niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_friedman.py

@@ -0,0 +1,226 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_FRIEDMAN_METADATA = Metadata(
+    id="39739dbe60149a8c929fe468d57b937cc221945c.boutiques",
+    name="3dFriedman",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dFriedmanParameters = typing.TypedDict('V3dFriedmanParameters', {
+    "__STYX_TYPE__": typing.Literal["3dFriedman"],
+    "levels": int,
+    "datasets": list[InputPathType],
+    "workmem": typing.NotRequired[int | None],
+    "voxel_num": typing.NotRequired[int | None],
+    "output_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dFriedman": v_3d_friedman_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 {
+        "3dFriedman": v_3d_friedman_outputs,
+    }.get(t)
+
+
+class V3dFriedmanOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_friedman(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Friedman statistics output file"""
+
+
+def v_3d_friedman_params(
+    levels: int,
+    datasets: list[InputPathType],
+    output_prefix: str,
+    workmem: int | None = None,
+    voxel_num: int | None = None,
+) -> V3dFriedmanParameters:
+    """
+    Build parameters.
+    
+    Args:
+        levels: Number of treatments.
+        datasets: Data sets for each treatment.
+        output_prefix: Prefix for the output files.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel_num: Screen output for a specific voxel number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dFriedman",
+        "levels": levels,
+        "datasets": datasets,
+        "output_prefix": output_prefix,
+    }
+    if workmem is not None:
+        params["workmem"] = workmem
+    if voxel_num is not None:
+        params["voxel_num"] = voxel_num
+    return params
+
+
+def v_3d_friedman_cargs(
+    params: V3dFriedmanParameters,
+    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("3dFriedman")
+    cargs.append(str(params.get("levels")))
+    cargs.extend([
+        "-dset",
+        *[execution.input_file(f) for f in params.get("datasets")]
+    ])
+    if params.get("workmem") is not None:
+        cargs.extend([
+            "-workmem",
+            str(params.get("workmem"))
+        ])
+    if params.get("voxel_num") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel_num"))
+        ])
+    cargs.extend([
+        "-out",
+        params.get("output_prefix")
+    ])
+    return cargs
+
+
+def v_3d_friedman_outputs(
+    params: V3dFriedmanParameters,
+    execution: Execution,
+) -> V3dFriedmanOutputs:
+    """
+    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 = V3dFriedmanOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + "*"),
+    )
+    return ret
+
+
+def v_3d_friedman_execute(
+    params: V3dFriedmanParameters,
+    execution: Execution,
+) -> V3dFriedmanOutputs:
+    """
+    Performs nonparametric Friedman test for randomized complete block design
+    experiments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dFriedmanOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_friedman_cargs(params, execution)
+    ret = v_3d_friedman_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_friedman(
+    levels: int,
+    datasets: list[InputPathType],
+    output_prefix: str,
+    workmem: int | None = None,
+    voxel_num: int | None = None,
+    runner: Runner | None = None,
+) -> V3dFriedmanOutputs:
+    """
+    Performs nonparametric Friedman test for randomized complete block design
+    experiments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        levels: Number of treatments.
+        datasets: Data sets for each treatment.
+        output_prefix: Prefix for the output files.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel_num: Screen output for a specific voxel number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dFriedmanOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FRIEDMAN_METADATA)
+    params = v_3d_friedman_params(
+        levels=levels,
+        datasets=datasets,
+        workmem=workmem,
+        voxel_num=voxel_num,
+        output_prefix=output_prefix,
+    )
+    return v_3d_friedman_execute(params, execution)
+
+
+__all__ = [
+    "V3dFriedmanOutputs",
+    "V3dFriedmanParameters",
+    "V_3D_FRIEDMAN_METADATA",
+    "v_3d_friedman",
+    "v_3d_friedman_params",
+]

