niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mean.py

@@ -0,0 +1,364 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MEAN_METADATA = Metadata(
+    id="e324408a8ad006ebdb33f912bb6b96f4f9350026.boutiques",
+    name="3dMean",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMeanParameters = typing.TypedDict('V3dMeanParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMean"],
+    "input_files": list[InputPathType],
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "fscale": bool,
+    "gscale": bool,
+    "nscale": bool,
+    "non_zero": bool,
+    "stdev": bool,
+    "sqr": bool,
+    "sum": bool,
+    "count": bool,
+    "max": bool,
+    "min": bool,
+    "absmax": bool,
+    "signed_absmax": bool,
+    "mask_inter": bool,
+    "mask_union": bool,
+    "weightset": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMean": v_3d_mean_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 {
+        "3dMean": v_3d_mean_outputs,
+    }.get(t)
+
+
+class V3dMeanOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mean(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output dataset"""
+
+
+def v_3d_mean_params(
+    input_files: list[InputPathType],
+    verbose: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    fscale: bool = False,
+    gscale: bool = False,
+    nscale: bool = False,
+    non_zero: bool = False,
+    stdev: bool = False,
+    sqr: bool = False,
+    sum_: bool = False,
+    count: bool = False,
+    max_: bool = False,
+    min_: bool = False,
+    absmax: bool = False,
+    signed_absmax: bool = False,
+    mask_inter: bool = False,
+    mask_union: bool = False,
+    weightset: InputPathType | None = None,
+) -> V3dMeanParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets.
+        verbose: Print out some information along the way.
+        prefix: Sets the prefix of the output dataset.
+        datum: Sets the datum of the output dataset.
+        fscale: Force scaling of the output to the maximum integer range.
+        gscale: Force scaling of the output to the maximum integer range, with\
+            uniform scaling factor for each sub-brick.
+        nscale: Don't do any scaling on output to byte or short datasets. Only\
+            use if you want the output dataset to be integer-valued.
+        non_zero: Use only non-zero values for calculation of mean, min, max,\
+            sum, squares.
+        stdev: Calculate the standard deviation, sqrt(variance), instead of the\
+            mean (cannot be used with -sqr, -sum or -non_zero).
+        sqr: Average the squares, instead of the values.
+        sum_: Just take the sum (don't divide by number of datasets).
+        count: Compute only the count of non-zero voxels.
+        max_: Find the maximum at each voxel.
+        min_: Find the minimum at each voxel.
+        absmax: Find maximum absolute value at each voxel.
+        signed_absmax: Find extremes with maximum absolute value but preserve\
+            sign.
+        mask_inter: Create a simple intersection mask.
+        mask_union: Create a simple union mask.
+        weightset: Sum of N dsets will be weighted by N volume WSET. This\
+            weight dataset must be of type float.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMean",
+        "input_files": input_files,
+        "verbose": verbose,
+        "fscale": fscale,
+        "gscale": gscale,
+        "nscale": nscale,
+        "non_zero": non_zero,
+        "stdev": stdev,
+        "sqr": sqr,
+        "sum": sum_,
+        "count": count,
+        "max": max_,
+        "min": min_,
+        "absmax": absmax,
+        "signed_absmax": signed_absmax,
+        "mask_inter": mask_inter,
+        "mask_union": mask_union,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    if weightset is not None:
+        params["weightset"] = weightset
+    return params
+
+
+def v_3d_mean_cargs(
+    params: V3dMeanParameters,
