From 9df14972fc54b5d37fe43bef01c46a7a0f57349e Mon Sep 17 00:00:00 2001
From: Nils Krah <krah.nils@gmail.com>
Date: Fri, 20 Sep 2024 18:16:44 +0200
Subject: [PATCH 01/19] Implement setter_hook for output_filename for
 StatsActor and remove property

---
 opengate/actors/miscactors.py | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/opengate/actors/miscactors.py b/opengate/actors/miscactors.py
index 4d1ac60a4..50fb1e63b 100644
--- a/opengate/actors/miscactors.py
+++ b/opengate/actors/miscactors.py
@@ -8,6 +8,15 @@
 from ..exception import warning
 
 
+def _setter_hook_output_filename(self, output_filename):
+    # By default, write_to_disk is False.
+    # However, if user actively sets the output_filename
+    # s/he most likely wants to write to disk also
+    if output_filename != "" and output_filename is not None:
+        self.write_to_disk = True
+    return output_filename
+
+
 class ActorOutputStatisticsActor(ActorOutputBase):
     """This is a hand-crafted ActorOutput specifically for the SimulationStatisticsActor."""
 
@@ -28,9 +37,9 @@ class ActorOutputStatisticsActor(ActorOutputBase):
             "auto",
             {
                 "doc": "Filename for the data represented by this actor output. "
-                "Relative paths and filenames are taken "
-                "relative to the global simulation output folder "
-                "set via the Simulation.output_dir option. ",
+                       "Relative paths and filenames are taken "
+                       "relative to the global simulation output folder "
+                       "set via the Simulation.output_dir option. ",
             },
         ),
         "write_to_disk": (
@@ -215,16 +224,6 @@ def __str__(self):
     def counts(self):
         return self.user_output.stats.merged_data
 
-    @ActorBase.output_filename.setter
-    def output_filename(self, val):
-        # special behavior:
-        # By default write_to_disk is False.
-        # However, if user set the output_filename while it is the default (auto)
-        # we set write_to_disk to True.
-        if self.output_filename == "auto":
-            self.write_to_disk = True
-        ActorBase.output_filename.fset(self, val)
-
     def store_output_data(self, output_name, run_index, *data):
         raise NotImplementedError
 
@@ -311,7 +310,6 @@ def _setter_hook_particles(self, value):
 
 
 class SplittingActorBase(ActorBase):
-
     # hints for IDE
     splitting_factor: int
     bias_primary_only: bool
@@ -350,7 +348,6 @@ class SplittingActorBase(ActorBase):
 
 
 class ComptSplittingActor(SplittingActorBase, g4.GateOptrComptSplittingActor):
-
     # hints for IDE
     weight_threshold: float
     min_weight_of_particle: float
@@ -415,7 +412,6 @@ def initialize(self):
 
 
 class BremSplittingActor(SplittingActorBase, g4.GateBOptrBremSplittingActor):
-
     # hints for IDE
     processes: list
 

From 9f6765c9a2002d3bf39bad5e64c1b301ead331f8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 20 Sep 2024 16:20:54 +0000
Subject: [PATCH 02/19] [pre-commit.ci] Automatic python and c++ formatting

---
 opengate/actors/miscactors.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/opengate/actors/miscactors.py b/opengate/actors/miscactors.py
index 50fb1e63b..7e5ed62d4 100644
--- a/opengate/actors/miscactors.py
+++ b/opengate/actors/miscactors.py
@@ -37,9 +37,9 @@ class ActorOutputStatisticsActor(ActorOutputBase):
             "auto",
             {
                 "doc": "Filename for the data represented by this actor output. "
-                       "Relative paths and filenames are taken "
-                       "relative to the global simulation output folder "
-                       "set via the Simulation.output_dir option. ",
+                "Relative paths and filenames are taken "
+                "relative to the global simulation output folder "
+                "set via the Simulation.output_dir option. ",
             },
         ),
         "write_to_disk": (

From 1d25696a6b804343fcf47a36d6fcbf5d66e52c43 Mon Sep 17 00:00:00 2001
From: Nils Krah <krah.nils@gmail.com>
Date: Fri, 20 Sep 2024 18:33:57 +0200
Subject: [PATCH 03/19] Implement a warning cache iin the Simulation class

---
 opengate/base.py     |  4 ++++
 opengate/engines.py  | 14 +++++++++++---
 opengate/managers.py |  6 ++++++
 opengate/physics.py  |  2 +-
 4 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/opengate/base.py b/opengate/base.py
index 6ccc18072..838d8b776 100644
--- a/opengate/base.py
+++ b/opengate/base.py
@@ -550,6 +550,10 @@ def from_dictionary(self, d):
                             f"In that case, simply ignore the warning. "
                         )
 
+    def warning(self, message):
+        self.simulation._warnings.append(message)
+        warning(message)
+
 
 class DynamicGateObject(GateObject):
 
diff --git a/opengate/engines.py b/opengate/engines.py
index 7412b21cf..fae1fcb88 100644
--- a/opengate/engines.py
+++ b/opengate/engines.py
@@ -101,7 +101,7 @@ def initialize(self, run_timing_intervals, progress_bar=False):
         self.run_timing_intervals = run_timing_intervals
         assert_run_timing(self.run_timing_intervals)
         if len(self.simulation_engine.simulation.source_manager.user_info_sources) == 0:
-            warning(f"No source: no particle will be generated")
+            self.simulation_engine.simulation.warning(f"No source: no particle will be generated")
         self.progress_bar = progress_bar
 
     def initialize_actors(self):
@@ -323,7 +323,7 @@ def initialize_global_cuts(self):
 
         # range
         if ui.energy_range_min is not None and ui.energy_range_max is not None:
-            warning(f"WARNING ! SetEnergyRange only works in MT mode")
+            self.simulation_engine.simulation.warning(f"WARNING ! SetEnergyRange only works in MT mode")
             pct = g4.G4ProductionCutsTable.GetProductionCutsTable()
             pct.SetEnergyRange(ui.energy_range_min, ui.energy_range_max)
 
@@ -424,7 +424,7 @@ def initialize_optical_material_properties(self):
                         self.g4_optical_material_tables[str(material_name)]
                     )
                 else:
-                    warning(
+                    self.simulation_engine.simulation.warning(
                         f"Could not load the optical material properties for material {material_name} "
                         f"found in volume {vol.name} from file {self.physics_manager.optical_properties_file}."
                     )
@@ -1153,6 +1153,14 @@ def run_engine(self):
         output.current_random_seed = self.current_random_seed
         output.expected_number_of_events = self.source_engine.expected_number_of_events
 
+        if len(self.simulation.warnings) > 0:
+            print("*" * 20)
+            print(f"{len(self.simulation.warnings)} warnings occurred in this simulation: ")
+            for w in self.simulation.warnings:
+                print(w)
+                print("-" * 10)
+            print("*" * 20)
+
         return output
 
     def start_and_stop(self):
diff --git a/opengate/managers.py b/opengate/managers.py
index 1b31a0591..b53aa00cb 100644
--- a/opengate/managers.py
+++ b/opengate/managers.py
@@ -1422,6 +1422,8 @@ def __init__(self, name="simulation"):
 
         # read-only info
         self._current_random_seed = None
+        self._warnings = []  # list to store warning messages issued somewhere in the simulation
+
 
     def __str__(self):
         s = (
@@ -1453,6 +1455,10 @@ def world(self):
     def current_random_seed(self):
         return self._current_random_seed
 
+    @property
+    def warnings(self):
+        return self._warnings
+
     def to_dictionary(self):
         d = super().to_dictionary()
         d["volume_manager"] = self.volume_manager.to_dictionary()
diff --git a/opengate/physics.py b/opengate/physics.py
index 822a32b0b..76a01e5e9 100644
--- a/opengate/physics.py
+++ b/opengate/physics.py
@@ -87,7 +87,7 @@ def ConstructProcess(self):
             ]
 
         if len(particle_keys_to_consider) == 0:
-            warning(
+            self.physics_engine.simulation_engine.simulation.warning(
                 "user_limits_particles is False for all particles. No tracking cuts will be applied. Use sim.physics_manager.set_user_limits_particles()."
             )
 

From 49f87ae5ae4f732a21b260fb3b4085e29c4a6a6e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 20 Sep 2024 16:41:11 +0000
Subject: [PATCH 04/19] [pre-commit.ci] Automatic python and c++ formatting

---
 opengate/engines.py  | 12 +++++++++---
 opengate/managers.py |  5 +++--
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/opengate/engines.py b/opengate/engines.py
index fae1fcb88..6dea928f8 100644
--- a/opengate/engines.py
+++ b/opengate/engines.py
@@ -101,7 +101,9 @@ def initialize(self, run_timing_intervals, progress_bar=False):
         self.run_timing_intervals = run_timing_intervals
         assert_run_timing(self.run_timing_intervals)
         if len(self.simulation_engine.simulation.source_manager.user_info_sources) == 0:
-            self.simulation_engine.simulation.warning(f"No source: no particle will be generated")
+            self.simulation_engine.simulation.warning(
+                f"No source: no particle will be generated"
+            )
         self.progress_bar = progress_bar
 
     def initialize_actors(self):
@@ -323,7 +325,9 @@ def initialize_global_cuts(self):
 
