niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__roi_corr_mat.py

@@ -0,0 +1,277 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ROI_CORR_MAT_METADATA = Metadata(
+    id="d30a28b9afde46895088e3c1489b3ceaf2e8ab86.boutiques",
+    name="@ROI_Corr_Mat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRoiCorrMatParameters = typing.TypedDict('VRoiCorrMatParameters', {
+    "__STYX_TYPE__": typing.Literal["@ROI_Corr_Mat"],
+    "ts_vol": InputPathType,
+    "roi_vol": InputPathType,
+    "prefix": str,
+    "roisel": typing.NotRequired[InputPathType | None],
+    "zval": bool,
+    "mat_opt": typing.NotRequired[str | None],
+    "dirty": bool,
+    "keep_tmp": bool,
+    "echo": bool,
+    "verb": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ROI_Corr_Mat": v__roi_corr_mat_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_Corr_Mat": v__roi_corr_mat_outputs,
+    }.get(t)
+
+
+class VRoiCorrMatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__roi_corr_mat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    matrix_1d: OutputPathType
+    """Correlation matrix in .1D format"""
+    matrix_brick: OutputPathType
+    """Correlation matrix in .BRIK format"""
+
+
+def v__roi_corr_mat_params(
+    ts_vol: InputPathType,
+    roi_vol: InputPathType,
+    prefix: str,
+    roisel: InputPathType | None = None,
+    zval: bool = False,
+    mat_opt: str | None = None,
+    dirty: bool = False,
+    keep_tmp: bool = False,
+    echo: bool = False,
+    verb: bool = False,
+) -> VRoiCorrMatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        ts_vol: Time series volume.
+        roi_vol: ROI volume.
+        prefix: Use output for a prefix.
+        roisel: Force processing of ROI label (integers) listed in ROISEL 1D\
+            file.
+        zval: Output a zscore version of the correlation matrix.
+        mat_opt: Output matrix in different manners.
+        dirty: Keep temporary files.
+        keep_tmp: Keep temporary files.
+        echo: Set echo (echo all commands to screen).
+        verb: Verbose flag.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ROI_Corr_Mat",
+        "ts_vol": ts_vol,
+        "roi_vol": roi_vol,
+        "prefix": prefix,
+        "zval": zval,
+        "dirty": dirty,
+        "keep_tmp": keep_tmp,
+        "echo": echo,
+        "verb": verb,
+    }
+    if roisel is not None:
+        params["roisel"] = roisel
+    if mat_opt is not None:
+        params["mat_opt"] = mat_opt
+    return params
+
+
+def v__roi_corr_mat_cargs(
+    params: VRoiCorrMatParameters,
+    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_Corr_Mat")
+    cargs.extend([
+        "-ts",
+        execution.input_file(params.get("ts_vol"))
+    ])
+    cargs.extend([
+        "-roi",
+        execution.input_file(params.get("roi_vol"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("roisel") is not None:
+        cargs.extend([
+            "-roisel",
+            execution.input_file(params.get("roisel"))
+        ])
+    if params.get("zval"):
+        cargs.append("-zval")
+    if params.get("mat_opt") is not None:
+        cargs.extend([
+            "-mat",
+            params.get("mat_opt")
+        ])
+    if params.get("dirty"):
+        cargs.append("-dirty")
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("verb"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v__roi_corr_mat_outputs(
+    params: VRoiCorrMatParameters,
+    execution: Execution,
+) -> VRoiCorrMatOutputs:
+    """
+    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 = VRoiCorrMatOutputs(
+        root=execution.output_file("."),
+        matrix_1d=execution.output_file(params.get("prefix") + "_matrix.1D"),
+        matrix_brick=execution.output_file(params.get("prefix") + "_matrix.BRIK"),
+    )
+    return ret
+
+
+def v__roi_corr_mat_execute(
+    params: VRoiCorrMatParameters,
+    execution: Execution,
+) -> VRoiCorrMatOutputs:
+    """
+    Script to produce an NxN ROI correlation matrix of N ROIs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRoiCorrMatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__roi_corr_mat_cargs(params, execution)
+    ret = v__roi_corr_mat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__roi_corr_mat(
+    ts_vol: InputPathType,
+    roi_vol: InputPathType,
+    prefix: str,
+    roisel: InputPathType | None = None,
+    zval: bool = False,
+    mat_opt: str | None = None,
+    dirty: bool = False,
+    keep_tmp: bool = False,
+    echo: bool = False,
+    verb: bool = False,
+    runner: Runner | None = None,
+) -> VRoiCorrMatOutputs:
+    """
+    Script to produce an NxN ROI correlation matrix of N ROIs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        ts_vol: Time series volume.
+        roi_vol: ROI volume.
+        prefix: Use output for a prefix.
+        roisel: Force processing of ROI label (integers) listed in ROISEL 1D\
+            file.
+        zval: Output a zscore version of the correlation matrix.
+        mat_opt: Output matrix in different manners.
+        dirty: Keep temporary files.
+        keep_tmp: Keep temporary files.
+        echo: Set echo (echo all commands to screen).
