niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_anhist.py

@@ -0,0 +1,260 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ANHIST_METADATA = Metadata(
+    id="00e44f2a97811aa464f9291074e3e9528d7e4939.boutiques",
+    name="3dAnhist",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAnhistParameters = typing.TypedDict('V3dAnhistParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAnhist"],
+    "dataset": InputPathType,
+    "quiet": bool,
+    "dump_histogram": bool,
+    "no_scurve": bool,
+    "winsorize": typing.NotRequired[str | None],
+    "top_2peaks": bool,
+    "label": typing.NotRequired[str | None],
+    "filename": 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 {
+        "3dAnhist": v_3d_anhist_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 {
+        "3dAnhist": v_3d_anhist_outputs,
+    }.get(t)
+
+
+class V3dAnhistOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_anhist(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_1_d: OutputPathType
+    """Dumped histogram data"""
+    output_ps: OutputPathType
+    """Plot of histogram data"""
+
+
+def v_3d_anhist_params(
+    dataset: InputPathType,
+    quiet: bool = False,
+    dump_histogram: bool = False,
+    no_scurve: bool = False,
+    winsorize: str | None = None,
+    top_2peaks: bool = False,
+    label: str | None = None,
+    filename: str | None = None,
+) -> V3dAnhistParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset, should be T1-weighted high-res brain image\
+            (shorts only).
+        quiet: Suppress progress reports.
+        dump_histogram: Dump histogram data to Anhist.1D and plot to Anhist.ps.
+        no_scurve: Do not fit histogram with curves.
+        winsorize: Apply Winsorizing filter prior to histogram scan. Can\
+            specify number of times (e.g., -w7).
+        top_2peaks: Analyze top 2 peaks only, for overlap, etc.
+        label: Use specified label for Anhist.ps plot file instead of the input\
+            dataset filename.
+        filename: Use specified filename instead of 'Anhist'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAnhist",
+        "dataset": dataset,
+        "quiet": quiet,
+        "dump_histogram": dump_histogram,
+        "no_scurve": no_scurve,
+        "top_2peaks": top_2peaks,
+    }
+    if winsorize is not None:
+        params["winsorize"] = winsorize
+    if label is not None:
+        params["label"] = label
+    if filename is not None:
+        params["filename"] = filename
+    return params
+
+
+def v_3d_anhist_cargs(
+    params: V3dAnhistParameters,
+    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("3dAnhist")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("quiet"):
+        cargs.append("-q")
+    if params.get("dump_histogram"):
+        cargs.append("-h")
+    if params.get("no_scurve"):
+        cargs.append("-F")
+    if params.get("winsorize") is not None:
+        cargs.extend([
+            "-w",
+            params.get("winsorize")
+        ])
+    if params.get("top_2peaks"):
+        cargs.append("-2")
+    if params.get("label") is not None:
+        cargs.extend([
+            "-label",
+            params.get("label")
+        ])
+    if params.get("filename") is not None:
+        cargs.extend([
+            "-fname",
+            params.get("filename")
+        ])
+    return cargs
+
+
+def v_3d_anhist_outputs(
+    params: V3dAnhistParameters,
+    execution: Execution,
+) -> V3dAnhistOutputs:
+    """
+    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 = V3dAnhistOutputs(
+        root=execution.output_file("."),
+        output_1_d=execution.output_file("Anhist.1D"),
+        output_ps=execution.output_file("Anhist.ps"),
+    )
+    return ret
+
+
+def v_3d_anhist_execute(
+    params: V3dAnhistParameters,
+    execution: Execution,
+) -> V3dAnhistOutputs:
+    """
+    Tool to analyze histogram peaks in a T1-weighted high-res brain image dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnhistOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_anhist_cargs(params, execution)
+    ret = v_3d_anhist_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_anhist(
+    dataset: InputPathType,
+    quiet: bool = False,
+    dump_histogram: bool = False,
+    no_scurve: bool = False,
+    winsorize: str | None = None,
+    top_2peaks: bool = False,
+    label: str | None = None,
+    filename: str | None = None,
+    runner: Runner | None = None,
+) -> V3dAnhistOutputs:
+    """
+    Tool to analyze histogram peaks in a T1-weighted high-res brain image dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset, should be T1-weighted high-res brain image\
+            (shorts only).
+        quiet: Suppress progress reports.
+        dump_histogram: Dump histogram data to Anhist.1D and plot to Anhist.ps.
+        no_scurve: Do not fit histogram with curves.
+        winsorize: Apply Winsorizing filter prior to histogram scan. Can\
+            specify number of times (e.g., -w7).
+        top_2peaks: Analyze top 2 peaks only, for overlap, etc.
+        label: Use specified label for Anhist.ps plot file instead of the input\
+            dataset filename.
