niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tfitter.py

@@ -0,0 +1,430 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TFITTER_METADATA = Metadata(
+    id="8451a7cd8aa8de8047fb4bbe324982a2fbf6f94a.boutiques",
+    name="3dTfitter",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTfitterParameters = typing.TypedDict('V3dTfitterParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTfitter"],
+    "RHS": str,
+    "LHS": typing.NotRequired[list[str] | None],
+    "polort": typing.NotRequired[float | None],
+    "vthr": typing.NotRequired[float | None],
+    "FALTUNG": typing.NotRequired[list[str] | None],
+    "lsqfit": bool,
+    "l1fit": bool,
+    "l2lasso": typing.NotRequired[list[str] | None],
+    "lasso_centro_block": typing.NotRequired[list[str] | None],
+    "l2sqrtlasso": typing.NotRequired[list[str] | None],
+    "consign": typing.NotRequired[list[str] | None],
+    "consFAL": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "label": typing.NotRequired[list[str] | None],
+    "fitts": typing.NotRequired[str | None],
+    "errsum": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[str | None],
+    "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 {
+        "3dTfitter": v_3d_tfitter_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 {
+        "3dTfitter": v_3d_tfitter_outputs,
+    }.get(t)
+
+
+class V3dTfitterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tfitter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_prefix: OutputPathType | None
+    """Output dataset for LHS parameters."""
+    fitted_time_series: OutputPathType | None
+    """Output fitted time series dataset."""
+    error_sums: OutputPathType | None
+    """Output error sums dataset."""
+
+
+def v_3d_tfitter_params(
+    rhs: str,
+    lhs: list[str] | None = None,
+    polort: float | None = None,
+    vthr: float | None = None,
+    faltung: list[str] | None = None,
+    lsqfit: bool = False,
+    l1fit: bool = False,
+    l2lasso: list[str] | None = None,
+    lasso_centro_block: list[str] | None = None,
+    l2sqrtlasso: list[str] | None = None,
+    consign: list[str] | None = None,
+    cons_fal: str | None = None,
+    prefix: str | None = None,
+    label: list[str] | None = None,
+    fitts: str | None = None,
+    errsum: str | None = None,
+    mask: str | None = None,
+    quiet: bool = False,
+) -> V3dTfitterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        rhs: Specifies the right-hand-side 3D+time dataset. ('rset' can also be\
+            a 1D file with 1 column).
+        lhs: Specifies a column (or columns) of the left-hand-side matrix. More\
+            than one 'lset' can follow the '-LHS' option.
+        polort: Add 'p+1' Legendre polynomial columns to the LHS matrix.
+        vthr: The value 'v' (between 0.0 and 0.09, inclusive) defines the\
+            threshold below which LHS vectors will be omitted from the regression\
+            analysis.
+        faltung: Specifies a convolution (German: Faltung) model to be added to\
+            the LHS matrix. Followed by four arguments: 'fset', 'fpre', 'pen',\
+            'fac'.
+        lsqfit: Solve equations via least squares [the default method].
+        l1fit: Solve equations via least sum of absolute residuals.
+        l2lasso: Solve equations via least squares with a LASSO (L1) penalty on\
+            the coefficients. Followed by 'lam' and optional 'i j k ...'.
+        lasso_centro_block: Defines a block of coefficients that will be\
+            penalized together.
+        l2sqrtlasso: Similar to '-l2lasso', but aims to minimize\
+            sqrt(Q2)+lam*L1.
+        consign: Indicates that the sign of some output LHS parameters should\
+            be constrained in the solution.
+        cons_fal: Constrain the deconvolution time series from '-FALTUNG' to be\
+            positive if 'c' is '+' or to be negative if 'c' is '-'.
+        prefix: Prefix for the output dataset (LHS parameters) filename.
+        label: Specifies sub-brick labels in the output LHS parameter dataset.
+        fitts: Prefix filename for the output fitted time series dataset.
+        errsum: Prefix filename for the error sums dataset.
+        mask: Read in dataset 'ms' to use as a mask; only voxels with nonzero\
+            values in the mask will be processed.