         # range
         if ui.energy_range_min is not None and ui.energy_range_max is not None:
-            self.simulation_engine.simulation.warning(f"WARNING ! SetEnergyRange only works in MT mode")
+            self.simulation_engine.simulation.warning(
+                f"WARNING ! SetEnergyRange only works in MT mode"
+            )
             pct = g4.G4ProductionCutsTable.GetProductionCutsTable()
             pct.SetEnergyRange(ui.energy_range_min, ui.energy_range_max)
 
@@ -1155,7 +1159,9 @@ def run_engine(self):
 
         if len(self.simulation.warnings) > 0:
             print("*" * 20)
-            print(f"{len(self.simulation.warnings)} warnings occurred in this simulation: ")
+            print(
+                f"{len(self.simulation.warnings)} warnings occurred in this simulation: "
+            )
             for w in self.simulation.warnings:
                 print(w)
                 print("-" * 10)
diff --git a/opengate/managers.py b/opengate/managers.py
index b53aa00cb..44f7cffb7 100644
--- a/opengate/managers.py
+++ b/opengate/managers.py
@@ -1422,8 +1422,9 @@ def __init__(self, name="simulation"):
 
         # read-only info
         self._current_random_seed = None
-        self._warnings = []  # list to store warning messages issued somewhere in the simulation
-
+        self._warnings = (
+            []
+        )  # list to store warning messages issued somewhere in the simulation
 
     def __str__(self):
         s = (

From ac76bd8b9b1a691eb1d974189ef56c022fee35bf Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Fri, 20 Sep 2024 18:40:40 +0200
Subject: [PATCH 05/19] update tolerance

---
 ...Nthreads.py => test041_dose_actor_mt_cp_images_n_threads.py} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename opengate/tests/src/{test041_dose_actor_mt_cp_images_Nthreads.py => test041_dose_actor_mt_cp_images_n_threads.py} (99%)

diff --git a/opengate/tests/src/test041_dose_actor_mt_cp_images_Nthreads.py b/opengate/tests/src/test041_dose_actor_mt_cp_images_n_threads.py
similarity index 99%
rename from opengate/tests/src/test041_dose_actor_mt_cp_images_Nthreads.py
rename to opengate/tests/src/test041_dose_actor_mt_cp_images_n_threads.py
index 7a48754b3..97a607bfe 100755
--- a/opengate/tests/src/test041_dose_actor_mt_cp_images_Nthreads.py
+++ b/opengate/tests/src/test041_dose_actor_mt_cp_images_n_threads.py
@@ -121,7 +121,7 @@ def run_test(doseFpath_IDD_singleImage, doseFpath_IDD_NthreadImages, stat):
         expected_ratio,
         doseFpath_IDD_singleImage,
         doseFpath_IDD_NthreadImages,
-        abs_tolerance=0.03,
+        abs_tolerance=0.05,
     )
     return is_ok
 

From 96b1708c3967a32ae4ec345f7fe3b912c6996e15 Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Fri, 20 Sep 2024 18:41:35 +0200
Subject: [PATCH 06/19] error message updated

---
 opengate/managers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opengate/managers.py b/opengate/managers.py
index 1b31a0591..08b164695 100644
--- a/opengate/managers.py
+++ b/opengate/managers.py
@@ -395,7 +395,7 @@ def dump_actor_types(self):
 
     def get_actor_user_info(self, name):
         warning(
-            f"Deprecation warning: This function will soon be removed."
+            f"Deprecation warning: The function 'get_actor_user_info' will soon be removed."
             f"Use my_actor.user_info instead, where 'my_actor' "
             f"should be replace by your actor object. "
             f"You can also access user input parameters directly, e.g. my_actor.attached_to=..."

From b1c07364069d597352ff530836afd4c87393f7fe Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Tue, 24 Sep 2024 20:58:26 +0200
Subject: [PATCH 07/19] Refactor digitizer actor to use properties for size and
 spacing

Removed the setter hooks for size and spacing and replaced them with output_size and output_spacing properties. This change simplifies the code and maintains the functionality of ensuring that size and spacing are treated as 2D vectors with an appended third dimension of 1.
---
 opengate/actors/digitizers.py | 62 ++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 34 deletions(-)

diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index baac7b6c7..7dc8c677f 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -762,28 +762,6 @@ def EndSimulationAction(self):
         g4.GateDigitizerHitsCollectionActor.EndSimulationAction(self)
 
 
-def _setter_hook_size_projection_actor(self, size):
-    size = list(size)
-    if len(size) != 2:
-        fatal(
-            f"Error, the size must be a 2-vector (2D) while it is {size}. "
-            f"Note: The size along the third dimension is automatically set to 1."
-        )
-    size.append(1)
-    return size
-
-
-def _setter_hook_spacing_projection_actor(self, spacing):
-    spacing = list(spacing)
-    if len(spacing) != 2:
-        fatal(
-            f"Error, the spacing must be a 2-vector (2D) while it is {spacing}. "
-            f"Note: The spacing along the third dimension is automatically determined."
-        )
-    spacing.append(1)
-    return spacing
-
-
 class DigitizerProjectionActor(ActorBase, g4.GateDigitizerProjectionActor):
     """
     This actor takes as input HitsCollections and performed binning in 2D images.
@@ -802,17 +780,11 @@ class DigitizerProjectionActor(ActorBase, g4.GateDigitizerProjectionActor):
         ),
         "spacing": (
             [4 * g4_units.mm, 4 * g4_units.mm],
-            {
-                "doc": "FIXME",
-                "setter_hook": _setter_hook_spacing_projection_actor,
-            },
+            {"doc": "FIXME"},
         ),
         "size": (
             [128, 128],
-            {
-                "doc": "FIXME",
-                "setter_hook": _setter_hook_size_projection_actor,
-            },
+            {"doc": "FIXME"},
         ),
         "physical_volume_index": (
             0,
@@ -853,12 +825,34 @@ def initialize(self):
                 f"Sorry, cannot (yet) use several attached_to volumes for "
                 f"DigitizerProjectionActor {self.user_info.name}"
             )
-
         ActorBase.initialize(self)
-
         self.InitializeUserInput(self.user_info)
         self.InitializeCpp()
 
+    @property
+    def output_size(self):
+        # consider 3D images, third dimension can be the energy windows
+        output_size = list(self.size)
+        if len(output_size) != 2:
+            fatal(
+                f"Error, the size must be a 2-vector (2D) while it is {output_size}. "
+                f"Note: The size along the third dimension is automatically set to 1."
+            )
+        output_size.append(1)
+        return output_size
+
+    @property
+    def output_spacing(self):
+        # consider 3D images, third dimension can be the energy windows
+        output_spacing = list(self.spacing)
+        if len(output_spacing) != 2:
+            fatal(
+                f"Error, the spacing must be a 2-vector (2D) while it is {output_spacing}. "
+                f"Note: The spacing along the third dimension is automatically set to 1."
+            )
+        output_spacing.append(1)
+        return output_spacing
+
     def compute_thickness(self, volume, channels):
         """
         Get the thickness of the detector volume, in the correct direction.
@@ -887,8 +881,8 @@ def StartSimulationAction(self):
 
         # define the new size and spacing according to the nb of channels
         # and according to the volume shape
-        size = self.size
-        spacing = self.spacing
+        size = self.output_size
+        spacing = self.output_spacing
         size[2] = len(self.input_digi_collections) * len(
             self.simulation.run_timing_intervals
         )

From 226451010eac43315c44e859e47e7eacfeb4920e Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Tue, 24 Sep 2024 20:58:47 +0200
Subject: [PATCH 08/19] Update .gitignore to exclude save_tests directory

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 1ec8a5d0c..856bb7270 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,6 +91,7 @@ opengate_temporaire
 /opengate/tests/src/demo_code_*.py
 /opengate/tests/src/test030_save
 /opengate/tests/src/test_log*
+/opengate/tests/src/save_tests
 
 /opengate/data/isomeric_transition/save
 /opengate/data/isomeric_transition/save2

From a275a2bf69e2d64f6af70ebab8be1dd94b577392 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Wed, 25 Sep 2024 10:24:46 +0200
Subject: [PATCH 09/19] Add explicit option for authorizing repeated volumes in
 digitizers (false by default)

---
 .../opengate_lib/GateHelpersGeometry.cpp      | 11 +++++
 opengate/actors/digitizers.py                 | 47 +++++++++++++++++--
 .../src/test028_ge_nm670_spect_2_helpers.py   |  2 +-
 .../tests/src/test036_adder_depth_helpers.py  |  4 +-
 4 files changed, 58 insertions(+), 6 deletions(-)

diff --git a/core/opengate_core/opengate_lib/GateHelpersGeometry.cpp b/core/opengate_core/opengate_lib/GateHelpersGeometry.cpp
index 4febe8557..bd789b2f3 100644
--- a/core/opengate_core/opengate_lib/GateHelpersGeometry.cpp
+++ b/core/opengate_core/opengate_lib/GateHelpersGeometry.cpp
@@ -19,6 +19,17 @@ void ComputeTransformationFromVolumeToWorld(const std::string &phys_volume_name,
   auto pvs = G4PhysicalVolumeStore::GetInstance();
   while (name != "world") {
     auto phys = pvs->GetVolume(name);
+    if (phys == nullptr) {
+      std::ostringstream oss;
+      oss << "The volume '" << name
+          << "' is not found. Here is the list of volumes: ";
+      auto map = pvs->GetMap();
+      for (auto m : map) {
+        oss << m.first << " ";
+      }
+      oss << std::endl;
+      Fatal(oss.str());
+    }
     auto tr = phys->GetObjectTranslation();
     // auto rot = *phys->GetObjectRotation();
     auto rot = phys->GetObjectRotationValue();
diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index 7dc8c677f..a1e5d95b5 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -196,6 +196,18 @@ def find_first_module(self, s):
 class DigitizerBase(ActorBase):
     _output_name_root = "root_output"
 
