niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1d_correlate.py

@@ -0,0 +1,218 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_CORRELATE_METADATA = Metadata(
+    id="be0ac3e4b1a192ead53f328b4b3ecf125d8d36fe.boutiques",
+    name="1dCorrelate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dCorrelateParameters = typing.TypedDict('V1dCorrelateParameters', {
+    "__STYX_TYPE__": typing.Literal["1dCorrelate"],
+    "ktaub": bool,
+    "nboot": typing.NotRequired[float | None],
+    "alpha": typing.NotRequired[float | None],
+    "blk": bool,
+    "input_files": 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 {
+        "1dCorrelate": v_1d_correlate_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 {
+    }.get(t)
+
+
+class V1dCorrelateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_correlate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_1d_correlate_params(
+    input_files: list[InputPathType],
+    ktaub: bool = False,
+    nboot: float | None = None,
+    alpha: float | None = None,
+    blk: bool = False,
+) -> V1dCorrelateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input 1D files.
+        ktaub: Kendall's tau_b correlation (popular somewhere, maybe).
+        nboot: Set the number of bootstrap replicates.
+        alpha: Set the 2-sided confidence interval width to '100-A' percent.
+        blk: Alternate flag for variable-length block resampling.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dCorrelate",
+        "ktaub": ktaub,
+        "blk": blk,
+        "input_files": input_files,
+    }
+    if nboot is not None:
+        params["nboot"] = nboot
+    if alpha is not None:
+        params["alpha"] = alpha
+    return params
+
+
+def v_1d_correlate_cargs(
+    params: V1dCorrelateParameters,
+    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("1dCorrelate")
+    if params.get("ktaub"):
+        cargs.append("-Ktaub")
+    if params.get("nboot") is not None:
+        cargs.extend([
+            "-nboot",
+            str(params.get("nboot"))
+        ])
+    if params.get("alpha") is not None:
+        cargs.extend([
+            "-alpha",
+            str(params.get("alpha"))
+        ])
+    if params.get("blk"):
+        cargs.append("-blk")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v_1d_correlate_outputs(
+    params: V1dCorrelateParameters,
+    execution: Execution,
+) -> V1dCorrelateOutputs:
+    """
+    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 = V1dCorrelateOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_1d_correlate_execute(
+    params: V1dCorrelateParameters,
+    execution: Execution,
+) -> V1dCorrelateOutputs:
+    """
+    1dCorrelate calculates the correlation coefficients between columns of input 1D
+    files along with confidence intervals via a bootstrap procedure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dCorrelateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_correlate_cargs(params, execution)
+    ret = v_1d_correlate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_correlate(
+    input_files: list[InputPathType],
+    ktaub: bool = False,
+    nboot: float | None = None,
+    alpha: float | None = None,
+    blk: bool = False,
+    runner: Runner | None = None,
+) -> V1dCorrelateOutputs:
+    """
+    1dCorrelate calculates the correlation coefficients between columns of input 1D
+    files along with confidence intervals via a bootstrap procedure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input 1D files.
+        ktaub: Kendall's tau_b correlation (popular somewhere, maybe).
+        nboot: Set the number of bootstrap replicates.
+        alpha: Set the 2-sided confidence interval width to '100-A' percent.
