niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__roi_modal_grow.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 *
+
+V__ROI_MODAL_GROW_METADATA = Metadata(
+    id="d33815ad6bfc8ff7ac694bacf23eb5bed10577bf.boutiques",
+    name="@ROI_modal_grow",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRoiModalGrowParameters = typing.TypedDict('VRoiModalGrowParameters', {
+    "__STYX_TYPE__": typing.Literal["@ROI_modal_grow"],
+    "input_dset": InputPathType,
+    "niters": float,
+    "outdir": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "neighborhood_type": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ROI_modal_grow": v__roi_modal_grow_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 {
+        "@ROI_modal_grow": v__roi_modal_grow_outputs,
+    }.get(t)
+
+
+class VRoiModalGrowOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__roi_modal_grow(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Final output dataset"""
+
+
+def v__roi_modal_grow_params(
+    input_dset: InputPathType,
+    niters: float,
+    outdir: str | None = None,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    neighborhood_type: int | None = None,
+) -> VRoiModalGrowParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dset: Required input dataset. This dataset should be a set of\
+            integer values, assuming approximate isotropic voxels.
+        niters: Number of iterations for modal growth, generally making sense\
+            for values from about 1-10.
+        outdir: Directory name for output. All output goes to this directory.\
+            Default is rmgrow.
+        mask: Mask dataset at the same grid as the input dataset. Could be a\
+            dilated version of the original mask or a larger region like a cortical\
+            ribbon mask. Not required but often desirable.
+        prefix: Base name of the final output dataset, i.e., baseprefix.nii.gz.\
+            Default is rmg, so output would be rmg.nii.gz.
+        neighborhood_type: Neighborhood type used in finding mode. 1 - facing\
+            neighbors, 2 - edges, 3 - corners.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ROI_modal_grow",
+        "input_dset": input_dset,
+        "niters": niters,
+    }
+    if outdir is not None:
+        params["outdir"] = outdir
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if neighborhood_type is not None:
+        params["neighborhood_type"] = neighborhood_type
+    return params
+
+
+def v__roi_modal_grow_cargs(
+    params: VRoiModalGrowParameters,
+    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("@ROI_modal_grow")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dset"))
+    ])
+    cargs.extend([
+        "-niters",
+        str(params.get("niters"))
+    ])
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "-outdir",
+            params.get("outdir")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("neighborhood_type") is not None:
+        cargs.extend([
+            "-NN",
+            str(params.get("neighborhood_type"))
+        ])
+    return cargs
+
+
+def v__roi_modal_grow_outputs(
+    params: VRoiModalGrowParameters,
+    execution: Execution,
+) -> VRoiModalGrowOutputs:
+    """
+    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 = VRoiModalGrowOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("outdir") + "/" + params.get("prefix") + ".nii.gz") if (params.get("outdir") is not None and params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__roi_modal_grow_execute(
+    params: VRoiModalGrowParameters,
+    execution: Execution,
+) -> VRoiModalGrowOutputs:
+    """
+    Script to grow a set of regions in a volumetric dataset using modal smoothing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRoiModalGrowOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__roi_modal_grow_cargs(params, execution)
+    ret = v__roi_modal_grow_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__roi_modal_grow(
+    input_dset: InputPathType,
+    niters: float,
+    outdir: str | None = None,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    neighborhood_type: int | None = None,
+    runner: Runner | None = None,
+) -> VRoiModalGrowOutputs:
+    """
+    Script to grow a set of regions in a volumetric dataset using modal smoothing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dset: Required input dataset. This dataset should be a set of\
+            integer values, assuming approximate isotropic voxels.
+        niters: Number of iterations for modal growth, generally making sense\
+            for values from about 1-10.
+        outdir: Directory name for output. All output goes to this directory.\
+            Default is rmgrow.
+        mask: Mask dataset at the same grid as the input dataset. Could be a\
+            dilated version of the original mask or a larger region like a cortical\
+            ribbon mask. Not required but often desirable.
+        prefix: Base name of the final output dataset, i.e., baseprefix.nii.gz.\
+            Default is rmg, so output would be rmg.nii.gz.
