niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelfilter.py

@@ -0,0 +1,616 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELFILTER_METADATA = Metadata(
+    id="de612300fec8260dbe9407acf8595be232354182.boutiques",
+    name="fixelfilter",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+FixelfilterConfigParameters = typing.TypedDict('FixelfilterConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+FixelfilterVariousStringParameters = typing.TypedDict('FixelfilterVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+FixelfilterVariousFileParameters = typing.TypedDict('FixelfilterVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+FixelfilterVariousString1Parameters = typing.TypedDict('FixelfilterVariousString1Parameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString_1"],
+    "obj": str,
+})
+
+
+FixelfilterVariousFile1Parameters = typing.TypedDict('FixelfilterVariousFile1Parameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile_1"],
+    "obj": InputPathType,
+})
+
+
+FixelfilterParameters = typing.TypedDict('FixelfilterParameters', {
+    "__STYX_TYPE__": typing.Literal["fixelfilter"],
+    "matrix": InputPathType,
+    "threshold_value": typing.NotRequired[float | None],
+    "threshold_connectivity": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "minweight": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelfilterConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": typing.Union[FixelfilterVariousStringParameters, FixelfilterVariousFileParameters],
+    "filter": str,
+    "output": typing.Union[FixelfilterVariousString1Parameters, FixelfilterVariousFile1Parameters],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixelfilter": fixelfilter_cargs,
+        "config": fixelfilter_config_cargs,
+        "VariousString": fixelfilter_various_string_cargs,
+        "VariousFile": fixelfilter_various_file_cargs,
+        "VariousString_1": fixelfilter_various_string_1_cargs,
+        "VariousFile_1": fixelfilter_various_file_1_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 fixelfilter_config_params(
+    key: str,
+    value: str,
+) -> FixelfilterConfigParameters:
+    """
+    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 fixelfilter_config_cargs(
+    params: FixelfilterConfigParameters,
+    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 fixelfilter_various_string_params(
+    obj: str,
+) -> FixelfilterVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_string_cargs(
+    params: FixelfilterVariousStringParameters,
+    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 fixelfilter_various_file_params(
+    obj: InputPathType,
+) -> FixelfilterVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_file_cargs(
+    params: FixelfilterVariousFileParameters,
+    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
+
+
+def fixelfilter_various_string_1_params(
+    obj: str,
+) -> FixelfilterVariousString1Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString_1",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_string_1_cargs(
+    params: FixelfilterVariousString1Parameters,
+    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 fixelfilter_various_file_1_params(
+    obj: InputPathType,
+) -> FixelfilterVariousFile1Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile_1",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_file_1_cargs(
+    params: FixelfilterVariousFile1Parameters,
+    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 FixelfilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixelfilter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fixelfilter_params(
+    matrix: InputPathType,
+    input_: typing.Union[FixelfilterVariousStringParameters, FixelfilterVariousFileParameters],
+    filter_: str,
+    output: typing.Union[FixelfilterVariousString1Parameters, FixelfilterVariousFile1Parameters],
+    threshold_value: float | None = None,
+    threshold_connectivity: float | None = None,
+    fwhm: float | None = None,
+    minweight: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelfilterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        matrix: provide a fixel-fixel connectivity matrix for filtering\
+            operations that require it.
+        input_: the input: either a fixel data file, or a fixel directory (see\
+            Description).
+        filter_: the filtering operation to perform; options are: connect,\
+            smooth.
+        output: the output: either a fixel data file, or a fixel directory (see\
+            Description).
+        threshold_value: specify a threshold for the input fixel data file\
+            values (default = 0.5).
+        threshold_connectivity: specify a fixel-fixel connectivity threshold\
+            for connected-component analysis (default = 0.10000000000000001).
+        fwhm: the full-width half-maximum (FWHM) of the spatial component of\
+            the smoothing filter (default = 10mm).
+        minweight: apply a minimum threshold to smoothing weights (default =\
+            0.01).
+        mask: only perform smoothing within a specified binary fixel mask.
