Feature/path use pathlib

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_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")

scripts/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/wall_effect.py

@@ -1,17 +1,15 @@
 #!/usr/bin/env python3
 
 import argparse
+import pathlib
 from math import pi, sqrt
-from os import makedirs
-from os.path import join
 from tempfile import mkdtemp
 
 from numpy import mean
 
 from simulator.factory import GeometryFactory, Plane, SimulationFactory
 from simulator.runner.legacy import SimulationRunner
 
-
 resolution = [40, 40, 40]
 spacing = [1, 1, 1]
 point_per_centroid = 30
@@ -26,7 +24,7 @@
 cluster_center = [0.5, 0.5, 0.5]
 
 
-def create_geometry(output_folder, output_naming, fibers_per_bundle):
+def create_geometry(output_folder: pathlib.Path, output_naming: str, fibers_per_bundle):
     geometry_handler = GeometryFactory.get_geometry_handler(resolution, spacing)
 
     bundle1 = GeometryFactory.create_bundle(
@@ -54,7 +52,7 @@ def create_geometry(output_folder, output_naming, fibers_per_bundle):
 
 
 def create_split_geometry(
-    output_folder, output_naming, fibers_per_bundle, rotation=None
+        output_folder: pathlib.Path, output_naming: str, fibers_per_bundle, rotation=None
 ):
     geometry_handler = GeometryFactory.get_geometry_handler(resolution, spacing)
 
@@ -142,7 +140,7 @@ def create_simulation_b1000(geometry_handler, output_folder, output_naming):
 
 
 def create_simulation_multishell(
-    geometry_handler, output_folder, output_naming
+        geometry_handler, output_folder, output_naming
 ):
     base_multishell_simulation_handler = get_base_simulation_handler(
         geometry_handler
@@ -166,18 +164,18 @@ def create_simulation_multishell(
 if __name__ == "__main__":
     parser = argparse.ArgumentParser("Wall Effect 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)
+        dest: pathlib.Path = args.out
+        dest.mkdir(parents=True, exist_ok=True)
     else:
-        dest = mkdtemp(prefix="wall_effect")
+        dest = pathlib.Path(mkdtemp(prefix="wall_effect"))
 
     print("Script execution results are in : {}".format(dest))
-    makedirs(join(dest, "runner_outputs"), exist_ok=True)
+    (dest / "runner_outputs").mkdir(parents=True, exist_ok=True)
 
     geometry_infos, geometry_handler = create_geometry(
         dest, "geometry", n_fibers_per_bundle
@@ -189,7 +187,7 @@ def create_simulation_multishell(
 
     SimulationRunner(
         "simulation_b1000", geometry_infos, simulation_b1000_infos
-    ).run(join(dest, "runner_outputs"), relative_fiber_compartment=False)
+    ).run(dest / "runner_outputs", relative_fiber_compartment=False)
 
     geometry_infos, geometry_handler = create_split_geometry(
         dest, "geometry_split_b1", 3000
@@ -201,7 +199,7 @@ def create_simulation_multishell(
 
     SimulationRunner(
         "simulation_split_b1_b1000", geometry_infos, simulation_b1000_infos
-    ).run(join(dest, "runner_outputs"))
+    ).run(dest / "runner_outputs")
 
     geometry_infos, geometry_handler = create_split_geometry(
         dest, "geometry_split_b2", 3000, pi
@@ -213,12 +211,12 @@ def create_simulation_multishell(
 
     SimulationRunner(
         "simulation_split_b2_b1000", geometry_infos, simulation_b1000_infos
-    ).run(join(dest, "runner_outputs"))
+    ).run(dest / "runner_outputs")
 
     simulation_multishell_infos = create_simulation_multishell(
         geometry_handler, dest, "simulation_multishell"
     )
 
     SimulationRunner(
         "simulation_multishell", geometry_infos, simulation_b1000_infos
-    ).run(join(dest, "runner_outputs"))
+    ).run(dest / "runner_outputs")

setup.py

@@ -3,18 +3,16 @@
 
 from simulator.utils.setup.documentation import DocCommand
 
-
 if __name__ == "__main__":
     setup(
         name="simulation_generator",
-        version="1.0.0",
+        version="1.0.5",
         packages=find_packages(exclude=("tests", "tests.*")),
         url="",
         license="",
         author="avcaron",
         author_email="",
         description="",
-        data_files=[(".", ["config.py", "config.json"])],
         scripts=list(
             filter(lambda s: "init" not in s, glob.glob("scripts/*.py"))
         ),

simulator/default.py

@@ -0,0 +1,7 @@
+import typing
+import pathlib
+
+SINGULARITY_PATH: typing.Final[pathlib.Path] = pathlib.Path()
+SINGULARITY_NAME: typing.Final[str] = "voxsim_singularity_latest.sif"
+SINGULARITY: typing.Final[pathlib.Path] = SINGULARITY_PATH / SINGULARITY_NAME
+SINGULARITY_EXEC: typing.Final[str] = "singularity"

simulator/factory/common/__init__.py

@@ -1 +1 @@
-from .common import AttributeAsDictClass
+from ._common import AttributeAsDictClass

simulator/factory/geometry_factory/__init__.py

@@ -1,3 +1,3 @@
-from .geometry_factory import GeometryFactory
+from ._geometry_factory import GeometryFactory
 from simulator.factory.geometry_factory.utils.plane import Plane
 from simulator.factory.geometry_factory.utils.rotation import Rotation

simulator/factory/geometry_factory/handlers/geometry_handler.py

@@ -1,11 +1,16 @@
+import logging
+import pathlib
+
 from copy import deepcopy
-from os import makedirs, path
 
 from ..features.ORM.config_builder import ConfigBuilder
 from .geometry_infos import GeometryInfos
 
+_logger = logging.getLogger(__name__)
+
 
 class GeometryHandler:
+
     def __init__(self, resolution, spacing, clusters=None, spheres=None):
         self._parameters_dict = {
             "resolution": resolution,
@@ -73,15 +78,21 @@ def _get_number_of_clusters(self):
         return len(self._parameters_dict["clusters"])
 
     def generate_json_configuration_files(
-        self, output_naming, simulation_path=""
-    ):
-        if not path.exists(simulation_path):
-            makedirs(simulation_path, exist_ok=True)
+            self, output_naming: str, simulation_path: pathlib.Path = pathlib.Path()
+    ) -> GeometryInfos:
+        simulation_path.mkdir(parents=True, exist_ok=True)
+
+        try:
+            simulation_path = simulation_path.resolve(strict=True)
+        except FileNotFoundError as exc:
+            _logger.exception(
+                f"simulation_path does not exist, even after the creation of its directories: {simulation_path}",
+                exc_info=exc)
+            raise exc
 
         with open(
-            path.join(simulation_path, output_naming + "_base.json"), "w+"
+                simulation_path / (output_naming + "_base.json"), "w+"
         ) as base_file:
-
             world = ConfigBuilder.create_world(
                 len(self.get_resolution()), self.get_resolution()
             )
@@ -109,11 +120,8 @@ def generate_json_configuration_files(
 
         for cluster_idx in range(len(self._parameters_dict["clusters"])):
             with open(
-                path.join(
-                    simulation_path,
-                    output_naming + "_f_{}.vspl".format(cluster_idx),
-                ),
-                "w+",
+                    simulation_path / (output_naming + "_f_{}.vspl".format(cluster_idx)),
+                    "w+",
             ) as f:
                 f.write(
                     self._parameters_dict["clusters"][cluster_idx].serialize()