niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tcorr1_d.py

@@ -0,0 +1,243 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TCORR1_D_METADATA = Metadata(
+    id="db33094375d3e7131beda2ef599c6bd0761a7d75.boutiques",
+    name="3dTcorr1D",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTcorr1DParameters = typing.TypedDict('V3dTcorr1DParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTcorr1D"],
+    "ktaub": bool,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "pearson": bool,
+    "quadrant": bool,
+    "spearman": bool,
+    "xset": InputPathType,
+    "y_1d": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTcorr1D": v_3d_tcorr1_d_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 {
+        "3dTcorr1D": v_3d_tcorr1_d_outputs,
+    }.get(t)
+
+
+class V3dTcorr1DOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tcorr1_d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output filename prefix."""
+    out_file_: OutputPathType
+    """Output file containing correlations."""
+
+
+def v_3d_tcorr1_d_params(
+    xset: InputPathType,
+    y_1d: InputPathType,
+    ktaub: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    pearson: bool = False,
+    quadrant: bool = False,
+    spearman: bool = False,
+) -> V3dTcorr1DParameters:
+    """
+    Build parameters.
+    
+    Args:
+        xset: 3d+time dataset input.
+        y_1d: 1d time series file input.
+        ktaub: Correlation is the kendall's tau_b correlation coefficient.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        pearson: Correlation is the normal pearson correlation coefficient.
+        quadrant: Correlation is the quadrant correlation coefficient.
+        spearman: Correlation is the spearman (rank) correlation coefficient.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTcorr1D",
+        "ktaub": ktaub,
+        "pearson": pearson,
+        "quadrant": quadrant,
+        "spearman": spearman,
+        "xset": xset,
+        "y_1d": y_1d,
+    }
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3d_tcorr1_d_cargs(
+    params: V3dTcorr1DParameters,
+    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("3dTcorr1D")
+    if params.get("ktaub"):
+        cargs.append("-ktaub")
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("pearson"):
+        cargs.append("-pearson")
+    if params.get("quadrant"):
+        cargs.append("-quadrant")
+    if params.get("spearman"):
+        cargs.append("-spearman" + execution.input_file(params.get("xset")) + execution.input_file(params.get("y_1d")))
+    return cargs
+
+
+def v_3d_tcorr1_d_outputs(
+    params: V3dTcorr1DParameters,
+    execution: Execution,
+) -> V3dTcorr1DOutputs:
+    """
+    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 = V3dTcorr1DOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("xset")).name + "_correlation.nii.gz"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3d_tcorr1_d_execute(
+    params: V3dTcorr1DParameters,
+    execution: Execution,
+) -> V3dTcorr1DOutputs:
+    """
+    Computes the correlation coefficient between each voxel time series in the input
+    3D+time dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorr1DOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tcorr1_d_cargs(params, execution)
+    ret = v_3d_tcorr1_d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tcorr1_d(
+    xset: InputPathType,
+    y_1d: InputPathType,
+    ktaub: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    pearson: bool = False,
+    quadrant: bool = False,
+    spearman: bool = False,
+    runner: Runner | None = None,
+) -> V3dTcorr1DOutputs:
+    """
+    Computes the correlation coefficient between each voxel time series in the input
+    3D+time dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        xset: 3d+time dataset input.
+        y_1d: 1d time series file input.
+        ktaub: Correlation is the kendall's tau_b correlation coefficient.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        pearson: Correlation is the normal pearson correlation coefficient.
+        quadrant: Correlation is the quadrant correlation coefficient.
