niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixel2voxel.py

@@ -0,0 +1,523 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXEL2VOXEL_METADATA = Metadata(
+    id="0e517d0eb23dea1741bca5bac37fc1918bda4919.boutiques",
+    name="fixel2voxel",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Fixel2voxelConfigParamsDictNoTag = typing.TypedDict('_Fixel2voxelConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Fixel2voxelConfigParamsDictTagged = typing.TypedDict('Fixel2voxelConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Fixel2voxelConfigParamsDict = _Fixel2voxelConfigParamsDictNoTag | Fixel2voxelConfigParamsDictTagged
+
+
+_Fixel2voxelParamsDictNoTag = typing.TypedDict('_Fixel2voxelParamsDictNoTag', {
+    "number": typing.NotRequired[int | None],
+    "fill": typing.NotRequired[float | None],
+    "weighted": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2voxelConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "operation": str,
+    "image_out": str,
+})
+Fixel2voxelParamsDictTagged = typing.TypedDict('Fixel2voxelParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixel2voxel"],
+    "number": typing.NotRequired[int | None],
+    "fill": typing.NotRequired[float | None],
+    "weighted": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2voxelConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "operation": str,
+    "image_out": str,
+})
+Fixel2voxelParamsDict = _Fixel2voxelParamsDictNoTag | Fixel2voxelParamsDictTagged
+
+
+def fixel2voxel_config(
+    key: str,
+    value: str,
+) -> Fixel2voxelConfigParamsDictTagged:
+    """
+    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 = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def fixel2voxel_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2voxelConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def fixel2voxel_config_cargs(
+    params: Fixel2voxelConfigParamsDict,
+    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", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class Fixel2voxelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Fixel2voxelParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    image_out: OutputPathType
+    """the output scalar image."""
+
+
+def fixel2voxel_params(
+    fixel_in: InputPathType,
+    operation: str,
+    image_out: str,
+    number: int | None = None,
+    fill: float | None = None,
+    weighted: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2voxelConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fixel2voxelParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_in: the input fixel data file.
+        operation: the operation to apply, one of: mean, sum, product, min,\
+            max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, none.
+        image_out: the output scalar image.
+        number: use only the largest N fixels in calculation of the voxel-wise\
+            statistic; in the case of operation "none", output only the largest N\
+            fixels in each voxel.
+        fill: for "none" operation, specify the value to fill when number of\
+            fixels is fewer than the maximum (default: 0.0).
+        weighted: weight the contribution of each fixel to the per-voxel result\
+            according to its volume.
+        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 = {
+        "@type": "mrtrix/fixel2voxel",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_in": fixel_in,
+        "operation": operation,
+        "image_out": image_out,
+    }
+    if number is not None:
+        params["number"] = number
+    if fill is not None:
+        params["fill"] = fill
+    if weighted is not None:
+        params["weighted"] = weighted
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixel2voxel_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2voxelParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("number", None) is not None:
+        if not isinstance(params["number"], int):
+            raise StyxValidationError(f'`number` has the wrong type: Received `{type(params.get("number", None))}` expected `int | None`')
+    if params.get("fill", None) is not None:
+        if not isinstance(params["fill"], (float, int)):
+            raise StyxValidationError(f'`fill` has the wrong type: Received `{type(params.get("fill", None))}` expected `float | None`')
+    if params.get("weighted", None) is not None:
+        if not isinstance(params["weighted"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`weighted` has the wrong type: Received `{type(params.get("weighted", None))}` expected `InputPathType | None`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[Fixel2voxelConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixel2voxel_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("fixel_in", None) is None:
+        raise StyxValidationError("`fixel_in` must not be None")
+    if not isinstance(params["fixel_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`fixel_in` has the wrong type: Received `{type(params.get("fixel_in", None))}` expected `InputPathType`')
+    if params.get("operation", None) is None:
+        raise StyxValidationError("`operation` must not be None")
+    if not isinstance(params["operation"], str):
+        raise StyxValidationError(f'`operation` has the wrong type: Received `{type(params.get("operation", None))}` expected `str`')
+    if params.get("image_out", None) is None:
+        raise StyxValidationError("`image_out` must not be None")
+    if not isinstance(params["image_out"], str):
+        raise StyxValidationError(f'`image_out` has the wrong type: Received `{type(params.get("image_out", None))}` expected `str`')
+
+
+def fixel2voxel_cargs(
+    params: Fixel2voxelParamsDict,
+    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("fixel2voxel")
+    if params.get("number", None) is not None:
+        cargs.extend([
+            "-number",
+            str(params.get("number", None))
+        ])
+    if params.get("fill", None) is not None:
+        cargs.extend([
+            "-fill",
+            str(params.get("fill", None))
+        ])
+    if params.get("weighted", None) is not None:
+        cargs.extend([
+            "-weighted",
+            execution.input_file(params.get("weighted", None))
+        ])
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [fixel2voxel_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("fixel_in", None)))
+    cargs.append(params.get("operation", None))
+    cargs.append(params.get("image_out", None))
+    return cargs
+
+
+def fixel2voxel_outputs(
+    params: Fixel2voxelParamsDict,
+    execution: Execution,
+) -> Fixel2voxelOutputs:
+    """
+    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 = Fixel2voxelOutputs(
+        root=execution.output_file("."),
+        image_out=execution.output_file(params.get("image_out", None)),
+    )
+    return ret
+
+
+def fixel2voxel_execute(
+    params: Fixel2voxelParamsDict,
+    runner: Runner | None = None,
+) -> Fixel2voxelOutputs:
+    """
+    fixel2voxel
+    
+    Convert a fixel-based sparse-data image into some form of scalar image.
