niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_intracranial.py

@@ -0,0 +1,275 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_INTRACRANIAL_METADATA = Metadata(
+    id="ea8145ebdfe6804031df6749fa5d0cbc04870c58.boutiques",
+    name="3dIntracranial",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dIntracranialParameters = typing.TypedDict('V3dIntracranialParameters', {
+    "__STYX_TYPE__": typing.Literal["3dIntracranial"],
+    "infile": InputPathType,
+    "prefix": str,
+    "min_val": typing.NotRequired[float | None],
+    "max_val": typing.NotRequired[float | None],
+    "min_conn": typing.NotRequired[float | None],
+    "max_conn": typing.NotRequired[float | None],
+    "no_smooth": bool,
+    "mask": bool,
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dIntracranial": v_3d_intracranial_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 {
+        "3dIntracranial": v_3d_intracranial_outputs,
+    }.get(t)
+
+
+class V3dIntracranialOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_intracranial(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    segmented_image: OutputPathType
+    """Output file containing segmented image"""
+
+
+def v_3d_intracranial_params(
+    infile: InputPathType,
+    prefix: str,
+    min_val: float | None = None,
+    max_val: float | None = None,
+    min_conn: float | None = None,
+    max_conn: float | None = None,
+    no_smooth: bool = False,
+    mask: bool = False,
+    quiet: bool = False,
+) -> V3dIntracranialParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Filename of anat dataset to be segmented.
+        prefix: Prefix name for file to contain segmented image.
+        min_val: Minimum voxel intensity limit. Default is internal PDF\
+            estimate for lower bound.
+        max_val: Maximum voxel intensity limit. Default is internal PDF\
+            estimate for upper bound.
+        min_conn: Minimum voxel connectivity to enter. Default is 4.
+        max_conn: Maximum voxel connectivity to leave. Default is 2.
+        no_smooth: Suppress spatial smoothing of segmentation mask.
+        mask: Generate functional image mask (complement). Default is to\
+            generate anatomical image.
+        quiet: Suppress output to screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dIntracranial",
+        "infile": infile,
+        "prefix": prefix,
+        "no_smooth": no_smooth,
+        "mask": mask,
+        "quiet": quiet,
+    }
+    if min_val is not None:
+        params["min_val"] = min_val
+    if max_val is not None:
+        params["max_val"] = max_val
+    if min_conn is not None:
+        params["min_conn"] = min_conn
+    if max_conn is not None:
+        params["max_conn"] = max_conn
+    return params
+
+
+def v_3d_intracranial_cargs(
+    params: V3dIntracranialParameters,
+    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("3dIntracranial")
+    cargs.extend([
+        "-anat",
+        execution.input_file(params.get("infile"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("min_val") is not None:
+        cargs.extend([
+            "-min_val",
+            str(params.get("min_val"))
+        ])
+    if params.get("max_val") is not None:
+        cargs.extend([
+            "-max_val",
+            str(params.get("max_val"))
+        ])
+    if params.get("min_conn") is not None:
+        cargs.extend([
+            "-min_conn",
+            str(params.get("min_conn"))
+        ])
+    if params.get("max_conn") is not None:
+        cargs.extend([
+            "-max_conn",
+            str(params.get("max_conn"))
+        ])
+    if params.get("no_smooth"):
+        cargs.append("-nosmooth")
+    if params.get("mask"):
+        cargs.append("-mask")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_intracranial_outputs(
+    params: V3dIntracranialParameters,
+    execution: Execution,
+) -> V3dIntracranialOutputs:
+    """
+    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 = V3dIntracranialOutputs(
+        root=execution.output_file("."),
+        segmented_image=execution.output_file(params.get("prefix") + "+orig"),
+    )
+    return ret
+
+
+def v_3d_intracranial_execute(
+    params: V3dIntracranialParameters,
+    execution: Execution,
+) -> V3dIntracranialOutputs:
+    """
+    Performs automatic segmentation of intracranial region.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dIntracranialOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_intracranial_cargs(params, execution)
+    ret = v_3d_intracranial_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_intracranial(
+    infile: InputPathType,
+    prefix: str,
+    min_val: float | None = None,
+    max_val: float | None = None,
+    min_conn: float | None = None,
+    max_conn: float | None = None,
+    no_smooth: bool = False,
+    mask: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dIntracranialOutputs:
+    """
+    Performs automatic segmentation of intracranial region.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Filename of anat dataset to be segmented.