+        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__": "fixelfilter",
+        "matrix": matrix,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "filter": filter_,
+        "output": output,
+    }
+    if threshold_value is not None:
+        params["threshold_value"] = threshold_value
+    if threshold_connectivity is not None:
+        params["threshold_connectivity"] = threshold_connectivity
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if minweight is not None:
+        params["minweight"] = minweight
+    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 fixelfilter_cargs(
+    params: FixelfilterParameters,
+    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("fixelfilter")
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("matrix"))
+    ])
+    if params.get("threshold_value") is not None:
+        cargs.extend([
+            "-threshold_value",
+            str(params.get("threshold_value"))
+        ])
+    if params.get("threshold_connectivity") is not None:
+        cargs.extend([
+            "-threshold_connectivity",
+            str(params.get("threshold_connectivity"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "-fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("minweight") is not None:
+        cargs.extend([
+            "-minweight",
+            str(params.get("minweight"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    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(dyn_cargs(params.get("input")["__STYXTYPE__"])(params.get("input"), execution))
+    cargs.append(params.get("filter"))
+    cargs.extend(dyn_cargs(params.get("output")["__STYXTYPE__"])(params.get("output"), execution))
+    return cargs
+
+
+def fixelfilter_outputs(
+    params: FixelfilterParameters,
+    execution: Execution,
+) -> FixelfilterOutputs:
+    """
+    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 = FixelfilterOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fixelfilter_execute(
+    params: FixelfilterParameters,
+    execution: Execution,
+) -> FixelfilterOutputs:
+    """
+    Perform filtering operations on fixel-based data.
+    
+    If the first input to the command is a specific fixel data file, then a
+    filtered version of only that file will be generated by the command.
+    Alternatively, if the input is the location of a fixel directory, then the
+    command will create a duplicate of the fixel directory, and apply the
+    specified filter operation to all fixel data files within the directory.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FixelfilterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixelfilter_cargs(params, execution)
+    ret = fixelfilter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelfilter(
+    matrix: InputPathType,
+    input_: typing.Union[FixelfilterVariousStringParameters, FixelfilterVariousFileParameters],
+    filter_: str,
+    output: typing.Union[FixelfilterVariousString1Parameters, FixelfilterVariousFile1Parameters],
+    threshold_value: float | None = None,
+    threshold_connectivity: float | None = None,
+    fwhm: float | None = None,
+    minweight: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelfilterOutputs:
+    """
+    Perform filtering operations on fixel-based data.
+    
+    If the first input to the command is a specific fixel data file, then a
+    filtered version of only that file will be generated by the command.
+    Alternatively, if the input is the location of a fixel directory, then the
+    command will create a duplicate of the fixel directory, and apply the
+    specified filter operation to all fixel data files within the directory.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        matrix: provide a fixel-fixel connectivity matrix for filtering\
+            operations that require it.
+        input_: the input: either a fixel data file, or a fixel directory (see\
+            Description).
+        filter_: the filtering operation to perform; options are: connect,\
+            smooth.
+        output: the output: either a fixel data file, or a fixel directory (see\
+            Description).
+        threshold_value: specify a threshold for the input fixel data file\
+            values (default = 0.5).
+        threshold_connectivity: specify a fixel-fixel connectivity threshold\
+            for connected-component analysis (default = 0.10000000000000001).
+        fwhm: the full-width half-maximum (FWHM) of the spatial component of\
+            the smoothing filter (default = 10mm).
+        minweight: apply a minimum threshold to smoothing weights (default =\
+            0.01).
+        mask: only perform smoothing within a specified binary fixel mask.
+        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 `FixelfilterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELFILTER_METADATA)
+    params = fixelfilter_params(
+        matrix=matrix,
+        threshold_value=threshold_value,
+        threshold_connectivity=threshold_connectivity,
+        fwhm=fwhm,
+        minweight=minweight,
+        mask=mask,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        filter_=filter_,
+        output=output,
+    )
+    return fixelfilter_execute(params, execution)
+
+
+__all__ = [
+    "FIXELFILTER_METADATA",
+    "FixelfilterConfigParameters",
+    "FixelfilterOutputs",
+    "FixelfilterParameters",
+    "FixelfilterVariousFile1Parameters",
+    "FixelfilterVariousFileParameters",
+    "FixelfilterVariousString1Parameters",
+    "FixelfilterVariousStringParameters",
+    "fixelfilter",
+    "fixelfilter_config_params",
+    "fixelfilter_params",
+    "fixelfilter_various_file_1_params",
+    "fixelfilter_various_file_params",
+    "fixelfilter_various_string_1_params",
+    "fixelfilter_various_string_params",
+]