+    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("3dMean")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("fscale"):
+        cargs.append("-fscale")
+    if params.get("gscale"):
+        cargs.append("-gscale")
+    if params.get("nscale"):
+        cargs.append("-nscale")
+    if params.get("non_zero"):
+        cargs.append("-non_zero")
+    if params.get("stdev"):
+        cargs.append("-sd")
+    if params.get("sqr"):
+        cargs.append("-sqr")
+    if params.get("sum"):
+        cargs.append("-sum")
+    if params.get("count"):
+        cargs.append("-count")
+    if params.get("max"):
+        cargs.append("-max")
+    if params.get("min"):
+        cargs.append("-min")
+    if params.get("absmax"):
+        cargs.append("-absmax")
+    if params.get("signed_absmax"):
+        cargs.append("-signed_absmax")
+    if params.get("mask_inter"):
+        cargs.append("-mask_inter")
+    if params.get("mask_union"):
+        cargs.append("-mask_union")
+    if params.get("weightset") is not None:
+        cargs.extend([
+            "-weightset",
+            execution.input_file(params.get("weightset"))
+        ])
+    return cargs
+
+
+def v_3d_mean_outputs(
+    params: V3dMeanParameters,
+    execution: Execution,
+) -> V3dMeanOutputs:
+    """
+    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 = V3dMeanOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + "<+optional_extension>") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_mean_execute(
+    params: V3dMeanParameters,
+    execution: Execution,
+) -> V3dMeanOutputs:
+    """
+    Takes the voxel-by-voxel mean of all input datasets; designed to be faster than
+    3dcalc.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMeanOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mean_cargs(params, execution)
+    ret = v_3d_mean_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mean(
+    input_files: list[InputPathType],
+    verbose: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    fscale: bool = False,
+    gscale: bool = False,
+    nscale: bool = False,
+    non_zero: bool = False,
+    stdev: bool = False,
+    sqr: bool = False,
+    sum_: bool = False,
+    count: bool = False,
+    max_: bool = False,
+    min_: bool = False,
+    absmax: bool = False,
+    signed_absmax: bool = False,
+    mask_inter: bool = False,
+    mask_union: bool = False,
+    weightset: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dMeanOutputs:
+    """
+    Takes the voxel-by-voxel mean of all input datasets; designed to be faster than
+    3dcalc.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets.
+        verbose: Print out some information along the way.
+        prefix: Sets the prefix of the output dataset.
+        datum: Sets the datum of the output dataset.
+        fscale: Force scaling of the output to the maximum integer range.
+        gscale: Force scaling of the output to the maximum integer range, with\
+            uniform scaling factor for each sub-brick.
+        nscale: Don't do any scaling on output to byte or short datasets. Only\
+            use if you want the output dataset to be integer-valued.
+        non_zero: Use only non-zero values for calculation of mean, min, max,\
+            sum, squares.
+        stdev: Calculate the standard deviation, sqrt(variance), instead of the\
+            mean (cannot be used with -sqr, -sum or -non_zero).
+        sqr: Average the squares, instead of the values.
+        sum_: Just take the sum (don't divide by number of datasets).
+        count: Compute only the count of non-zero voxels.
+        max_: Find the maximum at each voxel.
+        min_: Find the minimum at each voxel.
+        absmax: Find maximum absolute value at each voxel.
+        signed_absmax: Find extremes with maximum absolute value but preserve\
+            sign.
+        mask_inter: Create a simple intersection mask.
+        mask_union: Create a simple union mask.