+        prefix: Prefix name for file to contain segmented image.
+        min_val: Minimum voxel intensity limit. Default is internal PDF\
+            estimate for lower bound.
+        max_val: Maximum voxel intensity limit. Default is internal PDF\
+            estimate for upper bound.
+        min_conn: Minimum voxel connectivity to enter. Default is 4.
+        max_conn: Maximum voxel connectivity to leave. Default is 2.
+        no_smooth: Suppress spatial smoothing of segmentation mask.
+        mask: Generate functional image mask (complement). Default is to\
+            generate anatomical image.
+        quiet: Suppress output to screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dIntracranialOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_INTRACRANIAL_METADATA)
+    params = v_3d_intracranial_params(
+        infile=infile,
+        prefix=prefix,
+        min_val=min_val,
+        max_val=max_val,
+        min_conn=min_conn,
+        max_conn=max_conn,
+        no_smooth=no_smooth,
+        mask=mask,
+        quiet=quiet,
+    )
+    return v_3d_intracranial_execute(params, execution)
+
+
+__all__ = [
+    "V3dIntracranialOutputs",
+    "V3dIntracranialParameters",
+    "V_3D_INTRACRANIAL_METADATA",
+    "v_3d_intracranial",
+    "v_3d_intracranial_params",
+]

niwrap_afni/afni/v_3d_inv_fmri.py

@@ -0,0 +1,317 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_INV_FMRI_METADATA = Metadata(
+    id="0e98d6cd57d0addd162bfa97a9fce6949e7b4f85.boutiques",
+    name="3dInvFMRI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dInvFmriParameters = typing.TypedDict('V3dInvFmriParameters', {
+    "__STYX_TYPE__": typing.Literal["3dInvFMRI"],
+    "input_file": InputPathType,
+    "activation_map": InputPathType,
+    "map_weight": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "baseline_file": typing.NotRequired[list[InputPathType] | None],
+    "polynom_order": typing.NotRequired[float | None],
+    "output_file": typing.NotRequired[str | None],
+    "method": typing.NotRequired[str | None],
+    "alpha": typing.NotRequired[float | None],
+    "smooth_fir": bool,
+    "smooth_median": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dInvFMRI": v_3d_inv_fmri_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 {
+        "3dInvFMRI": v_3d_inv_fmri_outputs,
+    }.get(t)
+
+
+class V3dInvFmriOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_inv_fmri(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """The output 1D file."""
+
+
+def v_3d_inv_fmri_params(
+    input_file: InputPathType,
+    activation_map: InputPathType,
+    map_weight: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    baseline_file: list[InputPathType] | None = None,
+    polynom_order: float | None = None,
+    output_file: str | None = None,
+    method: str | None = None,
+    alpha: float | None = None,
+    smooth_fir: bool = False,
+    smooth_median: bool = False,
+) -> V3dInvFmriParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input 3D+time dataset.
+        activation_map: Defines activation map; should be a bucket dataset\
+            where each sub-brick defines the beta weight map for an unknown\
+            stimulus time series.
+        map_weight: Defines a weighting factor for the map. Dataset can have\
+            either 1 sub-brick or the same number as in the -map dataset.
+        mask: Defines a mask dataset to restrict input voxels from -data and\
+            -map.
+        baseline_file: Baseline time series file. Each column of the file\
+            defines a baseline time series.
+        polynom_order: Adds polynomials of specified order to the baseline\
+            collection.
+        output_file: Name of the 1D output file.
+        method: Determines the method to use: C for least squares fit to data\
+            matrix (default) or K for least squares fit to activation matrix.
+        alpha: Set the alpha factor to penalize large values of the output\
+            vectors.
+        smooth_fir: Smooth the results with a 5 point lowpass FIR filter.
