niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mss.py

@@ -0,0 +1,397 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MSS_METADATA = Metadata(
+    id="ecd8c02c668a204a461a0151f5ebbf32fbc74dce.boutiques",
+    name="3dMSS",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMssParameters = typing.TypedDict('V3dMssParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMSS"],
+    "prefix": str,
+    "jobs": typing.NotRequired[float | None],
+    "mrr_formula": typing.NotRequired[str | None],
+    "lme_formula": typing.NotRequired[str | None],
+    "random_effect": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bounds": typing.NotRequired[list[float] | None],
+    "prediction_table": typing.NotRequired[InputPathType | None],
+    "data_table": InputPathType,
+    "cio_flag": bool,
+    "rio_flag": bool,
+    "help_flag": bool,
+    "dbg_args_flag": bool,
+    "if_name": typing.NotRequired[str | None],
+    "show_allowed_options_flag": bool,
+    "sdiff_vars": typing.NotRequired[str | None],
+    "vt_formula": 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 {
+        "3dMSS": v_3d_mss_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 {
+        "3dMSS": v_3d_mss_outputs,
+    }.get(t)
+
+
+class V3dMssOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mss(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file in NIfTI format"""
+
+
+def v_3d_mss_params(
+    prefix: str,
+    data_table: InputPathType,
+    jobs: float | None = None,
+    mrr_formula: str | None = None,
+    lme_formula: str | None = None,
+    random_effect: str | None = None,
+    qvars: str | None = None,
+    mask: InputPathType | None = None,
+    bounds: list[float] | None = None,
+    prediction_table: InputPathType | None = None,
+    cio_flag: bool = False,
+    rio_flag: bool = False,
+    help_flag: bool = False,
+    dbg_args_flag: bool = False,
+    if_name: str | None = None,
+    show_allowed_options_flag: bool = False,
+    sdiff_vars: str | None = None,
+    vt_formula: str | None = None,
+) -> V3dMssParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file name. For AFNI format, provide prefix only, with no\
+            view+suffix needed. Filename for NIfTI format should have .nii\
+            attached.
+        data_table: List the data structure with a header as the first line.
+        jobs: Number of CPU cores for parallel processing.
+        mrr_formula: Model formulation through multilevel smoothing splines.
+        lme_formula: Specify the fixed effect components of the model.
+        random_effect: Specify the random effect components of the model.
+        qvars: Identify quantitative variables (or covariates). The list with\
+            more than one variable has to be separated with comma without any other\
+            characters.
+        mask: Process voxels inside this mask only.
+        bounds: Outlier removal bounds. Any values in the input data that are\
+            beyond the bounds will be removed and treated as missing.
+        prediction_table: Provide a data table so that predicted values could\
+            be generated for graphical illustration.
+        cio_flag: Use AFNI's C io functions, which is default.
+        rio_flag: Use R's io functions.
+        help_flag: Display help message.
+        dbg_args_flag: Enable R to save the parameters in a file called\
+            .3dMSS.dbg.AFNI.args for debugging.
+        if_name: Specify the column name that is designated for input files of\
+            effect estimate. Default is 'InputFile'.
+        show_allowed_options_flag: List of allowed options.
+        sdiff_vars: Specify the factors for group comparisons.
