niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/labelconvert.py

@@ -0,0 +1,377 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+LABELCONVERT_METADATA = Metadata(
+    id="70b1b32bfcb741c07b8d256b92dbe12ed0418e5f.boutiques",
+    name="labelconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+LabelconvertConfigParameters = typing.TypedDict('LabelconvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+LabelconvertParameters = typing.TypedDict('LabelconvertParameters', {
+    "__STYX_TYPE__": typing.Literal["labelconvert"],
+    "spine": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[LabelconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "path_in": InputPathType,
+    "lut_in": InputPathType,
+    "lut_out": InputPathType,
+    "image_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 {
+        "labelconvert": labelconvert_cargs,
+        "config": labelconvert_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 {
+        "labelconvert": labelconvert_outputs,
+    }.get(t)
+
+
+def labelconvert_config_params(
+    key: str,
+    value: str,
+) -> LabelconvertConfigParameters:
+    """
+    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 labelconvert_config_cargs(
+    params: LabelconvertConfigParameters,
+    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 LabelconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `labelconvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    image_out: OutputPathType
+    """the output image"""
+
+
+def labelconvert_params(
+    path_in: InputPathType,
+    lut_in: InputPathType,
+    lut_out: InputPathType,
+    image_out: str,
+    spine: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> LabelconvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        path_in: the input image.
+        lut_in: the connectome lookup table corresponding to the input image.
+        lut_out: the target connectome lookup table for the output image.
+        image_out: the output image.
+        spine: provide a manually-defined segmentation of the base of the spine\
+            where the streamlines terminate, so that this can become a node in the\
+            connection matrix.
+        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__": "labelconvert",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "path_in": path_in,
+        "lut_in": lut_in,
+        "lut_out": lut_out,
+        "image_out": image_out,
+    }
+    if spine is not None:
+        params["spine"] = spine
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def labelconvert_cargs(
+    params: LabelconvertParameters,
+    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("labelconvert")
+    if params.get("spine") is not None:
+        cargs.extend([
+            "-spine",
+            execution.input_file(params.get("spine"))
+        ])
+    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("path_in")))
+    cargs.append(execution.input_file(params.get("lut_in")))
+    cargs.append(execution.input_file(params.get("lut_out")))
+    cargs.append(params.get("image_out"))
+    return cargs
+
+
+def labelconvert_outputs(
+    params: LabelconvertParameters,
+    execution: Execution,
+) -> LabelconvertOutputs:
+    """
+    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 = LabelconvertOutputs(
+        root=execution.output_file("."),
+        image_out=execution.output_file(params.get("image_out")),
+    )
+    return ret
+
+
+def labelconvert_execute(
+    params: LabelconvertParameters,
+    execution: Execution,
+) -> LabelconvertOutputs:
+    """
+    Convert a connectome node image from one lookup table to another.
+    
+    Typical usage is to convert a parcellation image provided by some other
+    software, based on the lookup table provided by that software, to conform to
+    a new lookup table, particularly one where the node indices increment from
+    1, in preparation for connectome construction; examples of such target
+    lookup table files are provided in share//mrtrix3//labelconvert//, but can
+    be created by the user to provide the desired node set // ordering //
+    colours.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `LabelconvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = labelconvert_cargs(params, execution)
+    ret = labelconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def labelconvert(
+    path_in: InputPathType,
+    lut_in: InputPathType,
+    lut_out: InputPathType,
+    image_out: str,
+    spine: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> LabelconvertOutputs:
+    """
+    Convert a connectome node image from one lookup table to another.
+    
+    Typical usage is to convert a parcellation image provided by some other
+    software, based on the lookup table provided by that software, to conform to
+    a new lookup table, particularly one where the node indices increment from
+    1, in preparation for connectome construction; examples of such target
+    lookup table files are provided in share//mrtrix3//labelconvert//, but can
+    be created by the user to provide the desired node set // ordering //
+    colours.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        path_in: the input image.
+        lut_in: the connectome lookup table corresponding to the input image.
+        lut_out: the target connectome lookup table for the output image.
+        image_out: the output image.
+        spine: provide a manually-defined segmentation of the base of the spine\
+            where the streamlines terminate, so that this can become a node in the\
+            connection matrix.
+        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 `LabelconvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABELCONVERT_METADATA)
+    params = labelconvert_params(
+        spine=spine,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        path_in=path_in,
+        lut_in=lut_in,
+        lut_out=lut_out,
+        image_out=image_out,
+    )
+    return labelconvert_execute(params, execution)
+
+
+__all__ = [
+    "LABELCONVERT_METADATA",
+    "LabelconvertConfigParameters",
+    "LabelconvertOutputs",
+    "LabelconvertParameters",
+    "labelconvert",
+    "labelconvert_config_params",
+    "labelconvert_params",
+]

niwrap_mrtrix/mrtrix/labelstats.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 *
+
+LABELSTATS_METADATA = Metadata(
+    id="254f5ddf0636d16c200b150f7e9d225ebb08df1b.boutiques",
+    name="labelstats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+LabelstatsConfigParameters = typing.TypedDict('LabelstatsConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+LabelstatsParameters = typing.TypedDict('LabelstatsParameters', {
+    "__STYX_TYPE__": typing.Literal["labelstats"],
+    "output": typing.NotRequired[str | None],
+    "voxelspace": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[LabelstatsConfigParameters] | 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 {
+        "labelstats": labelstats_cargs,
+        "config": labelstats_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 labelstats_config_params(
+    key: str,
+    value: str,
+) -> LabelstatsConfigParameters:
+    """
+    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 labelstats_config_cargs(
+    params: LabelstatsConfigParameters,
+    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 LabelstatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `labelstats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def labelstats_params(
+    input_: InputPathType,
+    output: str | None = None,
+    voxelspace: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelstatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> LabelstatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input label image.
+        output: output only the field specified; options are: mass,centre.
+        voxelspace: report parcel centres 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__": "labelstats",
+        "voxelspace": voxelspace,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+    }
+    if output is not None:
+        params["output"] = output
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def labelstats_cargs(
+    params: LabelstatsParameters,
+    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("labelstats")
+    if params.get("output") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output")
+        ])
+    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 labelstats_outputs(
+    params: LabelstatsParameters,
+    execution: Execution,
+) -> LabelstatsOutputs:
+    """
+    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 = LabelstatsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def labelstats_execute(
+    params: LabelstatsParameters,
+    execution: Execution,
+) -> LabelstatsOutputs:
+    """
+    Compute statistics of parcels within a label image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `LabelstatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = labelstats_cargs(params, execution)
+    ret = labelstats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def labelstats(
+    input_: InputPathType,
+    output: str | None = None,
+    voxelspace: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelstatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> LabelstatsOutputs:
+    """
+    Compute statistics of parcels within a label image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input label image.
+        output: output only the field specified; options are: mass,centre.
+        voxelspace: report parcel centres 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 `LabelstatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABELSTATS_METADATA)
+    params = labelstats_params(
+        output=output,
+        voxelspace=voxelspace,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+    )
+    return labelstats_execute(params, execution)
+
+
+__all__ = [
+    "LABELSTATS_METADATA",
+    "LabelstatsConfigParameters",
+    "LabelstatsOutputs",
+    "LabelstatsParameters",
+    "labelstats",
+    "labelstats_config_params",
+    "labelstats_params",
+]