+        filename: Use specified filename instead of 'Anhist'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnhistOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ANHIST_METADATA)
+    params = v_3d_anhist_params(
+        dataset=dataset,
+        quiet=quiet,
+        dump_histogram=dump_histogram,
+        no_scurve=no_scurve,
+        winsorize=winsorize,
+        top_2peaks=top_2peaks,
+        label=label,
+        filename=filename,
+    )
+    return v_3d_anhist_execute(params, execution)
+
+
+__all__ = [
+    "V3dAnhistOutputs",
+    "V3dAnhistParameters",
+    "V_3D_ANHIST_METADATA",
+    "v_3d_anhist",
+    "v_3d_anhist_params",
+]

niwrap_afni/afni/v_3d_anova.py

@@ -0,0 +1,359 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ANOVA_METADATA = Metadata(
+    id="a6b18c124721654a7ec2ffc70584424d3b14a440.boutiques",
+    name="3dANOVA",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAnovaParameters = typing.TypedDict('V3dAnovaParameters', {
+    "__STYX_TYPE__": typing.Literal["3dANOVA"],
+    "levels": int,
+    "datasets": list[str],
+    "voxel": typing.NotRequired[int | None],
+    "diskspace": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "debug": typing.NotRequired[int | None],
+    "ftr": typing.NotRequired[str | None],
+    "mean": typing.NotRequired[str | None],
+    "diff": typing.NotRequired[str | None],
+    "contr": typing.NotRequired[str | None],
+    "old_method": bool,
+    "ok": bool,
+    "assume_sph": bool,
+    "bucket": 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 {
+        "3dANOVA": v_3d_anova_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 {
+        "3dANOVA": v_3d_anova_outputs,
+    }.get(t)
+
+
+class V3dAnovaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_anova(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    ftr_output: OutputPathType | None
+    """Output F-statistic dataset file"""
+    ftr_brick_output: OutputPathType | None
+    """Output F-statistic BRIK file"""
+    mean_output: OutputPathType | None
+    """Output mean dataset file"""
+    mean_brick_output: OutputPathType | None
+    """Output mean BRIK file"""
+    diff_output: OutputPathType | None
+    """Output difference dataset file"""
+    diff_brick_output: OutputPathType | None
+    """Output difference BRIK file"""
+    contr_output: OutputPathType | None
+    """Output contrast dataset file"""
+    contr_brick_output: OutputPathType | None
+    """Output contrast BRIK file"""
+    bucket_output: OutputPathType | None
+    """Output bucket dataset file"""
+    bucket_brick_output: OutputPathType | None
+    """Output bucket BRIK file"""
+
+
+def v_3d_anova_params(
+    levels: int,
+    datasets: list[str],
+    voxel: int | None = None,
+    diskspace: bool = False,
+    mask: InputPathType | None = None,
+    debug: int | None = None,
+    ftr: str | None = None,
+    mean: str | None = None,
+    diff: str | None = None,
+    contr: str | None = None,
+    old_method: bool = False,
+    ok: bool = False,
+    assume_sph: bool = False,
+    bucket: str | None = None,
+) -> V3dAnovaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        levels: Number of factor levels.
+        datasets: Datasets for each factor level.
+        voxel: Screen output for the specified voxel number.
+        diskspace: Print out the required disk space for program execution.
+        mask: Use sub-brick #0 of dataset to define which voxels to process.
+        debug: Request extra output verbosity.
+        ftr: F-statistic for treatment effect.
+        mean: Estimate of factor level mean.
+        diff: Difference between factor levels.
+        contr: Contrast in factor levels.
+        old_method: Perform ANOVA using the previous functionality.
+        ok: Confirm understanding of t-stats and sphericity assumptions with\
+            old method.
+        assume_sph: Assume sphericity (zero-sum contrasts only).