+    # hints for IDE
+    authorize_repeated_volumes: bool
+
+    user_info_defaults = {
+        "authorize_repeated_volumes": (
+            False,
+            {
+                "doc": "User must say explicitly that the digitizer can work with repeated volumes",
+            },
+        ),
+    }
+
     def __init__(self, *args, **kwargs):
         super().__init__(self, *args, **kwargs)
 
@@ -215,6 +227,22 @@ def _add_user_output_root(self, **kwargs):
             )
         return self._add_user_output(ActorOutputRoot, self._output_name_root, **kwargs)
 
+    def initialize(self):
+        ActorBase.initialize(self)
+        if self.authorize_repeated_volumes is True:
+            return
+        vm = self.simulation.volume_manager
+        current = vm.volumes[self.attached_to]
+        while current.name != "world":
+            if len(current.g4_transform) > 1:
+                fatal(
+                    f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}. "
+                    f"However, this volume is a daughter of the repeated volume '{current.name}'. It means it will "
+                    f"gather data from all repeated instances. If you are "
+                    f"sure, enable the option 'authorize_repeated_volumes'."
+                )
+            current = current.parent
+
 
 class DigitizerAdderActor(DigitizerBase, g4.GateDigitizerAdderActor):
     """
@@ -563,11 +591,12 @@ def initialize_blurring_parameters(self):
 
     def initialize(self):
         self.initialize_blurring_parameters()
-        ActorBase.initialize(self)
+        DigitizerBase.initialize(self)
         self.InitializeUserInput(self.user_info)
         self.InitializeCpp()
 
     def StartSimulationAction(self):
+        DigitizerBase.StartSimulationAction(self)
         g4.GateDigitizerSpatialBlurringActor.StartSimulationAction(self)
 
     def EndSimulationAction(self):
@@ -629,11 +658,12 @@ def initialize_blurring_parameters(self):
 
     def initialize(self):
         self.initialize_blurring_parameters()
-        ActorBase.initialize(self)
+        DigitizerBase.initialize(self)
         self.InitializeUserInput(self.user_info)
         self.InitializeCpp()
 
     def StartSimulationAction(self):
+        DigitizerBase.StartSimulationAction(self)
         g4.GateDigitizerEfficiencyActor.StartSimulationAction(self)
 
     def EndSimulationAction(self):
@@ -762,7 +792,7 @@ def EndSimulationAction(self):
         g4.GateDigitizerHitsCollectionActor.EndSimulationAction(self)
 
 
-class DigitizerProjectionActor(ActorBase, g4.GateDigitizerProjectionActor):
+class DigitizerProjectionActor(DigitizerBase, g4.GateDigitizerProjectionActor):
     """
     This actor takes as input HitsCollections and performed binning in 2D images.
     If there are several HitsCollection as input, the slices will correspond to each HC.
@@ -825,7 +855,12 @@ def initialize(self):
                 f"Sorry, cannot (yet) use several attached_to volumes for "
                 f"DigitizerProjectionActor {self.user_info.name}"
             )
-        ActorBase.initialize(self)
+        if self.authorize_repeated_volumes is True:
+            fatal(
+                f"Sorry, cannot (yet) use ProjectionActor with repeated volumes, "
+                f"set 'authorize_repeated_volumes' to False"
+            )
+        DigitizerBase.initialize(self)
         self.InitializeUserInput(self.user_info)
         self.InitializeCpp()
 
@@ -870,6 +905,7 @@ def compute_thickness(self, volume, channels):
         return thickness
 
     def StartSimulationAction(self):
+        DigitizerBase.StartSimulationAction(self)
         # for the moment, we cannot use this actor with several volumes
         if hasattr(self.attached_to, "__len__") and not isinstance(
             self.attached_to, str
@@ -907,6 +943,7 @@ def StartSimulationAction(self):
             self.attached_to_volume, self.user_output.projection.data_per_run[0].image
         )
         self.fPhysicalVolumeName = str(pv.GetName())
+        print(self.fPhysicalVolumeName)
 
         # update the cpp image and start
         update_image_py_to_cpp(
@@ -976,6 +1013,7 @@ def __initcpp__(self):
         self.AddActions({"StartSimulationAction", "EndSimulationAction"})
 
     def StartSimulationAction(self):
+        DigitizerBase.StartSimulationAction(self)
         DigitizerAdderActor.set_group_by_depth(self)
         if self.user_info.discretize_volume is None:
             fatal(f'Please, set the option "discretize_volume"')
@@ -1045,6 +1083,7 @@ def initialize(self):
         self.InitializeCpp()
 
     def StartSimulationAction(self):
+        DigitizerBase.StartSimulationAction(self)
         g4.GatePhaseSpaceActor.StartSimulationAction(self)
 
     def EndSimulationAction(self):
diff --git a/opengate/tests/src/test028_ge_nm670_spect_2_helpers.py b/opengate/tests/src/test028_ge_nm670_spect_2_helpers.py
index 25353cccb..9924a716e 100644
--- a/opengate/tests/src/test028_ge_nm670_spect_2_helpers.py
+++ b/opengate/tests/src/test028_ge_nm670_spect_2_helpers.py
@@ -342,7 +342,7 @@ def test_spect_proj(sim, paths, proj, version="3"):
     print("Compare images (old spacing/origin)")
     # read image and force change the offset to be similar to old Gate
     img = itk.imread(str(paths.output / "proj028.mhd"))
-    spacing = np.array(proj.user_info.spacing)
+    spacing = np.array(proj.projection.image.GetSpacing())  # user_info.spacing)
     origin = spacing / 2.0
     origin[2] = 0.5
     spacing[2] = 1
diff --git a/opengate/tests/src/test036_adder_depth_helpers.py b/opengate/tests/src/test036_adder_depth_helpers.py
index e67193d46..09376d29a 100644
--- a/opengate/tests/src/test036_adder_depth_helpers.py
+++ b/opengate/tests/src/test036_adder_depth_helpers.py
@@ -118,6 +118,7 @@ def create_simulation(geom, paths):
     # hits collection
     hc = sim.add_actor("DigitizerHitsCollectionActor", "Hits")
     hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
     hc.output_filename = "test036.root"
     hc.attributes = [
         "KineticEnergy",
@@ -134,6 +135,7 @@ def create_simulation(geom, paths):
     # singles collection
     sc = sim.add_actor("DigitizerAdderActor", "Singles")
     sc.attached_to = crystal.name
+    sc.authorize_repeated_volumes = True
     sc.input_digi_collection = "Hits"
     # sc.policy = 'EnergyWinnerPosition'
     sc.policy = "EnergyWeightedCentroidPosition"
@@ -148,7 +150,7 @@ def create_simulation(geom, paths):
     # print cuts
     print(sim.physics_manager.dump_production_cuts())
 
-    # add a user hook function to dump production cuts frmo Geant4
+    # add a user hook function to dump production cuts from Geant4
     sim.user_hook_after_init = check_production_cuts
 
     return sim

From 2442af081ee9b3a7cc82c4f6ee649fa858f42b35 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Wed, 25 Sep 2024 16:02:17 +0200
Subject: [PATCH 10/19] Handle null process and empty collections in digitizer
 actor.

Added null check for process in GateDigitizerHitsCollectionActor to prevent potential crashes. Additionally, included a safeguard for empty collections in GateDigiCollection::DumpLastDigi to avoid returning invalid data.
---
 .../opengate_lib/digitizer/GateDigiCollection.cpp    |  2 ++
 .../digitizer/GateDigitizerHitsCollectionActor.cpp   | 12 +++++++-----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/core/opengate_core/opengate_lib/digitizer/GateDigiCollection.cpp b/core/opengate_core/opengate_lib/digitizer/GateDigiCollection.cpp
index fdd7780b6..8880be26b 100644
--- a/core/opengate_core/opengate_lib/digitizer/GateDigiCollection.cpp
+++ b/core/opengate_core/opengate_lib/digitizer/GateDigiCollection.cpp
@@ -224,6 +224,8 @@ GateDigiCollection::Iterator GateDigiCollection::NewIterator() {
 }
 
 std::string GateDigiCollection::DumpLastDigi() const {
+  if (GetSize() == 0)
+    return "";
   std::ostringstream oss;
   auto n = GetSize() - 1;
   for (auto *att : fDigiAttributes) {
diff --git a/core/opengate_core/opengate_lib/digitizer/GateDigitizerHitsCollectionActor.cpp b/core/opengate_core/opengate_lib/digitizer/GateDigitizerHitsCollectionActor.cpp
index a54d178a8..d5ba13da3 100644
--- a/core/opengate_core/opengate_lib/digitizer/GateDigitizerHitsCollectionActor.cpp
+++ b/core/opengate_core/opengate_lib/digitizer/GateDigitizerHitsCollectionActor.cpp
@@ -98,11 +98,13 @@ void GateDigitizerHitsCollectionActor::SteppingAction(G4Step *step) {
     // nb transportation
     auto post = step->GetPostStepPoint();
     auto process = post->GetProcessDefinedStep();
-    auto pname = process->GetProcessName();
-    static int nb_tr = 0;
-    if (pname == "Transportation") {
-      nb_tr++;
-      std::cout << pname << " " << nb_tr << " " << id << x << std::endl;
+    if (process != nullptr) {
+      auto pname = process->GetProcessName();
+      static int nb_tr = 0;
+      if (pname == "Transportation") {
+        nb_tr++;
+        std::cout << pname << " " << nb_tr << " " << id << x << std::endl;
+      }
     }
   }
 }

