Feature/modern script simulation runner

.cache/doc/bat/build_doc.bat

@@ -1,7 +1,7 @@
-
-echo off
-SET pth=%~dp0
-SET pth=%pth:~0, -5%
-echo on
-
-bash %pth%/bash/build_doc.sh %*
+
+echo off
+SET pth=%~dp0
+SET pth=%pth:~0, -5%
+echo on
+
+bash %pth%/bash/build_doc.sh %*

.cache/doc/bat/generate_doc.bat

@@ -1,7 +1,7 @@
-
-echo off
-SET pth=%~dp0
-SET pth=%pth:~0, -5%
-echo on
-
-bash %pth%/bash/generate_doc.sh %*
+
+echo off
+SET pth=%~dp0
+SET pth=%pth:~0, -5%
+echo on
+
+bash %pth%/bash/generate_doc.sh %*

.github/workflows/sync-linum-mirror-repo.yml

@@ -0,0 +1,28 @@
+name: Sync LINUM mirror repository
+
+# GitHub App/Action mirror-repository: https://github.com/yesolutions/mirror-action
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  sync_mirror_repo:
+    runs-on: ubuntu-22.04
+
+    environment:
+      name: production
+      url: https://github.com/linum-uqam/inm5803-ete2022-benoit-dubreuil
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: 'master'
+          fetch-depth: 0
+
+      - uses: yesolutions/mirror-action@master
+        with:
+          REMOTE: 'git@github.com:linum-uqam/voxsim.git'
+          GIT_SSH_PRIVATE_KEY: ${{ secrets.LINUM_DEPLOY_GIT_SSH_PRIVATE_KEY }}  # The public key is a deploy key on the remote repository
+          GIT_SSH_NO_VERIFY_HOST: 'true'  # We're pushing from a public repo to a public repo, nothing can really be stolen.

scripts/geometry_factory.py

@@ -1,13 +1,12 @@
 #!/usr/bin/env python
 
 import argparse
+import pathlib
 from math import pi
-from os import makedirs
 from tempfile import mkdtemp
 
 from simulator.factory import GeometryFactory, Plane
 
-
 resolution = [10, 10, 10]
 spacing = [2, 2, 2]
 
@@ -42,7 +41,7 @@
 ]
 
 
-def get_geometry_parameters(output_folder, output_naming):
+def get_geometry_parameters(output_folder: pathlib.Path, output_naming: str):
     geometry_handler = GeometryFactory.get_geometry_handler(resolution, spacing)
 
     bundle1 = GeometryFactory.create_bundle(
@@ -76,15 +75,15 @@ def get_geometry_parameters(output_folder, output_naming):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser("Geometry Factory Example Script")
     parser.add_argument(
-        "--out", type=str, required=False, help="Output directory for the files"
+        "--out", type=pathlib.Path, help="Output directory for the files"
     )
 
     args = parser.parse_args()
-    if "out" in args and args.out:
-        dest = args.out
-        makedirs(args.out, exist_ok=True)
+    if args.out:
+        dest: pathlib.Path = args.out
+        dest.mkdir(parents=True, exist_ok=True)
     else:
-        dest = mkdtemp(prefix="geo_factory")
+        dest = pathlib.Path(mkdtemp(prefix="geo_factory"))
 
     print("Script execution results are in : {}".format(dest))
     get_geometry_parameters(dest, "geometry")

scripts/geometry_factory_multi_cluster.py

@@ -1,13 +1,12 @@
 #!/usr/bin/env python3
 
 import argparse
+import pathlib
 from math import pi
-from os import makedirs
 from tempfile import mkdtemp
 
 from simulator.factory import GeometryFactory, Plane
 
-
 resolution = [10, 10, 10]
 spacing = [2, 2, 2]
 
@@ -43,7 +42,7 @@
 ]
 
 
-def run_multi_clusters(output_folder, output_naming):
+def run_multi_clusters(output_folder: pathlib.Path, output_naming: str):
     geometry_handler = GeometryFactory.get_geometry_handler(resolution, spacing)
 
     bundle1 = GeometryFactory.create_bundle(
@@ -87,15 +86,15 @@ def run_multi_clusters(output_folder, output_naming):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser("Geometry Multi Clusters Example Script")
     parser.add_argument(
-        "--out", type=str, required=False, help="Output directory for the files"
+        "--out", type=pathlib.Path, help="Output directory for the files"
     )
 
