niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dirstat.py

@@ -0,0 +1,640 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DIRSTAT_METADATA = Metadata(
+    id="369098dbdbd016bf94682e0106a2f2e1711f2a5b.boutiques",
+    name="dirstat",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_DirstatFslgradParamsDictNoTag = typing.TypedDict('_DirstatFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+DirstatFslgradParamsDictTagged = typing.TypedDict('DirstatFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+DirstatFslgradParamsDict = _DirstatFslgradParamsDictNoTag | DirstatFslgradParamsDictTagged
+
+
+_DirstatConfigParamsDictNoTag = typing.TypedDict('_DirstatConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+DirstatConfigParamsDictTagged = typing.TypedDict('DirstatConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+DirstatConfigParamsDict = _DirstatConfigParamsDictNoTag | DirstatConfigParamsDictTagged
+
+
+_DirstatParamsDictNoTag = typing.TypedDict('_DirstatParamsDictNoTag', {
+    "output": typing.NotRequired[str | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DirstatFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirstatConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "dirs": InputPathType,
+})
+DirstatParamsDictTagged = typing.TypedDict('DirstatParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dirstat"],
+    "output": typing.NotRequired[str | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DirstatFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirstatConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "dirs": InputPathType,
+})
+DirstatParamsDict = _DirstatParamsDictNoTag | DirstatParamsDictTagged
+
+
+def dirstat_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> DirstatFslgradParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def dirstat_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirstatFslgradParamsDict` 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("bvecs", None) is None:
+        raise StyxValidationError("`bvecs` must not be None")
+    if not isinstance(params["bvecs"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvecs` has the wrong type: Received `{type(params.get("bvecs", None))}` expected `InputPathType`')
+    if params.get("bvals", None) is None:
+        raise StyxValidationError("`bvals` must not be None")
+    if not isinstance(params["bvals"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvals` has the wrong type: Received `{type(params.get("bvals", None))}` expected `InputPathType`')
+
+
+def dirstat_fslgrad_cargs(
+    params: DirstatFslgradParamsDict,
+    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("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
+    return cargs
+
+
+def dirstat_config(
+    key: str,
+    value: str,
+) -> DirstatConfigParamsDictTagged:
+    """
+    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 dirstat_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirstatConfigParamsDict` 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 dirstat_config_cargs(
+    params: DirstatConfigParamsDict,
+    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 DirstatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DirstatParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dirstat_params(
+    dirs: InputPathType,
+    output: str | None = None,
+    shells: list[float] | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: DirstatFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirstatConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DirstatParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        dirs: the text file or image containing the directions.
+        output: output selected metrics as a space-delimited list, suitable for\
+            use in scripts. This will produce one line of values per selected\
+            shell. Valid metrics are as specified in the description above.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        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/dirstat",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "dirs": dirs,
+    }
+    if output is not None:
+        params["output"] = output
+    if shells is not None:
+        params["shells"] = shells
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dirstat_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirstatParamsDict` 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("output", None) is not None:
+        if not isinstance(params["output"], str):
+            raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str | None`')
+    if params.get("shells", None) is not None:
+        if not isinstance(params["shells"], list):
+            raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+        for e in params["shells"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+    if params.get("grad", None) is not None:
+        if not isinstance(params["grad"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
+    if params.get("fslgrad", None) is not None:
+        dirstat_fslgrad_validate(params["fslgrad"])
+    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[DirstatConfigParamsDict] | None`')
+        for e in params["config"]:
+            dirstat_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("dirs", None) is None:
+        raise StyxValidationError("`dirs` must not be None")
+    if not isinstance(params["dirs"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`dirs` has the wrong type: Received `{type(params.get("dirs", None))}` expected `InputPathType`')
+
+
+def dirstat_cargs(
+    params: DirstatParamsDict,
+    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("dirstat")
+    if params.get("output", None) is not None:
+        cargs.extend([
+            "-output",
+            params.get("output", None)
+        ])
+    if params.get("shells", None) is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells", None)))
+        ])
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(dirstat_fslgrad_cargs(params.get("fslgrad", None), execution))
+    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 [dirstat_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("dirs", None)))
+    return cargs
+
+
+def dirstat_outputs(
+    params: DirstatParamsDict,
+    execution: Execution,
+) -> DirstatOutputs:
+    """
+    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 = DirstatOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dirstat_execute(
+    params: DirstatParamsDict,
+    runner: Runner | None = None,
+) -> DirstatOutputs:
+    """
+    dirstat
+    
+    Report statistics on a direction set.