+        spearman: Correlation is the spearman (rank) correlation coefficient.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorr1DOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCORR1_D_METADATA)
+    params = v_3d_tcorr1_d_params(
+        ktaub=ktaub,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        pearson=pearson,
+        quadrant=quadrant,
+        spearman=spearman,
+        xset=xset,
+        y_1d=y_1d,
+    )
+    return v_3d_tcorr1_d_execute(params, execution)
+
+
+__all__ = [
+    "V3dTcorr1DOutputs",
+    "V3dTcorr1DParameters",
+    "V_3D_TCORR1_D_METADATA",
+    "v_3d_tcorr1_d",
+    "v_3d_tcorr1_d_params",
+]

niwrap_afni/afni/v_3d_tcorr_map.py

@@ -0,0 +1,396 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TCORR_MAP_METADATA = Metadata(
+    id="197d89aea57496a500d08e514c10454efb723051.boutiques",
+    name="3dTcorrMap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTcorrMapParameters = typing.TypedDict('V3dTcorrMapParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTcorrMap"],
+    "input": InputPathType,
+    "seed": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "mean": typing.NotRequired[str | None],
+    "zmean": typing.NotRequired[str | None],
+    "qmean": typing.NotRequired[str | None],
+    "pmean": typing.NotRequired[str | None],
+    "thresh": typing.NotRequired[str | None],
+    "varthresh": typing.NotRequired[str | None],
+    "norm_varthresh": typing.NotRequired[str | None],
+    "corrmap": typing.NotRequired[str | None],
+    "corrmask": bool,
+    "aexpr": typing.NotRequired[str | None],
+    "cexpr": typing.NotRequired[str | None],
+    "sexpr": typing.NotRequired[str | None],
+    "hist": 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 {
+        "3dTcorrMap": v_3d_tcorr_map_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 {
+    }.get(t)
+
+
+class V3dTcorrMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tcorr_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_tcorr_map_params(
+    input_: InputPathType,
+    seed: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    mean: str | None = None,
+    zmean: str | None = None,
+    qmean: str | None = None,
+    pmean: str | None = None,
+    thresh: str | None = None,
+    varthresh: str | None = None,
+    norm_varthresh: str | None = None,
+    corrmap: str | None = None,
+    corrmask: bool = False,
+    aexpr: str | None = None,
+    cexpr: str | None = None,
+    sexpr: str | None = None,
+    hist: str | None = None,
+) -> V3dTcorrMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Read 3D+time dataset 'dd'. This provides the time series to be\
+            correlated en masse. This is a mandatory option.
+        seed: Read 3D+time dataset 'bb'. It correlates the -seed voxel time\
+            series with every voxel in the -input dataset.
+        mask: Read dataset 'mmm' as a voxel mask.
+        automask: Create a mask from the input dataset.
+        mean: Save average correlations into dataset prefix 'pp'.
+        zmean: Save tanh of mean arctanh(correlation) into 'pp'.
+        qmean: Save RMS(correlation) into 'pp'.
+        pmean: Save average of squared positive correlations into 'pp'.
+        thresh: Save the COUNT of how many voxels survived thresholding at\
+            level abs(correlation) >= tt.
+        varthresh: Save the COUNT of how many voxels survive thresholding at\
+            multiple levels abs(correlation) >= tt.
+        norm_varthresh: Like '-VarThresh', but the output counts are\
+            'Normalized'.
+        corrmap: Output at each voxel the entire correlation map, into a\
+            dataset with prefix 'pp'.
+        corrmask: By default, -CorrMap outputs a sub-brick for EACH input\
+            dataset voxel. Eliminates these sub-bricks using this option.
+        aexpr: For each correlation 'r', compute the calc-style expression\
+            'expr', and average these values to get the output that goes into\
+            dataset 'ppp'.
+        cexpr: As in '-Aexpr', but only average together nonzero values\
+            computed by 'expr'.
+        sexpr: As above, but the sum of the expressions is computed rather than\
+            the average.
+        hist: For each voxel, save a histogram of the correlation coefficients\
+            into dataset ppp.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTcorrMap",
+        "input": input_,
+        "automask": automask,
+        "corrmask": corrmask,
+    }
+    if seed is not None:
+        params["seed"] = seed
+    if mask is not None:
+        params["mask"] = mask
+    if mean is not None:
+        params["mean"] = mean
+    if zmean is not None:
+        params["zmean"] = zmean
+    if qmean is not None:
+        params["qmean"] = qmean
+    if pmean is not None:
+        params["pmean"] = pmean
+    if thresh is not None:
+        params["thresh"] = thresh
+    if varthresh is not None:
+        params["varthresh"] = varthresh
+    if norm_varthresh is not None:
+        params["norm_varthresh"] = norm_varthresh
+    if corrmap is not None:
+        params["corrmap"] = corrmap
+    if aexpr is not None:
+        params["aexpr"] = aexpr
+    if cexpr is not None:
+        params["cexpr"] = cexpr
+    if sexpr is not None:
+        params["sexpr"] = sexpr
+    if hist is not None:
+        params["hist"] = hist
+    return params
+
+
+def v_3d_tcorr_map_cargs(
+    params: V3dTcorrMapParameters,
+    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("3dTcorrMap")
+    cargs.append(execution.input_file(params.get("input")))
