niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_group_in_corr.py

@@ -0,0 +1,484 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_GROUP_IN_CORR_METADATA = Metadata(
+    id="c0af4482aaede4b9a649dd7f0c784cb42a8b0eb7.boutiques",
+    name="3dGroupInCorr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dGroupInCorrParameters = typing.TypedDict('V3dGroupInCorrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dGroupInCorr"],
+    "set_a": InputPathType,
+    "set_b": typing.NotRequired[InputPathType | None],
+    "apair": bool,
+    "label_a": typing.NotRequired[str | None],
+    "label_b": typing.NotRequired[str | None],
+    "pooled": bool,
+    "unpooled": bool,
+    "paired": bool,
+    "nosix": bool,
+    "covariates_file": typing.NotRequired[InputPathType | None],
+    "center": typing.NotRequired[str | None],
+    "seed_radius": typing.NotRequired[float | None],
+    "sendall": bool,
+    "donocov": bool,
+    "dospcov": bool,
+    "cluster": typing.NotRequired[str | None],
+    "read": bool,
+    "ztest": bool,
+    "ah": typing.NotRequired[str | None],
+    "port_offset": typing.NotRequired[float | None],
+    "port_offset_quiet": typing.NotRequired[float | None],
+    "port_bloc": typing.NotRequired[float | None],
+    "suma": bool,
+    "quiet": bool,
+    "verbose": bool,
+    "very_verbose": bool,
+    "debug": bool,
+    "batch": 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 {
+        "3dGroupInCorr": v_3d_group_in_corr_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 {
+        "3dGroupInCorr": v_3d_group_in_corr_outputs,
+    }.get(t)
+
+
+class V3dGroupInCorrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_group_in_corr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Results from analysis"""
+
+
+def v_3d_group_in_corr_params(
+    set_a: InputPathType,
+    set_b: InputPathType | None = None,
+    apair: bool = False,
+    label_a: str | None = None,
+    label_b: str | None = None,
+    pooled: bool = False,
+    unpooled: bool = False,
+    paired: bool = False,
+    nosix: bool = False,
+    covariates_file: InputPathType | None = None,
+    center: str | None = None,
+    seed_radius: float | None = None,
+    sendall: bool = False,
+    donocov: bool = False,
+    dospcov: bool = False,
+    cluster: str | None = None,
+    read: bool = False,
+    ztest: bool = False,
+    ah: str | None = None,
+    port_offset: float | None = None,
+    port_offset_quiet: float | None = None,
+    port_bloc: float | None = None,
+    suma: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
+    very_verbose: bool = False,
+    debug: bool = False,
+    batch: str | None = None,
+) -> V3dGroupInCorrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        set_a: Setup file describing the first dataset collection.
+        set_b: Setup file describing the second dataset collection for\
+            two-sample t-test analysis.
+        apair: Use -setA collection again but with different seed locations;\
+            produce paired t-test.
+        label_a: Label for sub-bricks corresponding to setA.
+        label_b: Label for sub-bricks corresponding to setB.
+        pooled: Use pooled variance estimator for two-sample un-paired t-test.
+        unpooled: Use unpooled variance estimator for two-sample un-paired\
+            t-test.
+        paired: Use a two-sample paired t-test.
+        nosix: Suppress the individual 1-sample t-tests and only return the\
+            difference 2-sample t-test.
+        covariates_file: File containing covariate values for each dataset.
+        center: Option for centering covariates.
+        seed_radius: Radius for seed voxel time series averaging (mm).
+        sendall: Send all individual subject results to AFNI along with group\
+            statistics.
+        donocov: Compute results both with and without covariates.
+        dospcov: Compute Spearman (rank) correlation coefficient of subject\
+            correlation results vs each covariate.
+        cluster: Input results from a 3dClustSim run to interface with AFNI.
+        read: Force program to read data into memory instead of memory mapping.
+        ztest: Debugging option to test if input data is all zero.
+        ah: Connect to AFNI/SUMA on a remote host.
+        port_offset: Provide a port offset.
+        port_offset_quiet: Provide a port offset, with less verbose output.
+        port_bloc: Provide a port offset bloc.
+        suma: Talk to SUMA instead of AFNI.
+        quiet: Suppress informational messages.
+        verbose: Print extra informational messages.
+        very_verbose: Print even more detailed informational messages.
+        debug: Enable internal testing.
