niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_xclust_sim.py

@@ -0,0 +1,370 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_XCLUST_SIM_METADATA = Metadata(
+    id="da8dfc6fd73a07401ddf1667768a4f16b84acebc.boutiques",
+    name="3dXClustSim",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dXclustSimParameters = typing.TypedDict('V3dXclustSimParameters', {
+    "__STYX_TYPE__": typing.Literal["3dXClustSim"],
+    "inset": InputPathType,
+    "insdat": typing.NotRequired[InputPathType | None],
+    "nn": typing.NotRequired[float | None],
+    "sid": typing.NotRequired[float | None],
+    "hpow": typing.NotRequired[list[float] | None],
+    "ncase": typing.NotRequired[list[str] | None],
+    "pthr": typing.NotRequired[list[float] | None],
+    "fpr": typing.NotRequired[float | None],
+    "multiFPR": bool,
+    "minclust": typing.NotRequired[float | None],
+    "local": bool,
+    "global": bool,
+    "nolocal": bool,
+    "noglobal": bool,
+    "splitfrac": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbose": 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 {
+        "3dXClustSim": v_3d_xclust_sim_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 {
+        "3dXClustSim": v_3d_xclust_sim_outputs,
+    }.get(t)
+
+
+class V3dXclustSimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_xclust_sim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_mthresh: OutputPathType | None
+    """Output multi-threshold files for each -ncase input"""
+
+
+def v_3d_xclust_sim_params(
+    inset: InputPathType,
+    insdat: InputPathType | None = None,
+    nn: float | None = None,
+    sid: float | None = None,
+    hpow: list[float] | None = None,
+    ncase: list[str] | None = None,
+    pthr: list[float] | None = None,
+    fpr: float | None = None,
+    multi_fpr: bool = False,
+    minclust: float | None = None,
+    local: bool = False,
+    global_: bool = False,
+    nolocal: bool = False,
+    noglobal: bool = False,
+    splitfrac: float | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+    quiet: bool = False,
+) -> V3dXclustSimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset: Mask sdata file (from 3dtoXdataset or 3dttest++).
+        insdat: Data files in the '.sdat' format.
+        nn: Neighborhood connectivity (1, 2, or 3). Default is 2.
+        sid: Sidedness: 1 (one-sided) or 2 (two-sided). Default is 2.
+        hpow: H power values (can be a subset of 0, 1, 2). Default is 2.
+        ncase: Number of cases with labels. Default is 1 A.
+        pthr: List of p-value thresholds. Default is 0.0100 0.0056 0.0031\
+            0.0018 0.0010.
+        fpr: Set global FPR goal to an integer ff between 2 and 9. Default is\
+            5.
+        multi_fpr: Compute results for multiple FPR goals (2%, 3%, ... 9%).
+        minclust: Minimum cluster size in voxels. Default is 5.
+        local: Do voxel-wise (local) ETAC computations.
+        global_: Do volume-wise (global) ETAC computations.
+        nolocal: Do not perform voxel-wise ETAC computations.
+        noglobal: Do not perform volume-wise ETAC computations.
+        splitfrac: Fraction to split simulations into pieces (0.2 < F < 0.8).
+        prefix: Output filename prefix.
+        verbose: Be more verbose.
