Merge pull request #483 from OpenGATE/consolidate5

Consolidate 5

.github/workflows/main.yml

@@ -397,10 +397,6 @@ jobs:
           if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then
               path=`opengate_library_path.py -p site_packages`
               export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH}
-              path=`opengate_library_path.py -p libG4processes`
-              export LD_PRELOAD=${path}:${LD_PRELOAD}
-              path=`opengate_library_path.py -p libG4geometry`
-              export LD_PRELOAD=${path}:${LD_PRELOAD}
           fi
           if [[ ${{ matrix.os }} == "windows-latest" ]]; then
               path=`opengate_library_path.py -p site_packages`

README.md

@@ -11,7 +11,7 @@ See the [User Guide](https://opengate-python.readthedocs.io/en/latest/user_guide
 
 ### How to install (short version)
 
-*Compatible with Python 3.9, 3.10, 3.11, 3.12. On Windows multithreading, Qt visualization and the "spawn new subprocess" are not (yet) available.*
+*Compatible with Python 3.9, 3.10, 3.11, 3.12. On Windows multithreading and Qt visualization are not (yet) available.*
 
 First, create an environment (not mandatory but highly advised)
 
@@ -23,7 +23,7 @@ source opengate_env/bin/activate
 or you can use the conda environment.
 
 ```
-conda create --name opengate_env python=3.9
+conda create --name opengate_env python=3.12
 conda activate opengate_env
 ```
 
@@ -33,6 +33,8 @@ pip install --upgrade pip
 pip install --pre opengate
 ```
 
+*Warning* while it is still beta, the `--pre` option is needed.
+
 If you already installed the packages and want to upgrade to the latest version:
 
