Create sim_reconstruct_single

Has ability to set processing directory directly (not the parent directory)
Can set the multiprocessing pool to be used

src/sim_recon/__init__.py

@@ -2,8 +2,13 @@
 
 
 if __name__ == "__main__":
-    from .main import sim_reconstruct, sim_psf_to_otf
+    from .main import sim_reconstruct, sim_psf_to_otf, sim_reconstruct_single
 
-    __all__ = ["__version__", "sim_reconstruct", "sim_psf_to_otf"]
+    __all__ = [
+        "__version__",
+        "sim_reconstruct",
+        "sim_reconstruct_single",
+        "sim_psf_to_otf",
+    ]
 else:
     __all__ = ["__version__"]

src/sim_recon/main.py

@@ -10,13 +10,14 @@
 )
 from .settings import ConfigManager
 from .otfs import convert_psfs_to_otfs
-from .recon import run_reconstructions
+from .recon import run_reconstructions, run_single_reconstruction
 
 
 if TYPE_CHECKING:
     from typing import Any
     from os import PathLike
     from pathlib import Path
+    from multiprocessing.pool import Pool
     from .recon import OutputFileTypes
 
 
@@ -101,9 +102,9 @@ def sim_reconstruct(
     overwrite: bool = False,
     cleanup: bool = True,
     stitch_channels: bool = True,
-    parallel_process: bool = False,
     allow_missing_channels: bool = False,
     output_file_type: OutputFileTypes = "dv",
+    parallel_process: bool = False,
     **recon_kwargs: Any,
 ) -> None:
     """
@@ -118,7 +119,7 @@ def sim_reconstruct(
     output_directory : str | PathLike[str] | None, optional
         Directory to save reconstructions in (reconstructions will be saved with the data files if not specified), by default None
     processing_directory : str | PathLike[str] | None, optional
-        The directory in which the temporary files will be stored for processing (otherwise the output directory will be used), by default None
+        The directory in which subdirectories of temporary files will be stored for processing (otherwise the output directory will be used), by default None
     otf_overrides : dict[int, Path] | None, optional
         A dictionary with emission wavelengths in nm as keys and paths to OTF files as values (these override configured OTFs), by default None
     overwrite : bool, optional
@@ -144,8 +145,71 @@ def sim_reconstruct(
         overwrite=overwrite,
         cleanup=cleanup,
         stitch_channels=stitch_channels,
+        allow_partial=allow_missing_channels,
+        output_file_type=output_file_type,
         parallel_process=parallel_process,
+        **recon_kwargs,
+    )
+
+
+def sim_reconstruct_single(
+    sim_data_path: str | PathLike[str],
+    config_path: str | PathLike[str] | None = None,
+    output_directory: str | PathLike[str] | None = None,
+    processing_directory: str | PathLike[str] | None = None,
+    otf_overrides: dict[int, Path] | None = None,
+    overwrite: bool = False,
+    cleanup: bool = True,
+    stitch_channels: bool = True,
+    allow_missing_channels: bool = False,
+    output_file_type: OutputFileTypes = "dv",
+    multiprocessing_pool: Pool | None = None,
+    parallel_process: bool = False,
+    **recon_kwargs: Any,
+) -> None:
+    """
+    Top level function for reconstructing SIM data
+
+    Parameters
+    ----------
+    sim_data_path : str | PathLike[str]
+        Path to SIM data files (DV expected)
+    config_path : str | PathLike[str] | None, optional
+        Path of the top level config file, by default None
+    output_directory : str | PathLike[str] | None, optional
+        Directory to save reconstructions in (reconstructions will be saved with the data files if not specified), by default None
+    processing_directory : str | PathLike[str] | None, optional
+        The directory in which the temporary files will be stored for processing (otherwise the output directory will be used), by default None
+    otf_overrides : dict[int, Path] | None, optional
+        A dictionary with emission wavelengths in nm as keys and paths to OTF files as values (these override configured OTFs), by default None
+    overwrite : bool, optional
+        Overwrite files if they already exist, by default False
+    cleanup : bool, optional
+        Clean up temporary directory and files after reconstruction, by default True
+    stitch_channels : bool, optional
+        Stitch channels back together after processing (otherwise output will be a separate DV per channel), by default True
+    allow_missing_channels: bool, optional
+        Attempt reconstruction of other channels in a multi-channel file if one or more are not configured, by default False
+    output_file_type: Literal["dv", "tiff"], optional
+        File type that output images will be saved as, by default "dv"
+    multiprocessing_pool : Pool | None, optional
+        Multiprocessing pool to run cudasirecon in (`maxtasksperchild=1` is recommended to avoid crashes), by default None
+    parallel_process : bool, optional
+        Run reconstructions in 2 processes concurrently (ignored if multiprocessing_pool is supplied), by default False
+    """
+    conf = load_configs(config_path, otf_overrides=otf_overrides)
+    logger.info("Starting reconstruction of %s", sim_data_path)
+    run_single_reconstruction(
+        conf,
+        sim_data_path,
+        output_directory=output_directory,
+        processing_directory=processing_directory,
+        overwrite=overwrite,
+        cleanup=cleanup,
+        stitch_channels=stitch_channels,
         allow_partial=allow_missing_channels,
         output_file_type=output_file_type,
+        multiprocessing_pool=multiprocessing_pool,
+        parallel_process=parallel_process,
         **recon_kwargs,
     )