niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_extrema.py

@@ -0,0 +1,279 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_EXTREMA_METADATA = Metadata(
+    id="84b854a87242a5d67c86897020fb70cd6c8e1945.boutiques",
+    name="SurfExtrema",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfExtremaParameters = typing.TypedDict('SurfExtremaParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfExtrema"],
+    "input": typing.NotRequired[InputPathType | None],
+    "hood": typing.NotRequired[float | None],
+    "thresh": typing.NotRequired[float | None],
+    "gthresh": typing.NotRequired[float | None],
+    "gscale": typing.NotRequired[typing.Literal["NONE", "LMEAN", "GMEAN"] | None],
+    "extype": typing.NotRequired[typing.Literal["MAX", "MIN", "ABS"] | None],
+    "prefix": str,
+    "table": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfExtrema": surf_extrema_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 {
+        "SurfExtrema": surf_extrema_outputs,
+    }.get(t)
+
+
+class SurfExtremaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_extrema(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_grd: OutputPathType
+    """Output file containing the scaled average gradient values."""
+    output_ext: OutputPathType
+    """Output file containing the nodes with maximum values."""
+
+
+def surf_extrema_params(
+    prefix: str,
+    input_: InputPathType | None = None,
+    hood: float | None = None,
+    thresh: float | None = None,
+    gthresh: float | None = None,
+    gscale: typing.Literal["NONE", "LMEAN", "GMEAN"] | None = None,
+    extype: typing.Literal["MAX", "MIN", "ABS"] | None = None,
+    table: str | None = None,
+) -> SurfExtremaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for the output datasets.
+        input_: Input dataset in which Extrema are to be identified.
+        hood: Neighborhood radius (R) in mm. Default is 8 mm.
+        thresh: Do not consider nodes with value less than this threshold.\
+            Default is 0.
+        gthresh: Do not consider nodes with gradient less than this threshold.\
+            Default is 0.01.
+        gscale: Scaling to apply to gradient computation.
+        extype: Find maxima, minima, or extrema. Options are MAX (default),\
+            MIN, ABS.
+        table: Name of file in which to store a record of the extrema found.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfExtrema",
+        "prefix": prefix,
+    }
+    if input_ is not None:
+        params["input"] = input_
+    if hood is not None:
+        params["hood"] = hood
+    if thresh is not None:
+        params["thresh"] = thresh
+    if gthresh is not None:
+        params["gthresh"] = gthresh
+    if gscale is not None:
+        params["gscale"] = gscale
+    if extype is not None:
+        params["extype"] = extype
+    if table is not None:
+        params["table"] = table
+    return params
+
+
+def surf_extrema_cargs(
+    params: SurfExtremaParameters,
+    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("SurfExtrema")
+    if params.get("input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input"))
+        ])
+    if params.get("hood") is not None:
+        cargs.extend([
+            "-nbhd_rad",
+            str(params.get("hood"))
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("thresh"))
+        ])
+    if params.get("gthresh") is not None:
+        cargs.extend([
+            "-gthresh",
+            str(params.get("gthresh"))
+        ])
+    if params.get("gscale") is not None:
+        cargs.extend([
+            "-gscale",
+            params.get("gscale")
+        ])
+    if params.get("extype") is not None:
+        cargs.extend([
+            "-extype",
+            params.get("extype")
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("table") is not None:
+        cargs.extend([
+            "-table",
+            params.get("table")
+        ])
+    return cargs
+
+
+def surf_extrema_outputs(
+    params: SurfExtremaParameters,
+    execution: Execution,
+) -> SurfExtremaOutputs:
+    """
+    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 = SurfExtremaOutputs(
+        root=execution.output_file("."),
+        output_grd=execution.output_file(params.get("prefix") + ".grd"),
+        output_ext=execution.output_file(params.get("prefix") + ".ext"),
+    )
+    return ret
+
+
+def surf_extrema_execute(
+    params: SurfExtremaParameters,
+    execution: Execution,
+) -> SurfExtremaOutputs:
+    """
+    A program finding the local extrema in a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfExtremaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_extrema_cargs(params, execution)
+    ret = surf_extrema_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_extrema(
+    prefix: str,
+    input_: InputPathType | None = None,
+    hood: float | None = None,
+    thresh: float | None = None,
+    gthresh: float | None = None,
+    gscale: typing.Literal["NONE", "LMEAN", "GMEAN"] | None = None,
+    extype: typing.Literal["MAX", "MIN", "ABS"] | None = None,
+    table: str | None = None,
+    runner: Runner | None = None,
+) -> SurfExtremaOutputs:
+    """
+    A program finding the local extrema in a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for the output datasets.
+        input_: Input dataset in which Extrema are to be identified.