+        quiet: Silent mode.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dXClustSim",
+        "inset": inset,
+        "multiFPR": multi_fpr,
+        "local": local,
+        "global": global_,
+        "nolocal": nolocal,
+        "noglobal": noglobal,
+        "verbose": verbose,
+        "quiet": quiet,
+    }
+    if insdat is not None:
+        params["insdat"] = insdat
+    if nn is not None:
+        params["nn"] = nn
+    if sid is not None:
+        params["sid"] = sid
+    if hpow is not None:
+        params["hpow"] = hpow
+    if ncase is not None:
+        params["ncase"] = ncase
+    if pthr is not None:
+        params["pthr"] = pthr
+    if fpr is not None:
+        params["fpr"] = fpr
+    if minclust is not None:
+        params["minclust"] = minclust
+    if splitfrac is not None:
+        params["splitfrac"] = splitfrac
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_xclust_sim_cargs(
+    params: V3dXclustSimParameters,
+    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("3dXClustSim")
+    cargs.append(execution.input_file(params.get("inset")))
+    if params.get("insdat") is not None:
+        cargs.append(execution.input_file(params.get("insdat")))
+    if params.get("nn") is not None:
+        cargs.extend([
+            "-NN",
+            str(params.get("nn"))
+        ])
+    if params.get("sid") is not None:
+        cargs.extend([
+            "-sid",
+            str(params.get("sid"))
+        ])
+    if params.get("hpow") is not None:
+        cargs.extend([
+            "-hpow",
+            *map(str, params.get("hpow"))
+        ])
+    if params.get("ncase") is not None:
+        cargs.extend([
+            "-ncase",
+            *params.get("ncase")
+        ])
+    if params.get("pthr") is not None:
+        cargs.extend([
+            "-pthr",
+            *map(str, params.get("pthr"))
+        ])
+    if params.get("fpr") is not None:
+        cargs.extend([
+            "-FPR",
+            str(params.get("fpr"))
+        ])
+    if params.get("multiFPR"):
+        cargs.append("-multiFPR")
+    if params.get("minclust") is not None:
+        cargs.extend([
+            "-minclust",
+            str(params.get("minclust"))
+        ])
+    if params.get("local"):
+        cargs.append("-local")
+    if params.get("global"):
+        cargs.append("-global")
+    if params.get("nolocal"):
+        cargs.append("-nolocal")
+    if params.get("noglobal"):
+        cargs.append("-noglobal")
+    if params.get("splitfrac") is not None:
+        cargs.extend([
+            "-splitfrac",
+            str(params.get("splitfrac"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_xclust_sim_outputs(
+    params: V3dXclustSimParameters,
+    execution: Execution,
+) -> V3dXclustSimOutputs:
+    """
+    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 = V3dXclustSimOutputs(
+        root=execution.output_file("."),
+        out_mthresh=execution.output_file(params.get("prefix") + ".mthresh.*.nii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_xclust_sim_execute(
+    params: V3dXclustSimParameters,
+    execution: Execution,
+) -> V3dXclustSimOutputs:
+    """
+    ETAC processing tool to find cluster figure of merit (FOM) thresholds.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dXclustSimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_xclust_sim_cargs(params, execution)
+    ret = v_3d_xclust_sim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_xclust_sim(
+    inset: InputPathType,
+    insdat: InputPathType | None = None,
+    nn: float | None = None,
+    sid: float | None = None,
+    hpow: list[float] | None = None,
+    ncase: list[str] | None = None,
+    pthr: list[float] | None = None,
+    fpr: float | None = None,
+    multi_fpr: bool = False,
+    minclust: float | None = None,
+    local: bool = False,
+    global_: bool = False,
+    nolocal: bool = False,
+    noglobal: bool = False,
+    splitfrac: float | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dXclustSimOutputs:
+    """
+    ETAC processing tool to find cluster figure of merit (FOM) thresholds.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset: Mask sdata file (from 3dtoXdataset or 3dttest++).
+        insdat: Data files in the '.sdat' format.
+        nn: Neighborhood connectivity (1, 2, or 3). Default is 2.
+        sid: Sidedness: 1 (one-sided) or 2 (two-sided). Default is 2.
+        hpow: H power values (can be a subset of 0, 1, 2). Default is 2.
+        ncase: Number of cases with labels. Default is 1 A.
+        pthr: List of p-value thresholds. Default is 0.0100 0.0056 0.0031\
+            0.0018 0.0010.
+        fpr: Set global FPR goal to an integer ff between 2 and 9. Default is\
+            5.
+        multi_fpr: Compute results for multiple FPR goals (2%, 3%, ... 9%).
+        minclust: Minimum cluster size in voxels. Default is 5.
+        local: Do voxel-wise (local) ETAC computations.
+        global_: Do volume-wise (global) ETAC computations.
+        nolocal: Do not perform voxel-wise ETAC computations.
+        noglobal: Do not perform volume-wise ETAC computations.
+        splitfrac: Fraction to split simulations into pieces (0.2 < F < 0.8).
