niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrmath.py

@@ -0,0 +1,413 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRMATH_METADATA = Metadata(
+    id="51b59bbaad9ca5110175fd6f6f0765499d38c928.boutiques",
+    name="mrmath",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrmathConfigParameters = typing.TypedDict('MrmathConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrmathParameters = typing.TypedDict('MrmathParameters', {
+    "__STYX_TYPE__": typing.Literal["mrmath"],
+    "axis": typing.NotRequired[int | None],
+    "keep_unary_axes": bool,
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmathConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "operation": str,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrmath": mrmath_cargs,
+        "config": mrmath_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 {
+        "mrmath": mrmath_outputs,
+    }.get(t)
+
+
+def mrmath_config_params(
+    key: str,
+    value: str,
+) -> MrmathConfigParameters:
+    """
+    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 mrmath_config_cargs(
+    params: MrmathConfigParameters,
+    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 MrmathOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrmath(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+
+
+def mrmath_params(
+    input_: list[InputPathType],
+    operation: str,
+    output: str,
+    axis: int | None = None,
+    keep_unary_axes: bool = False,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmathConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrmathParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image(s).
+        operation: the operation to apply, one of: mean, median, sum, product,\
+            rms, norm, var, std, min, max, absmax, magmax.
+        output: the output image.
+        axis: perform operation along a specified axis of a single input image.
+        keep_unary_axes: Keep unary axes in input images prior to calculating\
+            the stats. The default is to wipe axes with single elements.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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__": "mrmath",
+        "keep_unary_axes": keep_unary_axes,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "operation": operation,
+        "output": output,
+    }
+    if axis is not None:
+        params["axis"] = axis
+    if datatype is not None:
+        params["datatype"] = datatype
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrmath_cargs(
+    params: MrmathParameters,
+    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("mrmath")
+    if params.get("axis") is not None:
+        cargs.extend([
+            "-axis",
+            str(params.get("axis"))
+        ])
+    if params.get("keep_unary_axes"):
+        cargs.append("-keep_unary_axes")
+    if params.get("datatype") is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype")
+        ])
+    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.extend([execution.input_file(f) for f in params.get("input")])
+    cargs.append(params.get("operation"))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrmath_outputs(
+    params: MrmathParameters,
+    execution: Execution,
+) -> MrmathOutputs:
+    """
+    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 = MrmathOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def mrmath_execute(
+    params: MrmathParameters,
+    execution: Execution,
+) -> MrmathOutputs:
+    """
+    Compute summary statistic on image intensities either across images, or along a
+    specified axis of a single image.
+    
+    Supported operations are:
+    
+    mean, median, sum, product, rms (root-mean-square value), norm (vector
+    2-norm), var (unbiased variance), std (unbiased standard deviation), min,
+    max, absmax (maximum absolute value), magmax (value with maximum absolute
+    value, preserving its sign).
+    
+    This command is used to traverse either along an image axis, or across a set
+    of input images, calculating some statistic from the values along each
+    traversal. If you are seeking to instead perform mathematical calculations
+    that are done independently for each voxel, pleaase see the 'mrcalc'
+    command.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrmathOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrmath_cargs(params, execution)
+    ret = mrmath_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrmath(
+    input_: list[InputPathType],
+    operation: str,
+    output: str,
+    axis: int | None = None,
+    keep_unary_axes: bool = False,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmathConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrmathOutputs:
+    """
+    Compute summary statistic on image intensities either across images, or along a
+    specified axis of a single image.
+    
+    Supported operations are:
+    
+    mean, median, sum, product, rms (root-mean-square value), norm (vector
+    2-norm), var (unbiased variance), std (unbiased standard deviation), min,
+    max, absmax (maximum absolute value), magmax (value with maximum absolute
+    value, preserving its sign).
+    
+    This command is used to traverse either along an image axis, or across a set
+    of input images, calculating some statistic from the values along each
+    traversal. If you are seeking to instead perform mathematical calculations
+    that are done independently for each voxel, pleaase see the 'mrcalc'
+    command.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image(s).
+        operation: the operation to apply, one of: mean, median, sum, product,\
+            rms, norm, var, std, min, max, absmax, magmax.
+        output: the output image.
+        axis: perform operation along a specified axis of a single input image.
+        keep_unary_axes: Keep unary axes in input images prior to calculating\
+            the stats. The default is to wipe axes with single elements.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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 `MrmathOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRMATH_METADATA)
+    params = mrmath_params(
+        axis=axis,
+        keep_unary_axes=keep_unary_axes,
+        datatype=datatype,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        operation=operation,
+        output=output,
+    )
+    return mrmath_execute(params, execution)
+
+
+__all__ = [
+    "MRMATH_METADATA",
+    "MrmathConfigParameters",
+    "MrmathOutputs",
+    "MrmathParameters",
+    "mrmath",
+    "mrmath_config_params",
+    "mrmath_params",
+]