+        batch: Run program in batch mode with specified METHOD and command\
+            file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dGroupInCorr",
+        "set_a": set_a,
+        "apair": apair,
+        "pooled": pooled,
+        "unpooled": unpooled,
+        "paired": paired,
+        "nosix": nosix,
+        "sendall": sendall,
+        "donocov": donocov,
+        "dospcov": dospcov,
+        "read": read,
+        "ztest": ztest,
+        "suma": suma,
+        "quiet": quiet,
+        "verbose": verbose,
+        "very_verbose": very_verbose,
+        "debug": debug,
+    }
+    if set_b is not None:
+        params["set_b"] = set_b
+    if label_a is not None:
+        params["label_a"] = label_a
+    if label_b is not None:
+        params["label_b"] = label_b
+    if covariates_file is not None:
+        params["covariates_file"] = covariates_file
+    if center is not None:
+        params["center"] = center
+    if seed_radius is not None:
+        params["seed_radius"] = seed_radius
+    if cluster is not None:
+        params["cluster"] = cluster
+    if ah is not None:
+        params["ah"] = ah
+    if port_offset is not None:
+        params["port_offset"] = port_offset
+    if port_offset_quiet is not None:
+        params["port_offset_quiet"] = port_offset_quiet
+    if port_bloc is not None:
+        params["port_bloc"] = port_bloc
+    if batch is not None:
+        params["batch"] = batch
+    return params
+
+
+def v_3d_group_in_corr_cargs(
+    params: V3dGroupInCorrParameters,
+    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("3dGroupInCorr")
+    cargs.extend([
+        "-setA",
+        execution.input_file(params.get("set_a"))
+    ])
+    if params.get("set_b") is not None:
+        cargs.extend([
+            "-setB",
+            execution.input_file(params.get("set_b"))
+        ])
+    if params.get("apair"):
+        cargs.append("-Apair")
+    if params.get("label_a") is not None:
+        cargs.extend([
+            "-labelA",
+            params.get("label_a")
+        ])
+    if params.get("label_b") is not None:
+        cargs.extend([
+            "-labelB",
+            params.get("label_b")
+        ])
+    if params.get("pooled"):
+        cargs.append("-pooled")
+    if params.get("unpooled"):
+        cargs.append("-unpooled")
+    if params.get("paired"):
+        cargs.append("-paired")
+    if params.get("nosix"):
+        cargs.append("-nosix")
+    if params.get("covariates_file") is not None:
+        cargs.extend([
+            "-covariates",
+            execution.input_file(params.get("covariates_file"))
+        ])
+    if params.get("center") is not None:
+        cargs.extend([
+            "-center",
+            params.get("center")
+        ])
+    if params.get("seed_radius") is not None:
+        cargs.extend([
+            "-seedrad",
+            str(params.get("seed_radius"))
+        ])
+    if params.get("sendall"):
+        cargs.append("-sendall")
+    if params.get("donocov"):
+        cargs.append("-donocov")
+    if params.get("dospcov"):
+        cargs.append("-dospcov")
+    if params.get("cluster") is not None:
+        cargs.extend([
+            "-clust",
+            params.get("cluster")
+        ])
+    if params.get("read"):
+        cargs.append("-read")
+    if params.get("ztest"):
+        cargs.append("-ztest")
+    if params.get("ah") is not None:
+        cargs.extend([
+            "-ah",
+            params.get("ah")
+        ])
+    if params.get("port_offset") is not None:
+        cargs.extend([
+            "-np",
+            str(params.get("port_offset"))
+        ])
+    if params.get("port_offset_quiet") is not None:
+        cargs.extend([
+            "-npq",
+            str(params.get("port_offset_quiet"))
+        ])
+    if params.get("port_bloc") is not None:
+        cargs.extend([
+            "-npb",
+            str(params.get("port_bloc"))
+        ])
+    if params.get("suma"):
+        cargs.append("-suma")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("very_verbose"):
+        cargs.append("-VERB")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("batch") is not None:
+        cargs.extend([
+            "-batch",
+            params.get("batch")
+        ])
+    return cargs
+
+
+def v_3d_group_in_corr_outputs(
+    params: V3dGroupInCorrParameters,
+    execution: Execution,
+) -> V3dGroupInCorrOutputs:
+    """
+    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 = V3dGroupInCorrOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(pathlib.Path(params.get("set_a")).name + ".results.nii"),
+    )
+    return ret
+
+
+def v_3d_group_in_corr_execute(
