niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_brick_stat.py

@@ -0,0 +1,463 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_BRICK_STAT_METADATA = Metadata(
+    id="2171879e0c09931b6800be575110e0354a0a8e86.boutiques",
+    name="3dBrickStat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBrickStatParameters = typing.TypedDict('V3dBrickStatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBrickStat"],
+    "dataset": str,
+    "quick": bool,
+    "slow": bool,
+    "min": bool,
+    "max": bool,
+    "mean": bool,
+    "sum": bool,
+    "var": bool,
+    "stdev": bool,
+    "count": bool,
+    "volume": bool,
+    "positive": bool,
+    "negative": bool,
+    "zero": bool,
+    "non_positive": bool,
+    "non_negative": bool,
+    "non_zero": bool,
+    "absolute": bool,
+    "nan": bool,
+    "nonan": bool,
+    "mask": typing.NotRequired[str | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "mvalue": typing.NotRequired[float | None],
+    "automask": bool,
+    "percentile": typing.NotRequired[list[float] | None],
+    "perclist": typing.NotRequired[list[float] | None],
+    "median": bool,
+    "perc_quiet": bool,
+    "ver": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dBrickStat": v_3d_brick_stat_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 {
+        "3dBrickStat": v_3d_brick_stat_outputs,
+    }.get(t)
+
+
+class V3dBrickStatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_brick_stat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    console_output: OutputPathType
+    """Console output of computed statistics"""
+
+
+def v_3d_brick_stat_params(
+    dataset: str,
+    quick: bool = False,
+    slow: bool = False,
+    min_: bool = False,
+    max_: bool = False,
+    mean: bool = False,
+    sum_: bool = False,
+    var: bool = False,
+    stdev: bool = False,
+    count: bool = False,
+    volume: bool = False,
+    positive: bool = False,
+    negative: bool = False,
+    zero: bool = False,
+    non_positive: bool = False,
+    non_negative: bool = False,
+    non_zero: bool = False,
+    absolute: bool = False,
+    nan: bool = False,
+    nonan: bool = False,
+    mask: str | None = None,
+    mrange: list[float] | None = None,
+    mvalue: float | None = None,
+    automask: bool = False,
+    percentile: list[float] | None = None,
+    perclist: list[float] | None = None,
+    median: bool = False,
+    perc_quiet: bool = False,
+    ver: bool = False,
+    help_: bool = False,
+) -> V3dBrickStatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        quick: Get the information from the header only (default).
+        slow: Read the whole dataset to find the min and max values.
+        min_: Print the minimum value in dataset.
+        max_: Print the maximum value in dataset (default).
+        mean: Print the mean value in dataset.
+        sum_: Print the sum of values in the dataset.
+        var: Print the variance in the dataset.
+        stdev: Print the standard deviation in the dataset.
+        count: Print the number of voxels included.
+        volume: Print the volume of voxels included in microliters.
+        positive: Include only positive voxel values.
+        negative: Include only negative voxel values.
+        zero: Include only zero voxel values.
+        non_positive: Include only voxel values 0 or negative.
+        non_negative: Include only voxel values 0 or greater.
+        non_zero: Include only voxel values not equal to 0.
+        absolute: Use absolute value of voxel values for all calculations.
+        nan: Include only voxel values that are NaN or inf. Forces -slow mode.
+        nonan: Exclude voxel values that are NaN or inf.
+        mask: Use the specified dataset as mask to include/exclude voxels.
+        mrange: Only accept values between MIN and MAX (inclusive) from the\
+            mask.
+        mvalue: Only accept values equal to VAL from the mask.
+        automask: Automatically compute mask for dataset. Cannot be combined\
+            with -mask.
+        percentile: Compute and print percentile values from p0% to p1% at a\
+            step of ps%. Only one sub-brick is accepted as input with this option.
+        perclist: Like -percentile, but output the given percentiles.
+        median: Shortcut for -percentile 50 1 50 (or -perclist 1 50).
+        perc_quiet: Only print percentile results, not input percentile cutoffs.
+        ver: Print author and version info.
