niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixel2sh.py

@@ -0,0 +1,357 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXEL2SH_METADATA = Metadata(
+    id="ad311f3879760b3a8467869800c42a82cc4da4d8.boutiques",
+    name="fixel2sh",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Fixel2shConfigParameters = typing.TypedDict('Fixel2shConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Fixel2shParameters = typing.TypedDict('Fixel2shParameters', {
+    "__STYX_TYPE__": typing.Literal["fixel2sh"],
+    "lmax": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2shConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "sh_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 {
+        "fixel2sh": fixel2sh_cargs,
+        "config": fixel2sh_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 {
+        "fixel2sh": fixel2sh_outputs,
+    }.get(t)
+
+
+def fixel2sh_config_params(
+    key: str,
+    value: str,
+) -> Fixel2shConfigParameters:
+    """
+    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 fixel2sh_config_cargs(
+    params: Fixel2shConfigParameters,
+    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 Fixel2shOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixel2sh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sh_out: OutputPathType
+    """the output sh image."""
+
+
+def fixel2sh_params(
+    fixel_in: InputPathType,
+    sh_out: str,
+    lmax: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2shConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fixel2shParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_in: the input fixel data file.
+        sh_out: the output sh image.
+        lmax: set the maximum harmonic order for the output series (Default: 8).
+        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__": "fixel2sh",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_in": fixel_in,
+        "sh_out": sh_out,
+    }
+    if lmax is not None:
+        params["lmax"] = lmax
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixel2sh_cargs(
+    params: Fixel2shParameters,
+    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("fixel2sh")
+    if params.get("lmax") is not None:
+        cargs.extend([
+            "-lmax",
+            str(params.get("lmax"))
+        ])
+    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("fixel_in")))
+    cargs.append(params.get("sh_out"))
+    return cargs
+
+
+def fixel2sh_outputs(
+    params: Fixel2shParameters,
+    execution: Execution,
+) -> Fixel2shOutputs:
+    """
+    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 = Fixel2shOutputs(
+        root=execution.output_file("."),
+        sh_out=execution.output_file(params.get("sh_out")),
+    )
+    return ret
+
+
+def fixel2sh_execute(
+    params: Fixel2shParameters,
+    execution: Execution,
+) -> Fixel2shOutputs:
+    """
+    Convert a fixel-based sparse-data image into an spherical harmonic image.
+    
+    This command generates spherical harmonic data from fixels that can be
+    visualised using the ODF tool in MRview. The output ODF lobes are scaled
+    according to the values in the input fixel image.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Fixel2shOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixel2sh_cargs(params, execution)
+    ret = fixel2sh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixel2sh(
+    fixel_in: InputPathType,
+    sh_out: str,
+    lmax: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2shConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fixel2shOutputs:
+    """
+    Convert a fixel-based sparse-data image into an spherical harmonic image.
+    
+    This command generates spherical harmonic data from fixels that can be
+    visualised using the ODF tool in MRview. The output ODF lobes are scaled
+    according to the values in the input fixel image.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_in: the input fixel data file.
+        sh_out: the output sh image.
+        lmax: set the maximum harmonic order for the output series (Default: 8).
+        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 `Fixel2shOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2SH_METADATA)
+    params = fixel2sh_params(
+        lmax=lmax,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_in=fixel_in,
+        sh_out=sh_out,
+    )
+    return fixel2sh_execute(params, execution)
+
+
+__all__ = [
+    "FIXEL2SH_METADATA",
+    "Fixel2shConfigParameters",
+    "Fixel2shOutputs",
+    "Fixel2shParameters",
+    "fixel2sh",
+    "fixel2sh_config_params",
+    "fixel2sh_params",
+]