+    
+    This command will accept as inputs:
+    
+    - directions file in spherical coordinates (ASCII text, [ az el ]
+    space-separated values, one per line);
+    
+    - directions file in Cartesian coordinates (ASCII text, [ x y z ]
+    space-separated values, one per line);
+    
+    - DW gradient files (MRtrix format: ASCII text, [ x y z b ] space-separated
+    values, one per line);
+    
+    - image files, using the DW gradient scheme found in the header (or provided
+    using the appropriate command line options below).
+    
+    By default, this produces all relevant metrics for the direction set
+    provided. If the direction set contains multiple shells, metrics are
+    provided for each shell separately.
+    
+    Metrics are produced assuming a unipolar or bipolar electrostatic repulsion
+    model, producing the potential energy (total, mean, min & max), and the
+    nearest-neighbour angles (mean, min & max). The condition number is also
+    produced for the spherical harmonic fits up to the highest harmonic order
+    supported by the number of volumes. Finally, the norm of the mean direction
+    vector is provided as a measure of the overall symmetry of the direction set
+    (important with respect to eddy-current resilience).
+    
+    Specific metrics can also be queried independently via the "-output" option,
+    using these shorthands:
+    U/B for unipolar/bipolar model,
+    E/N for energy and nearest-neighbour respectively,
+    t/-/+ for total/min/max respectively (mean implied otherwise);
+    SHn for condition number of SH fit at order n (with n an even integer);
+    ASYM for asymmetry index (norm of mean direction vector);
+    N for the number of directions.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DirstatOutputs`).
+    """
+    dirstat_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRSTAT_METADATA)
+    params = execution.params(params)
+    cargs = dirstat_cargs(params, execution)
+    ret = dirstat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dirstat(
+    dirs: InputPathType,
+    output: str | None = None,
+    shells: list[float] | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: DirstatFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirstatConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DirstatOutputs:
+    """
+    dirstat
+    
+    Report statistics on a direction set.
+    
+    This command will accept as inputs:
+    
+    - directions file in spherical coordinates (ASCII text, [ az el ]
+    space-separated values, one per line);
+    
+    - directions file in Cartesian coordinates (ASCII text, [ x y z ]
+    space-separated values, one per line);
+    
+    - DW gradient files (MRtrix format: ASCII text, [ x y z b ] space-separated
+    values, one per line);
+    
+    - image files, using the DW gradient scheme found in the header (or provided
+    using the appropriate command line options below).
+    
+    By default, this produces all relevant metrics for the direction set
+    provided. If the direction set contains multiple shells, metrics are
+    provided for each shell separately.
+    
+    Metrics are produced assuming a unipolar or bipolar electrostatic repulsion
+    model, producing the potential energy (total, mean, min & max), and the
+    nearest-neighbour angles (mean, min & max). The condition number is also
+    produced for the spherical harmonic fits up to the highest harmonic order
+    supported by the number of volumes. Finally, the norm of the mean direction
+    vector is provided as a measure of the overall symmetry of the direction set
+    (important with respect to eddy-current resilience).
+    
+    Specific metrics can also be queried independently via the "-output" option,
+    using these shorthands:
+    U/B for unipolar/bipolar model,
+    E/N for energy and nearest-neighbour respectively,
+    t/-/+ for total/min/max respectively (mean implied otherwise);
+    SHn for condition number of SH fit at order n (with n an even integer);
+    ASYM for asymmetry index (norm of mean direction vector);
+    N for the number of directions.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        dirs: the text file or image containing the directions.
+        output: output selected metrics as a space-delimited list, suitable for\
+            use in scripts. This will produce one line of values per selected\
+            shell. Valid metrics are as specified in the description above.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        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 `DirstatOutputs`).
+    """
+    params = dirstat_params(
+        output=output,
+        shells=shells,
+        grad=grad,
+        fslgrad=fslgrad,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        dirs=dirs,
+    )
+    return dirstat_execute(params, runner)
+
+
+__all__ = [
+    "DIRSTAT_METADATA",
+    "DirstatConfigParamsDict",
+    "DirstatConfigParamsDictTagged",
+    "DirstatFslgradParamsDict",
+    "DirstatFslgradParamsDictTagged",
+    "DirstatOutputs",
+    "DirstatParamsDict",
+    "DirstatParamsDictTagged",
+    "dirstat",
+    "dirstat_config",
+    "dirstat_execute",
+    "dirstat_fslgrad",
+    "dirstat_params",
+]