+        vt_formula: Specify varying smoothing terms. Two components are\
+            required: the first one 'var' indicates the variable (e.g., subject)\
+            around which the smoothing will vary while the second component\
+            specifies the smoothing formulation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMSS",
+        "prefix": prefix,
+        "data_table": data_table,
+        "cio_flag": cio_flag,
+        "rio_flag": rio_flag,
+        "help_flag": help_flag,
+        "dbg_args_flag": dbg_args_flag,
+        "show_allowed_options_flag": show_allowed_options_flag,
+    }
+    if jobs is not None:
+        params["jobs"] = jobs
+    if mrr_formula is not None:
+        params["mrr_formula"] = mrr_formula
+    if lme_formula is not None:
+        params["lme_formula"] = lme_formula
+    if random_effect is not None:
+        params["random_effect"] = random_effect
+    if qvars is not None:
+        params["qvars"] = qvars
+    if mask is not None:
+        params["mask"] = mask
+    if bounds is not None:
+        params["bounds"] = bounds
+    if prediction_table is not None:
+        params["prediction_table"] = prediction_table
+    if if_name is not None:
+        params["if_name"] = if_name
+    if sdiff_vars is not None:
+        params["sdiff_vars"] = sdiff_vars
+    if vt_formula is not None:
+        params["vt_formula"] = vt_formula
+    return params
+
+
+def v_3d_mss_cargs(
+    params: V3dMssParameters,
+    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("3dMSS")
+    cargs.append(params.get("prefix"))
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    if params.get("mrr_formula") is not None:
+        cargs.extend([
+            "-mrr",
+            params.get("mrr_formula")
+        ])
+    if params.get("lme_formula") is not None:
+        cargs.extend([
+            "-lme",
+            params.get("lme_formula")
+        ])
+    if params.get("random_effect") is not None:
+        cargs.extend([
+            "-ranEff",
+            params.get("random_effect")
+        ])
+    if params.get("qvars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("qvars")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bounds") is not None:
+        cargs.extend([
+            "-bounds",
+            *map(str, params.get("bounds"))
+        ])
+    if params.get("prediction_table") is not None:
+        cargs.extend([
+            "-prediction",
+            execution.input_file(params.get("prediction_table"))
+        ])
+    cargs.extend([
+        "-dataTable",
+        execution.input_file(params.get("data_table"))
+    ])
+    if params.get("cio_flag"):
+        cargs.append("-cio")
+    if params.get("rio_flag"):
+        cargs.append("-Rio")
+    if params.get("help_flag"):
+        cargs.append("-help")
+    if params.get("dbg_args_flag"):
+        cargs.append("-dbgArgs")
+    if params.get("if_name") is not None:
+        cargs.extend([
+            "-IF",
+            params.get("if_name")
+        ])
+    if params.get("show_allowed_options_flag"):
+        cargs.append("-show_allowed_options")
+    if params.get("sdiff_vars") is not None:
+        cargs.extend([
+            "-sdiff",
+            params.get("sdiff_vars")
+        ])
+    if params.get("vt_formula") is not None:
+        cargs.extend([
+            "-vt",
+            params.get("vt_formula")
+        ])
+    return cargs
+
+
+def v_3d_mss_outputs(
+    params: V3dMssParameters,
+    execution: Execution,
+) -> V3dMssOutputs:
+    """
+    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 = V3dMssOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii"),
+    )
+    return ret
+
+
+def v_3d_mss_execute(
+    params: V3dMssParameters,
+    execution: Execution,
+) -> V3dMssOutputs:
+    """
+    Voxelwise Multilevel Smoothing Spline (MSS) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMssOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mss_cargs(params, execution)
+    ret = v_3d_mss_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mss(
+    prefix: str,
+    data_table: InputPathType,
+    jobs: float | None = None,
+    mrr_formula: str | None = None,
+    lme_formula: str | None = None,
+    random_effect: str | None = None,
+    qvars: str | None = None,
+    mask: InputPathType | None = None,
+    bounds: list[float] | None = None,
+    prediction_table: InputPathType | None = None,
+    cio_flag: bool = False,
+    rio_flag: bool = False,
+    help_flag: bool = False,
+    dbg_args_flag: bool = False,
+    if_name: str | None = None,
+    show_allowed_options_flag: bool = False,
+    sdiff_vars: str | None = None,
+    vt_formula: str | None = None,
+    runner: Runner | None = None,
+) -> V3dMssOutputs:
+    """
+    Voxelwise Multilevel Smoothing Spline (MSS) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file name. For AFNI format, provide prefix only, with no\
+            view+suffix needed. Filename for NIfTI format should have .nii\
+            attached.
+        data_table: List the data structure with a header as the first line.
+        jobs: Number of CPU cores for parallel processing.
+        mrr_formula: Model formulation through multilevel smoothing splines.
+        lme_formula: Specify the fixed effect components of the model.
+        random_effect: Specify the random effect components of the model.
+        qvars: Identify quantitative variables (or covariates). The list with\
+            more than one variable has to be separated with comma without any other\
+            characters.
+        mask: Process voxels inside this mask only.
+        bounds: Outlier removal bounds. Any values in the input data that are\
+            beyond the bounds will be removed and treated as missing.
+        prediction_table: Provide a data table so that predicted values could\
+            be generated for graphical illustration.
+        cio_flag: Use AFNI's C io functions, which is default.
+        rio_flag: Use R's io functions.
+        help_flag: Display help message.
+        dbg_args_flag: Enable R to save the parameters in a file called\
+            .3dMSS.dbg.AFNI.args for debugging.
+        if_name: Specify the column name that is designated for input files of\
+            effect estimate. Default is 'InputFile'.