+        help_: Print help screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBrickStat",
+        "dataset": dataset,
+        "quick": quick,
+        "slow": slow,
+        "min": min_,
+        "max": max_,
+        "mean": mean,
+        "sum": sum_,
+        "var": var,
+        "stdev": stdev,
+        "count": count,
+        "volume": volume,
+        "positive": positive,
+        "negative": negative,
+        "zero": zero,
+        "non_positive": non_positive,
+        "non_negative": non_negative,
+        "non_zero": non_zero,
+        "absolute": absolute,
+        "nan": nan,
+        "nonan": nonan,
+        "automask": automask,
+        "median": median,
+        "perc_quiet": perc_quiet,
+        "ver": ver,
+        "help": help_,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mrange is not None:
+        params["mrange"] = mrange
+    if mvalue is not None:
+        params["mvalue"] = mvalue
+    if percentile is not None:
+        params["percentile"] = percentile
+    if perclist is not None:
+        params["perclist"] = perclist
+    return params
+
+
+def v_3d_brick_stat_cargs(
+    params: V3dBrickStatParameters,
+    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("3dBrickStat")
+    cargs.append(params.get("dataset"))
+    if params.get("quick"):
+        cargs.append("-quick")
+    if params.get("slow"):
+        cargs.append("-slow")
+    if params.get("min"):
+        cargs.append("-min")
+    if params.get("max"):
+        cargs.append("-max")
+    if params.get("mean"):
+        cargs.append("-mean")
+    if params.get("sum"):
+        cargs.append("-sum")
+    if params.get("var"):
+        cargs.append("-var")
+    if params.get("stdev"):
+        cargs.append("-stdev")
+    if params.get("count"):
+        cargs.append("-count")
+    if params.get("volume"):
+        cargs.append("-volume")
+    if params.get("positive"):
+        cargs.append("-positive")
+    if params.get("negative"):
+        cargs.append("-negative")
+    if params.get("zero"):
+        cargs.append("-zero")
+    if params.get("non_positive"):
+        cargs.append("-non-positive")
+    if params.get("non_negative"):
+        cargs.append("-non-negative")
+    if params.get("non_zero"):
+        cargs.append("-non-zero")
+    if params.get("absolute"):
+        cargs.append("-absolute")
+    if params.get("nan"):
+        cargs.append("-nan")
+    if params.get("nonan"):
+        cargs.append("-nonan")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("mrange") is not None:
+        cargs.extend([
+            "-mrange",
+            *map(str, params.get("mrange"))
+        ])
+    if params.get("mvalue") is not None:
+        cargs.extend([
+            "-mvalue",
+            str(params.get("mvalue"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("percentile") is not None:
+        cargs.extend([
+            "-percentile",
+            *map(str, params.get("percentile"))
+        ])
+    if params.get("perclist") is not None:
+        cargs.extend([
+            "-perclist",
+            *map(str, params.get("perclist"))
+        ])
+    if params.get("median"):
+        cargs.append("-median")
+    if params.get("perc_quiet"):
+        cargs.append("-perc_quiet")
+    if params.get("ver"):
+        cargs.append("-ver")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v_3d_brick_stat_outputs(
+    params: V3dBrickStatParameters,
+    execution: Execution,
+) -> V3dBrickStatOutputs:
+    """
+    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 = V3dBrickStatOutputs(
+        root=execution.output_file("."),
+        console_output=execution.output_file("output.txt"),
+    )
+    return ret
+
+
+def v_3d_brick_stat_execute(
+    params: V3dBrickStatParameters,
+    execution: Execution,
+) -> V3dBrickStatOutputs:
+    """
+    Compute voxel statistics of an input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrickStatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_brick_stat_cargs(params, execution)
+    ret = v_3d_brick_stat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_brick_stat(
+    dataset: str,
+    quick: bool = False,
+    slow: bool = False,
+    min_: bool = False,
+    max_: bool = False,
+    mean: bool = False,
+    sum_: bool = False,
+    var: bool = False,
+    stdev: bool = False,
+    count: bool = False,
+    volume: bool = False,
+    positive: bool = False,
+    negative: bool = False,
+    zero: bool = False,
+    non_positive: bool = False,
+    non_negative: bool = False,
+    non_zero: bool = False,
+    absolute: bool = False,
+    nan: bool = False,
+    nonan: bool = False,
+    mask: str | None = None,
+    mrange: list[float] | None = None,
+    mvalue: float | None = None,
+    automask: bool = False,
+    percentile: list[float] | None = None,
+    perclist: list[float] | None = None,
+    median: bool = False,
+    perc_quiet: bool = False,
+    ver: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> V3dBrickStatOutputs:
+    """
+    Compute voxel statistics of an input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        quick: Get the information from the header only (default).
+        slow: Read the whole dataset to find the min and max values.
+        min_: Print the minimum value in dataset.
+        max_: Print the maximum value in dataset (default).
+        mean: Print the mean value in dataset.
+        sum_: Print the sum of values in the dataset.
+        var: Print the variance in the dataset.
+        stdev: Print the standard deviation in the dataset.