From 6e32ccf2910d9e9f0cb27f67e70554af32c11715 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 13:09:16 +0200
Subject: [PATCH 11/19] Add tests for DigitizerProjectionActor handling
 repeated volumes (prevent errors)

Introduced new test cases for the DigitizerProjectionActor, including scenarios with repeated volumes and invalid configurations. Enhanced the actor to handle lists/tuples for the `attached_to` property and added validations to prevent inappropriate attachment to parameterized volumes.
---
 opengate/actors/digitizers.py                 | 60 +++++++++++++++----
 .../tests/src/test036_adder_depth_helpers.py  | 25 ++++----
 opengate/tests/src/test036_proj_param_1.py    | 58 ++++++++++++++++++
 .../src/test036_proj_param_2_with_index.py    | 45 ++++++++++++++
 .../test036_proj_param_3_no_parent_repeat.py  | 33 ++++++++++
 ...t036_proj_param_4_not_attached_to_param.py | 39 ++++++++++++
 .../src/test037_pet_hits_singles_helpers.py   |  1 +
 7 files changed, 237 insertions(+), 24 deletions(-)
 create mode 100755 opengate/tests/src/test036_proj_param_1.py
 create mode 100755 opengate/tests/src/test036_proj_param_2_with_index.py
 create mode 100755 opengate/tests/src/test036_proj_param_3_no_parent_repeat.py
 create mode 100755 opengate/tests/src/test036_proj_param_4_not_attached_to_param.py

diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index a1e5d95b5..0fb7d3843 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -1,11 +1,13 @@
+from typing import List
+
 import numpy as np
 from scipy.spatial.transform import Rotation
 
 import opengate_core as g4
+from anytree import NodeMixin
 from .base import ActorBase
 from ..exception import fatal, warning
 from ..definitions import fwhm_to_sigma
-
 from ..utility import g4_units
 from ..image import (
     align_image_with_physical_volume,
@@ -232,16 +234,20 @@ def initialize(self):
         if self.authorize_repeated_volumes is True:
             return
         vm = self.simulation.volume_manager
-        current = vm.volumes[self.attached_to]
-        while current.name != "world":
-            if len(current.g4_transform) > 1:
-                fatal(
-                    f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}. "
-                    f"However, this volume is a daughter of the repeated volume '{current.name}'. It means it will "
-                    f"gather data from all repeated instances. If you are "
-                    f"sure, enable the option 'authorize_repeated_volumes'."
-                )
-            current = current.parent
+        att = self.attached_to
+        if not isinstance(self.attached_to, (list, tuple)):
+            att = [self.attached_to]
+        for a in att:
+            current = self.simulation.volume_manager.get_volume(a).parent
+            while current.name != "world" and not isinstance(current, NodeMixin):
+                if len(current.g4_transform) > 1:
+                    fatal(
+                        f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}. "
+                        f"However, this volume is a daughter of the repeated volume '{current.name}'. It means it will "
+                        f"gather data from all repeated instances. If you are "
+                        f"sure, enable the option 'authorize_repeated_volumes'."
+                    )
+                    current = current.parent
 
 
 class DigitizerAdderActor(DigitizerBase, g4.GateDigitizerAdderActor):
@@ -799,6 +805,14 @@ class DigitizerProjectionActor(DigitizerBase, g4.GateDigitizerProjectionActor):
     If there are several runs, images will also be slice-stacked.
     """
 
+    # hints for IDE
+    input_digi_collections: List[str]
+    spacing: List[float]
+    size: List[int]
+    physical_volume_index: int
+    origin_as_image_center: bool
+    detector_orientation_matrix: np.ndarray
+
     user_info_defaults = {
         # FIXME: implement a setter hook so the user can provided digitizer instances instead of their name,
         # like in attached_to
@@ -817,9 +831,9 @@ class DigitizerProjectionActor(DigitizerBase, g4.GateDigitizerProjectionActor):
             {"doc": "FIXME"},
         ),
         "physical_volume_index": (
-            0,
+            -1,
             {
-                "doc": "FIXME",
+                "doc": "When attached to a repeated volume, this option indicate which copy is used",
             },
         ),
         "origin_as_image_center": (
@@ -894,6 +908,13 @@ def compute_thickness(self, volume, channels):
         By default, it is Z. We use the 'projection_orientation' to get the correct one.
         """
         vol = self.actor_engine.simulation_engine.volume_engine.get_volume(volume)
+        if len(vol.g4_physical_volumes) < 1:
+            fatal(
+                f"The actor {self.name} is attached to '{self.attached_to}' which has "
+                f"no associated g4_physical_volumes (probably a parameterized volume?) and cannot "
+                f"be used. Try to attach it to the mother volume of the parameterized volume."
+            )
+
         solid = vol.g4_physical_volumes[0].GetLogicalVolume().GetSolid()
         pMin = g4.G4ThreeVector()
         pMax = g4.G4ThreeVector()
@@ -929,6 +950,19 @@ def StartSimulationAction(self):
         # to be able to work on a per-run basis
         self.user_output.projection.create_empty_image(0, size, spacing)
 
+        # check physical_volume_index and number of repeating
+        n = len(self.attached_to_volume.g4_physical_volumes)
+        if n > 1:
+            if self.physical_volume_index >= n or self.physical_volume_index < 0:
+                fatal(
+                    f"The actor '{self.name}' is attached to '{self.attached_to}' which is repeated {n} times. "
+                    f"You must set a valid 'physical_volume_index' between O to {n-1} while "
+                    f"it is {self.physical_volume_index}."
+                )
+        else:
+            # force the index to be zero
+            self.physical_volume_index = 0
+
         # initial position (will be anyway updated in BeginOfRunSimulation)
         try:
             pv = self.attached_to_volume.g4_physical_volumes[self.physical_volume_index]
diff --git a/opengate/tests/src/test036_adder_depth_helpers.py b/opengate/tests/src/test036_adder_depth_helpers.py
index 09376d29a..ede0281ca 100644
--- a/opengate/tests/src/test036_adder_depth_helpers.py
+++ b/opengate/tests/src/test036_adder_depth_helpers.py
@@ -187,17 +187,20 @@ def test_output(sim, paths):
     scalings = [1.0] * len(scalings2)
     tols[2] = 2  # Z
     # tols[4] = 0.01  # energy
-    is_ok = utility.compare_root3(
-        gate_file,
-        hc.get_output_path(),
-        "Hits",
-        "Hits",
-        keys1,
-        keys2,
-        tols,
-        scalings,
-        scalings2,
-        paths.output / "test036_hits.png",
+    is_ok = (
+        utility.compare_root3(
+            gate_file,
+            hc.get_output_path(),
+            "Hits",
+            "Hits",
+            keys1,
+            keys2,
+            tols,
+            scalings,
+            scalings2,
+            paths.output / "test036_hits.png",
+        )
+        and is_ok
     )
 