+        prefix: Output filename prefix.
+        verbose: Be more verbose.
+        quiet: Silent mode.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dXclustSimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_XCLUST_SIM_METADATA)
+    params = v_3d_xclust_sim_params(
+        inset=inset,
+        insdat=insdat,
+        nn=nn,
+        sid=sid,
+        hpow=hpow,
+        ncase=ncase,
+        pthr=pthr,
+        fpr=fpr,
+        multi_fpr=multi_fpr,
+        minclust=minclust,
+        local=local,
+        global_=global_,
+        nolocal=nolocal,
+        noglobal=noglobal,
+        splitfrac=splitfrac,
+        prefix=prefix,
+        verbose=verbose,
+        quiet=quiet,
+    )
+    return v_3d_xclust_sim_execute(params, execution)
+
+
+__all__ = [
+    "V3dXclustSimOutputs",
+    "V3dXclustSimParameters",
+    "V_3D_XCLUST_SIM_METADATA",
+    "v_3d_xclust_sim",
+    "v_3d_xclust_sim_params",
+]

niwrap_afni/afni/v_3d_xyzcat.py

@@ -0,0 +1,216 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_XYZCAT_METADATA = Metadata(
+    id="9d5a52a8f23a424216d7f4d255a606bf371620ee.boutiques",
+    name="3dXYZcat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dXyzcatParameters = typing.TypedDict('V3dXyzcatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dXYZcat"],
+    "direction": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "datasets": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dXYZcat": v_3d_xyzcat_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 {
+        "3dXYZcat": v_3d_xyzcat_outputs,
+    }.get(t)
+
+
+class V3dXyzcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_xyzcat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brainfile: OutputPathType | None
+    """Output concatenated dataset."""
+    output_headerfile: OutputPathType | None
+    """Output concatenated dataset header."""
+
+
+def v_3d_xyzcat_params(
+    datasets: list[InputPathType],
+    direction: str | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+) -> V3dXyzcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: Input datasets to concatenate.
+        direction: Catenate along direction 'Q' (X, Y, Z, or their synonyms I,\
+            J, K).
+        prefix: Use 'pname' for the output dataset prefix name.
+        verbose: Print out some verbositiness as the program proceeds.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dXYZcat",
+        "verbose": verbose,
+        "datasets": datasets,
+    }
+    if direction is not None:
+        params["direction"] = direction
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_xyzcat_cargs(
+    params: V3dXyzcatParameters,
+    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("3dXYZcat")
+    if params.get("direction") is not None:
+        cargs.extend([
+            "-dir",
+            params.get("direction")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    return cargs
+
+
+def v_3d_xyzcat_outputs(
+    params: V3dXyzcatParameters,
+    execution: Execution,
+) -> V3dXyzcatOutputs:
+    """
+    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 = V3dXyzcatOutputs(
+        root=execution.output_file("."),
+        output_brainfile=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_headerfile=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_xyzcat_execute(
+    params: V3dXyzcatParameters,
+    execution: Execution,
+) -> V3dXyzcatOutputs:
+    """
+    Catenates datasets spatially.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dXyzcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_xyzcat_cargs(params, execution)
+    ret = v_3d_xyzcat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_xyzcat(
+    datasets: list[InputPathType],
+    direction: str | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> V3dXyzcatOutputs:
+    """
+    Catenates datasets spatially.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: Input datasets to concatenate.
+        direction: Catenate along direction 'Q' (X, Y, Z, or their synonyms I,\
+            J, K).
+        prefix: Use 'pname' for the output dataset prefix name.
+        verbose: Print out some verbositiness as the program proceeds.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dXyzcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_XYZCAT_METADATA)
+    params = v_3d_xyzcat_params(
+        direction=direction,
+        prefix=prefix,
+        verbose=verbose,
+        datasets=datasets,
+    )
+    return v_3d_xyzcat_execute(params, execution)
+
+
+__all__ = [
+    "V3dXyzcatOutputs",
+    "V3dXyzcatParameters",
+    "V_3D_XYZCAT_METADATA",
+    "v_3d_xyzcat",
+    "v_3d_xyzcat_params",
+]