Add running test for linac to be used on VIP

MANIFEST.in

@@ -1,6 +1,7 @@
 global-include *.mac
 global-include *.md
 global-include *.bs
+global-include *.sh
 recursive-include opengate/contrib *
 recursive-include opengate/tests/src/gate/gate_test* *
 recursive-include opengate/tests/output_ref *

opengate/tests/src/advanced_tests/linacs/Dockerfile_opengate_vip

@@ -0,0 +1,27 @@
+
+#Docker for opengate_core
+#systemctl start docker
+#login: docker login
+#build: docker build -t tbaudier/opengate_castor_ci -f Dockerfile_opengate_vip.
+#push: docker push tbaudier/opengate_vip
+#run: docker run --rm -v $(Pipeline.Workspace):/home tbaudier/opengate_vip /home/.github/workflows/vip/run_linac_test.sh
+#interactive: docker run -ti --rm -v $PWD:/home quay.io/pypa/manylinux_2_34_x86_64 /bin/bash
+
+FROM quay.io/pypa/manylinux_2_34_x86_64
+MAINTAINER Thomas Baudier <thomas.baudier@creatis.insa-lyon.fr>
+#Install packages
+RUN     yum install -y wget \
+     && /opt/python/cp312-cp312/bin/pip install opengate \
+     && export PATH=/opt/python/cp312-cp312/bin:$PATH \
+     && opengate_info \
+     && cd /opt/python/cp312-cp312/lib/python3.12/site-packages/opengate/tests/src/advanced_tests/linacs/ \
+     && wget http://www.creatis.insa-lyon.fr/~baudier/data_advanced_test_linac.zip \
+     && unzip data_advanced_test_linac.zip \
+     && rm -f data_advanced_test_linac.zip \
+     && mkdir output \
+     && chmod a+rwX -R /opt/python/cp312-cp312/lib/python3.12/site-packages/opengate \
+     && /opt/python/cp312-cp312/bin/pip install "pymedphys[tests]==0.41.0"
+
+# docker commit <container_name>
+# docker tag <image_id> tbaudier/opengate_vip:0.1.1
+# docker run --rm tbaudier/opengate_vip:0.1.1 /opt/python/cp312-cp312/lib/python3.12/site-packages/opengate/tests/src/advanced_tests/linacs/run_linac_test.sh

opengate/tests/src/advanced_tests/linacs/README

@@ -1,11 +1,14 @@
 
+#Test for a linac
+#We use that test on VIP
+
 wget http://www.creatis.insa-lyon.fr/~baudier/data_advanced_test_linac.zip
 unzip data_advanced_test_linac.zip
 rm -f data_advanced_test_linac.zip
 mkdir output
 
 python run_vmat_mc.py --json_name data_advanced_test_linac/header.json
 python normalize_dose.py --path data_advanced_test_linac
-python comparison_deposited_dose_mc_tps.py --path data_advanced_test_linac data_advanced_test_linac --path_output output
+python comparison_deposited_dose_mc_tps.py --path data_advanced_test_linac --path_output output
 
-For the moment the test in comparison_deposited_dose_MC_TPS is a gamma index of 2%/2mm with 0.6 (60%) of passing rate between the gate dose and the TPS. Maybe chage the RAM for VIP
+#For the moment the test in comparison_deposited_dose_MC_TPS is a gamma index of 2%/2mm with 0.7 (70%) of passing rate between the gate dose and the TPS. Maybe chage the RAM for VIP

opengate/tests/src/advanced_tests/linacs/comparison_deposited_dose_mc_tps.py

@@ -3,6 +3,7 @@
 
 import os
 from pathlib import Path
+
 import click
 import itk
 import matplotlib.colors as mcolors
@@ -192,7 +193,8 @@ def gamma_index_comparison(path, path_output):
         "max_gamma": 1.5,
         "random_subset": None,
         "local_gamma": True,
-        "ram_available": 40 * 2**29,  # 40 * 1/2 GB
+        "ram_available": 7 * 2**30,  # < 8 GB
+        "interp_algo": "scipy",
     }
 
     gamma = pymedphys.gamma(
@@ -204,6 +206,7 @@ def gamma_index_comparison(path, path_output):
     )
     valid_gamma = gamma[~np.isnan(gamma)]
     pass_ratio = np.sum(valid_gamma <= 1) / len(valid_gamma)
+    print("pass ration: " + str(pass_ratio))
 
     height = 20
     width = height / 2
@@ -257,7 +260,7 @@ def gamma_index_comparison(path, path_output):
     ax1[1].set(ylabel="Y position [mm]", xlabel="X position [mm]")
     ax1[0].axes.get_xaxis().set_visible(False)
     fig1.savefig(f"{path_output}/MC_vs_TPS_dose.pdf")
-    is_ok = pass_ratio > 0.6
+    is_ok = pass_ratio > 0.70
     utility.test_ok(is_ok)
 
 

opengate/tests/src/advanced_tests/linacs/run_linac_test.sh

@@ -0,0 +1,7 @@
+
+#!/bin/bash
+cd /opt/python/cp312-cp312/lib/python3.12/site-packages/opengate/tests/src/advanced_tests/linacs/
+export PATH=/opt/python/cp312-cp312/bin:$PATH
+python run_vmat_mc.py --json_name data_advanced_test_linac/header.json
+python normalize_dose.py --path data_advanced_test_linac
+python comparison_deposited_dose_mc_tps.py --path data_advanced_test_linac --path_output output > output/output.log 2>&1

opengate/tests/src/advanced_tests/linacs/vmat_mc_helpers.py

@@ -1,9 +1,11 @@
+import itk
+import numpy as np
+
 import opengate as gate
-from opengate.tests import utility
-from opengate.contrib.linacs import elektaversa as versa
+from opengate import utility as ut
 from opengate.contrib.linacs import dicomrtplan as rtplan
-import numpy as np
-import itk
+from opengate.contrib.linacs import elektaversa as versa
+from opengate.tests import utility
 
 
 def information_img_patient(path_img=None, open_img=True, img=None):
@@ -90,8 +92,8 @@ def add_patient_image(
     patient.image = path_image + img
     patient.mother = name
     patient.material = "G4_AIR"  # material used by default
-    f1 = paths.data / "Schneider2000MaterialsTable.txt"
-    f2 = paths.data / "Schneider2000DensitiesTable.txt"
+    f1 = ut.get_data_folder() / "Schneider2000MaterialsTable.txt"
+    f2 = ut.get_data_folder() / "Schneider2000DensitiesTable.txt"
     tol = 0.05 * gcm3
     patient.voxel_materials, materials = (
         gate.geometry.materials.HounsfieldUnit_to_material(sim, tol, f1, f2)