     # Root compare SINGLES
diff --git a/opengate/tests/src/test036_proj_param_1.py b/opengate/tests/src/test036_proj_param_1.py
new file mode 100755
index 000000000..82450b199
--- /dev/null
+++ b/opengate/tests/src/test036_proj_param_1.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import test036_adder_depth_helpers as t036
+from opengate.tests import utility
+from opengate import g4_units
+
+if __name__ == "__main__":
+    paths = utility.get_default_test_paths(
+        __file__, "gate_test036_adder_depth", "test036"
+    )
+
+    # create and run the simulation
+    mm = g4_units.mm
+    sim = t036.create_simulation("param", paths)
+
+    # sim.visu = True
+    sim.visu_type = "qt"
+
+    # remove one head
+    head = sim.volume_manager.get_volume("SPECThead")
+    head.translation = head.translation[0]
+    head.rotation = head.rotation[0]
+
+    # enlarge the source
+    source = sim.source_manager.get_source_info("src2")
+    source.position.radius = 150 * mm
+
+    if sim.visu:
+        source = sim.source_manager.get_source_info("src2")
+        source.activity = source.activity / 1000
+        source = sim.source_manager.get_source_info("src1")
+        source.activity = source.activity / 1000
+
+    # add a proj actor
+    proj = sim.add_actor("DigitizerProjectionActor", "proj")
+    proj.attached_to = "crystal"
+    proj.output_filename = "proj1.mha"
+    proj.size = [128, 128]
+    proj.spacing = [5 * mm, 5 * mm]
+
+    # start simulation
+    sim.run()
+
+    # test the output
+    stats = sim.get_actor("Stats")
+    is_ok = utility.assert_images(
+        paths.output_ref / proj.output_filename,
+        proj.get_output_path(),
+        stats,
+        tolerance=38,
+        ignore_value=0,
+        axis="y",
+        sum_tolerance=1.5,
+        fig_name=paths.output / f"proj.png",
+    )
+    utility.print_test(is_ok, f"Compare image proj:")
+    utility.test_ok(is_ok)
diff --git a/opengate/tests/src/test036_proj_param_2_with_index.py b/opengate/tests/src/test036_proj_param_2_with_index.py
new file mode 100755
index 000000000..fa999108f
--- /dev/null
+++ b/opengate/tests/src/test036_proj_param_2_with_index.py
@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import test036_adder_depth_helpers as t036
+from opengate.tests import utility
+from opengate import g4_units
+
+if __name__ == "__main__":
+    paths = utility.get_default_test_paths(
+        __file__, "gate_test036_adder_depth", "test036"
+    )
+
+    # create and run the simulation
+    mm = g4_units.mm
+    sim = t036.create_simulation("param", paths)
+
+    # enlarge the source
+    source = sim.source_manager.get_source_info("src2")
+    source.position.radius = 150 * mm
+
+    # add a proj actor to a repeated volume
+    proj = sim.add_actor("DigitizerProjectionActor", "proj2")
+    proj.attached_to = "SPECThead"  # <-- there is two copy
+    proj.physical_volume_index = 0  # <-- the first one is considered
+    proj.output_filename = "proj2.mha"
+    proj.size = [128, 128]
+    proj.spacing = [5 * mm, 5 * mm]
+
+    # start simulation
+    sim.run()
+
+    # test the output
+    stats = sim.get_actor("Stats")
+    is_ok = utility.assert_images(
+        paths.output_ref / "proj1.mha",
+        proj.get_output_path(),
+        stats,
+        tolerance=38,
+        ignore_value=0,
+        axis="y",
+        sum_tolerance=1.5,
+        fig_name=paths.output / f"proj_index.png",
+    )
+    utility.print_test(is_ok, f"Compare image proj:")
+    utility.test_ok(is_ok)
diff --git a/opengate/tests/src/test036_proj_param_3_no_parent_repeat.py b/opengate/tests/src/test036_proj_param_3_no_parent_repeat.py
new file mode 100755
index 000000000..2058af678
--- /dev/null
+++ b/opengate/tests/src/test036_proj_param_3_no_parent_repeat.py
@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import test036_adder_depth_helpers as t036
+from opengate.tests import utility
+from opengate import g4_units
+
+if __name__ == "__main__":
+    paths = utility.get_default_test_paths(
+        __file__, "gate_test036_adder_depth", "test036"
+    )
+
+    # create and run the simulation
+    mm = g4_units.mm
+    sim = t036.create_simulation("param", paths)
+
+    # add a proj actor: it should not run because one of its parent is repeated
+    proj = sim.add_actor("DigitizerProjectionActor", "proj")
+    proj.attached_to = "crystal"
+    proj.output_filename = "proj1.mha"
+    proj.size = [128, 128]
+    proj.spacing = [5 * mm, 5 * mm]
+
+    # start simulation
+    is_ok = True
+    try:
+        sim.run()
+        is_ok = False
+    except:
+        pass
+    utility.print_test(is_ok, f"The simulation should not run")
+
+    utility.test_ok(is_ok)
diff --git a/opengate/tests/src/test036_proj_param_4_not_attached_to_param.py b/opengate/tests/src/test036_proj_param_4_not_attached_to_param.py
new file mode 100755
index 000000000..a8fac4949
--- /dev/null
+++ b/opengate/tests/src/test036_proj_param_4_not_attached_to_param.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import test036_adder_depth_helpers as t036
+from opengate.tests import utility
+from opengate import g4_units
+
+if __name__ == "__main__":
+    paths = utility.get_default_test_paths(
+        __file__, "gate_test036_adder_depth", "test036"
+    )
+
+    # create and run the simulation
+    mm = g4_units.mm
+    sim = t036.create_simulation("param", paths)
+
+    # sim.visu = True
+    sim.visu_type = "qt"
+
+    # remove one head
+    head = sim.volume_manager.get_volume("SPECThead")
+    head.translation = head.translation[0]
+    head.rotation = head.rotation[0]
+
+    # test another case that should fail
+    proj2 = sim.add_actor("DigitizerProjectionActor", "proj2")
+    proj2.attached_to = "crystal_pixel"
+    proj2.output_filename = "proj2.mha"
+    proj2.size = [128, 128]
+    proj2.spacing = [5 * mm, 5 * mm]
+
+    is_ok = True
+    try:
+        sim.run(start_new_process=True)
+        is_ok = False
+    except:
+        pass
+    utility.print_test(is_ok, f"The run should NOT be executed: ")
+    utility.test_ok(is_ok)
diff --git a/opengate/tests/src/test037_pet_hits_singles_helpers.py b/opengate/tests/src/test037_pet_hits_singles_helpers.py
index e006beb21..0a1ea511b 100644
--- a/opengate/tests/src/test037_pet_hits_singles_helpers.py
+++ b/opengate/tests/src/test037_pet_hits_singles_helpers.py
@@ -90,6 +90,7 @@ def add_digitizer(sim, paths, nb, crystal):
     # hits collection
     hc = sim.add_actor("DigitizerHitsCollectionActor", "Hits")
     hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
     print("Crystal :", crystal.name)
     hc.output_filename = f"test037_test{nb}.root"
     hc.attributes = [

From 4af9e80cdb121ee3434d1995f000b1d6958c821e Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 13:10:35 +0200
Subject: [PATCH 12/19] data for t036

---
 opengate/tests/data | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opengate/tests/data b/opengate/tests/data
index 714c1390a..e3d68b9c3 160000
--- a/opengate/tests/data
+++ b/opengate/tests/data
@@ -1 +1 @@
-Subproject commit 714c1390a3af3f70504bc263d237fd7c29e5eb41
+Subproject commit e3d68b9c3966f990c33ff3237965792c44407e73

From 399246572f49195fcaeb0783ab5ea3f0484ad4a1 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 16:39:55 +0200
Subject: [PATCH 13/19] remove debug message

---
 opengate/base.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/opengate/base.py b/opengate/base.py
index 838d8b776..4551a56d0 100644
--- a/opengate/base.py
+++ b/opengate/base.py
@@ -411,11 +411,11 @@ def __getstate__(self):
     def __setstate__(self, d):
         """Method needed for pickling. May be overridden in inheriting classes."""
         self.__dict__ = d
-        print(
+        """print(
             f"DEBUG: in __setstate__ of {type(self).__name__}: {type(self).known_attributes}"
         )
         print(f"DEBUG:    type(self).known_attributes: {type(self).known_attributes}")
-        print(f"DEBUG:    list(self.__dict__.keys()): {list(self.__dict__.keys())}")
+        print(f"DEBUG:    list(self.__dict__.keys()): {list(self.__dict__.keys())}")"""
 
     def __reduce__(self):
         """This method is called when the object is pickled.
@@ -450,7 +450,7 @@ def __setattr__(self, key, value):
         if len(self.known_attributes) > 0:
             if key not in self.known_attributes:
                 s = ", ".join(str(a) for a in self.known_attributes)
-                warning(
+                self.warn_user(
                     f'For object "{self.name}", attribute "{key}" is not known. Maybe a typo?\n'
                     f"Known attributes of this object are: {s}"
                 )
@@ -474,7 +474,9 @@ def __finalize_init__(self):
 
         # we define this at the class-level
         type(self).known_attributes = set(
-            list(self.user_info.keys()) + list(self.__dict__.keys())
+            list(self.user_info.keys())
+            + list(self.__dict__.keys())
+            + list(["__dict__"])
         )
 
     def __add_to_simulation__(self):
@@ -550,8 +552,12 @@ def from_dictionary(self, d):
                             f"In that case, simply ignore the warning. "
                         )
 
-    def warning(self, message):
-        self.simulation._warnings.append(message)
+    def warn_user(self, message):
+        # this may be called without simulation object, so we guard with try/except
+        try:
+            self.simulation._user_warnings.append(message)
+        except:
+            pass
         warning(message)
 
 

From a7305724365e6ee34fd89273f96d658f4c4080b1 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 16:41:12 +0200
Subject: [PATCH 14/19] remove fake attributes (checked by test 78)

---
 opengate/tests/src/test006_runs.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/opengate/tests/src/test006_runs.py b/opengate/tests/src/test006_runs.py
index d1c628701..a5e781a28 100755
--- a/opengate/tests/src/test006_runs.py
+++ b/opengate/tests/src/test006_runs.py
@@ -55,7 +55,6 @@
     source3.start_time = 0.50 * sec
     source3.direction.type = "momentum"
     source3.direction.momentum = [0, 0, 1]
-    source3.toto = 120  # raise a warning
 
     # Expected total of events
     # 100 + 175 + 120 = 395

From 42fdd0b2d0d1cf0662f30365c8570dc504631bc8 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 16:41:36 +0200
Subject: [PATCH 15/19] user spacing is 2D. We need the real 3D spacing from
 the output image

---
 opengate/tests/src/test073_helpers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opengate/tests/src/test073_helpers.py b/opengate/tests/src/test073_helpers.py
index 229b99ee5..56658c98b 100644
--- a/opengate/tests/src/test073_helpers.py
+++ b/opengate/tests/src/test073_helpers.py
@@ -162,7 +162,7 @@ def compare_proj_images(crystal, sim, stats, image_filename, path, n=1):
     f1 = path / f"projections_test{n}.mhd"
     f2 = path / f"projections_test{n}_offset.mhd"
     img = itk.imread(f1)
-    spacing = np.array(proj.user_info.spacing)
+    spacing = np.array(proj.projection.image.GetSpacing())
     origin = spacing / 2.0
     origin[2] = 0.5
     spacing[2] = 1