+        neighborhood_type: Neighborhood type used in finding mode. 1 - facing\
+            neighbors, 2 - edges, 3 - corners.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRoiModalGrowOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ROI_MODAL_GROW_METADATA)
+    params = v__roi_modal_grow_params(
+        input_dset=input_dset,
+        niters=niters,
+        outdir=outdir,
+        mask=mask,
+        prefix=prefix,
+        neighborhood_type=neighborhood_type,
+    )
+    return v__roi_modal_grow_execute(params, execution)
+
+
+__all__ = [
+    "VRoiModalGrowOutputs",
+    "VRoiModalGrowParameters",
+    "V__ROI_MODAL_GROW_METADATA",
+    "v__roi_modal_grow",
+    "v__roi_modal_grow_params",
+]

niwrap_afni/afni/v__scale_volume.py

@@ -0,0 +1,252 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SCALE_VOLUME_METADATA = Metadata(
+    id="4000996fdc6423040b991fc320209305f64cb474.boutiques",
+    name="@ScaleVolume",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VScaleVolumeParameters = typing.TypedDict('VScaleVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["@ScaleVolume"],
+    "input_dset": InputPathType,
+    "prefix": str,
+    "val_clip": typing.NotRequired[list[float] | None],
+    "perc_clip": typing.NotRequired[list[float] | None],
+    "scale_by_mean": bool,
+    "scale_by_median": bool,
+    "norm": bool,
+    "mask": 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 {
+        "@ScaleVolume": v__scale_volume_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 {
+        "@ScaleVolume": v__scale_volume_outputs,
+    }.get(t)
+
+
+class VScaleVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__scale_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output scaled dataset"""
+
+
+def v__scale_volume_params(
+    input_dset: InputPathType,
+    prefix: str,
+    val_clip: list[float] | None = None,
+    perc_clip: list[float] | None = None,
+    scale_by_mean: bool = False,
+    scale_by_median: bool = False,
+    norm: bool = False,
+    mask: InputPathType | None = None,
+) -> VScaleVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dset: Dataset to scale.
+        prefix: Prefix of output.
+        val_clip: Min and Max of output dataset. Default V0 = 0 and V1 = 255.
+        perc_clip: Set lowest P0 percentile to Min and highest P1 percentile to\
+            Max. Default P0 = 2 and P1 = 98.
+        scale_by_mean: Divide each sub-brick by mean of non-zero voxels.
+        scale_by_median: Divide each sub-brick by median of non-zero voxels.
+        norm: For each time series T, Tnorm = (T - mean(T)) / stdev(T).
+        mask: Restrict to non-zero values of given mask dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ScaleVolume",
+        "input_dset": input_dset,
+        "prefix": prefix,
+        "scale_by_mean": scale_by_mean,
+        "scale_by_median": scale_by_median,
+        "norm": norm,
+    }
+    if val_clip is not None:
+        params["val_clip"] = val_clip
+    if perc_clip is not None:
+        params["perc_clip"] = perc_clip
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v__scale_volume_cargs(
+    params: VScaleVolumeParameters,
+    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("@ScaleVolume")
+    cargs.append(execution.input_file(params.get("input_dset")))
+    cargs.append(params.get("prefix"))
+    if params.get("val_clip") is not None:
+        cargs.extend([
+            "-val_clip",
+            *map(str, params.get("val_clip"))
+        ])
+    if params.get("perc_clip") is not None:
+        cargs.extend([
+            "-perc_clip",
+            *map(str, params.get("perc_clip"))
+        ])
+    if params.get("scale_by_mean"):
+        cargs.append("-scale_by_mean")
+    if params.get("scale_by_median"):
+        cargs.append("-scale_by_median")
+    if params.get("norm"):
+        cargs.append("-norm")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    return cargs
+
+
+def v__scale_volume_outputs(
+    params: VScaleVolumeParameters,
+    execution: Execution,
+) -> VScaleVolumeOutputs:
+    """
+    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 = VScaleVolumeOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("<-prefix PREFIX>_scaled"),
+    )
+    return ret
+
+
+def v__scale_volume_execute(
+    params: VScaleVolumeParameters,
+    execution: Execution,
+) -> VScaleVolumeOutputs:
+    """
+    A tool to scale the volume of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VScaleVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__scale_volume_cargs(params, execution)
+    ret = v__scale_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__scale_volume(
+    input_dset: InputPathType,
+    prefix: str,
+    val_clip: list[float] | None = None,
+    perc_clip: list[float] | None = None,
+    scale_by_mean: bool = False,
+    scale_by_median: bool = False,
+    norm: bool = False,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> VScaleVolumeOutputs:
+    """
+    A tool to scale the volume of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dset: Dataset to scale.
+        prefix: Prefix of output.
+        val_clip: Min and Max of output dataset. Default V0 = 0 and V1 = 255.