     args = parser.parse_args()
-    if "out" in args and args.out:
-        dest = args.out
-        makedirs(args.out, exist_ok=True)
+    if args.out:
+        dest: pathlib.Path = args.out
+        dest.mkdir(parents=True, exist_ok=True)
     else:
-        dest = mkdtemp(prefix="geo_factory_mc")
+        dest = pathlib.Path(mkdtemp(prefix="geo_factory_mc"))
 
     print("Script execution results are in : {}".format(dest))
     run_multi_clusters(dest, "multi_clusters")

scripts/simulation_runner.py → scripts/legacy_simulation_runner.py

@@ -1,16 +1,15 @@
 #!/usr/bin/env python3
 
 import argparse
-from os import makedirs
-from os.path import join
+import pathlib
 from tempfile import mkdtemp
 
 from scripts.geometry_factory import get_geometry_parameters
 from scripts.simulation_factory import get_simulation_parameters
 from simulator.runner.legacy import SimulationRunner
 
 
-def run_simulation(output_folder):
+def run_simulation(output_folder: pathlib.Path):
     geometry_parameters = get_geometry_parameters(
         output_folder, "runner_test_geometry"
     )
@@ -32,7 +31,7 @@ def run_simulation(output_folder):
         output_folder, "runner_test_simulation_standalone"
     )
 
-    standalone_output = join(output_folder, "standalone_test")
+    standalone_output = output_folder / "standalone_test"
 
     runner.run_simulation_standalone(
         standalone_output, output_folder, simulation_parameters, "standalone"
@@ -42,15 +41,15 @@ def run_simulation(output_folder):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser("Simulation Runner Example Script")
     parser.add_argument(
-        "--out", type=str, required=False, help="Output directory for the files"
+        "--out", type=pathlib.Path, help="Output directory for the files"
     )
 
     args = parser.parse_args()
-    if "out" in args and args.out:
-        dest = args.out
-        makedirs(args.out, exist_ok=True)
+    if args.out:
+        dest: pathlib.Path = args.out
+        dest.mkdir(parents=True, exist_ok=True)
     else:
-        dest = mkdtemp(prefix="sim_runner")
+        dest = pathlib.Path(mkdtemp(prefix="sim_runner"))
 
     print("Script execution results are in : {}".format(dest))
     run_simulation(dest)

scripts/phantom_generation_runner.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+
+import argparse
+import pathlib
+
+from scripts.geometry_factory import get_geometry_parameters
+from simulator.runner.simulation_runner import SimulationRunner
+
+
+def run_simulation(output_folder: pathlib.Path):
+    geometry_parameters = get_geometry_parameters(
+        output_folder, "runner_test_geometry"
+    )
+
+    runner = SimulationRunner()
+    runner.generate_phantom(
+        run_name="runner_test_simulation_standalone",
+        phantom_infos=geometry_parameters,
+        output_folder=output_folder,
+        output_nifti=False,
+    )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser("Simulation Runner Example Script")
+    parser.add_argument(
+        "--out", type=pathlib.Path, default="./out/", help="Output directory for the files"
+    )
+
+    args = parser.parse_args()
+    dest: pathlib.Path = args.out
+    dest.mkdir(parents=True, exist_ok=True)
+    dest = dest.resolve(strict=True)
+
+    print("Script execution results are in : {}".format(dest))
+    run_simulation(dest)

scripts/simulation_factory.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import argparse
-from os import makedirs
+import pathlib
 from tempfile import mkdtemp
 from random import uniform
 
@@ -12,7 +12,7 @@
 from simulator.utils.test_helpers import GeometryHelper
 
 
-def get_simulation_parameters(output_folder, output_naming):
+def get_simulation_parameters(output_folder: pathlib.Path, output_naming: str):
     fiber_compartment = SimulationFactory.generate_fiber_stick_compartment(
         0.007, 900, 80, SimulationFactory.CompartmentType.INTRA_AXONAL
     )
@@ -71,15 +71,15 @@ def get_simulation_parameters(output_folder, output_naming):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser("Simulation Factory Example Script")
     parser.add_argument(
-        "--out", type=str, required=False, help="Output directory for the files"
+        "--out", type=pathlib.Path, help="Output directory for the files"
     )
 
     args = parser.parse_args()
-    if "out" in args and args.out:
-        dest = args.out
-        makedirs(args.out, exist_ok=True)
+    if args.out:
+        dest: pathlib.Path = args.out
+        dest.mkdir(parents=True, exist_ok=True)
     else:
-        dest = mkdtemp(prefix="sim_factory")
+        dest = pathlib.Path(mkdtemp(prefix="sim_factory"))
 
     print("Script execution results are in : {}".format(dest))
     get_simulation_parameters(dest, "simulation")