+        quiet: Don't print progress report messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTfitter",
+        "RHS": rhs,
+        "lsqfit": lsqfit,
+        "l1fit": l1fit,
+        "quiet": quiet,
+    }
+    if lhs is not None:
+        params["LHS"] = lhs
+    if polort is not None:
+        params["polort"] = polort
+    if vthr is not None:
+        params["vthr"] = vthr
+    if faltung is not None:
+        params["FALTUNG"] = faltung
+    if l2lasso is not None:
+        params["l2lasso"] = l2lasso
+    if lasso_centro_block is not None:
+        params["lasso_centro_block"] = lasso_centro_block
+    if l2sqrtlasso is not None:
+        params["l2sqrtlasso"] = l2sqrtlasso
+    if consign is not None:
+        params["consign"] = consign
+    if cons_fal is not None:
+        params["consFAL"] = cons_fal
+    if prefix is not None:
+        params["prefix"] = prefix
+    if label is not None:
+        params["label"] = label
+    if fitts is not None:
+        params["fitts"] = fitts
+    if errsum is not None:
+        params["errsum"] = errsum
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_tfitter_cargs(
+    params: V3dTfitterParameters,
+    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("3dTfitter")
+    cargs.extend([
+        "-RHS",
+        params.get("RHS")
+    ])
+    if params.get("LHS") is not None:
+        cargs.extend([
+            "-LHS",
+            *params.get("LHS")
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("vthr") is not None:
+        cargs.extend([
+            "-vthr",
+            str(params.get("vthr"))
+        ])
+    if params.get("FALTUNG") is not None:
+        cargs.extend([
+            "-FALTUNG",
+            *params.get("FALTUNG")
+        ])
+    if params.get("lsqfit"):
+        cargs.append("-lsqfit")
+    if params.get("l1fit"):
+        cargs.append("-l1fit")
+    if params.get("l2lasso") is not None:
+        cargs.extend([
+            "-l2lasso",
+            *params.get("l2lasso")
+        ])
+    if params.get("lasso_centro_block") is not None:
+        cargs.extend([
+            "-lasso_centro_block",
+            *params.get("lasso_centro_block")
+        ])
+    if params.get("l2sqrtlasso") is not None:
+        cargs.extend([
+            "-l2sqrtlasso",
+            *params.get("l2sqrtlasso")
+        ])
+    if params.get("consign") is not None:
+        cargs.extend([
+            "-consign",
+            *params.get("consign")
+        ])
+    if params.get("consFAL") is not None:
+        cargs.extend([
+            "-consFAL",
+            params.get("consFAL")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("label") is not None:
+        cargs.extend([
+            "-label",
+            *params.get("label")
+        ])
+    if params.get("fitts") is not None:
+        cargs.extend([
+            "-fitts",
+            params.get("fitts")
+        ])
+    if params.get("errsum") is not None:
+        cargs.extend([
+            "-errsum",
+            params.get("errsum")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_tfitter_outputs(
+    params: V3dTfitterParameters,
+    execution: Execution,
+) -> V3dTfitterOutputs:
+    """
+    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 = V3dTfitterOutputs(
+        root=execution.output_file("."),
+        output_prefix=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        fitted_time_series=execution.output_file(params.get("fitts") + ".nii.gz") if (params.get("fitts") is not None) else None,
+        error_sums=execution.output_file(params.get("errsum") + ".nii.gz") if (params.get("errsum") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tfitter_execute(
+    params: V3dTfitterParameters,
+    execution: Execution,
+) -> V3dTfitterOutputs:
+    """
+    * At each voxel, assembles and solves a set of linear equations.
+    ++ The matrix at each voxel may be the same or may be different.
+    ++ This flexibility (for voxel-wise regressors) is one feature
+    that makes 3dTfitter different from 3dDeconvolve.
+    ++ Another distinguishing feature is that 3dTfitter allows for
+    L2, L1, and L2+L1 (LASSO) regression solvers, and allows you
+    to impose sign constraints on the solution parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTfitterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tfitter_cargs(params, execution)
+    ret = v_3d_tfitter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tfitter(
+    rhs: str,
+    lhs: list[str] | None = None,
+    polort: float | None = None,
+    vthr: float | None = None,
+    faltung: list[str] | None = None,
+    lsqfit: bool = False,
+    l1fit: bool = False,
+    l2lasso: list[str] | None = None,
+    lasso_centro_block: list[str] | None = None,
+    l2sqrtlasso: list[str] | None = None,
+    consign: list[str] | None = None,
+    cons_fal: str | None = None,
+    prefix: str | None = None,
+    label: list[str] | None = None,
+    fitts: str | None = None,
+    errsum: str | None = None,
+    mask: str | None = None,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dTfitterOutputs:
+    """
+    * At each voxel, assembles and solves a set of linear equations.