+        perc_clip: Set lowest P0 percentile to Min and highest P1 percentile to\
+            Max. Default P0 = 2 and P1 = 98.
+        scale_by_mean: Divide each sub-brick by mean of non-zero voxels.
+        scale_by_median: Divide each sub-brick by median of non-zero voxels.
+        norm: For each time series T, Tnorm = (T - mean(T)) / stdev(T).
+        mask: Restrict to non-zero values of given mask dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VScaleVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SCALE_VOLUME_METADATA)
+    params = v__scale_volume_params(
+        input_dset=input_dset,
+        prefix=prefix,
+        val_clip=val_clip,
+        perc_clip=perc_clip,
+        scale_by_mean=scale_by_mean,
+        scale_by_median=scale_by_median,
+        norm=norm,
+        mask=mask,
+    )
+    return v__scale_volume_execute(params, execution)
+
+
+__all__ = [
+    "VScaleVolumeOutputs",
+    "VScaleVolumeParameters",
+    "V__SCALE_VOLUME_METADATA",
+    "v__scale_volume",
+    "v__scale_volume_params",
+]

niwrap_afni/afni/v__script_check.py

@@ -0,0 +1,201 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SCRIPT_CHECK_METADATA = Metadata(
+    id="1ec7bab89de6f0062a23a1361628a4abde50ae24.boutiques",
+    name="@ScriptCheck",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VScriptCheckParameters = typing.TypedDict('VScriptCheckParameters', {
+    "__STYX_TYPE__": typing.Literal["@ScriptCheck"],
+    "clean": bool,
+    "suffix": typing.NotRequired[str | None],
+    "scripts": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ScriptCheck": v__script_check_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 {
+        "@ScriptCheck": v__script_check_outputs,
+    }.get(t)
+
+
+class VScriptCheckOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__script_check(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    uncleaned_file: OutputPathType
+    """Uncleaned original file with specified suffix"""
+    cleaned_file: OutputPathType
+    """Cleaned file if -clean option is used"""
+
+
+def v__script_check_params(
+    scripts: list[InputPathType],
+    clean: bool = False,
+    suffix: str | None = None,
+) -> VScriptCheckParameters:
+    """
+    Build parameters.
+    
+    Args:
+        scripts: Scripts to be checked for improperly terminated lines.
+        clean: Clean bad line breaks.
+        suffix: Rename uncleaned file with specified suffix. Default is .uncln.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ScriptCheck",
+        "clean": clean,
+        "scripts": scripts,
+    }
+    if suffix is not None:
+        params["suffix"] = suffix
+    return params
+
+
+def v__script_check_cargs(
+    params: VScriptCheckParameters,
+    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("@ScriptCheck")
+    if params.get("clean"):
+        cargs.append("-clean")
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("scripts")])
+    return cargs
+
+
+def v__script_check_outputs(
+    params: VScriptCheckParameters,
+    execution: Execution,
+) -> VScriptCheckOutputs:
+    """
+    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 = VScriptCheckOutputs(
+        root=execution.output_file("."),
+        uncleaned_file=execution.output_file("{SCRIPT}.uncln"),
+        cleaned_file=execution.output_file("{SCRIPT}"),
+    )
+    return ret
+
+
+def v__script_check_execute(
+    params: VScriptCheckParameters,
+    execution: Execution,
+) -> VScriptCheckOutputs:
+    """
+    Checks scripts for improperly terminated lines and optionally cleans them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VScriptCheckOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__script_check_cargs(params, execution)
+    ret = v__script_check_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__script_check(
+    scripts: list[InputPathType],
+    clean: bool = False,
+    suffix: str | None = None,
+    runner: Runner | None = None,
+) -> VScriptCheckOutputs:
+    """
+    Checks scripts for improperly terminated lines and optionally cleans them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        scripts: Scripts to be checked for improperly terminated lines.
+        clean: Clean bad line breaks.
+        suffix: Rename uncleaned file with specified suffix. Default is .uncln.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VScriptCheckOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SCRIPT_CHECK_METADATA)
+    params = v__script_check_params(
+        clean=clean,
+        suffix=suffix,
+        scripts=scripts,
+    )
+    return v__script_check_execute(params, execution)
+
+
+__all__ = [
+    "VScriptCheckOutputs",
+    "VScriptCheckParameters",
+    "V__SCRIPT_CHECK_METADATA",
+    "v__script_check",
+    "v__script_check_params",
+]