niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrstats.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRSTATS_METADATA = Metadata(
+    id="ac3503467263b1605cd6395c44e756384ef84457.boutiques",
+    name="mrstats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrstatsOutputParameters = typing.TypedDict('MrstatsOutputParameters', {
+    "__STYX_TYPE__": typing.Literal["output"],
+    "field": str,
+})
+
+
+MrstatsConfigParameters = typing.TypedDict('MrstatsConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrstatsParameters = typing.TypedDict('MrstatsParameters', {
+    "__STYX_TYPE__": typing.Literal["mrstats"],
+    "output": typing.NotRequired[list[MrstatsOutputParameters] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "ignorezero": bool,
+    "allvolumes": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrstatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrstats": mrstats_cargs,
+        "output": mrstats_output_cargs,
+        "config": mrstats_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 {
+    }.get(t)
+
+
+def mrstats_output_params(
+    field: str,
+) -> MrstatsOutputParameters:
+    """
+    Build parameters.
+    
+    Args:
+        field: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "output",
+        "field": field,
+    }
+    return params
+
+
+def mrstats_output_cargs(
+    params: MrstatsOutputParameters,
+    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("-output")
+    cargs.append(params.get("field"))
+    return cargs
+
+
+def mrstats_config_params(
+    key: str,
+    value: str,
+) -> MrstatsConfigParameters:
+    """
+    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 mrstats_config_cargs(
+    params: MrstatsConfigParameters,
+    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 MrstatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrstats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mrstats_params(
+    image: InputPathType,
+    output: list[MrstatsOutputParameters] | None = None,
+    mask: InputPathType | None = None,
+    ignorezero: bool = False,
+    allvolumes: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrstatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrstatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        image: the input image from which statistics will be computed.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+        mask: only perform computation within the specified binary mask image.
+        ignorezero: ignore zero values during statistics calculation.
+        allvolumes: generate statistics across all image volumes, rather than\
+            one set of statistics per image 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 = {
+        "__STYXTYPE__": "mrstats",
+        "ignorezero": ignorezero,
+        "allvolumes": allvolumes,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "image": image,
+    }
+    if output is not None:
+        params["output"] = output
+    if mask is not None:
+        params["mask"] = mask
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrstats_cargs(
+    params: MrstatsParameters,
+    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("mrstats")
+    if params.get("output") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("output")] for a in c])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("ignorezero"):
+        cargs.append("-ignorezero")
+    if params.get("allvolumes"):
+        cargs.append("-allvolumes")
+    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("image")))
+    return cargs
+
+
+def mrstats_outputs(
+    params: MrstatsParameters,
+    execution: Execution,
+) -> MrstatsOutputs:
+    """
+    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 = MrstatsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mrstats_execute(
+    params: MrstatsParameters,
+    execution: Execution,
+) -> MrstatsOutputs:
+    """
+    Compute images statistics.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrstatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrstats_cargs(params, execution)
+    ret = mrstats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrstats(
+    image: InputPathType,
+    output: list[MrstatsOutputParameters] | None = None,
+    mask: InputPathType | None = None,
+    ignorezero: bool = False,
+    allvolumes: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrstatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrstatsOutputs:
+    """
+    Compute images statistics.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        image: the input image from which statistics will be computed.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, std_rv, min, max,\
+            count. Useful for use in scripts. Both std options refer to the\
+            unbiased (sample) standard deviation. For complex data, min, max and\
+            std are calculated separately for real and imaginary parts, std_rv is\
+            based on the real valued variance (equals sqrt of sum of variances of\
+            imaginary and real parts).
+        mask: only perform computation within the specified binary mask image.
+        ignorezero: ignore zero values during statistics calculation.
+        allvolumes: generate statistics across all image volumes, rather than\
+            one set of statistics per image 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 `MrstatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRSTATS_METADATA)
+    params = mrstats_params(
+        output=output,
+        mask=mask,
+        ignorezero=ignorezero,
+        allvolumes=allvolumes,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        image=image,
+    )
+    return mrstats_execute(params, execution)
+
+
+__all__ = [
+    "MRSTATS_METADATA",
+    "MrstatsConfigParameters",
+    "MrstatsOutputParameters",
+    "MrstatsOutputs",
+    "MrstatsParameters",
+    "mrstats",
+    "mrstats_config_params",
+    "mrstats_output_params",
+    "mrstats_params",
+]