+        blk: Alternate flag for variable-length block resampling.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dCorrelateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_CORRELATE_METADATA)
+    params = v_1d_correlate_params(
+        ktaub=ktaub,
+        nboot=nboot,
+        alpha=alpha,
+        blk=blk,
+        input_files=input_files,
+    )
+    return v_1d_correlate_execute(params, execution)
+
+
+__all__ = [
+    "V1dCorrelateOutputs",
+    "V1dCorrelateParameters",
+    "V_1D_CORRELATE_METADATA",
+    "v_1d_correlate",
+    "v_1d_correlate_params",
+]

niwrap_afni/afni/v_1d_dw_grad_o_mat__.py

@@ -0,0 +1,429 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_DW_GRAD_O_MAT___METADATA = Metadata(
+    id="46eee009ed5251cf0654dc7e2305bcbaecf3782b.boutiques",
+    name="1dDW_Grad_o_Mat++",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dDwGradOMatParameters = typing.TypedDict('V1dDwGradOMatParameters', {
+    "__STYX_TYPE__": typing.Literal["1dDW_Grad_o_Mat++"],
+    "in_row_vec": InputPathType,
+    "in_col_vec": InputPathType,
+    "in_col_matA": InputPathType,
+    "in_col_matT": InputPathType,
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "no_flip": bool,
+    "out_row_vec": str,
+    "out_col_vec": str,
+    "out_col_matA": str,
+    "out_col_matT": str,
+    "in_bvals": typing.NotRequired[InputPathType | None],
+    "out_col_bval": bool,
+    "out_row_bval_sep": typing.NotRequired[str | None],
+    "out_col_bval_sep": typing.NotRequired[str | None],
+    "unit_mag_out": bool,
+    "check_abs_min": typing.NotRequired[float | None],
+    "bref_mean_top": bool,
+    "put_zeros_top": bool,
+    "bmax_ref": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dDW_Grad_o_Mat++": v_1d_dw_grad_o_mat___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 {
+        "1dDW_Grad_o_Mat++": v_1d_dw_grad_o_mat___outputs,
+    }.get(t)
+
+
+class V1dDwGradOMatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_dw_grad_o_mat__(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output file of gradients or matrices"""
+    out_row_bval_file: OutputPathType | None
+    """Output b-values file in a single row"""
+    out_col_bval_file: OutputPathType | None
+    """Output b-values file in a single column"""
+
+
+def v_1d_dw_grad_o_mat___params(
+    in_row_vec: InputPathType,
+    in_col_vec: InputPathType,
+    in_col_mat_a: InputPathType,
+    in_col_mat_t: InputPathType,
+    out_row_vec: str,
+    out_col_vec: str,
+    out_col_mat_a: str,
+    out_col_mat_t: str,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    in_bvals: InputPathType | None = None,
+    out_col_bval: bool = False,
+    out_row_bval_sep: str | None = None,
+    out_col_bval_sep: str | None = None,
+    unit_mag_out: bool = False,
+    check_abs_min: float | None = None,
+    bref_mean_top: bool = False,
+    put_zeros_top: bool = False,
+    bmax_ref: float | None = None,
+) -> V1dDwGradOMatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_row_vec: Input file of 3 rows of gradients (e.g., dcm2nii-format\
+            output).
+        in_col_vec: Input file of 3 columns of gradients.
+        in_col_mat_a: Input file of 6 columns of b- or g-matrix in 'A(FNI)'\
+            diagonal first format.
+        in_col_mat_t: Input file of 6 columns of b- or g-matrix in 'T(ORTOISE)'\
+            row first format.
+        out_row_vec: Output file of 3 rows of gradients.
+        out_col_vec: Output file of 3 columns of gradients.
+        out_col_mat_a: Output file of 6 columns of b- or g-matrix in 'A(FNI)'\
+            diagonal first format.
+        out_col_mat_t: Output file of 6 columns of b- or g-matrix in\
+            'T(ORTOISE)' row first format.
+        flip_x: Change sign of first column of gradients (or of the x-component\
+            parts of the matrix).
+        flip_y: Change sign of second column of gradients (or of the\
+            y-component parts of the matrix).
+        flip_z: Change sign of third column of gradients (or of the z-component\
+            parts of the matrix).
+        no_flip: Don't change any gradient/matrix signs (default behavior).
+        in_bvals: BVAL_FILE is a file of b-values either in a single row or a\
+            single column.
+        out_col_bval: Switch to put a column of the bvalues as the first column\
+            in the output data.
+        out_row_bval_sep: Output a file of bvalues in a single row.
+        out_col_bval_sep: Output a file of bvalues in a single column.
+        unit_mag_out: Switch to scale each vector/matrix from the INFILE to\
+            either unit or zero magnitude.
+        check_abs_min: Specify the threshold to replace small negative diagonal\
+            elements with zero in the input matrix.
+        bref_mean_top: When averaging the reference 'b0' values, represent the\
+            mean of X values in the top row.
+        put_zeros_top: Add a row at the top with all zeros in the output format.