+    params: V3dGroupInCorrParameters,
+    execution: Execution,
+) -> V3dGroupInCorrOutputs:
+    """
+    Functional connectivity analysis in group of subjects.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dGroupInCorrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_group_in_corr_cargs(params, execution)
+    ret = v_3d_group_in_corr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_group_in_corr(
+    set_a: InputPathType,
+    set_b: InputPathType | None = None,
+    apair: bool = False,
+    label_a: str | None = None,
+    label_b: str | None = None,
+    pooled: bool = False,
+    unpooled: bool = False,
+    paired: bool = False,
+    nosix: bool = False,
+    covariates_file: InputPathType | None = None,
+    center: str | None = None,
+    seed_radius: float | None = None,
+    sendall: bool = False,
+    donocov: bool = False,
+    dospcov: bool = False,
+    cluster: str | None = None,
+    read: bool = False,
+    ztest: bool = False,
+    ah: str | None = None,
+    port_offset: float | None = None,
+    port_offset_quiet: float | None = None,
+    port_bloc: float | None = None,
+    suma: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
+    very_verbose: bool = False,
+    debug: bool = False,
+    batch: str | None = None,
+    runner: Runner | None = None,
+) -> V3dGroupInCorrOutputs:
+    """
+    Functional connectivity analysis in group of subjects.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        set_a: Setup file describing the first dataset collection.
+        set_b: Setup file describing the second dataset collection for\
+            two-sample t-test analysis.
+        apair: Use -setA collection again but with different seed locations;\
+            produce paired t-test.
+        label_a: Label for sub-bricks corresponding to setA.
+        label_b: Label for sub-bricks corresponding to setB.
+        pooled: Use pooled variance estimator for two-sample un-paired t-test.
+        unpooled: Use unpooled variance estimator for two-sample un-paired\
+            t-test.
+        paired: Use a two-sample paired t-test.
+        nosix: Suppress the individual 1-sample t-tests and only return the\
+            difference 2-sample t-test.
+        covariates_file: File containing covariate values for each dataset.
+        center: Option for centering covariates.
+        seed_radius: Radius for seed voxel time series averaging (mm).
+        sendall: Send all individual subject results to AFNI along with group\
+            statistics.
+        donocov: Compute results both with and without covariates.
+        dospcov: Compute Spearman (rank) correlation coefficient of subject\
+            correlation results vs each covariate.
+        cluster: Input results from a 3dClustSim run to interface with AFNI.
+        read: Force program to read data into memory instead of memory mapping.
+        ztest: Debugging option to test if input data is all zero.
+        ah: Connect to AFNI/SUMA on a remote host.
+        port_offset: Provide a port offset.
+        port_offset_quiet: Provide a port offset, with less verbose output.
+        port_bloc: Provide a port offset bloc.
+        suma: Talk to SUMA instead of AFNI.
+        quiet: Suppress informational messages.
+        verbose: Print extra informational messages.
+        very_verbose: Print even more detailed informational messages.
+        debug: Enable internal testing.
+        batch: Run program in batch mode with specified METHOD and command\
+            file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dGroupInCorrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GROUP_IN_CORR_METADATA)
+    params = v_3d_group_in_corr_params(
+        set_a=set_a,
+        set_b=set_b,
+        apair=apair,
+        label_a=label_a,
+        label_b=label_b,
+        pooled=pooled,
+        unpooled=unpooled,
+        paired=paired,
+        nosix=nosix,
+        covariates_file=covariates_file,
+        center=center,
+        seed_radius=seed_radius,
+        sendall=sendall,
+        donocov=donocov,
+        dospcov=dospcov,
+        cluster=cluster,
+        read=read,
+        ztest=ztest,
+        ah=ah,
+        port_offset=port_offset,
+        port_offset_quiet=port_offset_quiet,
+        port_bloc=port_bloc,
+        suma=suma,
+        quiet=quiet,
+        verbose=verbose,
+        very_verbose=very_verbose,
+        debug=debug,
+        batch=batch,
+    )
+    return v_3d_group_in_corr_execute(params, execution)
+
+
+__all__ = [
+    "V3dGroupInCorrOutputs",
+    "V3dGroupInCorrParameters",
+    "V_3D_GROUP_IN_CORR_METADATA",
+    "v_3d_group_in_corr",
+    "v_3d_group_in_corr_params",
+]