+        verb: Verbose flag.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRoiCorrMatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ROI_CORR_MAT_METADATA)
+    params = v__roi_corr_mat_params(
+        ts_vol=ts_vol,
+        roi_vol=roi_vol,
+        prefix=prefix,
+        roisel=roisel,
+        zval=zval,
+        mat_opt=mat_opt,
+        dirty=dirty,
+        keep_tmp=keep_tmp,
+        echo=echo,
+        verb=verb,
+    )
+    return v__roi_corr_mat_execute(params, execution)
+
+
+__all__ = [
+    "VRoiCorrMatOutputs",
+    "VRoiCorrMatParameters",
+    "V__ROI_CORR_MAT_METADATA",
+    "v__roi_corr_mat",
+    "v__roi_corr_mat_params",
+]

niwrap_afni/afni/v__roi_decluster.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__ROI_DECLUSTER_METADATA = Metadata(
+    id="c565e19b7f5a74c17db9a508d6eb500dd6dc0e98.boutiques",
+    name="@ROI_decluster",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRoiDeclusterParameters = typing.TypedDict('VRoiDeclusterParameters', {
+    "__STYX_TYPE__": typing.Literal["@ROI_decluster"],
+    "input_dset": InputPathType,
+    "output_dir": typing.NotRequired[str | None],
+    "nvox_thresh": typing.NotRequired[float | None],
+    "frac_thresh": typing.NotRequired[float | 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_decluster": v__roi_decluster_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_decluster": v__roi_decluster_outputs,
+    }.get(t)
+
+
+class VRoiDeclusterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__roi_decluster(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Final output dataset"""
+
+
+def v__roi_decluster_params(
+    input_dset: InputPathType,
+    output_dir: str | None = None,
+    nvox_thresh: float | None = None,
+    frac_thresh: float | None = None,
+    prefix: str | None = None,
+    neighborhood_type: int | None = None,
+) -> VRoiDeclusterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dset: Required input dataset. This dataset should be set of\
+            integer values. The program mostly assumes approximate isotropic\
+            voxels.
+        output_dir: Directory name for output. All output goes to this\
+            directory.
+        nvox_thresh: Number of voxels in a cluster to keep.
+        frac_thresh: Fraction of voxels in a cluster to keep [0.0-1.0].
+        prefix: Base name of final output dataset, i.e. baseprefix.nii.gz.
+        neighborhood_type: Neighborhood type using in finding mode: 1 - facing\
+            neighbors, 2 - edges, 3 - corners.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ROI_decluster",
+        "input_dset": input_dset,
+    }
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    if nvox_thresh is not None:
+        params["nvox_thresh"] = nvox_thresh
+    if frac_thresh is not None:
+        params["frac_thresh"] = frac_thresh
+    if prefix is not None:
+        params["prefix"] = prefix
+    if neighborhood_type is not None:
+        params["neighborhood_type"] = neighborhood_type
+    return params
+
+
+def v__roi_decluster_cargs(
+    params: VRoiDeclusterParameters,
+    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_decluster")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dset"))
+    ])
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-outdir",
+            params.get("output_dir")
+        ])
+    if params.get("nvox_thresh") is not None:
+        cargs.extend([
+            "-nvox_thresh",
+            str(params.get("nvox_thresh"))
+        ])
+    if params.get("frac_thresh") is not None:
+        cargs.extend([
+            "-frac_thresh",
+            str(params.get("frac_thresh"))
+        ])
+    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_decluster_outputs(
+    params: VRoiDeclusterParameters,
+    execution: Execution,
+) -> VRoiDeclusterOutputs:
+    """
+    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 = VRoiDeclusterOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__roi_decluster_execute(
+    params: VRoiDeclusterParameters,
+    execution: Execution,
+) -> VRoiDeclusterOutputs:
+    """
+    Script to remove small clusters or standalone voxels from an ROI/atlas dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRoiDeclusterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__roi_decluster_cargs(params, execution)
+    ret = v__roi_decluster_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__roi_decluster(
+    input_dset: InputPathType,
+    output_dir: str | None = None,
+    nvox_thresh: float | None = None,
+    frac_thresh: float | None = None,
+    prefix: str | None = None,
+    neighborhood_type: int | None = None,
+    runner: Runner | None = None,
+) -> VRoiDeclusterOutputs:
+    """
+    Script to remove small clusters or standalone voxels from an ROI/atlas dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dset: Required input dataset. This dataset should be set of\
+            integer values. The program mostly assumes approximate isotropic\
+            voxels.
+        output_dir: Directory name for output. All output goes to this\
+            directory.
+        nvox_thresh: Number of voxels in a cluster to keep.
+        frac_thresh: Fraction of voxels in a cluster to keep [0.0-1.0].
+        prefix: Base name of final output dataset, i.e. baseprefix.nii.gz.
+        neighborhood_type: Neighborhood type using in finding mode: 1 - facing\
+            neighbors, 2 - edges, 3 - corners.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRoiDeclusterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ROI_DECLUSTER_METADATA)
+    params = v__roi_decluster_params(
+        input_dset=input_dset,
+        output_dir=output_dir,
+        nvox_thresh=nvox_thresh,
+        frac_thresh=frac_thresh,
+        prefix=prefix,
+        neighborhood_type=neighborhood_type,
+    )
+    return v__roi_decluster_execute(params, execution)
+
+
+__all__ = [
+    "VRoiDeclusterOutputs",
+    "VRoiDeclusterParameters",
+    "V__ROI_DECLUSTER_METADATA",
+    "v__roi_decluster",
+    "v__roi_decluster_params",
+]