+        bmax_ref: THRESH is a scalar number below which b-values are considered\
+            zero or reference.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dDW_Grad_o_Mat++",
+        "in_row_vec": in_row_vec,
+        "in_col_vec": in_col_vec,
+        "in_col_matA": in_col_mat_a,
+        "in_col_matT": in_col_mat_t,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+        "no_flip": no_flip,
+        "out_row_vec": out_row_vec,
+        "out_col_vec": out_col_vec,
+        "out_col_matA": out_col_mat_a,
+        "out_col_matT": out_col_mat_t,
+        "out_col_bval": out_col_bval,
+        "unit_mag_out": unit_mag_out,
+        "bref_mean_top": bref_mean_top,
+        "put_zeros_top": put_zeros_top,
+    }
+    if in_bvals is not None:
+        params["in_bvals"] = in_bvals
+    if out_row_bval_sep is not None:
+        params["out_row_bval_sep"] = out_row_bval_sep
+    if out_col_bval_sep is not None:
+        params["out_col_bval_sep"] = out_col_bval_sep
+    if check_abs_min is not None:
+        params["check_abs_min"] = check_abs_min
+    if bmax_ref is not None:
+        params["bmax_ref"] = bmax_ref
+    return params
+
+
+def v_1d_dw_grad_o_mat___cargs(
+    params: V1dDwGradOMatParameters,
+    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("1dDW_Grad_o_Mat++")
+    cargs.extend([
+        "-in_row_vec",
+        execution.input_file(params.get("in_row_vec"))
+    ])
+    cargs.extend([
+        "-in_col_vec",
+        execution.input_file(params.get("in_col_vec"))
+    ])
+    cargs.extend([
+        "-in_col_matA",
+        execution.input_file(params.get("in_col_matA"))
+    ])
+    cargs.extend([
+        "-in_col_matT",
+        execution.input_file(params.get("in_col_matT"))
+    ])
+    if params.get("flip_x"):
+        cargs.append("-flip_x")
+    if params.get("flip_y"):
+        cargs.append("-flip_y")
+    if params.get("flip_z"):
+        cargs.append("-flip_z")
+    if params.get("no_flip"):
+        cargs.append("-no_flip")
+    cargs.extend([
+        "-out_row_vec",
+        params.get("out_row_vec")
+    ])
+    cargs.extend([
+        "-out_col_vec",
+        params.get("out_col_vec")
+    ])
+    cargs.extend([
+        "-out_col_matA",
+        params.get("out_col_matA")
+    ])
+    cargs.extend([
+        "-out_col_matT",
+        params.get("out_col_matT")
+    ])
+    if params.get("in_bvals") is not None:
+        cargs.extend([
+            "-in_bvals",
+            execution.input_file(params.get("in_bvals"))
+        ])
+    if params.get("out_col_bval"):
+        cargs.append("-out_col_bval")
+    if params.get("out_row_bval_sep") is not None:
+        cargs.extend([
+            "-out_row_bval_sep",
+            params.get("out_row_bval_sep")
+        ])
+    if params.get("out_col_bval_sep") is not None:
+        cargs.extend([
+            "-out_col_bval_sep",
+            params.get("out_col_bval_sep")
+        ])
+    if params.get("unit_mag_out"):
+        cargs.append("-unit_mag_out")
+    if params.get("check_abs_min") is not None:
+        cargs.extend([
+            "-check_abs_min",
+            str(params.get("check_abs_min"))
+        ])
+    if params.get("bref_mean_top"):
+        cargs.append("-bref_mean_top")
+    if params.get("put_zeros_top"):
+        cargs.append("-put_zeros_top")
+    if params.get("bmax_ref") is not None:
+        cargs.extend([
+            "-bmax_ref",
+            str(params.get("bmax_ref"))
+        ])
+    return cargs
+
+
+def v_1d_dw_grad_o_mat___outputs(
+    params: V1dDwGradOMatParameters,
+    execution: Execution,
+) -> V1dDwGradOMatOutputs:
+    """
+    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 = V1dDwGradOMatOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("out_row_vec")),
+        out_row_bval_file=execution.output_file(params.get("out_row_bval_sep")) if (params.get("out_row_bval_sep") is not None) else None,
+        out_col_bval_file=execution.output_file(params.get("out_row_bval_sep")) if (params.get("out_row_bval_sep") is not None) else None,
+    )
+    return ret
+
+
+def v_1d_dw_grad_o_mat___execute(
+    params: V1dDwGradOMatParameters,
+    execution: Execution,
+) -> V1dDwGradOMatOutputs:
+    """
+    Manipulation of diffusion-weighted (DW) gradient vector files, b-value files,
+    and b- or g-matrices with various input and output configurations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dDwGradOMatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_dw_grad_o_mat___cargs(params, execution)
+    ret = v_1d_dw_grad_o_mat___outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_dw_grad_o_mat__(
+    in_row_vec: InputPathType,
+    in_col_vec: InputPathType,
+    in_col_mat_a: InputPathType,
+    in_col_mat_t: InputPathType,
+    out_row_vec: str,
+    out_col_vec: str,
+    out_col_mat_a: str,
+    out_col_mat_t: str,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    in_bvals: InputPathType | None = None,
+    out_col_bval: bool = False,
+    out_row_bval_sep: str | None = None,
+    out_col_bval_sep: str | None = None,
+    unit_mag_out: bool = False,
+    check_abs_min: float | None = None,
+    bref_mean_top: bool = False,
+    put_zeros_top: bool = False,
+    bmax_ref: float | None = None,
+    runner: Runner | None = None,
+) -> V1dDwGradOMatOutputs:
+    """
+    Manipulation of diffusion-weighted (DW) gradient vector files, b-value files,
+    and b- or g-matrices with various input and output configurations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_row_vec: Input file of 3 rows of gradients (e.g., dcm2nii-format\
+            output).