From 3609e07634bd1f17e939a0646c4c2dd5a6c507d4 Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 16:42:06 +0200
Subject: [PATCH 16/19] Refactor warning calls to warn_user method

Replaced all instances of the deprecated warning function with the new warn_user method for consistency and clarity. Additionally, updated attribute handling in several classes to avoid unnecessary warnings and cleaned up unused imports and commented-out code.
---
 opengate/actors/actoroutput.py |  2 +-
 opengate/actors/base.py        | 16 +++++++---------
 opengate/actors/digitizers.py  | 20 +++++++++++++-------
 opengate/actors/miscactors.py  | 12 ++++++------
 opengate/engines.py            |  8 ++++----
 opengate/managers.py           | 10 +++++-----
 opengate/physics.py            |  2 +-
 7 files changed, 37 insertions(+), 33 deletions(-)

diff --git a/opengate/actors/actoroutput.py b/opengate/actors/actoroutput.py
index deedb86cd..011716734 100644
--- a/opengate/actors/actoroutput.py
+++ b/opengate/actors/actoroutput.py
@@ -808,7 +808,7 @@ class ActorOutputRoot(ActorOutputBase):
 
     def get_output_path(self, *args, **kwargs):
         if "which" in kwargs and kwargs["which"] != "merged":
-            warning(
+            self.warn_user(
                 "Currently, GATE 10 only stores cumulative ROOT output per simulation ('merged'), "
                 "not data per run. Showing you the path to the ROOT file with cumulative data."
             )
diff --git a/opengate/actors/base.py b/opengate/actors/base.py
index 1110e83aa..e8ed5c28f 100644
--- a/opengate/actors/base.py
+++ b/opengate/actors/base.py
@@ -149,15 +149,13 @@ def __setstate__(self, state):
         self.__initcpp__()
         self.__update_interface_properties__()
 
-    # def __finalize_init__(self):
-    #     super().__finalize_init__()
-    #     # The following attributes exist. They are declared here to avoid warning
-    #     self.known_attributes.append("fFilters")
-    #     self.known_attributes.append("actor_engine")
-    #     self.known_attributes.append("user_output")
-    #     self.known_attributes.append("simulation")
-    #     self.known_attributes.append("__dict__")
-    #     self.known_attributes.append("output_filename")
+    def __finalize_init__(self):
+        super().__finalize_init__()
+        # The following attributes exist. They are declared here to avoid warning
+        # fFilters is not known here because ActorBase does not inherit from a cpp counterpart.
+        self.known_attributes.add("fFilters")
+        # output_filename is a property
+        self.known_attributes.add("output_filename")
 
     def to_dictionary(self):
         d = super().to_dictionary()
diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index 0fb7d3843..2092bf90f 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -4,9 +4,8 @@
 from scipy.spatial.transform import Rotation
 
 import opengate_core as g4
-from anytree import NodeMixin
 from .base import ActorBase
-from ..exception import fatal, warning
+from ..exception import fatal
 from ..definitions import fwhm_to_sigma
 from ..utility import g4_units
 from ..image import (
@@ -233,13 +232,12 @@ def initialize(self):
         ActorBase.initialize(self)
         if self.authorize_repeated_volumes is True:
             return
-        vm = self.simulation.volume_manager
         att = self.attached_to
         if not isinstance(self.attached_to, (list, tuple)):
             att = [self.attached_to]
         for a in att:
             current = self.simulation.volume_manager.get_volume(a).parent
-            while current.name != "world" and not isinstance(current, NodeMixin):
+            while current.name != "world" and hasattr(current, "g4_transform"):
                 if len(current.g4_transform) > 1:
                     fatal(
                         f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}. "
@@ -660,7 +658,9 @@ def __initcpp__(self):
 
     def initialize_blurring_parameters(self):
         if not (0.0 <= self.efficiency <= 1.0):
-            warning(f"Efficency set to {self.efficiency}, which is not in [0;1].")
+            self.warn_user(
+                f"Efficency set to {self.efficiency}, which is not in [0;1]."
+            )
 
     def initialize(self):
         self.initialize_blurring_parameters()
@@ -851,7 +851,7 @@ class DigitizerProjectionActor(DigitizerBase, g4.GateDigitizerProjectionActor):
     }
 
     def __init__(self, *args, **kwargs):
-        ActorBase.__init__(self, *args, **kwargs)
+        DigitizerBase.__init__(self, *args, **kwargs)
         self._add_user_output(ActorOutputSingleImage, "projection")
         self.start_output_origin = None
         self.__initcpp__()
@@ -861,6 +861,10 @@ def __initcpp__(self):
         g4.GateDigitizerProjectionActor.__init__(self, self.user_info)
         self.AddActions({"StartSimulationAction", "EndSimulationAction"})
 
+    """def __finalize_init__(self):
+        super().__finalize_init__()
+        self.known_attributes.add("fPhysicalVolumeName")"""
+
     def initialize(self):
         # for the moment, we cannot use this actor with several volumes
         m = self.attached_to
@@ -1124,5 +1128,7 @@ def EndSimulationAction(self):
         self.number_of_absorbed_events = self.GetNumberOfAbsorbedEvents()
         self.total_number_of_entries = self.GetTotalNumberOfEntries()
         if self.total_number_of_entries == 0:
-            warning(f"Empty output, no particles stored in {self.get_output_path()}")
+            self.warn_user(
+                f"Empty output, no particles stored in {self.get_output_path()}"
+            )
         g4.GatePhaseSpaceActor.EndSimulationAction(self)
diff --git a/opengate/actors/miscactors.py b/opengate/actors/miscactors.py
index 7e5ed62d4..d8bc9d49a 100644
--- a/opengate/actors/miscactors.py
+++ b/opengate/actors/miscactors.py
@@ -202,7 +202,7 @@ class SimulationStatisticsActor(ActorBase, g4.GateSimulationStatisticsActor):
 
     def __init__(self, *args, **kwargs):
         ActorBase.__init__(self, *args, **kwargs)
-        output = self._add_user_output(ActorOutputStatisticsActor, "stats")
+        self._add_user_output(ActorOutputStatisticsActor, "stats")
         self.__initcpp__()
         self.__finalize_init__()
 
@@ -210,11 +210,11 @@ def __initcpp__(self):
         g4.GateSimulationStatisticsActor.__init__(self, self.user_info)
         self.AddActions({"StartSimulationAction", "EndSimulationAction"})
 
-    # def __finalize_init__(self):
-    #     super().__finalize_init__()
-    #     # this attribute is considered sometimes in the read_stat_file
-    #     # we declare it here to avoid warning
-    #     self.known_attributes.append("date")
+    def __finalize_init__(self):
+        super().__finalize_init__()
+        # this attribute is considered sometimes in the read_stat_file
+        # we declare it here to avoid warning
+        self.known_attributes.add("date")
 
     def __str__(self):
         s = self.user_output["stats"].__str__()
diff --git a/opengate/engines.py b/opengate/engines.py
index 6dea928f8..881a6d4c3 100644
--- a/opengate/engines.py
+++ b/opengate/engines.py
@@ -101,7 +101,7 @@ def initialize(self, run_timing_intervals, progress_bar=False):
         self.run_timing_intervals = run_timing_intervals
         assert_run_timing(self.run_timing_intervals)
         if len(self.simulation_engine.simulation.source_manager.user_info_sources) == 0:
-            self.simulation_engine.simulation.warning(
+            self.simulation_engine.simulation.warn_user(
                 f"No source: no particle will be generated"
             )
         self.progress_bar = progress_bar
@@ -325,7 +325,7 @@ def initialize_global_cuts(self):
 
         # range
         if ui.energy_range_min is not None and ui.energy_range_max is not None:
-            self.simulation_engine.simulation.warning(
+            self.physics_manager.warn_user(
                 f"WARNING ! SetEnergyRange only works in MT mode"
             )
             pct = g4.G4ProductionCutsTable.GetProductionCutsTable()
@@ -428,7 +428,7 @@ def initialize_optical_material_properties(self):
                         self.g4_optical_material_tables[str(material_name)]
                     )
                 else:
-                    self.simulation_engine.simulation.warning(
+                    self.simulation_engine.simulation.warn_user(
                         f"Could not load the optical material properties for material {material_name} "
                         f"found in volume {vol.name} from file {self.physics_manager.optical_properties_file}."
                     )
@@ -865,7 +865,7 @@ def initialize_visualisation(self):
     def initialize_visualisation_gdml(self):
         # Check when GDML is activated, if G4 was compiled with GDML
         if not g4.GateInfo.get_G4GDML():
-            warning(
+            self.simulation.warn_user(
                 "Visualization with GDML not available in Geant4. Check G4 compilation."
             )
         if self.current_visu_filename is None:
diff --git a/opengate/managers.py b/opengate/managers.py
index edd4c0773..47cdbc406 100644
--- a/opengate/managers.py
+++ b/opengate/managers.py
@@ -394,7 +394,7 @@ def dump_actor_types(self):
         return "\n".join(list(actor_types.keys()))
 
     def get_actor_user_info(self, name):
-        warning(
+        self.warn_user(
             f"Deprecation warning: The function 'get_actor_user_info' will soon be removed."
             f"Use my_actor.user_info instead, where 'my_actor' "
             f"should be replace by your actor object. "
@@ -1422,9 +1422,9 @@ def __init__(self, name="simulation"):
 