+        show_allowed_options_flag: List of allowed options.
+        sdiff_vars: Specify the factors for group comparisons.
+        vt_formula: Specify varying smoothing terms. Two components are\
+            required: the first one 'var' indicates the variable (e.g., subject)\
+            around which the smoothing will vary while the second component\
+            specifies the smoothing formulation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMssOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MSS_METADATA)
+    params = v_3d_mss_params(
+        prefix=prefix,
+        jobs=jobs,
+        mrr_formula=mrr_formula,
+        lme_formula=lme_formula,
+        random_effect=random_effect,
+        qvars=qvars,
+        mask=mask,
+        bounds=bounds,
+        prediction_table=prediction_table,
+        data_table=data_table,
+        cio_flag=cio_flag,
+        rio_flag=rio_flag,
+        help_flag=help_flag,
+        dbg_args_flag=dbg_args_flag,
+        if_name=if_name,
+        show_allowed_options_flag=show_allowed_options_flag,
+        sdiff_vars=sdiff_vars,
+        vt_formula=vt_formula,
+    )
+    return v_3d_mss_execute(params, execution)
+
+
+__all__ = [
+    "V3dMssOutputs",
+    "V3dMssParameters",
+    "V_3D_MSS_METADATA",
+    "v_3d_mss",
+    "v_3d_mss_params",
+]

niwrap_afni/afni/v_3d_multi_thresh.py

@@ -0,0 +1,306 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MULTI_THRESH_METADATA = Metadata(
+    id="ac6c6a539a206612134e8a96c0fd7291780ddc36.boutiques",
+    name="3dMultiThresh",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMultiThreshParameters = typing.TypedDict('V3dMultiThreshParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMultiThresh"],
+    "mthresh_file": InputPathType,
+    "input_file": InputPathType,
+    "index": typing.NotRequired[float | None],
+    "signed_flag": typing.NotRequired[str | None],
+    "positive_sign_flag": bool,
+    "negative_sign_flag": bool,
+    "prefix": typing.NotRequired[str | None],
+    "mask_only_flag": bool,
+    "all_mask": typing.NotRequired[str | None],
+    "no_zero_flag": bool,
+    "quiet_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMultiThresh": v_3d_multi_thresh_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 {
+        "3dMultiThresh": v_3d_multi_thresh_outputs,
+    }.get(t)
+
+
+class V3dMultiThreshOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_multi_thresh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Thresholded version of the input dataset."""
+    mask_output: OutputPathType | None
+    """0/1 mask dataset of voxels that survive the process."""
+    all_mask_output: OutputPathType | None
+    """Multi-volume dataset where each volume is the binary mask of voxels that
+    pass ONE of the tests."""
+
+
+def v_3d_multi_thresh_params(
+    mthresh_file: InputPathType,
+    input_file: InputPathType,
+    index: float | None = None,
+    signed_flag: str | None = None,
+    positive_sign_flag: bool = False,
+    negative_sign_flag: bool = False,
+    prefix: str | None = None,
+    mask_only_flag: bool = False,
+    all_mask: str | None = None,
+    no_zero_flag: bool = False,
+    quiet_flag: bool = False,
+) -> V3dMultiThreshParameters:
+    """
+    Build parameters.
+    
+    Args:
+        mthresh_file: Multi-threshold dataset from 3dXClustSim, usually via\
+            running '3dttest++ -ETAC'.
+        input_file: Dataset to threshold.
+        index: Index (sub-brick) on which to threshold.
+        signed_flag: Indicates if the .mthresh.nii file from 3dXClustSim was\
+            created using 1-sided thresholding. Choose sign + or -.
+        positive_sign_flag: Same as '-signed +'.
+        negative_sign_flag: Same as '-signed -'.
+        prefix: Prefix for output dataset. Can be 'NULL' to get no output\
+            dataset.
+        mask_only_flag: Instead of outputting a thresholded version of the\
+            input dataset, just output a 0/1 mask dataset of voxels that survive\
+            the process.
+        all_mask: Write out a multi-volume dataset with prefix 'qqq' where each\
+            volume is the binary mask of voxels that pass ONE of the tests.
+        no_zero_flag: Prevents the output of a dataset if it would be all zero.