niwrap_afni/afni/v_3d_fwhmx.py

@@ -0,0 +1,321 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_FWHMX_METADATA = Metadata(
+    id="b5663599ab067623b1ae3ff871361e65e6cc2740.boutiques",
+    name="3dFWHMx",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dFwhmxParameters = typing.TypedDict('V3dFwhmxParameters', {
+    "__STYX_TYPE__": typing.Literal["3dFWHMx"],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "demed": bool,
+    "unif": bool,
+    "detrend": typing.NotRequired[float | None],
+    "detprefix": typing.NotRequired[str | None],
+    "geom": bool,
+    "arith": bool,
+    "combine": bool,
+    "out": typing.NotRequired[str | None],
+    "compat": bool,
+    "acf": typing.NotRequired[str | None],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dFWHMx": v_3d_fwhmx_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 {
+        "3dFWHMx": v_3d_fwhmx_outputs,
+    }.get(t)
+
+
+class V3dFwhmxOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_fwhmx(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output file containing FWHM/ACF estimates"""
+    detrended_dataset: OutputPathType | None
+    """Detrended dataset file"""
+
+
+def v_3d_fwhmx_params(
+    infile: InputPathType,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    demed: bool = False,
+    unif: bool = False,
+    detrend: float | None = None,
+    detprefix: str | None = None,
+    geom: bool = False,
+    arith: bool = False,
+    combine: bool = False,
+    out: str | None = None,
+    compat: bool = False,
+    acf: str | None = None,
+) -> V3dFwhmxParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input dataset.
+        mask: Use only voxels that are nonzero in dataset 'mmm'.
+        automask: Compute a mask from THIS dataset.
+        demed: if the input dataset has more than one sub-brick then subtract\
+            the median of each voxel's time series before processing FWHM.
+        unif: Normalize each voxel's time series to have the same MAD before\
+            processing FWHM, implies -demed.
+        detrend: Detrend to order 'q'. If q is not given, the program picks\
+            q=NT/30; -detrend disables -demed, and includes -unif.
+        detprefix: Save the detrended file into a dataset with prefix 'd'.
+        geom: Compute the final estimate as the geometric mean.
+        arith: Compute the final estimate as the arithmetic mean.
+        combine: Combine the final measurements along each axis into one result.
+        out: Write output to file 'ttt' (3 columns of numbers). If not given,\
+            the sub-brick outputs are not written. Use '-out -' to write to stdout,\
+            if desired.
+        compat: Be compatible with the older 3dFWHM.
+        acf: Compute the spatial autocorrelation of the data as a function of\
+            radius, then fit that to a model and output the model parameters.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dFWHMx",
+        "automask": automask,
+        "demed": demed,
+        "unif": unif,
+        "geom": geom,
+        "arith": arith,
+        "combine": combine,
+        "compat": compat,
+        "infile": infile,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if detrend is not None:
+        params["detrend"] = detrend
+    if detprefix is not None:
+        params["detprefix"] = detprefix
+    if out is not None:
+        params["out"] = out
+    if acf is not None:
+        params["acf"] = acf
+    return params
+
+
+def v_3d_fwhmx_cargs(
+    params: V3dFwhmxParameters,
+    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("3dFWHMx")
+    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("demed"):
+        cargs.append("-demed")
+    if params.get("unif"):
+        cargs.append("-unif")
+    if params.get("detrend") is not None:
+        cargs.extend([
+            "-detrend",
+            str(params.get("detrend"))
+        ])
+    if params.get("detprefix") is not None:
+        cargs.extend([
+            "-detprefix",
+            params.get("detprefix")
+        ])
+    if params.get("geom"):
+        cargs.append("-geom")
+    if params.get("arith"):
+        cargs.append("-arith")
+    if params.get("combine"):
+        cargs.append("-combine")
+    if params.get("out") is not None:
+        cargs.extend([
+            "-out",
+            params.get("out")
+        ])
+    if params.get("compat"):
+        cargs.append("-compat")
+    if params.get("acf") is not None:
+        cargs.extend([
+            "-acf",
+            params.get("acf")
+        ])
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v_3d_fwhmx_outputs(
+    params: V3dFwhmxParameters,
+    execution: Execution,
+) -> V3dFwhmxOutputs:
+    """
+    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 = V3dFwhmxOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("out") + ".1D") if (params.get("out") is not None) else None,
+        detrended_dataset=execution.output_file(params.get("detprefix") + ".nii.gz") if (params.get("detprefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_fwhmx_execute(
+    params: V3dFwhmxParameters,
+    execution: Execution,
+) -> V3dFwhmxOutputs:
+    """
+    Compute Full Width at Half Maximum (FWHM) for FMRI datasets using
+    AutoCorrelation Function (ACF).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dFwhmxOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_fwhmx_cargs(params, execution)
+    ret = v_3d_fwhmx_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_fwhmx(
+    infile: InputPathType,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    demed: bool = False,
+    unif: bool = False,
+    detrend: float | None = None,
+    detprefix: str | None = None,
+    geom: bool = False,
+    arith: bool = False,
+    combine: bool = False,
+    out: str | None = None,
+    compat: bool = False,
+    acf: str | None = None,
+    runner: Runner | None = None,
+) -> V3dFwhmxOutputs:
+    """
+    Compute Full Width at Half Maximum (FWHM) for FMRI datasets using
+    AutoCorrelation Function (ACF).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input dataset.
+        mask: Use only voxels that are nonzero in dataset 'mmm'.
+        automask: Compute a mask from THIS dataset.
+        demed: if the input dataset has more than one sub-brick then subtract\
+            the median of each voxel's time series before processing FWHM.
+        unif: Normalize each voxel's time series to have the same MAD before\
+            processing FWHM, implies -demed.
+        detrend: Detrend to order 'q'. If q is not given, the program picks\
+            q=NT/30; -detrend disables -demed, and includes -unif.
+        detprefix: Save the detrended file into a dataset with prefix 'd'.
+        geom: Compute the final estimate as the geometric mean.
+        arith: Compute the final estimate as the arithmetic mean.
+        combine: Combine the final measurements along each axis into one result.
+        out: Write output to file 'ttt' (3 columns of numbers). If not given,\
+            the sub-brick outputs are not written. Use '-out -' to write to stdout,\
+            if desired.
+        compat: Be compatible with the older 3dFWHM.
+        acf: Compute the spatial autocorrelation of the data as a function of\
+            radius, then fit that to a model and output the model parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dFwhmxOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FWHMX_METADATA)
+    params = v_3d_fwhmx_params(
+        mask=mask,
+        automask=automask,
+        demed=demed,
+        unif=unif,
+        detrend=detrend,
+        detprefix=detprefix,
+        geom=geom,
+        arith=arith,
+        combine=combine,
+        out=out,
+        compat=compat,
+        acf=acf,
+        infile=infile,
+    )
+    return v_3d_fwhmx_execute(params, execution)
+
+
+__all__ = [
+    "V3dFwhmxOutputs",
+    "V3dFwhmxParameters",
+    "V_3D_FWHMX_METADATA",
+    "v_3d_fwhmx",
+    "v_3d_fwhmx_params",
+]