+    
+    Fixel data can be reduced to voxel data in a number of ways:
+    
+    - Some statistic computed across all fixel values within a voxel: mean, sum,
+    product, min, max, absmax, magmax
+    
+    - The number of fixels in each voxel: count
+    
+    - Some measure of crossing-fibre organisation: complexity, sf
+    ('single-fibre')
+    
+    - A 4D directionally-encoded colour image: dec_unit, dec_scaled
+    
+    - A 4D image containing all fixel data values in each voxel unmodified: none
+    
+    The -weighted option deals with the case where there is some per-fixel
+    metric of interest that you wish to collapse into a single scalar measure
+    per voxel, but each fixel possesses a different volume, and you wish for
+    those fixels with greater volume to have a greater influence on the
+    calculation than fixels with lesser volume. For instance, when estimating a
+    voxel-based measure of mean axon diameter from per-fixel mean axon
+    diameters, a fixel's mean axon diameter should be weigthed by its relative
+    volume within the voxel in the calculation of that voxel mean.
+    
+    References:
+    
+    * Reference for 'complexity' operation:
+    Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. Beyond
+    Fractional Anisotropy: Extraction of bundle-specific structural metrics from
+    crossing fibre models. NeuroImage, 2014, 100, 176-191.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Fixel2voxelOutputs`).
+    """
+    fixel2voxel_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2VOXEL_METADATA)
+    params = execution.params(params)
+    cargs = fixel2voxel_cargs(params, execution)
+    ret = fixel2voxel_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixel2voxel(
+    fixel_in: InputPathType,
+    operation: str,
+    image_out: str,
+    number: int | None = None,
+    fill: float | None = None,
+    weighted: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2voxelConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fixel2voxelOutputs:
+    """
+    fixel2voxel
+    
+    Convert a fixel-based sparse-data image into some form of scalar image.
+    
+    Fixel data can be reduced to voxel data in a number of ways:
+    
+    - Some statistic computed across all fixel values within a voxel: mean, sum,
+    product, min, max, absmax, magmax
+    
+    - The number of fixels in each voxel: count
+    
+    - Some measure of crossing-fibre organisation: complexity, sf
+    ('single-fibre')
+    
+    - A 4D directionally-encoded colour image: dec_unit, dec_scaled
+    
+    - A 4D image containing all fixel data values in each voxel unmodified: none
+    
+    The -weighted option deals with the case where there is some per-fixel
+    metric of interest that you wish to collapse into a single scalar measure
+    per voxel, but each fixel possesses a different volume, and you wish for
+    those fixels with greater volume to have a greater influence on the
+    calculation than fixels with lesser volume. For instance, when estimating a
+    voxel-based measure of mean axon diameter from per-fixel mean axon
+    diameters, a fixel's mean axon diameter should be weigthed by its relative
+    volume within the voxel in the calculation of that voxel mean.
+    
+    References:
+    
+    * Reference for 'complexity' operation:
+    Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. Beyond
+    Fractional Anisotropy: Extraction of bundle-specific structural metrics from
+    crossing fibre models. NeuroImage, 2014, 100, 176-191.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_in: the input fixel data file.
+        operation: the operation to apply, one of: mean, sum, product, min,\
+            max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, none.
+        image_out: the output scalar image.
+        number: use only the largest N fixels in calculation of the voxel-wise\
+            statistic; in the case of operation "none", output only the largest N\
+            fixels in each voxel.
+        fill: for "none" operation, specify the value to fill when number of\
+            fixels is fewer than the maximum (default: 0.0).
+        weighted: weight the contribution of each fixel to the per-voxel result\
+            according to its volume.
+        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 `Fixel2voxelOutputs`).
+    """
+    params = fixel2voxel_params(
+        number=number,
+        fill=fill,
+        weighted=weighted,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_in=fixel_in,
+        operation=operation,
+        image_out=image_out,
+    )
+    return fixel2voxel_execute(params, runner)
+
+
+__all__ = [
+    "FIXEL2VOXEL_METADATA",
+    "Fixel2voxelConfigParamsDict",
+    "Fixel2voxelConfigParamsDictTagged",
+    "Fixel2voxelOutputs",
+    "Fixel2voxelParamsDict",
+    "Fixel2voxelParamsDictTagged",
+    "fixel2voxel",
+    "fixel2voxel_config",
+    "fixel2voxel_execute",
+    "fixel2voxel_params",
+]