niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrcentroid.py

@@ -0,0 +1,344 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRCENTROID_METADATA = Metadata(
+    id="d45d49e8b930b948a798b910b254792bd30544a6.boutiques",
+    name="mrcentroid",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrcentroidConfigParameters = typing.TypedDict('MrcentroidConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrcentroidParameters = typing.TypedDict('MrcentroidParameters', {
+    "__STYX_TYPE__": typing.Literal["mrcentroid"],
+    "mask": typing.NotRequired[InputPathType | None],
+    "voxelspace": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcentroidConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrcentroid": mrcentroid_cargs,
+        "config": mrcentroid_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 {
+    }.get(t)
+
+
+def mrcentroid_config_params(
+    key: str,
+    value: str,
+) -> MrcentroidConfigParameters:
+    """
+    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 mrcentroid_config_cargs(
+    params: MrcentroidConfigParameters,
+    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 MrcentroidOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrcentroid(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mrcentroid_params(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    voxelspace: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcentroidConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrcentroidParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image.
+        mask: only include voxels within a mask in the calculation.
+        voxelspace: report image centre of mass in voxel space rather than\
+            scanner 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__": "mrcentroid",
+        "voxelspace": voxelspace,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrcentroid_cargs(
+    params: MrcentroidParameters,
+    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("mrcentroid")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("voxelspace"):
+        cargs.append("-voxelspace")
+    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("input")))
+    return cargs
+
+
+def mrcentroid_outputs(
+    params: MrcentroidParameters,
+    execution: Execution,
+) -> MrcentroidOutputs:
+    """
+    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 = MrcentroidOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mrcentroid_execute(
+    params: MrcentroidParameters,
+    execution: Execution,
+) -> MrcentroidOutputs:
+    """
+    Determine the centre of mass / centre of gravity of an image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrcentroidOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrcentroid_cargs(params, execution)
+    ret = mrcentroid_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrcentroid(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    voxelspace: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcentroidConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrcentroidOutputs:
+    """
+    Determine the centre of mass / centre of gravity of an image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image.
+        mask: only include voxels within a mask in the calculation.
+        voxelspace: report image centre of mass in voxel space rather than\
+            scanner 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 `MrcentroidOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCENTROID_METADATA)
+    params = mrcentroid_params(
+        mask=mask,
+        voxelspace=voxelspace,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+    )
+    return mrcentroid_execute(params, execution)
+
+
+__all__ = [
+    "MRCENTROID_METADATA",
+    "MrcentroidConfigParameters",
+    "MrcentroidOutputs",
+    "MrcentroidParameters",
+    "mrcentroid",
+    "mrcentroid_config_params",
+    "mrcentroid_params",
+]

niwrap_mrtrix/mrtrix/mrcheckerboardmask.py

@@ -0,0 +1,363 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRCHECKERBOARDMASK_METADATA = Metadata(
+    id="d3e361c565ddae09545311ba3dafc739a0f94a5f.boutiques",
+    name="mrcheckerboardmask",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrcheckerboardmaskConfigParameters = typing.TypedDict('MrcheckerboardmaskConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrcheckerboardmaskParameters = typing.TypedDict('MrcheckerboardmaskParameters', {
+    "__STYX_TYPE__": typing.Literal["mrcheckerboardmask"],
+    "tiles": typing.NotRequired[int | None],
+    "invert": bool,
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcheckerboardmaskConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrcheckerboardmask": mrcheckerboardmask_cargs,
+        "config": mrcheckerboardmask_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 {
+        "mrcheckerboardmask": mrcheckerboardmask_outputs,
+    }.get(t)
+
+
+def mrcheckerboardmask_config_params(
+    key: str,
+    value: str,
+) -> MrcheckerboardmaskConfigParameters:
+    """
+    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 mrcheckerboardmask_config_cargs(
+    params: MrcheckerboardmaskConfigParameters,
+    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 MrcheckerboardmaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrcheckerboardmask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output binary image mask."""
+
+
+def mrcheckerboardmask_params(
+    input_: InputPathType,
+    output: str,
+    tiles: int | None = None,
+    invert: bool = False,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcheckerboardmaskConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrcheckerboardmaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image to be used as a template.
+        output: the output binary image mask.
+        tiles: specify the number of tiles in any direction.
+        invert: invert output binary mask.
+        nan: use NaN as the output zero value.
+        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__": "mrcheckerboardmask",
+        "invert": invert,
+        "nan": nan,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if tiles is not None:
+        params["tiles"] = tiles
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrcheckerboardmask_cargs(
+    params: MrcheckerboardmaskParameters,
+    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("mrcheckerboardmask")
+    if params.get("tiles") is not None:
+        cargs.extend([
+            "-tiles",
+            str(params.get("tiles"))
+        ])
+    if params.get("invert"):
+        cargs.append("-invert")
+    if params.get("nan"):
+        cargs.append("-nan")
+    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("input")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrcheckerboardmask_outputs(
+    params: MrcheckerboardmaskParameters,
+    execution: Execution,
+) -> MrcheckerboardmaskOutputs:
+    """
+    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 = MrcheckerboardmaskOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def mrcheckerboardmask_execute(
+    params: MrcheckerboardmaskParameters,
+    execution: Execution,
+) -> MrcheckerboardmaskOutputs:
+    """
+    Create bitwise checkerboard image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrcheckerboardmaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrcheckerboardmask_cargs(params, execution)
+    ret = mrcheckerboardmask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrcheckerboardmask(
+    input_: InputPathType,
+    output: str,
+    tiles: int | None = None,
+    invert: bool = False,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcheckerboardmaskConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrcheckerboardmaskOutputs:
+    """
+    Create bitwise checkerboard image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image to be used as a template.
+        output: the output binary image mask.
+        tiles: specify the number of tiles in any direction.
+        invert: invert output binary mask.
+        nan: use NaN as the output zero value.
+        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 `MrcheckerboardmaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCHECKERBOARDMASK_METADATA)
+    params = mrcheckerboardmask_params(
+        tiles=tiles,
+        invert=invert,
+        nan=nan,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return mrcheckerboardmask_execute(params, execution)
+
+
+__all__ = [
+    "MRCHECKERBOARDMASK_METADATA",
+    "MrcheckerboardmaskConfigParameters",
+    "MrcheckerboardmaskOutputs",
+    "MrcheckerboardmaskParameters",
+    "mrcheckerboardmask",
+    "mrcheckerboardmask_config_params",
+    "mrcheckerboardmask_params",
+]