 ```
@@ -44,19 +46,24 @@ Once installed, you can run all tests:
 opengate_tests
 ````
 
-**WARNING** The first time you run this command, the geant4 data and the test data will be downloaded. If the download fails (on some systems), try to add the following command before running opengate_tests:
+**WARNING (1)** The first time you run this command, the geant4 data and the test data will be downloaded. If the download fails (on some systems), try to add the following command before running opengate_tests:
 ````
 export GIT_SSL_NO_VERIFY=1
 ````
 
 All tests are in the folder [here](https://github.com/OpenGATE/opengate/tree/master/opengate/tests/src). The test data (binary files) are stored, for technical reasons, in this git: https://gitlab.in2p3.fr/opengamgate/gam_tests_data (which is stored as a git submodule).
 
-**WARNING** Some tests (e.g. test034) needs [gaga-phsp](https://github.com/dsarrut/gaga-phsp) which needs [pytorch](https://pytorch.org/) that cannot really be automatically installed by the previous pip install (at least we don't know how to do). So, in order to run those tests, you will have to install both PyTorch and gaga-phsp first with
+**WARNING (2)** Some tests (e.g. test034) needs [gaga-phsp](https://github.com/dsarrut/gaga-phsp) which needs [pytorch](https://pytorch.org/) that cannot really be automatically installed by the previous pip install (at least we don't know how to do). So, in order to run those tests, you will have to install both PyTorch and gaga-phsp first with
 ````
 pip install torch
 pip install gaga-phsp
 ````
 
+**WARNING (3)** With some linux systems (not all), you may encounter an error similar to “cannot allocate memory in static TLS block”. In that case, you must add a specific path to the linker as follows:
+````
+export LD_PRELOAD=<path to libG4processes>:<path to libG4geometry>:${LD_PRELOAD}
+````
+
 The documentation is here: https://opengate-python.readthedocs.io/en/latest/user_guide.html
 
 The test history can be visualized here: https://opengate.github.io/opengate_tests_results/

core/CMakeLists.txt

@@ -14,6 +14,9 @@ project(opengate_core)
 
 set(CMAKE_CXX_STANDARD 17)
 
+# Enable Position Independent Code for all targets (-fPIC)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
 # Need Geant4
 find_package(Geant4 REQUIRED OPTIONAL_COMPONENTS qt)
 include(${Geant4_USE_FILE})
@@ -103,13 +106,8 @@ if (WIN32)
     endif ()
 endif ()
 
-# correct one on OSX
-#target_link_libraries(opengate_core PRIVATE pybind11::module ${Geant4_LIBRARIES} Threads::Threads ${ITK_LIBRARIES})
-
 # additional utilities
 target_include_directories(opengate_core PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/external/)
 
 #set(CMAKE_VERBOSE_MAKEFILE on)
 target_link_libraries(opengate_core PRIVATE pybind11::module ${Geant4_LIBRARIES} Threads::Threads ${ITK_LIBRARIES} fmt::fmt-header-only)
-
-# Do not not add ${PYTHON_LIBRARIES}) here (seg fault)

core/opengate_core/__init__.py

@@ -41,37 +41,23 @@ def get_libG4_path(lib):
         "site-packages" in pathCurrentFile
     ):  # opengate_core is installed using wheel (for "pip install -e .", the paths are different)
         reloadPython = False
-        if (
-            "LD_LIBRARY_PATH" not in os.environ
-            or os.path.join(get_site_packages_dir(), "opengate_core.libs")
-            not in os.environ["LD_LIBRARY_PATH"]
-        ):
-            reloadPython = True
+        # if (
+        #    "LD_LIBRARY_PATH" not in os.environ
+        #    or os.path.join(get_site_packages_dir(), "opengate_core.libs")
+        #    not in os.environ["LD_LIBRARY_PATH"]
+        # ):
+        #    reloadPython = True
 
-        if (
-            "LD_PRELOAD" not in os.environ
-            or get_libG4_path("processes") not in os.environ["LD_PRELOAD"]
-            or get_libG4_path("geometry") not in os.environ["LD_PRELOAD"]
-        ):
-            reloadPython = True
-
-        if reloadPython:
-            print(
-                "opengate_core is not detected. Be sure to execute these lines before to run python:"
-            )
-            print(
-                "export LD_LIBRARY_PATH="
-                + os.path.join(get_site_packages_dir(), "opengate_core.libs")
-                + ":${LD_LIBRARY_PATH}"
-            )
-            print(
-                "export LD_PRELOAD="
-                + get_libG4_path("processes")
-                + ":"
-                + get_libG4_path("geometry")
-                + ":${LD_PRELOAD}"
-            )
-            sys.exit(-1)
+        # if reloadPython:
+        #    print(
+        #        "opengate_core is not detected. Be sure to execute these lines before to run python:"
+        #    )
+        #    print(
+        #        "export LD_LIBRARY_PATH="
+        #        + os.path.join(get_site_packages_dir(), "opengate_core.libs")
+        #        + ":${LD_LIBRARY_PATH}"
+        #    )
+        #    sys.exit(-1)
 elif sys.platform == "win32":
     print(os.path.dirname(pathCurrentFile))
     os.add_dll_directory(os.path.dirname(pathCurrentFile))

opengate/__init__.py

@@ -1,36 +1,38 @@
 # This file handles the way opengate is imported.
+import os
+import sys
 
-"""
-import colored
-import threading
-print(
-    colored.stylize(
-        f"Importing opengate (thread " f"{threading.get_native_id()}) ... ",
-        colored.fore("dark_gray"),
-    ),
-    end="",
-    flush=True,
-)
-print(colored.stylize("done", colored.fore("dark_gray")))
-"""
-
-# the following modules are imported respecting the package structure
-# they will be available via