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            execution.input_file(params.get("seed"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mean") is not None:
+        cargs.extend([
+            "-Mean",
+            params.get("mean")
+        ])
+    if params.get("zmean") is not None:
+        cargs.extend([
+            "-Zmean",
+            params.get("zmean")
+        ])
+    if params.get("qmean") is not None:
+        cargs.extend([
+            "-Qmean",
+            params.get("qmean")
+        ])
+    if params.get("pmean") is not None:
+        cargs.extend([
+            "-Pmean",
+            params.get("pmean")
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "-Thresh",
+            params.get("thresh")
+        ])
+    if params.get("varthresh") is not None:
+        cargs.extend([
+            "-VarThresh",
+            params.get("varthresh")
+        ])
+    if params.get("norm_varthresh") is not None:
+        cargs.extend([
+            "-VarThreshN",
+            params.get("norm_varthresh")
+        ])
+    if params.get("corrmap") is not None:
+        cargs.extend([
+            "-CorrMap",
+            params.get("corrmap")
+        ])
+    if params.get("corrmask"):
+        cargs.append("-CorrMask")
+    if params.get("aexpr") is not None:
+        cargs.extend([
+            "-Aexpr",
+            params.get("aexpr")
+        ])
+    if params.get("cexpr") is not None:
+        cargs.extend([
+            "-Cexpr",
+            params.get("cexpr")
+        ])
+    if params.get("sexpr") is not None:
+        cargs.extend([
+            "-Sexpr",
+            params.get("sexpr")
+        ])
+    if params.get("hist") is not None:
+        cargs.extend([
+            "-Hist",
+            params.get("hist")
+        ])
+    return cargs
+
+
+def v_3d_tcorr_map_outputs(
+    params: V3dTcorrMapParameters,
+    execution: Execution,
+) -> V3dTcorrMapOutputs:
+    """
+    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 = V3dTcorrMapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_tcorr_map_execute(
+    params: V3dTcorrMapParameters,
+    execution: Execution,
+) -> V3dTcorrMapOutputs:
+    """
+    AFNI program to compute correlation maps of input time series data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorrMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tcorr_map_cargs(params, execution)
+    ret = v_3d_tcorr_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tcorr_map(
+    input_: InputPathType,
+    seed: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    mean: str | None = None,
+    zmean: str | None = None,
+    qmean: str | None = None,
+    pmean: str | None = None,
+    thresh: str | None = None,
+    varthresh: str | None = None,
+    norm_varthresh: str | None = None,
+    corrmap: str | None = None,
+    corrmask: bool = False,
+    aexpr: str | None = None,
+    cexpr: str | None = None,
+    sexpr: str | None = None,
+    hist: str | None = None,
+    runner: Runner | None = None,
+) -> V3dTcorrMapOutputs:
+    """
+    AFNI program to compute correlation maps of input time series data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Read 3D+time dataset 'dd'. This provides the time series to be\
+            correlated en masse. This is a mandatory option.
+        seed: Read 3D+time dataset 'bb'. It correlates the -seed voxel time\
+            series with every voxel in the -input dataset.
+        mask: Read dataset 'mmm' as a voxel mask.
+        automask: Create a mask from the input dataset.
+        mean: Save average correlations into dataset prefix 'pp'.
+        zmean: Save tanh of mean arctanh(correlation) into 'pp'.
+        qmean: Save RMS(correlation) into 'pp'.
+        pmean: Save average of squared positive correlations into 'pp'.
+        thresh: Save the COUNT of how many voxels survived thresholding at\
+            level abs(correlation) >= tt.
+        varthresh: Save the COUNT of how many voxels survive thresholding at\
+            multiple levels abs(correlation) >= tt.
+        norm_varthresh: Like '-VarThresh', but the output counts are\
+            'Normalized'.
+        corrmap: Output at each voxel the entire correlation map, into a\
+            dataset with prefix 'pp'.
+        corrmask: By default, -CorrMap outputs a sub-brick for EACH input\
+            dataset voxel. Eliminates these sub-bricks using this option.
+        aexpr: For each correlation 'r', compute the calc-style expression\
+            'expr', and average these values to get the output that goes into\
+            dataset 'ppp'.
+        cexpr: As in '-Aexpr', but only average together nonzero values\
+            computed by 'expr'.
+        sexpr: As above, but the sum of the expressions is computed rather than\
+            the average.
+        hist: For each voxel, save a histogram of the correlation coefficients\
+            into dataset ppp.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorrMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCORR_MAP_METADATA)
+    params = v_3d_tcorr_map_params(
+        input_=input_,
+        seed=seed,
+        mask=mask,
+        automask=automask,
+        mean=mean,
+        zmean=zmean,
+        qmean=qmean,
+        pmean=pmean,
+        thresh=thresh,
+        varthresh=varthresh,
+        norm_varthresh=norm_varthresh,
+        corrmap=corrmap,
+        corrmask=corrmask,
+        aexpr=aexpr,
+        cexpr=cexpr,
+        sexpr=sexpr,
+        hist=hist,
+    )
+    return v_3d_tcorr_map_execute(params, execution)
+
+
+__all__ = [
+    "V3dTcorrMapOutputs",
+    "V3dTcorrMapParameters",
+    "V_3D_TCORR_MAP_METADATA",
+    "v_3d_tcorr_map",
+    "v_3d_tcorr_map_params",
+]