+    ++ The matrix at each voxel may be the same or may be different.
+    ++ This flexibility (for voxel-wise regressors) is one feature
+    that makes 3dTfitter different from 3dDeconvolve.
+    ++ Another distinguishing feature is that 3dTfitter allows for
+    L2, L1, and L2+L1 (LASSO) regression solvers, and allows you
+    to impose sign constraints on the solution parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        rhs: Specifies the right-hand-side 3D+time dataset. ('rset' can also be\
+            a 1D file with 1 column).
+        lhs: Specifies a column (or columns) of the left-hand-side matrix. More\
+            than one 'lset' can follow the '-LHS' option.
+        polort: Add 'p+1' Legendre polynomial columns to the LHS matrix.
+        vthr: The value 'v' (between 0.0 and 0.09, inclusive) defines the\
+            threshold below which LHS vectors will be omitted from the regression\
+            analysis.
+        faltung: Specifies a convolution (German: Faltung) model to be added to\
+            the LHS matrix. Followed by four arguments: 'fset', 'fpre', 'pen',\
+            'fac'.
+        lsqfit: Solve equations via least squares [the default method].
+        l1fit: Solve equations via least sum of absolute residuals.
+        l2lasso: Solve equations via least squares with a LASSO (L1) penalty on\
+            the coefficients. Followed by 'lam' and optional 'i j k ...'.
+        lasso_centro_block: Defines a block of coefficients that will be\
+            penalized together.
+        l2sqrtlasso: Similar to '-l2lasso', but aims to minimize\
+            sqrt(Q2)+lam*L1.
+        consign: Indicates that the sign of some output LHS parameters should\
+            be constrained in the solution.
+        cons_fal: Constrain the deconvolution time series from '-FALTUNG' to be\
+            positive if 'c' is '+' or to be negative if 'c' is '-'.
+        prefix: Prefix for the output dataset (LHS parameters) filename.
+        label: Specifies sub-brick labels in the output LHS parameter dataset.
+        fitts: Prefix filename for the output fitted time series dataset.
+        errsum: Prefix filename for the error sums dataset.
+        mask: Read in dataset 'ms' to use as a mask; only voxels with nonzero\
+            values in the mask will be processed.
+        quiet: Don't print progress report messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTfitterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TFITTER_METADATA)
+    params = v_3d_tfitter_params(
+        rhs=rhs,
+        lhs=lhs,
+        polort=polort,
+        vthr=vthr,
+        faltung=faltung,
+        lsqfit=lsqfit,
+        l1fit=l1fit,
+        l2lasso=l2lasso,
+        lasso_centro_block=lasso_centro_block,
+        l2sqrtlasso=l2sqrtlasso,
+        consign=consign,
+        cons_fal=cons_fal,
+        prefix=prefix,
+        label=label,
+        fitts=fitts,
+        errsum=errsum,
+        mask=mask,
+        quiet=quiet,
+    )
+    return v_3d_tfitter_execute(params, execution)
+
+
+__all__ = [
+    "V3dTfitterOutputs",
+    "V3dTfitterParameters",
+    "V_3D_TFITTER_METADATA",
+    "v_3d_tfitter",
+    "v_3d_tfitter_params",
+]

niwrap_afni/afni/v_3d_threeto_rgb.py

@@ -0,0 +1,265 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_THREETO_RGB_METADATA = Metadata(
+    id="0e50efb1e4d4adac2b47669f62f58516c895a1cf.boutiques",
+    name="3dThreetoRGB",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dThreetoRgbParameters = typing.TypedDict('V3dThreetoRgbParameters', {
+    "__STYX_TYPE__": typing.Literal["3dThreetoRGB"],
+    "output_prefix": typing.NotRequired[str | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "fim": bool,
+    "anat": bool,
+    "input_dataset": InputPathType,
+    "input_dataset2": typing.NotRequired[InputPathType | None],
+    "input_dataset3": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dThreetoRGB": v_3d_threeto_rgb_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 {
+        "3dThreetoRGB": v_3d_threeto_rgb_outputs,
+    }.get(t)
+
+
+class V3dThreetoRgbOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_threeto_rgb(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset_head: OutputPathType | None
+    """RGB-valued dataset output"""
+    output_dataset_brik: OutputPathType | None
+    """RGB-valued dataset output"""
+
+
+def v_3d_threeto_rgb_params(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    scale_factor: float | None = None,
+    mask_dataset: InputPathType | None = None,
+    fim: bool = False,
+    anat: bool = False,
+    input_dataset2: InputPathType | None = None,
+    input_dataset3: InputPathType | None = None,
+) -> V3dThreetoRgbParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset or first dataset if three datasets are\
+            provided.
