niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warpconvert.py

@@ -0,0 +1,411 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARPCONVERT_METADATA = Metadata(
+    id="aa820be224a359dcdb4d3911882f1ee399c31903.boutiques",
+    name="warpconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+WarpconvertConfigParameters = typing.TypedDict('WarpconvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+WarpconvertParameters = typing.TypedDict('WarpconvertParameters', {
+    "__STYX_TYPE__": typing.Literal["warpconvert"],
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "from": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "type": str,
+    "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 {
+        "warpconvert": warpconvert_cargs,
+        "config": warpconvert_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 {
+        "warpconvert": warpconvert_outputs,
+    }.get(t)
+
+
+def warpconvert_config_params(
+    key: str,
+    value: str,
+) -> WarpconvertConfigParameters:
+    """
+    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 warpconvert_config_cargs(
+    params: WarpconvertConfigParameters,
+    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 WarpconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `warpconvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output warp image."""
+
+
+def warpconvert_params(
+    in_: InputPathType,
+    type_: str,
+    out: str,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    from_: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> WarpconvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input warp image.
+        type_: the conversion type required. Valid choices are:\
+            deformation2displacement, displacement2deformation,\
+            warpfull2deformation, warpfull2displacement.
+        out: the output warp image.
+        template: define a template image when converting a warpfull file\
+            (which is defined on a grid in the midway space between image 1 & 2).\
+            For example to generate the deformation field that maps image1 to\
+            image2, then supply image2 as the template image.
+        midway_space: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. The output will only contain\
+            the non-linear warp to map an input image to the midway space (defined\
+            by the warpfull grid). If a linear transform exists in the warpfull\
+            file header then it will be composed and included in the output.
+        from_: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. Used to define the direction of\
+            the desired output field.Use -from 1 to obtain the image1->image2 field\
+            and from 2 for image2->image1. Can be used in combination with the\
+            -midway_space option to produce a field that only maps to midway space.
+        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__": "warpconvert",
+        "midway_space": midway_space,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "type": type_,
+        "out": out,
+    }
+    if template is not None:
+        params["template"] = template
+    if from_ is not None:
+        params["from"] = from_
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warpconvert_cargs(
+    params: WarpconvertParameters,
+    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("warpconvert")
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    if params.get("midway_space"):
+        cargs.append("-midway_space")
+    if params.get("from") is not None:
+        cargs.extend([
+            "-from",
+            str(params.get("from"))
+        ])
+    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("in")))
+    cargs.append(params.get("type"))
+    cargs.append(params.get("out"))
+    return cargs
+
+
+def warpconvert_outputs(
+    params: WarpconvertParameters,
+    execution: Execution,
+) -> WarpconvertOutputs:
+    """
+    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 = WarpconvertOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out")),
+    )
+    return ret
+
+
+def warpconvert_execute(
+    params: WarpconvertParameters,
+    execution: Execution,
+) -> WarpconvertOutputs:
+    """
+    Convert between different representations of a non-linear warp.
+    
+    A deformation field is defined as an image where each voxel defines the
+    corresponding position in the other image (in scanner space coordinates). A
+    displacement field stores the displacements (in mm) to the other image from
+    the each voxel's position (in scanner space). The warpfull file is the 5D
+    format output from mrregister -nl_warp_full, which contains linear
+    transforms, warps and their inverses that map each image to a midway space.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WarpconvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = warpconvert_cargs(params, execution)
+    ret = warpconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warpconvert(
+    in_: InputPathType,
+    type_: str,
+    out: str,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    from_: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> WarpconvertOutputs:
+    """
+    Convert between different representations of a non-linear warp.
+    
+    A deformation field is defined as an image where each voxel defines the
+    corresponding position in the other image (in scanner space coordinates). A
+    displacement field stores the displacements (in mm) to the other image from
+    the each voxel's position (in scanner space). The warpfull file is the 5D
+    format output from mrregister -nl_warp_full, which contains linear
+    transforms, warps and their inverses that map each image to a midway space.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input warp image.
+        type_: the conversion type required. Valid choices are:\
+            deformation2displacement, displacement2deformation,\
+            warpfull2deformation, warpfull2displacement.
+        out: the output warp image.
+        template: define a template image when converting a warpfull file\
+            (which is defined on a grid in the midway space between image 1 & 2).\
+            For example to generate the deformation field that maps image1 to\
+            image2, then supply image2 as the template image.
+        midway_space: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. The output will only contain\
+            the non-linear warp to map an input image to the midway space (defined\
+            by the warpfull grid). If a linear transform exists in the warpfull\
+            file header then it will be composed and included in the output.
+        from_: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. Used to define the direction of\
+            the desired output field.Use -from 1 to obtain the image1->image2 field\
+            and from 2 for image2->image1. Can be used in combination with the\
+            -midway_space option to produce a field that only maps to midway space.
+        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 `WarpconvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPCONVERT_METADATA)
+    params = warpconvert_params(
+        template=template,
+        midway_space=midway_space,
+        from_=from_,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        type_=type_,
+        out=out,
+    )
+    return warpconvert_execute(params, execution)
+
+
+__all__ = [
+    "WARPCONVERT_METADATA",
+    "WarpconvertConfigParameters",
+    "WarpconvertOutputs",
+    "WarpconvertParameters",
+    "warpconvert",
+    "warpconvert_config_params",
+    "warpconvert_params",
+]