niwrap_mrtrix/mrtrix/fixel2tsf.py

@@ -0,0 +1,357 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXEL2TSF_METADATA = Metadata(
+    id="0bbc1887f97398283810259c9bfc2ba108df6a97.boutiques",
+    name="fixel2tsf",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Fixel2tsfConfigParameters = typing.TypedDict('Fixel2tsfConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Fixel2tsfParameters = typing.TypedDict('Fixel2tsfParameters', {
+    "__STYX_TYPE__": typing.Literal["fixel2tsf"],
+    "angle": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2tsfConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "tracks": InputPathType,
+    "tsf": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixel2tsf": fixel2tsf_cargs,
+        "config": fixel2tsf_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 {
+        "fixel2tsf": fixel2tsf_outputs,
+    }.get(t)
+
+
+def fixel2tsf_config_params(
+    key: str,
+    value: str,
+) -> Fixel2tsfConfigParameters:
+    """
+    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 fixel2tsf_config_cargs(
+    params: Fixel2tsfConfigParameters,
+    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 Fixel2tsfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixel2tsf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    tsf: OutputPathType
+    """the output track scalar file"""
+
+
+def fixel2tsf_params(
+    fixel_in: InputPathType,
+    tracks: InputPathType,
+    tsf: str,
+    angle: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2tsfConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fixel2tsfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_in: the input fixel data file (within the fixel directory).
+        tracks: the input track file.
+        tsf: the output track scalar file.
+        angle: the max anglular threshold for computing correspondence between\
+            a fixel direction and track tangent (default = 45 degrees).
+        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__": "fixel2tsf",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_in": fixel_in,
+        "tracks": tracks,
+        "tsf": tsf,
+    }
+    if angle is not None:
+        params["angle"] = angle
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixel2tsf_cargs(
+    params: Fixel2tsfParameters,
+    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("fixel2tsf")
+    if params.get("angle") is not None:
+        cargs.extend([
+            "-angle",
+            str(params.get("angle"))
+        ])
+    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("fixel_in")))
+    cargs.append(execution.input_file(params.get("tracks")))
+    cargs.append(params.get("tsf"))
+    return cargs
+
+
+def fixel2tsf_outputs(
+    params: Fixel2tsfParameters,
+    execution: Execution,
+) -> Fixel2tsfOutputs:
+    """
+    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 = Fixel2tsfOutputs(
+        root=execution.output_file("."),
+        tsf=execution.output_file(params.get("tsf")),
+    )
+    return ret
+
+
+def fixel2tsf_execute(
+    params: Fixel2tsfParameters,
+    execution: Execution,
+) -> Fixel2tsfOutputs:
+    """
+    Map fixel values to a track scalar file based on an input tractogram.
+    
+    This command is useful for visualising all brain fixels (e.g. the output
+    from fixelcfestats) in 3D.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Fixel2tsfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixel2tsf_cargs(params, execution)
+    ret = fixel2tsf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixel2tsf(
+    fixel_in: InputPathType,
+    tracks: InputPathType,
+    tsf: str,
+    angle: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2tsfConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fixel2tsfOutputs:
+    """
+    Map fixel values to a track scalar file based on an input tractogram.
+    
+    This command is useful for visualising all brain fixels (e.g. the output
+    from fixelcfestats) in 3D.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_in: the input fixel data file (within the fixel directory).
+        tracks: the input track file.
+        tsf: the output track scalar file.
+        angle: the max anglular threshold for computing correspondence between\
+            a fixel direction and track tangent (default = 45 degrees).
+        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 `Fixel2tsfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2TSF_METADATA)
+    params = fixel2tsf_params(
+        angle=angle,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_in=fixel_in,
+        tracks=tracks,
+        tsf=tsf,
+    )
+    return fixel2tsf_execute(params, execution)
+
+
+__all__ = [
+    "FIXEL2TSF_METADATA",
+    "Fixel2tsfConfigParameters",
+    "Fixel2tsfOutputs",
+    "Fixel2tsfParameters",
+    "fixel2tsf",
+    "fixel2tsf_config_params",
+    "fixel2tsf_params",
+]