+        output_prefix: Write output into dataset with specified prefix.
+        scale_factor: Multiply input values by this factor before using as RGB.
+        mask_dataset: Only output nonzero values where the mask dataset is\
+            nonzero.
+        fim: Write result as a 'fim' type dataset (default behavior).
+        anat: Write result as a anatomical type dataset.
+        input_dataset2: Second dataset, required only if three datasets are\
+            provided.
+        input_dataset3: Third dataset, required only if three datasets are\
+            provided.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dThreetoRGB",
+        "fim": fim,
+        "anat": anat,
+        "input_dataset": input_dataset,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if scale_factor is not None:
+        params["scale_factor"] = scale_factor
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if input_dataset2 is not None:
+        params["input_dataset2"] = input_dataset2
+    if input_dataset3 is not None:
+        params["input_dataset3"] = input_dataset3
+    return params
+
+
+def v_3d_threeto_rgb_cargs(
+    params: V3dThreetoRgbParameters,
+    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("3dThreetoRGB")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("scale_factor") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale_factor"))
+        ])
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("fim"):
+        cargs.append("-fim")
+    if params.get("anat"):
+        cargs.append("-anat")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.append("[DATASET1]")
+    if params.get("input_dataset2") is not None:
+        cargs.append(execution.input_file(params.get("input_dataset2")))
+    if params.get("input_dataset3") is not None:
+        cargs.append(execution.input_file(params.get("input_dataset3")))
+    return cargs
+
+
+def v_3d_threeto_rgb_outputs(
+    params: V3dThreetoRgbParameters,
+    execution: Execution,
+) -> V3dThreetoRgbOutputs:
+    """
+    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 = V3dThreetoRgbOutputs(
+        root=execution.output_file("."),
+        output_dataset_head=execution.output_file(params.get("output_prefix") + "+rgb.HEAD") if (params.get("output_prefix") is not None) else None,
+        output_dataset_brik=execution.output_file(params.get("output_prefix") + "+rgb.BRIK") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_threeto_rgb_execute(
+    params: V3dThreetoRgbParameters,
+    execution: Execution,
+) -> V3dThreetoRgbOutputs:
+    """
+    Converts 3 sub-bricks of input to an RGB-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dThreetoRgbOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_threeto_rgb_cargs(params, execution)
+    ret = v_3d_threeto_rgb_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_threeto_rgb(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    scale_factor: float | None = None,
+    mask_dataset: InputPathType | None = None,
+    fim: bool = False,
+    anat: bool = False,
+    input_dataset2: InputPathType | None = None,
+    input_dataset3: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dThreetoRgbOutputs:
+    """
+    Converts 3 sub-bricks of input to an RGB-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset or first dataset if three datasets are\
+            provided.
+        output_prefix: Write output into dataset with specified prefix.
+        scale_factor: Multiply input values by this factor before using as RGB.
+        mask_dataset: Only output nonzero values where the mask dataset is\
+            nonzero.
+        fim: Write result as a 'fim' type dataset (default behavior).
+        anat: Write result as a anatomical type dataset.
+        input_dataset2: Second dataset, required only if three datasets are\
+            provided.
+        input_dataset3: Third dataset, required only if three datasets are\
+            provided.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dThreetoRgbOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_THREETO_RGB_METADATA)
+    params = v_3d_threeto_rgb_params(
+        output_prefix=output_prefix,
+        scale_factor=scale_factor,
+        mask_dataset=mask_dataset,
+        fim=fim,
+        anat=anat,
+        input_dataset=input_dataset,
+        input_dataset2=input_dataset2,
+        input_dataset3=input_dataset3,
+    )
+    return v_3d_threeto_rgb_execute(params, execution)
+
+
+__all__ = [
+    "V3dThreetoRgbOutputs",
+    "V3dThreetoRgbParameters",
+    "V_3D_THREETO_RGB_METADATA",
+    "v_3d_threeto_rgb",
+    "v_3d_threeto_rgb_params",
+]