+        in_col_vec: Input file of 3 columns of gradients.
+        in_col_mat_a: Input file of 6 columns of b- or g-matrix in 'A(FNI)'\
+            diagonal first format.
+        in_col_mat_t: Input file of 6 columns of b- or g-matrix in 'T(ORTOISE)'\
+            row first format.
+        out_row_vec: Output file of 3 rows of gradients.
+        out_col_vec: Output file of 3 columns of gradients.
+        out_col_mat_a: Output file of 6 columns of b- or g-matrix in 'A(FNI)'\
+            diagonal first format.
+        out_col_mat_t: Output file of 6 columns of b- or g-matrix in\
+            'T(ORTOISE)' row first format.
+        flip_x: Change sign of first column of gradients (or of the x-component\
+            parts of the matrix).
+        flip_y: Change sign of second column of gradients (or of the\
+            y-component parts of the matrix).
+        flip_z: Change sign of third column of gradients (or of the z-component\
+            parts of the matrix).
+        no_flip: Don't change any gradient/matrix signs (default behavior).
+        in_bvals: BVAL_FILE is a file of b-values either in a single row or a\
+            single column.
+        out_col_bval: Switch to put a column of the bvalues as the first column\
+            in the output data.
+        out_row_bval_sep: Output a file of bvalues in a single row.
+        out_col_bval_sep: Output a file of bvalues in a single column.
+        unit_mag_out: Switch to scale each vector/matrix from the INFILE to\
+            either unit or zero magnitude.
+        check_abs_min: Specify the threshold to replace small negative diagonal\
+            elements with zero in the input matrix.
+        bref_mean_top: When averaging the reference 'b0' values, represent the\
+            mean of X values in the top row.
+        put_zeros_top: Add a row at the top with all zeros in the output format.
+        bmax_ref: THRESH is a scalar number below which b-values are considered\
+            zero or reference.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dDwGradOMatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_DW_GRAD_O_MAT___METADATA)
+    params = v_1d_dw_grad_o_mat___params(
+        in_row_vec=in_row_vec,
+        in_col_vec=in_col_vec,
+        in_col_mat_a=in_col_mat_a,
+        in_col_mat_t=in_col_mat_t,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+        no_flip=no_flip,
+        out_row_vec=out_row_vec,
+        out_col_vec=out_col_vec,
+        out_col_mat_a=out_col_mat_a,
+        out_col_mat_t=out_col_mat_t,
+        in_bvals=in_bvals,
+        out_col_bval=out_col_bval,
+        out_row_bval_sep=out_row_bval_sep,
+        out_col_bval_sep=out_col_bval_sep,
+        unit_mag_out=unit_mag_out,
+        check_abs_min=check_abs_min,
+        bref_mean_top=bref_mean_top,
+        put_zeros_top=put_zeros_top,
+        bmax_ref=bmax_ref,
+    )
+    return v_1d_dw_grad_o_mat___execute(params, execution)
+
+
+__all__ = [
+    "V1dDwGradOMatOutputs",
+    "V1dDwGradOMatParameters",
+    "V_1D_DW_GRAD_O_MAT___METADATA",
+    "v_1d_dw_grad_o_mat__",
+    "v_1d_dw_grad_o_mat___params",
+]