         # read-only info
         self._current_random_seed = None
-        self._warnings = (
-            []
-        )  # list to store warning messages issued somewhere in the simulation
+
+        # list to store warning messages issued somewhere in the simulation
+        self._user_warnings = []
 
     def __str__(self):
         s = (
@@ -1458,7 +1458,7 @@ def current_random_seed(self):
 
     @property
     def warnings(self):
-        return self._warnings
+        return self._user_warnings
 
     def to_dictionary(self):
         d = super().to_dictionary()
diff --git a/opengate/physics.py b/opengate/physics.py
index 76a01e5e9..f25a9559d 100644
--- a/opengate/physics.py
+++ b/opengate/physics.py
@@ -87,7 +87,7 @@ def ConstructProcess(self):
             ]
 
         if len(particle_keys_to_consider) == 0:
-            self.physics_engine.simulation_engine.simulation.warning(
+            self.physics_engine.simulation_engine.simulation.warn_user(
                 "user_limits_particles is False for all particles. No tracking cuts will be applied. Use sim.physics_manager.set_user_limits_particles()."
             )
 

From 02f77484598341344f4e105d24033d72f4c6454a Mon Sep 17 00:00:00 2001
From: David <david.sarrut@gmail.com>
Date: Thu, 26 Sep 2024 16:50:40 +0200
Subject: [PATCH 17/19] Fix indentation error in digitizers.py

---
 opengate/actors/digitizers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index 2092bf90f..5f95ab800 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -245,7 +245,7 @@ def initialize(self):
                         f"gather data from all repeated instances. If you are "
                         f"sure, enable the option 'authorize_repeated_volumes'."
                     )
-                    current = current.parent
+                current = current.parent
 
 
 class DigitizerAdderActor(DigitizerBase, g4.GateDigitizerAdderActor):

From 956119fbed00ad5721dec42d06d2a9575065f09a Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Fri, 27 Sep 2024 09:00:06 +0200
Subject: [PATCH 18/19] Update physical volume name handling in
 DigitizerProjectionActor

Replaced direct access to `fPhysicalVolumeName` with a setter method `SetPhysicalVolumeName`. This change enhances encapsulation and allows for more controlled modifications of the `fPhysicalVolumeName` attribute. Also initialized `fPhysicalVolumeName` to "None" by default in the constructor.
---
 .../opengate_lib/digitizer/GateDigitizerProjectionActor.cpp | 5 +++++
 .../opengate_lib/digitizer/GateDigitizerProjectionActor.h   | 6 ++++--
 .../digitizer/pyGateDigitizerProjectionActor.cpp            | 4 ++--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.cpp b/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.cpp
index 41668b195..445b5ced9 100644
--- a/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.cpp
+++ b/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.cpp
@@ -19,6 +19,7 @@ GateDigitizerProjectionActor::GateDigitizerProjectionActor(py::dict &user_info)
   fActions.insert("StartSimulationAction");
   fActions.insert("EndOfEventAction");
   fActions.insert("BeginOfRunAction");
+  fPhysicalVolumeName = "None";
 }
 
 GateDigitizerProjectionActor::~GateDigitizerProjectionActor() = default;
@@ -35,6 +36,10 @@ void GateDigitizerProjectionActor::InitializeCpp() {
   fImage = ImageType::New();
 }
 
+void GateDigitizerProjectionActor::SetPhysicalVolumeName(std::string name) {
+  fPhysicalVolumeName = name;
+}
+
 // Called when the simulation start
 void GateDigitizerProjectionActor::StartSimulationAction() {
   // Get input hits collection
diff --git a/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.h b/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.h
index f1482254b..ddfef7188 100644
--- a/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.h
+++ b/core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.h
@@ -29,9 +29,9 @@ class GateDigitizerProjectionActor : public GateVActor {
 
   ~GateDigitizerProjectionActor() override;
 
-  virtual void InitializeUserInput(py::dict &user_info) override;
+  void InitializeUserInput(py::dict &user_info) override;
 
-  virtual void InitializeCpp() override;
+  void InitializeCpp() override;
 
   // Called when the simulation start (master thread only)
   void StartSimulationAction() override;
@@ -42,6 +42,8 @@ class GateDigitizerProjectionActor : public GateVActor {
   // Called every time an Event ends (all threads)
   void EndOfEventAction(const G4Event *event) override;
 
+  void SetPhysicalVolumeName(std::string name);
+
   // Image type is 3D float by default
   typedef itk::Image<float, 3> ImageType;
   ImageType::Pointer fImage;
diff --git a/core/opengate_core/opengate_lib/digitizer/pyGateDigitizerProjectionActor.cpp b/core/opengate_core/opengate_lib/digitizer/pyGateDigitizerProjectionActor.cpp
index f3e4ae31d..6b6a12709 100644
--- a/core/opengate_core/opengate_lib/digitizer/pyGateDigitizerProjectionActor.cpp
+++ b/core/opengate_core/opengate_lib/digitizer/pyGateDigitizerProjectionActor.cpp
@@ -19,6 +19,6 @@ void init_GateDigitizerProjectionActor(py::module &m) {
              GateVActor>(m, "GateDigitizerProjectionActor")
       .def(py::init<py::dict &>())
       .def_readwrite("fImage", &GateDigitizerProjectionActor::fImage)
-      .def_readwrite("fPhysicalVolumeName",
-                     &GateDigitizerProjectionActor::fPhysicalVolumeName);
+      .def("SetPhysicalVolumeName",
+           &GateDigitizerProjectionActor::SetPhysicalVolumeName);
 }

From 0b97605c98c42c737a17f54a478fe71d55bccd5c Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Fri, 27 Sep 2024 09:00:46 +0200
Subject: [PATCH 19/19] Fix typos and enhance digitizer configurability.

Correct typos in the code, standardize filename and output property names, and enable support for repeated volumes in multiple digitizer actors.
---
 opengate/actors/digitizers.py                        | 12 ++++--------
 opengate/contrib/pet/siemensbiograph.py              |  2 ++
 opengate/tests/src/test017_repeater.py               |  2 --
 .../src/test029_volume_time_rotation_helpers.py      |  2 +-
 opengate/tests/src/test037_pet_hits_singles_2.py     |  2 ++
 .../src/test040_gan_phsp_pet_training_dataset.py     |  2 +-
 opengate/tests/src/test043_garf_training_dataset.py  |  2 +-
 opengate/tests/src/test053_phid_helpers2.py          |  2 +-
 opengate/tests/src/test059_tpsource_weights.py       |  2 +-
 opengate/tests/src/test072_coinc_sorter_1.py         |  2 ++
 opengate/tests/src/test073_test3_intevo_tc99m_mt.py  |  2 +-
 opengate/tests/src/test073_test4_intevo_lu177_mt.py  |  2 +-
 .../tests/src/test073_test5_discovery_lu177_mt.py    |  2 +-
 .../tests/src/test073_test5_discovery_tc99m_mt.py    |  2 +-
 14 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/opengate/actors/digitizers.py b/opengate/actors/digitizers.py
index 5f95ab800..59e5038b1 100644
--- a/opengate/actors/digitizers.py
+++ b/opengate/actors/digitizers.py
@@ -177,7 +177,8 @@ def add_module(self, module_type, module_name=None):
         mod.attached_to = self.actors[index - 1].attached_to
         if "input_digi_collection" in mod.user_info:
             mod.input_digi_collection = self.actors[index - 1].name
-        mod.write_to_disk = False
+        first_key = next(iter(mod.user_output))
+        mod.user_output[first_key].write_to_disk = False
         self.actors.append(mod)
         return mod
 
@@ -240,7 +241,7 @@ def initialize(self):
             while current.name != "world" and hasattr(current, "g4_transform"):
                 if len(current.g4_transform) > 1:
                     fatal(
-                        f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}. "
+                        f"This digitizer actor name '{self.name}' is attached to the volume '{self.attached_to}'. "
                         f"However, this volume is a daughter of the repeated volume '{current.name}'. It means it will "
                         f"gather data from all repeated instances. If you are "
                         f"sure, enable the option 'authorize_repeated_volumes'."
@@ -861,10 +862,6 @@ def __initcpp__(self):
         g4.GateDigitizerProjectionActor.__init__(self, self.user_info)
         self.AddActions({"StartSimulationAction", "EndSimulationAction"})
 
-    """def __finalize_init__(self):
-        super().__finalize_init__()
-        self.known_attributes.add("fPhysicalVolumeName")"""
-
     def initialize(self):
         # for the moment, we cannot use this actor with several volumes
         m = self.attached_to
@@ -980,8 +977,7 @@ def StartSimulationAction(self):
         align_image_with_physical_volume(
             self.attached_to_volume, self.user_output.projection.data_per_run[0].image
         )
-        self.fPhysicalVolumeName = str(pv.GetName())
-        print(self.fPhysicalVolumeName)
+        self.SetPhysicalVolumeName(str(pv.GetName()))
 
         # update the cpp image and start
         update_image_py_to_cpp(
diff --git a/opengate/contrib/pet/siemensbiograph.py b/opengate/contrib/pet/siemensbiograph.py
index 4b9707034..529880bc0 100644
--- a/opengate/contrib/pet/siemensbiograph.py
+++ b/opengate/contrib/pet/siemensbiograph.py
@@ -81,6 +81,7 @@ def add_digitizer(
     # hits collection
     hc = sim.add_actor("DigitizerHitsCollectionActor", hits_name)
     hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
     hc.output_filename = output_filename
     hc.attributes = [
         "PostPosition",
@@ -91,6 +92,7 @@ def add_digitizer(
 