+        quiet_flag: Turn off progress report messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMultiThresh",
+        "mthresh_file": mthresh_file,
+        "input_file": input_file,
+        "positive_sign_flag": positive_sign_flag,
+        "negative_sign_flag": negative_sign_flag,
+        "mask_only_flag": mask_only_flag,
+        "no_zero_flag": no_zero_flag,
+        "quiet_flag": quiet_flag,
+    }
+    if index is not None:
+        params["index"] = index
+    if signed_flag is not None:
+        params["signed_flag"] = signed_flag
+    if prefix is not None:
+        params["prefix"] = prefix
+    if all_mask is not None:
+        params["all_mask"] = all_mask
+    return params
+
+
+def v_3d_multi_thresh_cargs(
+    params: V3dMultiThreshParameters,
+    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("3dMultiThresh")
+    cargs.extend([
+        "-mthresh",
+        execution.input_file(params.get("mthresh_file"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("index") is not None:
+        cargs.extend([
+            "-1tindex",
+            str(params.get("index"))
+        ])
+    if params.get("signed_flag") is not None:
+        cargs.extend([
+            "-signed",
+            params.get("signed_flag")
+        ])
+    if params.get("positive_sign_flag"):
+        cargs.append("-pos")
+    if params.get("negative_sign_flag"):
+        cargs.append("-neg")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("mask_only_flag"):
+        cargs.append("-maskonly")
+    if params.get("all_mask") is not None:
+        cargs.extend([
+            "-allmask",
+            params.get("all_mask")
+        ])
+    if params.get("no_zero_flag"):
+        cargs.append("-nozero")
+    if params.get("quiet_flag"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_multi_thresh_outputs(
+    params: V3dMultiThreshParameters,
+    execution: Execution,
+) -> V3dMultiThreshOutputs:
+    """
+    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 = V3dMultiThreshOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        mask_output=execution.output_file(params.get("prefix") + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
+        all_mask_output=execution.output_file(params.get("all_mask") + ".nii.gz") if (params.get("all_mask") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_multi_thresh_execute(
+    params: V3dMultiThreshParameters,
+    execution: Execution,
+) -> V3dMultiThreshOutputs:
+    """
+    Program to apply a multi-threshold (mthresh) dataset to an input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMultiThreshOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_multi_thresh_cargs(params, execution)
+    ret = v_3d_multi_thresh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_multi_thresh(
+    mthresh_file: InputPathType,
+    input_file: InputPathType,
+    index: float | None = None,
+    signed_flag: str | None = None,
+    positive_sign_flag: bool = False,
+    negative_sign_flag: bool = False,
+    prefix: str | None = None,
+    mask_only_flag: bool = False,
+    all_mask: str | None = None,
+    no_zero_flag: bool = False,
+    quiet_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3dMultiThreshOutputs:
+    """
+    Program to apply a multi-threshold (mthresh) dataset to an input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        mthresh_file: Multi-threshold dataset from 3dXClustSim, usually via\
+            running '3dttest++ -ETAC'.
+        input_file: Dataset to threshold.
+        index: Index (sub-brick) on which to threshold.
+        signed_flag: Indicates if the .mthresh.nii file from 3dXClustSim was\
+            created using 1-sided thresholding. Choose sign + or -.
+        positive_sign_flag: Same as '-signed +'.
+        negative_sign_flag: Same as '-signed -'.
+        prefix: Prefix for output dataset. Can be 'NULL' to get no output\
+            dataset.
+        mask_only_flag: Instead of outputting a thresholded version of the\
+            input dataset, just output a 0/1 mask dataset of voxels that survive\
+            the process.
+        all_mask: Write out a multi-volume dataset with prefix 'qqq' where each\
+            volume is the binary mask of voxels that pass ONE of the tests.
+        no_zero_flag: Prevents the output of a dataset if it would be all zero.
+        quiet_flag: Turn off progress report messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMultiThreshOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MULTI_THRESH_METADATA)
+    params = v_3d_multi_thresh_params(
+        mthresh_file=mthresh_file,
+        input_file=input_file,
+        index=index,
+        signed_flag=signed_flag,
+        positive_sign_flag=positive_sign_flag,
+        negative_sign_flag=negative_sign_flag,
+        prefix=prefix,
+        mask_only_flag=mask_only_flag,
+        all_mask=all_mask,
+        no_zero_flag=no_zero_flag,
+        quiet_flag=quiet_flag,
+    )
+    return v_3d_multi_thresh_execute(params, execution)
+
+
+__all__ = [
+    "V3dMultiThreshOutputs",
+    "V3dMultiThreshParameters",
+    "V_3D_MULTI_THRESH_METADATA",
+    "v_3d_multi_thresh",
+    "v_3d_multi_thresh_params",
+]