niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tcorrelate.py

@@ -0,0 +1,368 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TCORRELATE_METADATA = Metadata(
+    id="a874b3865df8702baf89b243d1e11b051abda5bf.boutiques",
+    name="3dTcorrelate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTcorrelateParameters = typing.TypedDict('V3dTcorrelateParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTcorrelate"],
+    "xset": InputPathType,
+    "yset": InputPathType,
+    "pearson": bool,
+    "spearman": bool,
+    "quadrant": bool,
+    "ktaub": bool,
+    "covariance": bool,
+    "partial": typing.NotRequired[InputPathType | None],
+    "ycoef": bool,
+    "fisher": bool,
+    "polort": typing.NotRequired[int | None],
+    "ort": typing.NotRequired[InputPathType | None],
+    "autoclip": bool,
+    "automask": bool,
+    "zcensor": bool,
+    "prefix": 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 {
+        "3dTcorrelate": v_3d_tcorrelate_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 {
+        "3dTcorrelate": v_3d_tcorrelate_outputs,
+    }.get(t)
+
+
+class V3dTcorrelateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tcorrelate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output image file name."""
+
+
+def v_3d_tcorrelate_params(
+    xset: InputPathType,
+    yset: InputPathType,
+    pearson: bool = False,
+    spearman: bool = False,
+    quadrant: bool = False,
+    ktaub: bool = False,
+    covariance: bool = False,
+    partial: InputPathType | None = None,
+    ycoef: bool = False,
+    fisher: bool = False,
+    polort: int | None = None,
+    ort: InputPathType | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    zcensor: bool = False,
+    prefix: str | None = None,
+) -> V3dTcorrelateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        xset: Input xset.
+        yset: Input yset.
+        pearson: Correlation is the normal pearson correlation coefficient.
+        spearman: Correlation is the Spearman (rank) correlation coefficient.
+        quadrant: Correlation is the quadrant coefficient.
+        ktaub: Correlation is Kendall's tau_b coefficient. For continuous or\
+            finely discretized data, tau_b and rank correlation are nearly\
+            equivalent.
+        covariance: Covariance instead of correlation. That would be Pearson\
+            correlation without scaling by the product of the standard deviations.
+        partial: Partial Pearson's correlation of X & Y, adjusting for Z (the\
+            dataset provided here).
+        ycoef: Least squares coefficient that best fits y(t) to x(t), after\
+            detrending. That is, if yd(t) is the detrended y(t) and xd(t) is the\
+            detrended x(t), then the ycoef value is from the OLSQ fit to xd(t) =\
+            ycoef & y(t) + error.
+        fisher: Apply the Fisher (inverse hyperbolic tangent) transformation to\
+            correlation results. Does not make sense with ktaub, covariance, or\
+            ycoef.
+        polort: Remove polynomial trend of order m. Using m=-1 mean no\
+            detrending; this is only useful fro data that has been preprocessed.
+        ort: A 1D file. Also detrend using the columbs of the 1D file provided\
+            here. Only one -ort option can be given, so if you would like to use\
+            more than one, create a temporary file using 1dcat.
+        autoclip: Clip off low-intensity regions in the two datasets, so that\
+            the correlation is only computed between high-intensity (presumably\
+            brain) voxels. The intensity level is determined the same way that\
+            3dClipLevel works.
+        automask: Clip off low-intensity regions in the two datasets, so that\
+            the correlation is only computed between high-intensity (presumably\
+            brain) voxels. The intensity level is determined the same way that\
+            3dClipLevel works.
+        zcensor: Omit (censor out) any time points where the xset volume is all\
+            zero OR where the yset volume is all zero (in mask). Please note that\
+            using -zcensor with any detrending is unlikely to be useful.