-# `import opengate`
-# `opengate.xxx.yyy`
-# Modules that are mainly for internal use, such as runtiming.py or uisessions.py
-# are not automatically imported. If a user needs them, s/he must import
-# them specifically, e.g. `import opengate.uisessions`
+
+def restart_with_glibc_tunables():
+    """
+    Restart the current process with GLIBC_TUNABLES set.
+    """
+    # tunables_value = "glibc.rtld.optional_static_tls=2048000"
+    tunables_value = "glibc.rtld.optional_static_tls=1500000"
+
+    # Check if the environment variable is already set correctly
+    if os.environ.get("GLIBC_TUNABLES") != tunables_value:
+        # Set the environment variable
+        new_env = os.environ.copy()
+        new_env["GLIBC_TUNABLES"] = tunables_value
+
+        # Restart the process with the new environment
+        os.execve(sys.executable, [sys.executable] + sys.argv, new_env)
+
+        # Exit the current process
+        sys.exit()
+
+
+if sys.platform.startswith("linux"):
+    restart_with_glibc_tunables()
 
 # subpackages
 import opengate.sources
-
 import opengate.geometry
 import opengate.geometry.materials
 import opengate.geometry.solids
 import opengate.geometry.utility
 import opengate.geometry.volumes
-
 import opengate.actors
 import opengate.contrib
 

opengate/contrib/phantoms/jaszczak.py

@@ -0,0 +1,85 @@
+from opengate.contrib.phantoms.nemaiec import dump_bg_activity
+from opengate.utility import g4_units
+
+
+def add_phantom_material(simulation):
+    elems = ["H", "C", "O"]
+    w = [0.080538, 0.599848, 0.319614]
+    gcm3 = g4_units.g_cm3
+    simulation.volume_manager.material_database.add_material_weights(
+        "JASZCZAK_PMMA", elems, w, 1.19 * gcm3
+    )
+
+
+def add_jaszczak_phantom(simulation, name="jaszczak", check_overlap=False):
+    # https://www.meditest.fr/documentation/4.pdf
+    # unit
+    add_phantom_material(simulation)
+
+    # check overlap only for debug
+    original_check_overlap_flag = simulation.check_volumes_overlap
+    simulation.check_volumes_overlap = check_overlap
+
+    # Outside structure
+    jaszczak, internal_cylinder = add_jaszczak_body(simulation, name)
+    jaszczak.material = "JASZCZAK_PMMA"
+
+    simulation.check_volumes_overlap = original_check_overlap_flag
+    return jaszczak, internal_cylinder
+
+
+def add_jaszczak_body(sim, name):
+    cm = g4_units.cm
+    mm = g4_units.mm
+    deg = g4_units.deg
+    white = [1, 1, 1, 1]
+    thickness = 3.2 * mm
+
+    # main cylinder interior
+    external_cylinder = sim.add_volume("Tubs", name=f"{name}_cylinder")
+    external_cylinder.rmax = 21.6 * cm / 2.0 + thickness
+    external_cylinder.rmin = 0
+    external_cylinder.dz = 18.6 * cm / 2 + thickness * 2
+    external_cylinder.sphi = 0 * deg
+    external_cylinder.dphi = 360 * deg
+    external_cylinder.material = "JASZCZAK_PMMA"
+    external_cylinder.color = white
+
+    # main cylinder interior
+    internal_cylinder = sim.add_volume("Tubs", name=f"{name}_internal_cylinder")
+    internal_cylinder.mother = external_cylinder.name
+    internal_cylinder.rmax = 21.6 * cm / 2
+    internal_cylinder.rmin = 0
+    internal_cylinder.dz = 18.6 * cm / 2
+    internal_cylinder.sphi = 0 * deg
+    internal_cylinder.dphi = 360 * deg
+    internal_cylinder.material = "G4_AIR"
+
+    return external_cylinder, internal_cylinder
+
+
+def add_background_source(
+    simulation, jaszczak_name, src_name, activity_bqml, verbose=False
+):
+    # source
+    bg = simulation.add_source("GenericSource", f"{jaszczak_name}_{src_name}")
+    bg.mother = f"{jaszczak_name}_internal_cylinder"
+    v = simulation.volume_manager.volumes[bg.mother]
+    v_info = v.solid_info
+    # (1 cm3 = 1 mL)
+    """
+    # no need to confine yet, nothing inside the cylinder -> should be done later
+    bg.position.type = "box"
+    bg.position.size = simulation.volume_manager.volumes[bg.mother].bounding_box_size
+    # this source is confined only within the mother volume, it does not include daughter volumes
+    # it is a tubs inside the box
+    bg.position.confine = bg.mother
+    """
+    bg.particle = "e+"
+    bg.energy.type = "F18"
+    bg.activity = activity_bqml * v_info.cubic_volume
+
+    if verbose:
+        s = dump_bg_activity(simulation, jaszczak_name, src_name)
+        print(s)
+    return bg, v_info.cubic_volume

opengate/contrib/phantoms/nemaiec.py

@@ -39,6 +39,7 @@ def add_iec_phantom(
     create_material(simulation)
 
     # check overlap only for debug
+    original_check_overlap_flag = simulation.check_volumes_overlap
     simulation.check_volumes_overlap = check_overlap
 
     # Outside structure
@@ -64,6 +65,7 @@ def add_iec_phantom(
         simulation, name, thickness_z, sphere_starting_angle, toggle_sphere_order
     )
 
+    simulation.check_volumes_overlap = original_check_overlap_flag
     return iec
 
 
@@ -544,7 +546,7 @@ def get_n_samples_from_ratio(n, ratio):
     return n_samples
 
 
-def compute_sphere_centers_and_volumes(sim, name):
+def compute_sphere_centers_and_volumes_OLD_NEVER_CALLED(sim, name):
     spheres_diam = [10, 13, 17, 22, 28, 37]
     centers = []
     volumes = []

opengate/tests/src/test015_iec_phantom_4.py

@@ -22,7 +22,7 @@
 
     # main options
     sim.check_volumes_overlap = True
-    sim.random_seed = "auto"  # 123456789
+    sim.random_seed = 87456321
     sim.output_dir = paths.output
     sim.progress_bar = True
 
@@ -74,7 +74,7 @@
         axis="y",
         tolerance=50,
         ignore_value=0,
-        sum_tolerance=1.0,
+        sum_tolerance=1.1,
         sad_profile_tolerance=3.0,
     )