kvp):
         sourcebox.mother = f"{self.machine_name}_xray_tank"
         sourcebox.translation = [0 * cm, 0 * cm, 10 * cm]
         sourcebox.size = [1 * cm, 1 * cm, 1 * cm]
-        sourcebox.rotation = Rotation.from_euler("ZYX", [0, 90, 90], degrees=True).as_matrix()
+        sourcebox.rotation = Rotation.from_euler(
+            "ZYX", [0, 90, 90], degrees=True
+        ).as_matrix()
 
         source = self.sim.add_source("GenericSource", f"{self.machine_name}_source")
         source.mother = sourcebox.name
@@ -109,9 +112,9 @@ def add_carm_source(self, kvp):
         source.direction.histogram_theta_angle = [85 * deg, 95 * deg]
 
         # TODO: Need real values for the anode heel effect
-        data = np.load(current_path / 'anodeheeleffect.npz')
-        source.direction.histogram_phi_weight = data['weight']
-        source.direction.histogram_phi_angle = data['angle']
+        data = np.load(current_path / "anodeheeleffect.npz")
+        source.direction.histogram_phi_weight = data["weight"]
+        source.direction.histogram_phi_angle = data["angle"]
 
         source.energy.type = "histogram"
         source.energy.histogram_weight = weights
diff --git a/opengate/tests/src/test075_siemens_cios_alpha.py b/opengate/tests/src/test075_siemens_cios_alpha.py
index 6d4bc0ab4..8845c457a 100644
--- a/opengate/tests/src/test075_siemens_cios_alpha.py
+++ b/opengate/tests/src/test075_siemens_cios_alpha.py
@@ -43,7 +43,7 @@
     carm = Ciosalpha(sim, kvp, source_only=False)
     carm.rotation = Rotation.from_euler("ZYX", [0, 20, 0], degrees=True).as_matrix()
     carm.translation = [0 * cm, 0 * cm, 0 * cm]
-    carm.collimation = [25* mm, 25 * mm]
+    carm.collimation = [25 * mm, 25 * mm]
 
     carm.source.n = 1e6
     if sim.visu:

From ec4f93c0665d5061ba0c13ca74a5b75c799e8a06 Mon Sep 17 00:00:00 2001
From: Thomas BAUDIER <thomas.baudier@creatis.insa-lyon.fr>
Date: Mon, 19 Aug 2024 16:58:34 +0200
Subject: [PATCH 13/14] Install spekpy for test075

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bba7cc5e4..5c0f229ab 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -394,6 +394,7 @@ jobs:
           fi
           pip install SimpleITK
           pip install gaga_phsp==0.7.2
+          pip install spekpy
           pip install dist/opengate_core-*-${PYTHONFOLDER}-${OSNAME}*_${PLATFORM}64.whl
           pip install dist/opengate-*.whl
           export GIT_SSL_NO_VERIFY=1

From 4bf906ca001e4a7a67b699f783b4633dd14383c5 Mon Sep 17 00:00:00 2001
From: Thomas BAUDIER <thomas.baudier@creatis.insa-lyon.fr>
Date: Wed, 21 Aug 2024 10:40:23 +0200
Subject: [PATCH 14/14] For tests 072 coinc, we need the output of
 test072_coinc_sorter_1.py

---
 opengate/contrib/carm/siemensciosalpha.py                | 2 +-
 opengate/tests/src/test068_rotation_source.py            | 2 +-
 opengate/tests/src/test072_coinc_sorter_2keepAll.py      | 9 +++++++++
 .../tests/src/test072_coinc_sorter_2removeMultiples.py   | 8 ++++++++
 4 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/opengate/contrib/carm/siemensciosalpha.py b/opengate/contrib/carm/siemensciosalpha.py
index 362f1c14f..5eb4d271a 100644
--- a/opengate/contrib/carm/siemensciosalpha.py
+++ b/opengate/contrib/carm/siemensciosalpha.py
@@ -106,7 +106,7 @@ def add_carm_source(self, kvp):
         source.position.type = "disc"
         source.position.radius = 0 * mm
 
-        source.direction_relative_to_volume = True
+        source.direction_relative_to_attached_volume = True
         source.direction.type = "histogram"
         source.direction.histogram_theta_weight = [0, 1]
         source.direction.histogram_theta_angle = [85 * deg, 95 * deg]
diff --git a/opengate/tests/src/test068_rotation_source.py b/opengate/tests/src/test068_rotation_source.py
index 96d9d40b7..9f07368d2 100755
--- a/opengate/tests/src/test068_rotation_source.py
+++ b/opengate/tests/src/test068_rotation_source.py
@@ -103,7 +103,7 @@ def test068(tab, nb_run, nb_part, nb_source):
     source3.direction.type = "iso"
     source3.direction.theta = [0 * deg, 10 * deg]
     source3.direction.phi = [0 * deg, 360 * deg]
-    source3.direction_relative_to_volume = True
+    source3.direction_relative_to_attached_volume = True
     source3.energy.type = "mono"
     source3.energy.mono = 1 * MeV
     source3.activity = n * Bq / sim.number_of_threads
diff --git a/opengate/tests/src/test072_coinc_sorter_2keepAll.py b/opengate/tests/src/test072_coinc_sorter_2keepAll.py
index 41d576fa9..92d21fc80 100755
--- a/opengate/tests/src/test072_coinc_sorter_2keepAll.py
+++ b/opengate/tests/src/test072_coinc_sorter_2keepAll.py
@@ -7,6 +7,8 @@
     coincidences_sorter,
     copy_tree_for_dump,
 )
+import os
+import subprocess
 import uproot
 
 if __name__ == "__main__":
@@ -15,6 +17,13 @@
         __file__, output_folder="test072_coinc_sorter"
     )
 
+    # The test needs the output of test072_coinc_sorter_1.py
+    # If the output of test072_coinc_sorter_1.py does not exist, create it
+    if not os.path.isfile(paths.output / "test72_output_1.root"):
+        print("---------- Begin of test072_coinc_sorter_1.py ----------")
+        subprocess.call(["python", paths.current / "test072_coinc_sorter_1.py"])
+        print("----------- End of test072_coinc_sorter_1.py -----------")
+
     # open root file
     root_filename = paths.output / "test72_output_1.root"
     print(f"Opening {root_filename} ...")
diff --git a/opengate/tests/src/test072_coinc_sorter_2removeMultiples.py b/opengate/tests/src/test072_coinc_sorter_2removeMultiples.py
index 1d80f07c6..a7ab2a952 100755
--- a/opengate/tests/src/test072_coinc_sorter_2removeMultiples.py
+++ b/opengate/tests/src/test072_coinc_sorter_2removeMultiples.py
@@ -8,6 +8,7 @@
     copy_tree_for_dump,
 )
 import uproot
+import subprocess
 import os
 
 if __name__ == "__main__":
@@ -16,6 +17,13 @@
         __file__, output_folder="test072_coinc_sorter"
     )
 
+    # The test needs the output of test072_coinc_sorter_1.py
+    # If the output of test072_coinc_sorter_1.py does not exist, create it
+    if not os.path.isfile(paths.output / "test72_output_1.root"):
+        print("---------- Begin of test072_coinc_sorter_1.py ----------")
+        subprocess.call(["python", paths.current / "test072_coinc_sorter_1.py"])
+        print("----------- End of test072_coinc_sorter_1.py -----------")
+
     # open root file
     root_filename = paths.output / "test72_output_1.root"
     print(f"Opening {root_filename} ...")