+        bucket: Create one AFNI 'bucket' dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dANOVA",
+        "levels": levels,
+        "datasets": datasets,
+        "diskspace": diskspace,
+        "old_method": old_method,
+        "ok": ok,
+        "assume_sph": assume_sph,
+    }
+    if voxel is not None:
+        params["voxel"] = voxel
+    if mask is not None:
+        params["mask"] = mask
+    if debug is not None:
+        params["debug"] = debug
+    if ftr is not None:
+        params["ftr"] = ftr
+    if mean is not None:
+        params["mean"] = mean
+    if diff is not None:
+        params["diff"] = diff
+    if contr is not None:
+        params["contr"] = contr
+    if bucket is not None:
+        params["bucket"] = bucket
+    return params
+
+
+def v_3d_anova_cargs(
+    params: V3dAnovaParameters,
+    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("3dANOVA")
+    cargs.extend([
+        "-levels",
+        str(params.get("levels"))
+    ])
+    cargs.extend([
+        "-dset",
+        *params.get("datasets")
+    ])
+    if params.get("voxel") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel"))
+        ])
+    if params.get("diskspace"):
+        cargs.append("-diskspace")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("ftr") is not None:
+        cargs.extend([
+            "-ftr",
+            params.get("ftr")
+        ])
+    if params.get("mean") is not None:
+        cargs.extend([
+            "-mean",
+            params.get("mean")
+        ])
+    if params.get("diff") is not None:
+        cargs.extend([
+            "-diff",
+            params.get("diff")
+        ])
+    if params.get("contr") is not None:
+        cargs.extend([
+            "-contr",
+            params.get("contr")
+        ])
+    if params.get("old_method"):
+        cargs.append("-old_method")
+    if params.get("ok"):
+        cargs.append("-OK")
+    if params.get("assume_sph"):
+        cargs.append("-assume_sph")
+    if params.get("bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket")
+        ])
+    return cargs
+
+
+def v_3d_anova_outputs(
+    params: V3dAnovaParameters,
+    execution: Execution,
+) -> V3dAnovaOutputs:
+    """
+    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 = V3dAnovaOutputs(
+        root=execution.output_file("."),
+        ftr_output=execution.output_file(params.get("ftr") + ".HEAD") if (params.get("ftr") is not None) else None,
+        ftr_brick_output=execution.output_file(params.get("ftr") + ".BRIK") if (params.get("ftr") is not None) else None,
+        mean_output=execution.output_file(params.get("mean") + "_mean.HEAD") if (params.get("mean") is not None) else None,
+        mean_brick_output=execution.output_file(params.get("mean") + "_mean.BRIK") if (params.get("mean") is not None) else None,
+        diff_output=execution.output_file(params.get("diff") + "_diff.HEAD") if (params.get("diff") is not None) else None,
+        diff_brick_output=execution.output_file(params.get("diff") + "_diff.BRIK") if (params.get("diff") is not None) else None,
+        contr_output=execution.output_file(params.get("contr") + "_contr.HEAD") if (params.get("contr") is not None) else None,
+        contr_brick_output=execution.output_file(params.get("contr") + "_contr.BRIK") if (params.get("contr") is not None) else None,
+        bucket_output=execution.output_file(params.get("bucket") + ".HEAD") if (params.get("bucket") is not None) else None,
+        bucket_brick_output=execution.output_file(params.get("bucket") + ".BRIK") if (params.get("bucket") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_anova_execute(
+    params: V3dAnovaParameters,
+    execution: Execution,
+) -> V3dAnovaOutputs:
+    """
+    Performs single-factor Analysis of Variance (ANOVA) on 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnovaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_anova_cargs(params, execution)
+    ret = v_3d_anova_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_anova(
+    levels: int,
+    datasets: list[str],
+    voxel: int | None = None,
+    diskspace: bool = False,
+    mask: InputPathType | None = None,
+    debug: int | None = None,
+    ftr: str | None = None,
+    mean: str | None = None,
+    diff: str | None = None,
+    contr: str | None = None,
+    old_method: bool = False,
+    ok: bool = False,
+    assume_sph: bool = False,
+    bucket: str | None = None,
+    runner: Runner | None = None,
+) -> V3dAnovaOutputs:
+    """
+    Performs single-factor Analysis of Variance (ANOVA) on 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        levels: Number of factor levels.
+        datasets: Datasets for each factor level.
+        voxel: Screen output for the specified voxel number.
+        diskspace: Print out the required disk space for program execution.
+        mask: Use sub-brick #0 of dataset to define which voxels to process.
+        debug: Request extra output verbosity.
+        ftr: F-statistic for treatment effect.
+        mean: Estimate of factor level mean.
+        diff: Difference between factor levels.
+        contr: Contrast in factor levels.
+        old_method: Perform ANOVA using the previous functionality.
+        ok: Confirm understanding of t-stats and sphericity assumptions with\
+            old method.
+        assume_sph: Assume sphericity (zero-sum contrasts only).
+        bucket: Create one AFNI 'bucket' dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnovaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ANOVA_METADATA)
+    params = v_3d_anova_params(
+        levels=levels,
+        datasets=datasets,
+        voxel=voxel,
+        diskspace=diskspace,
+        mask=mask,
+        debug=debug,
+        ftr=ftr,
+        mean=mean,
+        diff=diff,
+        contr=contr,
+        old_method=old_method,
+        ok=ok,
+        assume_sph=assume_sph,
+        bucket=bucket,
+    )
+    return v_3d_anova_execute(params, execution)
+
+
+__all__ = [
+    "V3dAnovaOutputs",
+    "V3dAnovaParameters",
+    "V_3D_ANOVA_METADATA",
+    "v_3d_anova",
+    "v_3d_anova_params",
+]