+        weightset: Sum of N dsets will be weighted by N volume WSET. This\
+            weight dataset must be of type float.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMeanOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEAN_METADATA)
+    params = v_3d_mean_params(
+        input_files=input_files,
+        verbose=verbose,
+        prefix=prefix,
+        datum=datum,
+        fscale=fscale,
+        gscale=gscale,
+        nscale=nscale,
+        non_zero=non_zero,
+        stdev=stdev,
+        sqr=sqr,
+        sum_=sum_,
+        count=count,
+        max_=max_,
+        min_=min_,
+        absmax=absmax,
+        signed_absmax=signed_absmax,
+        mask_inter=mask_inter,
+        mask_union=mask_union,
+        weightset=weightset,
+    )
+    return v_3d_mean_execute(params, execution)
+
+
+__all__ = [
+    "V3dMeanOutputs",
+    "V3dMeanParameters",
+    "V_3D_MEAN_METADATA",
+    "v_3d_mean",
+    "v_3d_mean_params",
+]

niwrap_afni/afni/v_3d_median_filter.py

@@ -0,0 +1,238 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MEDIAN_FILTER_METADATA = Metadata(
+    id="e4ff1f00010a20a209cf31d2f6355a6142d17c25.boutiques",
+    name="3dMedianFilter",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMedianFilterParameters = typing.TypedDict('V3dMedianFilterParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMedianFilter"],
+    "irad": typing.NotRequired[float | None],
+    "iter": typing.NotRequired[float | None],
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "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 {
+        "3dMedianFilter": v_3d_median_filter_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 {
+        "3dMedianFilter": v_3d_median_filter_outputs,
+    }.get(t)
+
+
+class V3dMedianFilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_median_filter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType | None
+    """Output dataset is stored in float format."""
+    output_head: OutputPathType | None
+    """Output dataset header file."""
+
+
+def v_3d_median_filter_params(
+    dataset: InputPathType,
+    irad: float | None = None,
+    iter_: float | None = None,
+    verbose: bool = False,
+    prefix: str | None = None,
+    automask: bool = False,
+) -> V3dMedianFilterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        irad: Radius in voxels of spherical regions.
+        iter_: Iterate 'n' times [default=1].
+        verbose: Be verbose during run.
+        prefix: Use 'pp' for prefix of output dataset.
+        automask: Create a mask (a la 3dAutomask).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMedianFilter",
+        "verbose": verbose,
+        "automask": automask,
+        "dataset": dataset,
+    }
+    if irad is not None:
+        params["irad"] = irad
+    if iter_ is not None:
+        params["iter"] = iter_
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_median_filter_cargs(
+    params: V3dMedianFilterParameters,
+    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("3dMedianFilter")
+    if params.get("irad") is not None:
+        cargs.extend([
+            "-irad",
+            str(params.get("irad"))
+        ])
+    if params.get("iter") is not None:
+        cargs.extend([
+            "-iter",
+            str(params.get("iter"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_median_filter_outputs(
+    params: V3dMedianFilterParameters,
+    execution: Execution,
+) -> V3dMedianFilterOutputs:
+    """
+    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 = V3dMedianFilterOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file(params.get("prefix") + "+tlrc.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix") + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_median_filter_execute(
+    params: V3dMedianFilterParameters,
+    execution: Execution,
+) -> V3dMedianFilterOutputs:
+    """
+    Computes the median in a spherical neighborhood around each point in the input
+    to produce the output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMedianFilterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_median_filter_cargs(params, execution)
+    ret = v_3d_median_filter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_median_filter(
+    dataset: InputPathType,
+    irad: float | None = None,
+    iter_: float | None = None,
+    verbose: bool = False,
+    prefix: str | None = None,
+    automask: bool = False,
+    runner: Runner | None = None,
+) -> V3dMedianFilterOutputs:
+    """
+    Computes the median in a spherical neighborhood around each point in the input
+    to produce the output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        irad: Radius in voxels of spherical regions.
+        iter_: Iterate 'n' times [default=1].
+        verbose: Be verbose during run.
+        prefix: Use 'pp' for prefix of output dataset.
+        automask: Create a mask (a la 3dAutomask).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMedianFilterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEDIAN_FILTER_METADATA)
+    params = v_3d_median_filter_params(
+        irad=irad,
+        iter_=iter_,
+        verbose=verbose,
+        prefix=prefix,
+        automask=automask,
+        dataset=dataset,
+    )
+    return v_3d_median_filter_execute(params, execution)
+
+
+__all__ = [
+    "V3dMedianFilterOutputs",
+    "V3dMedianFilterParameters",
+    "V_3D_MEDIAN_FILTER_METADATA",
+    "v_3d_median_filter",
+    "v_3d_median_filter_params",
+]