+        smooth_median: Smooth the results with a 5 point median filter.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dInvFMRI",
+        "input_file": input_file,
+        "activation_map": activation_map,
+        "smooth_fir": smooth_fir,
+        "smooth_median": smooth_median,
+    }
+    if map_weight is not None:
+        params["map_weight"] = map_weight
+    if mask is not None:
+        params["mask"] = mask
+    if baseline_file is not None:
+        params["baseline_file"] = baseline_file
+    if polynom_order is not None:
+        params["polynom_order"] = polynom_order
+    if output_file is not None:
+        params["output_file"] = output_file
+    if method is not None:
+        params["method"] = method
+    if alpha is not None:
+        params["alpha"] = alpha
+    return params
+
+
+def v_3d_inv_fmri_cargs(
+    params: V3dInvFmriParameters,
+    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("3dInvFMRI")
+    cargs.extend([
+        "-data",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-map",
+        execution.input_file(params.get("activation_map"))
+    ])
+    if params.get("map_weight") is not None:
+        cargs.extend([
+            "-mapwt",
+            execution.input_file(params.get("map_weight"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("baseline_file") is not None:
+        cargs.extend([
+            "-base",
+            *[execution.input_file(f) for f in params.get("baseline_file")]
+        ])
+    if params.get("polynom_order") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polynom_order"))
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-out",
+            params.get("output_file")
+        ])
+    if params.get("method") is not None:
+        cargs.extend([
+            "-method",
+            params.get("method")
+        ])
+    if params.get("alpha") is not None:
+        cargs.extend([
+            "-alpha",
+            str(params.get("alpha"))
+        ])
+    if params.get("smooth_fir"):
+        cargs.append("-fir5")
+    if params.get("smooth_median"):
+        cargs.append("-median5")
+    return cargs
+
+
+def v_3d_inv_fmri_outputs(
+    params: V3dInvFmriParameters,
+    execution: Execution,
+) -> V3dInvFmriOutputs:
+    """
+    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 = V3dInvFmriOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_inv_fmri_execute(
+    params: V3dInvFmriParameters,
+    execution: Execution,
+) -> V3dInvFmriOutputs:
+    """
+    Program to compute stimulus time series, given a 3D+time dataset and an
+    activation map (the inverse of the usual FMRI analysis problem).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dInvFmriOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_inv_fmri_cargs(params, execution)
+    ret = v_3d_inv_fmri_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_inv_fmri(
+    input_file: InputPathType,
+    activation_map: InputPathType,
+    map_weight: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    baseline_file: list[InputPathType] | None = None,
+    polynom_order: float | None = None,
+    output_file: str | None = None,
+    method: str | None = None,
+    alpha: float | None = None,
+    smooth_fir: bool = False,
+    smooth_median: bool = False,
+    runner: Runner | None = None,
+) -> V3dInvFmriOutputs:
+    """
+    Program to compute stimulus time series, given a 3D+time dataset and an
+    activation map (the inverse of the usual FMRI analysis problem).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input 3D+time dataset.
+        activation_map: Defines activation map; should be a bucket dataset\
+            where each sub-brick defines the beta weight map for an unknown\
+            stimulus time series.
+        map_weight: Defines a weighting factor for the map. Dataset can have\
+            either 1 sub-brick or the same number as in the -map dataset.
+        mask: Defines a mask dataset to restrict input voxels from -data and\
+            -map.
+        baseline_file: Baseline time series file. Each column of the file\
+            defines a baseline time series.
+        polynom_order: Adds polynomials of specified order to the baseline\
+            collection.
+        output_file: Name of the 1D output file.
+        method: Determines the method to use: C for least squares fit to data\
+            matrix (default) or K for least squares fit to activation matrix.
+        alpha: Set the alpha factor to penalize large values of the output\
+            vectors.
+        smooth_fir: Smooth the results with a 5 point lowpass FIR filter.
+        smooth_median: Smooth the results with a 5 point median filter.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dInvFmriOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_INV_FMRI_METADATA)
+    params = v_3d_inv_fmri_params(
+        input_file=input_file,
+        activation_map=activation_map,
+        map_weight=map_weight,
+        mask=mask,
+        baseline_file=baseline_file,
+        polynom_order=polynom_order,
+        output_file=output_file,
+        method=method,
+        alpha=alpha,
+        smooth_fir=smooth_fir,
+        smooth_median=smooth_median,
+    )
+    return v_3d_inv_fmri_execute(params, execution)
+
+
+__all__ = [
+    "V3dInvFmriOutputs",
+    "V3dInvFmriParameters",
+    "V_3D_INV_FMRI_METADATA",
+    "v_3d_inv_fmri",
+    "v_3d_inv_fmri_params",
+]