     # singles collection
     sc = sim.add_actor("DigitizerReadoutActor", singles_name)
+    sc.authorize_repeated_volumes = True
     sc.attached_to = crystal.name
     sc.input_digi_collection = hc.name
     sc.group_volume = block.name
diff --git a/opengate/tests/src/test017_repeater.py b/opengate/tests/src/test017_repeater.py
index 7f7321636..fd0afb173 100755
--- a/opengate/tests/src/test017_repeater.py
+++ b/opengate/tests/src/test017_repeater.py
@@ -4,7 +4,6 @@
 import opengate as gate
 from opengate.tests import utility
 import opengate_core as g4
-from scipy.spatial.transform import Rotation
 
 if __name__ == "__main__":
     paths = utility.get_default_test_paths(__file__, "", "test017")
@@ -84,7 +83,6 @@
     dose.size = [150, 150, 150]
     dose.spacing = [1 * mm, 1 * mm, 1 * mm]
     dose.translation = [5 * mm, 0 * mm, 0 * mm]
-    dose.physical_volume_index = 0
     print(
         "The Dose actor is triggered every time a hit occurs in the (logical volume) "
         '"crystal" (and any of its associated repeated physical volumes).'
diff --git a/opengate/tests/src/test029_volume_time_rotation_helpers.py b/opengate/tests/src/test029_volume_time_rotation_helpers.py
index a5f314a3d..1ec5b0b96 100644
--- a/opengate/tests/src/test029_volume_time_rotation_helpers.py
+++ b/opengate/tests/src/test029_volume_time_rotation_helpers.py
@@ -109,7 +109,7 @@ def create_simulation(sim, aa_flag, paths):
     hc.attached_to = "spect_crystal"
     hc.output_filename = "test029.root"
     if sim.number_of_threads == 1:
-        hc.write_to_disk = False
+        hc.root_output.write_to_disk = False
     hc.attributes = [
         "PostPosition",
         "TotalEnergyDeposit",
diff --git a/opengate/tests/src/test037_pet_hits_singles_2.py b/opengate/tests/src/test037_pet_hits_singles_2.py
index 813fb3144..ed5e9acf8 100755
--- a/opengate/tests/src/test037_pet_hits_singles_2.py
+++ b/opengate/tests/src/test037_pet_hits_singles_2.py
@@ -21,6 +21,7 @@
     # digitizer hits
     hc = sim.add_actor("DigitizerHitsCollectionActor", "Hits")
     hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
     hc.output_filename = f"test037_test{v}.root"
     hc.attributes = [
         "PostPosition",
@@ -31,6 +32,7 @@
 
     # Readout (not need for adder)
     sc = sim.add_actor("DigitizerReadoutActor", "Singles2_1")
+    sc.authorize_repeated_volumes = True
     sc.output_filename = f"test037_test{v}.root"
     sc.input_digi_collection = "Hits"
     sc.group_volume = stack.name  # should be depth=1 in Gate
diff --git a/opengate/tests/src/test040_gan_phsp_pet_training_dataset.py b/opengate/tests/src/test040_gan_phsp_pet_training_dataset.py
index 2a063e364..39b3bacc8 100755
--- a/opengate/tests/src/test040_gan_phsp_pet_training_dataset.py
+++ b/opengate/tests/src/test040_gan_phsp_pet_training_dataset.py
@@ -77,7 +77,7 @@
 
     # add stat actor
     stats = sim.add_actor("SimulationStatisticsActor", "Stats")
-    stats.output = paths.output / "test040_train_stats.txt"
+    stats.output_filename = "test040_train_stats.txt"
 
     # filter gamma only
     f = sim.add_filter("ParticleFilter", "f")
diff --git a/opengate/tests/src/test043_garf_training_dataset.py b/opengate/tests/src/test043_garf_training_dataset.py
index 68a164968..57cbf2a8c 100755
--- a/opengate/tests/src/test043_garf_training_dataset.py
+++ b/opengate/tests/src/test043_garf_training_dataset.py
@@ -88,7 +88,7 @@
     stats = sim.add_actor("SimulationStatisticsActor", "stats")
     stats.track_types_flag = True
     stats.output_filename = "test043_arf_training_dataset_stats.txt"
-    stats.write_to_disk = True
+    stats.stats.write_to_disk = True
 
     # start simulation
     sim.run(start_new_process=True)
diff --git a/opengate/tests/src/test053_phid_helpers2.py b/opengate/tests/src/test053_phid_helpers2.py
index 99ce02a6b..d72736edc 100644
--- a/opengate/tests/src/test053_phid_helpers2.py
+++ b/opengate/tests/src/test053_phid_helpers2.py
@@ -34,7 +34,7 @@ def create_sim_test053(sim, sim_name, output=paths.output):
     # add stat actor
     s = sim.add_actor("SimulationStatisticsActor", "stats")
     s.track_types_flag = True
-    s.output = output / f"test053_{sim_name}.txt"
+    s.output_filename = output / f"test053_{sim_name}.txt"
 
     # phsp actor
     phsp = sim.add_actor("PhaseSpaceActor", "phsp")
diff --git a/opengate/tests/src/test059_tpsource_weights.py b/opengate/tests/src/test059_tpsource_weights.py
index afccb464f..2e61f3034 100755
--- a/opengate/tests/src/test059_tpsource_weights.py
+++ b/opengate/tests/src/test059_tpsource_weights.py
@@ -66,7 +66,7 @@
     # add dose actor
     dose = sim.add_actor("DoseActor", "doseInYZ_1")
     filename = "phantom_a_1.mhd"
-    dose.output_filename_filename = filename
+    dose.output_filename = filename
     dose.attached_to = "phantom_a_1"
     dose.size = [250, 250, 1]
     dose.spacing = [0.4, 0.4, 2]
diff --git a/opengate/tests/src/test072_coinc_sorter_1.py b/opengate/tests/src/test072_coinc_sorter_1.py
index a2d05253a..24a89f011 100755
--- a/opengate/tests/src/test072_coinc_sorter_1.py
+++ b/opengate/tests/src/test072_coinc_sorter_1.py
@@ -115,6 +115,7 @@
     # Hits
     hc = sim.add_actor("DigitizerHitsCollectionActor", f"Hits_{crystal.name}")
     hc.attached_to = crystal
+    hc.authorize_repeated_volumes = True
     hc.output_filename = "test72_output_1.root"
     hc.attributes = [
         "EventID",
@@ -127,6 +128,7 @@
     # 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
diff --git a/opengate/tests/src/test073_test3_intevo_tc99m_mt.py b/opengate/tests/src/test073_test3_intevo_tc99m_mt.py
index 10e56b0e4..b177ef922 100755
--- a/opengate/tests/src/test073_test3_intevo_tc99m_mt.py
+++ b/opengate/tests/src/test073_test3_intevo_tc99m_mt.py
@@ -24,7 +24,7 @@
     c = {"name": f"spectrum", "min": 3 * keV, "max": 160 * keV}
     ew = digit.find_first_module("energy_window")
     ew.output_filename = "output_tc99m.root"
-    ew.write_to_disk = True
+    ew.root_output.write_to_disk = True
     ew.channels.append(c)
 
     # output
diff --git a/opengate/tests/src/test073_test4_intevo_lu177_mt.py b/opengate/tests/src/test073_test4_intevo_lu177_mt.py
index 8bdb1e135..75c626347 100755
--- a/opengate/tests/src/test073_test4_intevo_lu177_mt.py
+++ b/opengate/tests/src/test073_test4_intevo_lu177_mt.py
@@ -24,7 +24,7 @@
     c = {"name": "spectrum", "min": 35 * keV, "max": 588 * keV}
     ew = digit.find_first_module("energy_window")
     ew.output_filename = "output_intevo_lu177.root"
-    ew.write_to_disk = True
+    ew.root_output.write_to_disk = True
     ew.channels.append(c)
 
     # output
diff --git a/opengate/tests/src/test073_test5_discovery_lu177_mt.py b/opengate/tests/src/test073_test5_discovery_lu177_mt.py
index 8b27bd031..f9e28b3a0 100755
--- a/opengate/tests/src/test073_test5_discovery_lu177_mt.py
+++ b/opengate/tests/src/test073_test5_discovery_lu177_mt.py
@@ -21,7 +21,7 @@
     digit = discovery.add_digitizer_lu177(sim, crystal.name, "digit_lu177")
     ew = digit.find_first_module("energy_window")
     ew.output_filename = "output_discovery_lu177.root"
-    ew.write_to_disk = True
+    ew.root_output.write_to_disk = True
 
     # output
     stats.output_filename = "stats_discovery_lu177.txt"
diff --git a/opengate/tests/src/test073_test5_discovery_tc99m_mt.py b/opengate/tests/src/test073_test5_discovery_tc99m_mt.py
index bcd4dfe6a..9b3741d1c 100755
--- a/opengate/tests/src/test073_test5_discovery_tc99m_mt.py
+++ b/opengate/tests/src/test073_test5_discovery_tc99m_mt.py
@@ -21,7 +21,7 @@
     digit = discovery.add_digitizer_tc99m(sim, crystal.name, "digit_tc99m")
     ew = digit.find_first_module("energy_window")
     ew.output_filename = "output_discovery_tc99m.root"
-    ew.write_to_disk = True
+    ew.root_output.write_to_disk = True
 
     # output
     stats.output_filename = "stats_discovery_tc99m.txt"