+        hood: Neighborhood radius (R) in mm. Default is 8 mm.
+        thresh: Do not consider nodes with value less than this threshold.\
+            Default is 0.
+        gthresh: Do not consider nodes with gradient less than this threshold.\
+            Default is 0.01.
+        gscale: Scaling to apply to gradient computation.
+        extype: Find maxima, minima, or extrema. Options are MAX (default),\
+            MIN, ABS.
+        table: Name of file in which to store a record of the extrema found.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfExtremaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_EXTREMA_METADATA)
+    params = surf_extrema_params(
+        input_=input_,
+        hood=hood,
+        thresh=thresh,
+        gthresh=gthresh,
+        gscale=gscale,
+        extype=extype,
+        prefix=prefix,
+        table=table,
+    )
+    return surf_extrema_execute(params, execution)
+
+
+__all__ = [
+    "SURF_EXTREMA_METADATA",
+    "SurfExtremaOutputs",
+    "SurfExtremaParameters",
+    "surf_extrema",
+    "surf_extrema_params",
+]

niwrap_afni/afni/surf_fwhm.py

@@ -0,0 +1,350 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_FWHM_METADATA = Metadata(
+    id="e55aebb6889c141305f83d758c57177bec4ec628.boutiques",
+    name="SurfFWHM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfFwhmParameters = typing.TypedDict('SurfFwhmParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfFWHM"],
+    "input_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "surf_1": typing.NotRequired[str | None],
+    "surf_sphere": typing.NotRequired[str | None],
+    "clean": bool,
+    "detrend": typing.NotRequired[float | None],
+    "detpoly": typing.NotRequired[float | None],
+    "detprefix": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "vox_size": typing.NotRequired[float | None],
+    "neighborhood": typing.NotRequired[float | None],
+    "ok_warn": bool,
+    "examples": bool,
+    "slice": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfFWHM": surf_fwhm_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 {
+        "SurfFWHM": surf_fwhm_outputs,
+    }.get(t)
+
+
+class SurfFwhmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_fwhm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    detrended_output: OutputPathType | None
+    """Detrended dataset."""
+    main_output: OutputPathType | None
+    """Main output dataset."""
+    histogram_output: OutputPathType | None
+    """Histogram showing the distribution of local FWHM."""
+    mask_output: OutputPathType | None
+    """Mask output dataset."""
+
+
+def surf_fwhm_params(
+    input_file: InputPathType,
+    mask: InputPathType | None = None,
+    surf_1: str | None = None,
+    surf_sphere: str | None = None,
+    clean: bool = False,
+    detrend: float | None = None,
+    detpoly: float | None = None,
+    detprefix: str | None = None,
+    prefix: str | None = None,
+    vox_size: float | None = None,
+    neighborhood: float | None = None,
+    ok_warn: bool = False,
+    examples: bool = False,
+    slice_: bool = False,
+) -> SurfFwhmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Dataset for which the FWHM is to be calculated.
+        mask: Node mask so that only nodes in the mask are used to obtain\
+            estimates.
+        surf_1: Option for specifying the surface over which the input dataset\
+            is defined.
+        surf_sphere: Spherical version of -SURF_1 for Local FWHM estimates.
+        clean: Strip text from output to simplify parsing.
+        detrend: Detrend to order 'q'. If q is not given, the program picks\
+            q=NT/30.
+        detpoly: Detrend with polynomials of order p.
+        detprefix: Save the detrended file into a dataset with prefix 'd'.
+        prefix: Prefix of output data set.
+        vox_size: Specify the nominal voxel size in mm.
+        neighborhood: Neighborhood radius R for local FWHM estimates.
+        ok_warn: Flag to set the mode to ok_warn.
+        examples: Show command line examples and quit.
