niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelreorient.py

@@ -0,0 +1,361 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELREORIENT_METADATA = Metadata(
+    id="131439582b6a79c991d4bdc5b5ebe9896e2ee937.boutiques",
+    name="fixelreorient",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+FixelreorientConfigParameters = typing.TypedDict('FixelreorientConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+FixelreorientParameters = typing.TypedDict('FixelreorientParameters', {
+    "__STYX_TYPE__": typing.Literal["fixelreorient"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelreorientConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "warp": InputPathType,
+    "fixel_out": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixelreorient": fixelreorient_cargs,
+        "config": fixelreorient_config_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "fixelreorient": fixelreorient_outputs,
+    }.get(t)
+
+
+def fixelreorient_config_params(
+    key: str,
+    value: str,
+) -> FixelreorientConfigParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def fixelreorient_config_cargs(
+    params: FixelreorientConfigParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-config")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class FixelreorientOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixelreorient(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fixel_out: OutputPathType
+    """the output fixel directory. If the the input and output directories are
+    the same, the existing directions file will be replaced (providing the
+    -force option is supplied). If a new directory is supplied then the fixel
+    directions and all other fixel data will be copied to the new directory."""
+
+
+def fixelreorient_params(
+    fixel_in: InputPathType,
+    warp: InputPathType,
+    fixel_out: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelreorientConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelreorientParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_in: the input fixel directory.
+        warp: a 4D deformation field used to perform reorientation.\
+            Reorientation is performed by applying the Jacobian affine transform in\
+            each voxel in the warp, then re-normalising the vector representing the\
+            fixel direction.
+        fixel_out: the output fixel directory. If the the input and output\
+            directories are the same, the existing directions file will be replaced\
+            (providing the -force option is supplied). If a new directory is\
+            supplied then the fixel directions and all other fixel data will be\
+            copied to the new directory.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fixelreorient",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_in": fixel_in,
+        "warp": warp,
+        "fixel_out": fixel_out,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelreorient_cargs(
+    params: FixelreorientParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("fixelreorient")
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("fixel_in")))
+    cargs.append(execution.input_file(params.get("warp")))
+    cargs.append(params.get("fixel_out"))
+    return cargs
+
+
+def fixelreorient_outputs(
+    params: FixelreorientParameters,
+    execution: Execution,
+) -> FixelreorientOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = FixelreorientOutputs(
+        root=execution.output_file("."),
+        fixel_out=execution.output_file(params.get("fixel_out")),
+    )
+    return ret
+
+
+def fixelreorient_execute(
+    params: FixelreorientParameters,
+    execution: Execution,
+) -> FixelreorientOutputs:
+    """
+    Reorient fixel directions.
+    
+    Reorientation is performed by transforming the vector representing the fixel
+    direction with the Jacobian (local affine transform) computed at each voxel
+    in the warp, then re-normalising the vector.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FixelreorientOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixelreorient_cargs(params, execution)
+    ret = fixelreorient_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelreorient(
+    fixel_in: InputPathType,
+    warp: InputPathType,
+    fixel_out: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelreorientConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelreorientOutputs:
+    """
+    Reorient fixel directions.
+    
+    Reorientation is performed by transforming the vector representing the fixel
+    direction with the Jacobian (local affine transform) computed at each voxel
+    in the warp, then re-normalising the vector.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_in: the input fixel directory.
+        warp: a 4D deformation field used to perform reorientation.\
+            Reorientation is performed by applying the Jacobian affine transform in\
+            each voxel in the warp, then re-normalising the vector representing the\
+            fixel direction.
+        fixel_out: the output fixel directory. If the the input and output\
+            directories are the same, the existing directions file will be replaced\
+            (providing the -force option is supplied). If a new directory is\
+            supplied then the fixel directions and all other fixel data will be\
+            copied to the new directory.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelreorientOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELREORIENT_METADATA)
+    params = fixelreorient_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_in=fixel_in,
+        warp=warp,
+        fixel_out=fixel_out,
+    )
+    return fixelreorient_execute(params, execution)
+
+
+__all__ = [
+    "FIXELREORIENT_METADATA",
+    "FixelreorientConfigParameters",
+    "FixelreorientOutputs",
+    "FixelreorientParameters",
+    "fixelreorient",
+    "fixelreorient_config_params",
+    "fixelreorient_params",
+]