Fix/str join takes path

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="1.0.3",
         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.PurePath] = pathlib.PurePath()
+SINGULARITY_NAME: typing.Final[str] = "voxsim_singularity_latest.sif"
+SINGULARITY: typing.Final[pathlib.PurePath] = 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/simulation_factory/__init__.py

@@ -1 +1 @@
-from .simulation_factory import SimulationFactory
+from ._simulation_factory import SimulationFactory

simulator/runner/__init__.py

@@ -1 +1,2 @@
+from .config import SingularityConfig
 from .simulation_runner import SimulationRunner

simulator/runner/config.py

@@ -0,0 +1,10 @@
+import dataclasses
+import pathlib
+
+import simulator.default as default
+
+
+@dataclasses.dataclass
+class SingularityConfig:
+    singularity: pathlib.PurePath = default.SINGULARITY
+    singularity_exec: str = default.SINGULARITY_EXEC

simulator/runner/legacy.py

@@ -10,21 +10,21 @@
 from numpy import ones_like, sum
 import nrrd
 
-from config import get_config
+from .config import SingularityConfig
 from ..exceptions import SimulationRunnerException
 from ..utils.logging import RTLogging
 
-
 logger = logging.getLogger(basename(__file__).split(".")[0])
 
 
 class SimulationRunner:
+
     def __init__(
         self,
         base_naming,
         geometry_infos,
         simulation_infos=None,
-        singularity_conf=get_config(),
+        singularity_conf=SingularityConfig(),
         output_nifti=False,
     ):
         self._geometry_path = geometry_infos["file_path"]
@@ -40,17 +40,10 @@ def __init__(
             self._compartment_ids = simulation_infos["compartment_ids"]
 
         singularity_conf = (
-            singularity_conf if singularity_conf else get_config()
-        )
-        self._singularity = path.join(
-            singularity_conf["singularity_path"],
-            singularity_conf["singularity_name"],
-        )
-        self._singularity_exec = (
-            singularity_conf["singularity_exec"]
-            if "singularity_exec" in singularity_conf
-            else "singularity"
+            singularity_conf if singularity_conf else SingularityConfig()
         )
+        self._singularity = singularity_conf.singularity
+        self._singularity_exec = singularity_conf.singularity_exec
 
         self._run_simulation = True if simulation_infos else False
         self._extension = "nii.gz" if output_nifti else "nrrd"
@@ -80,7 +73,7 @@ def run_simulation_dwimage(
             "{} run -B {} --app launch_mitk {} -p {} -i {} -o {} {}".format(
                 self._singularity_exec,
                 ",".join(
-                    [simulation_infos["file_path"], simulation_output_folder]
+                    [str(simulation_infos["file_path"]), str(simulation_output_folder)]
                 ),
                 self._singularity,
                 path.join(
@@ -156,9 +149,9 @@ def run_simulation_standalone(
                 self._singularity_exec,
                 ",".join(
                     [
-                        geometry_folder,
-                        simulation_infos["file_path"],
-                        simulation_output_folder,
+                        str(geometry_folder),
+                        str(simulation_infos["file_path"]),
+                        str(simulation_output_folder),
                     ]
                 ),
                 self._singularity,
@@ -238,7 +231,7 @@ def run(
         geometry_command = (
             "singularity run -B {} --app launch_voxsim {} -f {} -r {} "
             "-s {} -o {} --comp-map {} --quiet{}".format(
-                ",".join([self._geometry_path, geometry_output_folder]),
+                ",".join([str(self._geometry_path), str(geometry_output_folder)]),
                 self._singularity,
                 path.join(self._geometry_path, self._geometry_base_file),
                 ",".join([str(r) for r in self._geometry_resolution]),
@@ -255,9 +248,9 @@ def run(
                 "-p {} -i {} -o {} {}".format(
                     ",".join(
                         [
-                            self._simulation_path,
-                            geometry_output_folder,
-                            simulation_output_folder,
+                            str(self._simulation_path),
+                            str(geometry_output_folder),
+                            str(simulation_output_folder),
                         ]
                     ),
                     self._singularity,

simulator/runner/simulation_runner.py

@@ -1,19 +1,19 @@
 import logging
 
 from asyncio import get_event_loop, new_event_loop, set_event_loop
-from os import makedirs, path
-from os.path import basename
+from os import makedirs
+import os
 from subprocess import PIPE, Popen
 
-from config import get_config
+from .config import SingularityConfig
 from .datastore import Datastore
 from ..utils.logging import RTLogging
 
-
-logger = logging.getLogger(basename(__file__).split(".")[0])
+logger = logging.getLogger(os.path.basename(__file__).split(".")[0])
 
 
 class AsyncRunner:
+
     def __init__(self):
         self._event_loop = new_event_loop()
 
