Adapt PCT to GATE 10.1.1

.github/workflows/build-test-package.yml

@@ -51,7 +51,8 @@ jobs:
         echo "Installing wheel: $wheel"
         pip install $wheel
 
-        pip install pytest uproot opengate hepunits
+        # Install dependencies for tests as specified in pyproject.toml
+        pip install --group test
 
         # Force the installation of Geant4 data, required by opengate
         opengate_info

applications/pctdoublelut/pctdoublelut.py

@@ -108,6 +108,7 @@ def tof_fit_mc(
     # Geometry
     sim.world.material = "G4_AIR"
     sim.world.size = [4 * m, 4 * m, 4 * m]
+    sim.world.set_max_step_size(1.0 * mm)
 
     # Phantom
     if wepl > 0.0:
@@ -119,7 +120,6 @@ def tof_fit_mc(
         ]
         phantom.material = material
         phantom.color = blue
-        phantom.set_max_step_size(1.0 * mm)
 
     # Beam
     source = sim.add_source("GenericSource", "mybeam")
@@ -139,7 +139,7 @@ def tof_fit_mc(
 
     # Physics list
     sim.physics_manager.physics_list_name = "G4EmStandardPhysics_option4"
-    sim.physics_manager.set_user_limits_particles(["proton"])
+    sim.physics_manager.user_limits_particles = "proton"
 
     # Phase spaces
     def add_detector(name, translation, attach_to_phantom=False):
@@ -163,12 +163,8 @@ def add_detector(name, translation, attach_to_phantom=False):
             "LocalTime",
             "PostVelocity",
         ]
-        if int(gate.utility.version("opengate").split(".")[1]) > 0:
-            F = gate.actors.filters.GateFilterBuilder()
-            phase_space.filter = F.ParticleName == "proton"
-        else:
-            particle_filter = sim.add_filter("ParticleFilter", "Filter" + name)
-            particle_filter.particle = "proton"
+        F = gate.actors.filters.GateFilterBuilder()
+        phase_space.filter = F.ParticleName == "proton"
 
     add_detector("In", [0.0 * mm, 0.0 * mm, (-wepl / 2) * mm])
     add_detector("Out", [0.0 * mm, 0.0 * mm, (wepl / 2) * mm])

applications/pctweplfit/pctweplfit.py

@@ -90,7 +90,7 @@ def tof_fit_mc(
 
     # Physics list
     sim.physics_manager.physics_list_name = "G4EmStandardPhysics_option4"
-    sim.physics_manager.set_user_limits_particles(["proton"])
+    sim.physics_manager.user_limits_particles = "proton"
 
     # Phase spaces
     def add_detector(name, translation, attach_to_phantom=False):

pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
     "itk-rtk == 2.7.*"
 ]
 [dependency-groups]
-test = ["pytest", "uproot", "opengate"]
+test = ["pytest", "uproot", "opengate == 10.1.1"]
 
 [project.scripts]
 pctbinning = "itk.pctbinning:main"

test/pct_application_test.py

@@ -50,7 +50,7 @@ def test_pairprotons_application(
 def test_weplfit_application(tmp_path):
     output = tmp_path / "weplfit"
     pct.pctweplfit(
-        f"-o {output} --path-type phantom_length -d 220 -e 200 -l 220 --seed 1234 -v"
+        f"-o {output} --path-type phantom_length -d 220 -e 200 -l 220 --seed 1234"
     )
 
     with open(output / "tof_to_wepl_fit_deg3.json", encoding="utf-8") as f:
@@ -84,33 +84,33 @@ def test_doublelut_application(tmp_path):
     tof_coeffs = np.loadtxt(output / "tof_coeffs_9.txt")
     tof_reference = np.array(
         [
-            -1.290921042580240798e-19,
-            1.351207981731195971e-16,
-            -5.963202845355236675e-14,
-            1.443362133502381465e-11,
-            -2.084980429067098285e-09,
-            1.829330424219974866e-07,
-            -9.443542359443581318e-06,
-            2.631908622195730887e-04,
-            2.921848578064085208e-03,
-            2.715972855380448421e-03,
+            -1.304835138529633472e-19,
+            1.356468922636278510e-16,
+            -5.942720434270841880e-14,
+            1.427297715745322610e-11,
+            -2.045269455668975767e-09,
+            1.780062155625161403e-07,
+            -9.118495781246014652e-06,
+            2.525195871208434648e-04,
+            3.058213313702242298e-03,
+            2.589942534059123773e-03,
         ]
     )
     assert np.allclose(tof_coeffs, tof_reference)
 
     vel_coeffs = np.loadtxt(output / "vel_coeffs_9.txt")
     vel_reference = np.array(
         [
-            5.023900900539231649e-18,
-            -5.304589281207117926e-15,
-            2.358303897263661076e-12,
-            -5.748047473922940780e-10,
-            8.360830241840195663e-08,
-            -7.391334678087265226e-06,
-            3.842573655671269075e-04,
-            -1.096847900269657186e-02,
-            -1.773574286549965684e-02,
-            1.696161111400466552e02,
+            4.582905610876915593e-18,
+            -4.742816184714826704e-15,
+            2.062923179381136339e-12,
+            -4.910573707663995126e-10,
+            6.964091908878167104e-08,
+            -5.995324018840303797e-06,
+            3.031542041296401437e-04,
+            -8.476856480304249125e-03,
+            -4.918237198608615968e-02,
+            1.696467164517849255e02,
         ]
     )
     assert np.allclose(vel_reference, vel_coeffs)
@@ -193,7 +193,7 @@ def test_lomalinda_application(
 ):
     output = tmp_path_factory.getbasetemp() / "lomalinda.mhd"
     pct.pctlomalinda(
-        f"-i {lomalinda_data} -o {output} --plane-in -167.2 --plane-out 167.2 --ps recoENTRY -v"
+        f"-i {lomalinda_data} -o {output} --plane-in -167.2 --plane-out 167.2 --ps recoENTRY"
     )
     output0000 = str(output).replace(".", "0000.")
     test_lomalinda = itk.array_from_image(itk.imread(output0000))