+        prefix: Save output into a dataset with this prefix.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTcorrelate",
+        "xset": xset,
+        "yset": yset,
+        "pearson": pearson,
+        "spearman": spearman,
+        "quadrant": quadrant,
+        "ktaub": ktaub,
+        "covariance": covariance,
+        "ycoef": ycoef,
+        "fisher": fisher,
+        "autoclip": autoclip,
+        "automask": automask,
+        "zcensor": zcensor,
+    }
+    if partial is not None:
+        params["partial"] = partial
+    if polort is not None:
+        params["polort"] = polort
+    if ort is not None:
+        params["ort"] = ort
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_tcorrelate_cargs(
+    params: V3dTcorrelateParameters,
+    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("3dTcorrelate")
+    cargs.append(execution.input_file(params.get("xset")))
+    cargs.append(execution.input_file(params.get("yset")))
+    if params.get("pearson"):
+        cargs.append("-pearson")
+    if params.get("spearman"):
+        cargs.append("-spearman")
+    if params.get("quadrant"):
+        cargs.append("-quadrant")
+    if params.get("ktaub"):
+        cargs.append("-ktaub")
+    if params.get("covariance"):
+        cargs.append("-covariance")
+    if params.get("partial") is not None:
+        cargs.extend([
+            "-partial",
+            execution.input_file(params.get("partial"))
+        ])
+    if params.get("ycoef"):
+        cargs.append("-ycoef")
+    if params.get("fisher"):
+        cargs.append("-Fisher")
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("ort") is not None:
+        cargs.extend([
+            "-ort",
+            execution.input_file(params.get("ort"))
+        ])
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("zcensor"):
+        cargs.append("-zcensor")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3d_tcorrelate_outputs(
+    params: V3dTcorrelateParameters,
+    execution: Execution,
+) -> V3dTcorrelateOutputs:
+    """
+    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 = V3dTcorrelateOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tcorrelate_execute(
+    params: V3dTcorrelateParameters,
+    execution: Execution,
+) -> V3dTcorrelateOutputs:
+    """
+    3dTcorrelate. Computes the correlation coefficient between corresponding voxel
+    time series in two input 3D+time datasets 'xset' and 'yset'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorrelateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tcorrelate_cargs(params, execution)
+    ret = v_3d_tcorrelate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tcorrelate(
+    xset: InputPathType,
+    yset: InputPathType,
+    pearson: bool = False,
+    spearman: bool = False,
+    quadrant: bool = False,
+    ktaub: bool = False,
+    covariance: bool = False,
+    partial: InputPathType | None = None,
+    ycoef: bool = False,
+    fisher: bool = False,
+    polort: int | None = None,
+    ort: InputPathType | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    zcensor: bool = False,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dTcorrelateOutputs:
+    """
+    3dTcorrelate. Computes the correlation coefficient between corresponding voxel
+    time series in two input 3D+time datasets 'xset' and 'yset'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        xset: Input xset.
+        yset: Input yset.
+        pearson: Correlation is the normal pearson correlation coefficient.
+        spearman: Correlation is the Spearman (rank) correlation coefficient.
+        quadrant: Correlation is the quadrant coefficient.
+        ktaub: Correlation is Kendall's tau_b coefficient. For continuous or\
+            finely discretized data, tau_b and rank correlation are nearly\
+            equivalent.
+        covariance: Covariance instead of correlation. That would be Pearson\
+            correlation without scaling by the product of the standard deviations.
+        partial: Partial Pearson's correlation of X & Y, adjusting for Z (the\
+            dataset provided here).
+        ycoef: Least squares coefficient that best fits y(t) to x(t), after\
+            detrending. That is, if yd(t) is the detrended y(t) and xd(t) is the\
+            detrended x(t), then the ycoef value is from the OLSQ fit to xd(t) =\
+            ycoef & y(t) + error.
+        fisher: Apply the Fisher (inverse hyperbolic tangent) transformation to\
+            correlation results. Does not make sense with ktaub, covariance, or\
+            ycoef.
+        polort: Remove polynomial trend of order m. Using m=-1 mean no\
+            detrending; this is only useful fro data that has been preprocessed.
+        ort: A 1D file. Also detrend using the columbs of the 1D file provided\
+            here. Only one -ort option can be given, so if you would like to use\
+            more than one, create a temporary file using 1dcat.
+        autoclip: Clip off low-intensity regions in the two datasets, so that\
+            the correlation is only computed between high-intensity (presumably\
+            brain) voxels. The intensity level is determined the same way that\
+            3dClipLevel works.
