niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/transformcompose.py

@@ -0,0 +1,465 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TRANSFORMCOMPOSE_METADATA = Metadata(
+    id="8e378625408e1058e736b1bc94ac29bb3d2555e8.boutiques",
+    name="transformcompose",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TransformcomposeConfigParameters = typing.TypedDict('TransformcomposeConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TransformcomposeVariousStringParameters = typing.TypedDict('TransformcomposeVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+TransformcomposeVariousFileParameters = typing.TypedDict('TransformcomposeVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+TransformcomposeParameters = typing.TypedDict('TransformcomposeParameters', {
+    "__STYX_TYPE__": typing.Literal["transformcompose"],
+    "template": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TransformcomposeConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "output": typing.Union[TransformcomposeVariousStringParameters, TransformcomposeVariousFileParameters],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "transformcompose": transformcompose_cargs,
+        "config": transformcompose_config_cargs,
+        "VariousString": transformcompose_various_string_cargs,
+        "VariousFile": transformcompose_various_file_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 {
+    }.get(t)
+
+
+def transformcompose_config_params(
+    key: str,
+    value: str,
+) -> TransformcomposeConfigParameters:
+    """
+    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 transformcompose_config_cargs(
+    params: TransformcomposeConfigParameters,
+    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
+
+
+def transformcompose_various_string_params(
+    obj: str,
+) -> TransformcomposeVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def transformcompose_various_string_cargs(
+    params: TransformcomposeVariousStringParameters,
+    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(params.get("obj"))
+    return cargs
+
+
+def transformcompose_various_file_params(
+    obj: InputPathType,
+) -> TransformcomposeVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def transformcompose_various_file_cargs(
+    params: TransformcomposeVariousFileParameters,
+    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(execution.input_file(params.get("obj")))
+    return cargs
+
+
+class TransformcomposeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `transformcompose(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def transformcompose_params(
+    input_: list[InputPathType],
+    output: typing.Union[TransformcomposeVariousStringParameters, TransformcomposeVariousFileParameters],
+    template: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformcomposeConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TransformcomposeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input transforms (either linear or non-linear warps).
+        output: the output file (may be a linear transformation text file, or a\
+            deformation warp field image, depending on usage).
+        template: define the output grid defined by a template image.
+        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__": "transformcompose",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if template is not None:
+        params["template"] = template
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def transformcompose_cargs(
+    params: TransformcomposeParameters,
+    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("transformcompose")
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    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.extend([execution.input_file(f) for f in params.get("input")])
+    cargs.extend(dyn_cargs(params.get("output")["__STYXTYPE__"])(params.get("output"), execution))
+    return cargs
+
+
+def transformcompose_outputs(
+    params: TransformcomposeParameters,
+    execution: Execution,
+) -> TransformcomposeOutputs:
+    """
+    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 = TransformcomposeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def transformcompose_execute(
+    params: TransformcomposeParameters,
+    execution: Execution,
+) -> TransformcomposeOutputs:
+    """
+    Compose any number of linear transformations and/or warps into a single
+    transformation.
+    
+    Any linear transforms must be supplied as a 4x4 matrix in a text file (e.g.
+    as per the output of mrregister). Any warp fields must be supplied as a 4D
+    image representing a deformation field (e.g. as output from mrrregister
+    -nl_warp).
+    
+    Input transformations should be provided to the command in the order in
+    which they would be applied to an image if they were to be applied
+    individually.
+    
+    If all input transformations are linear, and the -template option is not
+    provided, then the file output by the command will also be a linear
+    transformation saved as a 4x4 matrix in a text file. If a template image is
+    supplied, then the output will always be a deformation field. If at least
+    one of the inputs is a warp field, then the output will be a deformation
+    field, which will be defined on the grid of the last input warp image
+    supplied if the -template option is not used.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TransformcomposeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = transformcompose_cargs(params, execution)
+    ret = transformcompose_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def transformcompose(
+    input_: list[InputPathType],
+    output: typing.Union[TransformcomposeVariousStringParameters, TransformcomposeVariousFileParameters],
+    template: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformcomposeConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TransformcomposeOutputs:
+    """
+    Compose any number of linear transformations and/or warps into a single
+    transformation.
+    
+    Any linear transforms must be supplied as a 4x4 matrix in a text file (e.g.
+    as per the output of mrregister). Any warp fields must be supplied as a 4D
+    image representing a deformation field (e.g. as output from mrrregister
+    -nl_warp).
+    
+    Input transformations should be provided to the command in the order in
+    which they would be applied to an image if they were to be applied
+    individually.
+    
+    If all input transformations are linear, and the -template option is not
+    provided, then the file output by the command will also be a linear
+    transformation saved as a 4x4 matrix in a text file. If a template image is
+    supplied, then the output will always be a deformation field. If at least
+    one of the inputs is a warp field, then the output will be a deformation
+    field, which will be defined on the grid of the last input warp image
+    supplied if the -template option is not used.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input transforms (either linear or non-linear warps).
+        output: the output file (may be a linear transformation text file, or a\
+            deformation warp field image, depending on usage).
+        template: define the output grid defined by a template image.
+        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 `TransformcomposeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRANSFORMCOMPOSE_METADATA)
+    params = transformcompose_params(
+        template=template,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return transformcompose_execute(params, execution)
+
+
+__all__ = [
+    "TRANSFORMCOMPOSE_METADATA",
+    "TransformcomposeConfigParameters",
+    "TransformcomposeOutputs",
+    "TransformcomposeParameters",
+    "TransformcomposeVariousFileParameters",
+    "TransformcomposeVariousStringParameters",
+    "transformcompose",
+    "transformcompose_config_params",
+    "transformcompose_params",
+    "transformcompose_various_file_params",
+    "transformcompose_various_string_params",
+]