+        count: Print the number of voxels included.
+        volume: Print the volume of voxels included in microliters.
+        positive: Include only positive voxel values.
+        negative: Include only negative voxel values.
+        zero: Include only zero voxel values.
+        non_positive: Include only voxel values 0 or negative.
+        non_negative: Include only voxel values 0 or greater.
+        non_zero: Include only voxel values not equal to 0.
+        absolute: Use absolute value of voxel values for all calculations.
+        nan: Include only voxel values that are NaN or inf. Forces -slow mode.
+        nonan: Exclude voxel values that are NaN or inf.
+        mask: Use the specified dataset as mask to include/exclude voxels.
+        mrange: Only accept values between MIN and MAX (inclusive) from the\
+            mask.
+        mvalue: Only accept values equal to VAL from the mask.
+        automask: Automatically compute mask for dataset. Cannot be combined\
+            with -mask.
+        percentile: Compute and print percentile values from p0% to p1% at a\
+            step of ps%. Only one sub-brick is accepted as input with this option.
+        perclist: Like -percentile, but output the given percentiles.
+        median: Shortcut for -percentile 50 1 50 (or -perclist 1 50).
+        perc_quiet: Only print percentile results, not input percentile cutoffs.
+        ver: Print author and version info.
+        help_: Print help screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrickStatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRICK_STAT_METADATA)
+    params = v_3d_brick_stat_params(
+        dataset=dataset,
+        quick=quick,
+        slow=slow,
+        min_=min_,
+        max_=max_,
+        mean=mean,
+        sum_=sum_,
+        var=var,
+        stdev=stdev,
+        count=count,
+        volume=volume,
+        positive=positive,
+        negative=negative,
+        zero=zero,
+        non_positive=non_positive,
+        non_negative=non_negative,
+        non_zero=non_zero,
+        absolute=absolute,
+        nan=nan,
+        nonan=nonan,
+        mask=mask,
+        mrange=mrange,
+        mvalue=mvalue,
+        automask=automask,
+        percentile=percentile,
+        perclist=perclist,
+        median=median,
+        perc_quiet=perc_quiet,
+        ver=ver,
+        help_=help_,
+    )
+    return v_3d_brick_stat_execute(params, execution)
+
+
+__all__ = [
+    "V3dBrickStatOutputs",
+    "V3dBrickStatParameters",
+    "V_3D_BRICK_STAT_METADATA",
+    "v_3d_brick_stat",
+    "v_3d_brick_stat_params",
+]

niwrap_afni/afni/v_3d_clip_level.py

@@ -0,0 +1,175 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CLIP_LEVEL_METADATA = Metadata(
+    id="d74c5cd045e053e286d1b5c8e3587d88d871f128.boutiques",
+    name="3dClipLevel",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dClipLevelParameters = typing.TypedDict('V3dClipLevelParameters', {
+    "__STYX_TYPE__": typing.Literal["3dClipLevel"],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dClipLevel": v_3d_clip_level_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)
+
+
+class V3dClipLevelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_clip_level(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_clip_level_params(
+    dataset: InputPathType,
+) -> V3dClipLevelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset (e.g. dataset.nii.gz).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dClipLevel",
+        "dataset": dataset,
+    }
+    return params
+
+
+def v_3d_clip_level_cargs(
+    params: V3dClipLevelParameters,
+    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("3dClipLevel")
+    cargs.append("[options]")
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_clip_level_outputs(
+    params: V3dClipLevelParameters,
+    execution: Execution,
+) -> V3dClipLevelOutputs:
+    """
+    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 = V3dClipLevelOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_clip_level_execute(
+    params: V3dClipLevelParameters,
+    execution: Execution,
+) -> V3dClipLevelOutputs:
+    """
+    Estimates the value at which to clip the anatomical dataset so that background
+    regions are set to zero.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dClipLevelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_clip_level_cargs(params, execution)
+    ret = v_3d_clip_level_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_clip_level(
+    dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dClipLevelOutputs:
+    """
+    Estimates the value at which to clip the anatomical dataset so that background
+    regions are set to zero.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset (e.g. dataset.nii.gz).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dClipLevelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLIP_LEVEL_METADATA)
+    params = v_3d_clip_level_params(
+        dataset=dataset,
+    )
+    return v_3d_clip_level_execute(params, execution)
+
+
+__all__ = [
+    "V3dClipLevelOutputs",
+    "V3dClipLevelParameters",
+    "V_3D_CLIP_LEVEL_METADATA",
+    "v_3d_clip_level",
+    "v_3d_clip_level_params",
+]