+        automask: Clip off low-intensity regions in the two datasets, so that\
+            the correlation is only computed between high-intensity (presumably\
+            brain) voxels. The intensity level is determined the same way that\
+            3dClipLevel works.
+        zcensor: Omit (censor out) any time points where the xset volume is all\
+            zero OR where the yset volume is all zero (in mask). Please note that\
+            using -zcensor with any detrending is unlikely to be useful.
+        prefix: Save output into a dataset with this prefix.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcorrelateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCORRELATE_METADATA)
+    params = v_3d_tcorrelate_params(
+        xset=xset,
+        yset=yset,
+        pearson=pearson,
+        spearman=spearman,
+        quadrant=quadrant,
+        ktaub=ktaub,
+        covariance=covariance,
+        partial=partial,
+        ycoef=ycoef,
+        fisher=fisher,
+        polort=polort,
+        ort=ort,
+        autoclip=autoclip,
+        automask=automask,
+        zcensor=zcensor,
+        prefix=prefix,
+    )
+    return v_3d_tcorrelate_execute(params, execution)
+
+
+__all__ = [
+    "V3dTcorrelateOutputs",
+    "V3dTcorrelateParameters",
+    "V_3D_TCORRELATE_METADATA",
+    "v_3d_tcorrelate",
+    "v_3d_tcorrelate_params",
+]

niwrap_afni/afni/v_3d_tfilter.py

@@ -0,0 +1,203 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TFILTER_METADATA = Metadata(
+    id="4735e83a23f97826ec3c39f708b0bfaeaff9f5e9.boutiques",
+    name="3dTfilter",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTfilterParameters = typing.TypedDict('V3dTfilterParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTfilter"],
+    "inputdataset": InputPathType,
+    "outputdataset": str,
+    "filters": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTfilter": v_3d_tfilter_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 {
+        "3dTfilter": v_3d_tfilter_outputs,
+    }.get(t)
+
+
+class V3dTfilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tfilter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Filtered output dataset"""
+
+
+def v_3d_tfilter_params(
+    inputdataset: InputPathType,
+    outputdataset: str,
+    filters: list[str],
+) -> V3dTfilterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inputdataset: Input dataset.
+        outputdataset: Output dataset.
+        filters: Filter function(s) to apply.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTfilter",
+        "inputdataset": inputdataset,
+        "outputdataset": outputdataset,
+        "filters": filters,
+    }
+    return params
+
+
+def v_3d_tfilter_cargs(
+    params: V3dTfilterParameters,
+    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("3dTfilter")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("inputdataset"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("outputdataset")
+    ])
+    cargs.extend([
+        "-filter",
+        *params.get("filters")
+    ])
+    return cargs
+
+
+def v_3d_tfilter_outputs(
+    params: V3dTfilterParameters,
+    execution: Execution,
+) -> V3dTfilterOutputs:
+    """
+    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 = V3dTfilterOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("outputdataset")),
+    )
+    return ret
+
+
+def v_3d_tfilter_execute(
+    params: V3dTfilterParameters,
+    execution: Execution,
+) -> V3dTfilterOutputs:
+    """
+    3dTfilter filters the time series in each voxel according to the user-specified
+    filter functions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTfilterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tfilter_cargs(params, execution)
+    ret = v_3d_tfilter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tfilter(
+    inputdataset: InputPathType,
+    outputdataset: str,
+    filters: list[str],
+    runner: Runner | None = None,
+) -> V3dTfilterOutputs:
+    """
+    3dTfilter filters the time series in each voxel according to the user-specified
+    filter functions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inputdataset: Input dataset.
+        outputdataset: Output dataset.
+        filters: Filter function(s) to apply.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTfilterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TFILTER_METADATA)
+    params = v_3d_tfilter_params(
+        inputdataset=inputdataset,
+        outputdataset=outputdataset,
+        filters=filters,
+    )
+    return v_3d_tfilter_execute(params, execution)
+
+
+__all__ = [
+    "V3dTfilterOutputs",
+    "V3dTfilterParameters",
+    "V_3D_TFILTER_METADATA",
+    "v_3d_tfilter",
+    "v_3d_tfilter_params",
+]