+        slice_: Use the contours from planar intersections to estimate\
+            gradients. For testing and development purposes only.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfFWHM",
+        "input_file": input_file,
+        "clean": clean,
+        "ok_warn": ok_warn,
+        "examples": examples,
+        "slice": slice_,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if surf_1 is not None:
+        params["surf_1"] = surf_1
+    if surf_sphere is not None:
+        params["surf_sphere"] = surf_sphere
+    if detrend is not None:
+        params["detrend"] = detrend
+    if detpoly is not None:
+        params["detpoly"] = detpoly
+    if detprefix is not None:
+        params["detprefix"] = detprefix
+    if prefix is not None:
+        params["prefix"] = prefix
+    if vox_size is not None:
+        params["vox_size"] = vox_size
+    if neighborhood is not None:
+        params["neighborhood"] = neighborhood
+    return params
+
+
+def surf_fwhm_cargs(
+    params: SurfFwhmParameters,
+    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("SurfFWHM")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-MASK",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("surf_1") is not None:
+        cargs.extend([
+            "-SURF_1",
+            params.get("surf_1")
+        ])
+    if params.get("surf_sphere") is not None:
+        cargs.extend([
+            "-SURF_SPHERE",
+            params.get("surf_sphere")
+        ])
+    if params.get("clean"):
+        cargs.append("-clean")
+    if params.get("detrend") is not None:
+        cargs.extend([
+            "-detrend",
+            str(params.get("detrend"))
+        ])
+    if params.get("detpoly") is not None:
+        cargs.extend([
+            "-detpoly",
+            str(params.get("detpoly"))
+        ])
+    if params.get("detprefix") is not None:
+        cargs.extend([
+            "-detprefix",
+            params.get("detprefix")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("vox_size") is not None:
+        cargs.extend([
+            "-vox_size",
+            str(params.get("vox_size"))
+        ])
+    if params.get("neighborhood") is not None:
+        cargs.extend([
+            "-hood",
+            str(params.get("neighborhood"))
+        ])
+    if params.get("ok_warn"):
+        cargs.append("-ok_warn")
+    if params.get("examples"):
+        cargs.append("-examples")
+    if params.get("slice"):
+        cargs.append("-slice")
+    cargs.append("[TALK_SUMA_OPTIONS]")
+    cargs.append("[NIML_OPTIONS]")
+    cargs.append("[DEBUG_OPTIONS]")
+    cargs.append("[HELP_OPTIONS]")
+    return cargs
+
+
+def surf_fwhm_outputs(
+    params: SurfFwhmParameters,
+    execution: Execution,
+) -> SurfFwhmOutputs:
+    """
+    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 = SurfFwhmOutputs(
+        root=execution.output_file("."),
+        detrended_output=execution.output_file(params.get("prefix") + ".1D.dset") if (params.get("prefix") is not None) else None,
+        main_output=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        histogram_output=execution.output_file(params.get("prefix") + "_histog.1D") if (params.get("prefix") is not None) else None,
+        mask_output=execution.output_file(params.get("prefix") + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def surf_fwhm_execute(
+    params: SurfFwhmParameters,
+    execution: Execution,
+) -> SurfFwhmOutputs:
+    """
+    A program for calculating local and global FWHM.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfFwhmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_fwhm_cargs(params, execution)
+    ret = surf_fwhm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_fwhm(
+    input_file: InputPathType,
+    mask: InputPathType | None = None,
+    surf_1: str | None = None,
+    surf_sphere: str | None = None,
+    clean: bool = False,
+    detrend: float | None = None,
+    detpoly: float | None = None,
+    detprefix: str | None = None,
+    prefix: str | None = None,
+    vox_size: float | None = None,
+    neighborhood: float | None = None,
+    ok_warn: bool = False,
+    examples: bool = False,
+    slice_: bool = False,
+    runner: Runner | None = None,
+) -> SurfFwhmOutputs:
+    """
+    A program for calculating local and global FWHM.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Dataset for which the FWHM is to be calculated.
+        mask: Node mask so that only nodes in the mask are used to obtain\
+            estimates.
+        surf_1: Option for specifying the surface over which the input dataset\
+            is defined.
+        surf_sphere: Spherical version of -SURF_1 for Local FWHM estimates.
+        clean: Strip text from output to simplify parsing.
+        detrend: Detrend to order 'q'. If q is not given, the program picks\
+            q=NT/30.
+        detpoly: Detrend with polynomials of order p.
+        detprefix: Save the detrended file into a dataset with prefix 'd'.
+        prefix: Prefix of output data set.
+        vox_size: Specify the nominal voxel size in mm.
+        neighborhood: Neighborhood radius R for local FWHM estimates.
+        ok_warn: Flag to set the mode to ok_warn.
+        examples: Show command line examples and quit.
+        slice_: Use the contours from planar intersections to estimate\
+            gradients. For testing and development purposes only.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfFwhmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_FWHM_METADATA)
+    params = surf_fwhm_params(
+        input_file=input_file,
+        mask=mask,
+        surf_1=surf_1,
+        surf_sphere=surf_sphere,
+        clean=clean,
+        detrend=detrend,
+        detpoly=detpoly,
+        detprefix=detprefix,
+        prefix=prefix,
+        vox_size=vox_size,
+        neighborhood=neighborhood,
+        ok_warn=ok_warn,
+        examples=examples,
+        slice_=slice_,
+    )
+    return surf_fwhm_execute(params, execution)
+
+
+__all__ = [
+    "SURF_FWHM_METADATA",
+    "SurfFwhmOutputs",
+    "SurfFwhmParameters",
+    "surf_fwhm",
+    "surf_fwhm_params",
+]