niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/peaks2amp.py

@@ -0,0 +1,334 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+PEAKS2AMP_METADATA = Metadata(
+    id="90ed8fa8022a8bb67e41e995c1aaf7cea334db02.boutiques",
+    name="peaks2amp",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Peaks2ampConfigParameters = typing.TypedDict('Peaks2ampConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Peaks2ampParameters = typing.TypedDict('Peaks2ampParameters', {
+    "__STYX_TYPE__": typing.Literal["peaks2amp"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Peaks2ampConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "directions": InputPathType,
+    "amplitudes": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "peaks2amp": peaks2amp_cargs,
+        "config": peaks2amp_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 {
+        "peaks2amp": peaks2amp_outputs,
+    }.get(t)
+
+
+def peaks2amp_config_params(
+    key: str,
+    value: str,
+) -> Peaks2ampConfigParameters:
+    """
+    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 peaks2amp_config_cargs(
+    params: Peaks2ampConfigParameters,
+    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 Peaks2ampOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `peaks2amp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    amplitudes: OutputPathType
+    """the output amplitudes image."""
+
+
+def peaks2amp_params(
+    directions: InputPathType,
+    amplitudes: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Peaks2ampConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Peaks2ampParameters:
+    """
+    Build parameters.
+    
+    Args:
+        directions: the input directions image. Each volume corresponds to the\
+            x, y & z component of each direction vector in turn.
+        amplitudes: the output amplitudes image.
+        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__": "peaks2amp",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "directions": directions,
+        "amplitudes": amplitudes,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def peaks2amp_cargs(
+    params: Peaks2ampParameters,
+    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("peaks2amp")
+    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("directions")))
+    cargs.append(params.get("amplitudes"))
+    return cargs
+
+
+def peaks2amp_outputs(
+    params: Peaks2ampParameters,
+    execution: Execution,
+) -> Peaks2ampOutputs:
+    """
+    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 = Peaks2ampOutputs(
+        root=execution.output_file("."),
+        amplitudes=execution.output_file(params.get("amplitudes")),
+    )
+    return ret
+
+
+def peaks2amp_execute(
+    params: Peaks2ampParameters,
+    execution: Execution,
+) -> Peaks2ampOutputs:
+    """
+    Extract amplitudes from a peak directions image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Peaks2ampOutputs`).
+    """
+    params = execution.params(params)
+    cargs = peaks2amp_cargs(params, execution)
+    ret = peaks2amp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def peaks2amp(
+    directions: InputPathType,
+    amplitudes: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Peaks2ampConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Peaks2ampOutputs:
+    """
+    Extract amplitudes from a peak directions image.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        directions: the input directions image. Each volume corresponds to the\
+            x, y & z component of each direction vector in turn.
+        amplitudes: the output amplitudes image.
+        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 `Peaks2ampOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PEAKS2AMP_METADATA)
+    params = peaks2amp_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        directions=directions,
+        amplitudes=amplitudes,
+    )
+    return peaks2amp_execute(params, execution)
+
+
+__all__ = [
+    "PEAKS2AMP_METADATA",
+    "Peaks2ampConfigParameters",
+    "Peaks2ampOutputs",
+    "Peaks2ampParameters",
+    "peaks2amp",
+    "peaks2amp_config_params",
+    "peaks2amp_params",
+]

niwrap_mrtrix/mrtrix/peaks2fixel.py

@@ -0,0 +1,349 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+PEAKS2FIXEL_METADATA = Metadata(
+    id="d7a45807f5df2a3ff0f6456f9bc36be6cdae2250.boutiques",
+    name="peaks2fixel",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Peaks2fixelConfigParameters = typing.TypedDict('Peaks2fixelConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Peaks2fixelParameters = typing.TypedDict('Peaks2fixelParameters', {
+    "__STYX_TYPE__": typing.Literal["peaks2fixel"],
+    "dataname": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Peaks2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "directions": InputPathType,
+    "fixels": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "peaks2fixel": peaks2fixel_cargs,
+        "config": peaks2fixel_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 {
+        "peaks2fixel": peaks2fixel_outputs,
+    }.get(t)
+
+
+def peaks2fixel_config_params(
+    key: str,
+    value: str,
+) -> Peaks2fixelConfigParameters:
+    """
+    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 peaks2fixel_config_cargs(
+    params: Peaks2fixelConfigParameters,
+    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 Peaks2fixelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `peaks2fixel(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fixels: OutputPathType
+    """the output fixel directory."""
+
+
+def peaks2fixel_params(
+    directions: InputPathType,
+    fixels: str,
+    dataname: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Peaks2fixelConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Peaks2fixelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        directions: the input directions image; each volume corresponds to the\
+            x, y & z component of each direction vector in turn.
+        fixels: the output fixel directory.
+        dataname: the name of the output fixel data file encoding peak\
+            amplitudes.
+        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__": "peaks2fixel",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "directions": directions,
+        "fixels": fixels,
+    }
+    if dataname is not None:
+        params["dataname"] = dataname
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def peaks2fixel_cargs(
+    params: Peaks2fixelParameters,
+    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("peaks2fixel")
+    if params.get("dataname") is not None:
+        cargs.extend([
+            "-dataname",
+            params.get("dataname")
+        ])
+    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("directions")))
+    cargs.append(params.get("fixels"))
+    return cargs
+
+
+def peaks2fixel_outputs(
+    params: Peaks2fixelParameters,
+    execution: Execution,
+) -> Peaks2fixelOutputs:
+    """
+    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 = Peaks2fixelOutputs(
+        root=execution.output_file("."),
+        fixels=execution.output_file(params.get("fixels")),
+    )
+    return ret
+
+
+def peaks2fixel_execute(
+    params: Peaks2fixelParameters,
+    execution: Execution,
+) -> Peaks2fixelOutputs:
+    """
+    Convert peak directions image to a fixel directory.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Peaks2fixelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = peaks2fixel_cargs(params, execution)
+    ret = peaks2fixel_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def peaks2fixel(
+    directions: InputPathType,
+    fixels: str,
+    dataname: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Peaks2fixelConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Peaks2fixelOutputs:
+    """
+    Convert peak directions image to a fixel directory.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        directions: the input directions image; each volume corresponds to the\
+            x, y & z component of each direction vector in turn.
+        fixels: the output fixel directory.
+        dataname: the name of the output fixel data file encoding peak\
+            amplitudes.
+        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 `Peaks2fixelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PEAKS2FIXEL_METADATA)
+    params = peaks2fixel_params(
+        dataname=dataname,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        directions=directions,
+        fixels=fixels,
+    )
+    return peaks2fixel_execute(params, execution)
+
+
+__all__ = [
+    "PEAKS2FIXEL_METADATA",
+    "Peaks2fixelConfigParameters",
+    "Peaks2fixelOutputs",
+    "Peaks2fixelParameters",
+    "peaks2fixel",
+    "peaks2fixel_config_params",
+    "peaks2fixel_params",
+]