@@ -49,16 +49,11 @@ async def _run_async(self, command, log_file, log_tag):
 class SimulationRunner(AsyncRunner):
     _apps = {"phantom": "launch_voxsim", "diffusion mri": "launch_mitk"}
 
-    def __init__(self, singularity_conf=get_config()):
-        self._singularity = path.join(
-            singularity_conf["singularity_path"],
-            singularity_conf["singularity_name"],
-        )
+    def __init__(self, singularity_conf=SingularityConfig()):
+        self._singularity = singularity_conf.singularity
         super().__init__()
 
-        self._singularity_exec = "singularity"
-        if "singularity_exec" in singularity_conf:
-            self._singularity_exec = singularity_conf["singularity_exec"]
+        self._singularity_exec = singularity_conf.singularity_exec
 
     def _bind_singularity(self, step, paths, arguments):
         return "{} run -B {} --app {} {} {}".format(
@@ -69,8 +64,9 @@ def _bind_singularity(self, step, paths, arguments):
             arguments,
         )
 
-    def _create_outputs(self, path):
-        if not path.exists(path):
+    @staticmethod
+    def _create_outputs(path):
+        if not os.path.exists(path):
             makedirs(path, exist_ok=True)
 
         return path
@@ -97,8 +93,8 @@ def run(
         )
 
         datastore = Datastore(
-            path.join(output_folder, "simulation"),
-            path.join(
+            os.path.join(output_folder, "simulation"),
+            os.path.join(
                 output_folder,
                 "phantom",
                 "{}_phantom_merged_bundles.fib".format(run_name),
@@ -108,7 +104,7 @@ def run(
         )
 
         datastore.load_compartments(
-            path.join(output_folder, "phantom"), run_name, output_nifti
+            os.path.join(output_folder, "phantom"), run_name, output_nifti
         )
         datastore.stage_compartments(run_name)
 
@@ -140,17 +136,17 @@ def generate_phantom(
 
         base_output_folder = output_folder
         output_folder = self._create_outputs(
-            path.join(output_folder, "phantom")
+            os.path.join(output_folder, "phantom")
         )
 
-        phantom_def = path.join(
+        phantom_def = os.path.join(
             phantom_infos["file_path"], phantom_infos["base_file"]
         )
 
         resolution = ",".join([str(r) for r in phantom_infos["resolution"]])
         spacing = ",".join([str(s) for s in phantom_infos["spacing"]])
         fiber_fraction = "rel" if relative_fiber_fraction else "abs"
-        out_name = path.join(
+        out_name = os.path.join(
             output_folder, "phantom, " "{}_phantom".format(run_name)
         )
 
@@ -161,9 +157,9 @@ def generate_phantom(
         if output_nifti:
             arguments += " --nii"
 
-        bind_paths = ",".join([phantom_infos["file_path"], output_folder])
+        bind_paths = ",".join([str(phantom_infos["file_path"]), str(output_folder)])
         command = self._bind_singularity("phantom", bind_paths, arguments)
-        log_file = path.join(base_output_folder, "{}.log".format(run_name))
+        log_file = os.path.join(base_output_folder, "{}.log".format(run_name))
         self._run_command(command, log_file, "[PHANTOM]")
 
         loop_managed or self.stop()
@@ -185,18 +181,18 @@ def simulate_diffusion_mri(
         bind_paths = [] if bind_paths is None else bind_paths
         base_output_folder = output_folder
         output_folder = self._create_outputs(
-            path.join(output_folder, "simulation")
+            os.path.join(output_folder, "simulation")
         )
 
         name = "{}_simulation".format(run_name)
 
-        bind_paths += [simulation_infos["file_path"], output_folder]
+        bind_paths += [str(simulation_infos["file_path"]), str(output_folder)]
         bind_paths = ",".join(bind_paths)
-        ffp_file = path.join(
+        ffp_file = os.path.join(
             simulation_infos["file_path"], simulation_infos["param_file"]
         )
         extension = "nii.gz" if output_nifti else "nrrd"
-        out_name = path.join(output_folder, "{}.{}".format(name, extension))
+        out_name = os.path.join(output_folder, "{}.{}".format(name, extension))
 
         if not compartments_staged and compartment_maps is not None:
             datastore = Datastore(
@@ -211,7 +207,7 @@ def simulate_diffusion_mri(
         arguments = "-p {} -i {} -o {}".format(ffp_file, fibers_file, out_name)
 
         command = self._bind_singularity("diffusion mri", bind_paths, arguments)
-        log_file = path.join(base_output_folder, "{}.log".format(run_name))
+        log_file = os.path.join(base_output_folder, "{}.log".format(run_name))
         self._run_command(command, log_file, "[DIFFUSION MRI]")
 
         loop_managed or self.stop()