niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/xmat_tool_py.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+XMAT_TOOL_PY_METADATA = Metadata(
+    id="3a6bcb8aee2e7ab05a9a212e21f7dfef419b3b43.boutiques",
+    name="xmat_tool.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+XmatToolPyParameters = typing.TypedDict('XmatToolPyParameters', {
+    "__STYX_TYPE__": typing.Literal["xmat_tool.py"],
+    "no_gui": bool,
+    "load_xmat": typing.NotRequired[InputPathType | None],
+    "load_1d": typing.NotRequired[InputPathType | None],
+    "choose_cols": typing.NotRequired[str | None],
+    "choose_nonzero_cols": bool,
+    "chrono": bool,
+    "cormat_cutoff": typing.NotRequired[float | None],
+    "cosmat_cutoff": typing.NotRequired[float | None],
+    "cosmat_motion": bool,
+    "verb": typing.NotRequired[float | None],
+    "show_col_types": bool,
+    "show_conds": bool,
+    "show_cormat": bool,
+    "show_cormat_warnings": bool,
+    "show_cosmat": bool,
+    "show_cosmat_warnings": bool,
+    "show_fit_betas": bool,
+    "show_fit_ts": bool,
+    "show_xmat": bool,
+    "show_1d": bool,
+    "gui_plot_xmat_as_one": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "xmat_tool.py": xmat_tool_py_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 {
+        "xmat_tool.py": xmat_tool_py_outputs,
+    }.get(t)
+
+
+class XmatToolPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `xmat_tool_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_fitts: OutputPathType
+    """Output fit time series"""
+
+
+def xmat_tool_py_params(
+    no_gui: bool = False,
+    load_xmat: InputPathType | None = None,
+    load_1d: InputPathType | None = None,
+    choose_cols: str | None = None,
+    choose_nonzero_cols: bool = False,
+    chrono: bool = False,
+    cormat_cutoff: float | None = None,
+    cosmat_cutoff: float | None = None,
+    cosmat_motion: bool = False,
+    verb: float | None = None,
+    show_col_types: bool = False,
+    show_conds: bool = False,
+    show_cormat: bool = False,
+    show_cormat_warnings: bool = False,
+    show_cosmat: bool = False,
+    show_cosmat_warnings: bool = False,
+    show_fit_betas: bool = False,
+    show_fit_ts: bool = False,
+    show_xmat: bool = False,
+    show_1d: bool = False,
+    gui_plot_xmat_as_one: bool = False,
+) -> XmatToolPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        no_gui: Do not start the GUI.
+        load_xmat: Load the AFNI X-matrix.
+        load_1d: Load the 1D time series.
+        choose_cols: Select columns to fit against.
+        choose_nonzero_cols: Select only non-zero columns.
+        chrono: Apply options chronologically.
+        cormat_cutoff: Set min cutoff for correlation matrix warnings.
+        cosmat_cutoff: Set min cutoff for cosine matrix warnings.
+        cosmat_motion: Include motion in cosine matrix warnings.
+        verb: Set the verbose level. Valid levels are currently 0..5.
+        show_col_types: Display columns by regressor types.
+        show_conds: Display a list of condition numbers.
+        show_cormat: Display the correlation matrix.
+        show_cormat_warnings: Show correlation matrix warnings.
+        show_cosmat: Display the cosine matrix.
+        show_cosmat_warnings: Show cosine matrix warnings.
+        show_fit_betas: Show fit betas.
+        show_fit_ts: Show fit time series.
+        show_xmat: Display general X-matrix information.
+        show_1d: Display general 1D information.
+        gui_plot_xmat_as_one: Plot Xmat columns on single axis.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "xmat_tool.py",
+        "no_gui": no_gui,
+        "choose_nonzero_cols": choose_nonzero_cols,
+        "chrono": chrono,
+        "cosmat_motion": cosmat_motion,
+        "show_col_types": show_col_types,
+        "show_conds": show_conds,
+        "show_cormat": show_cormat,
+        "show_cormat_warnings": show_cormat_warnings,
+        "show_cosmat": show_cosmat,
+        "show_cosmat_warnings": show_cosmat_warnings,
+        "show_fit_betas": show_fit_betas,
+        "show_fit_ts": show_fit_ts,
+        "show_xmat": show_xmat,
+        "show_1d": show_1d,
+        "gui_plot_xmat_as_one": gui_plot_xmat_as_one,
+    }
+    if load_xmat is not None:
+        params["load_xmat"] = load_xmat
+    if load_1d is not None:
+        params["load_1d"] = load_1d
+    if choose_cols is not None:
+        params["choose_cols"] = choose_cols
+    if cormat_cutoff is not None:
+        params["cormat_cutoff"] = cormat_cutoff
+    if cosmat_cutoff is not None:
+        params["cosmat_cutoff"] = cosmat_cutoff
+    if verb is not None:
+        params["verb"] = verb
+    return params
+
+
+def xmat_tool_py_cargs(
+    params: XmatToolPyParameters,
+    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("xmat_tool.py")
+    if params.get("no_gui"):
+        cargs.append("-no_gui")
+    if params.get("load_xmat") is not None:
+        cargs.extend([
+            "-load_xmat",
+            execution.input_file(params.get("load_xmat"))
+        ])
+    if params.get("load_1d") is not None:
+        cargs.extend([
+            "-load_1D",
+            execution.input_file(params.get("load_1d"))
+        ])
+    if params.get("choose_cols") is not None:
+        cargs.extend([
+            "-choose_cols",
+            params.get("choose_cols")
+        ])
+    if params.get("choose_nonzero_cols"):
+        cargs.append("-choose_nonzero_cols")
+    if params.get("chrono"):
+        cargs.append("-chrono")
+    if params.get("cormat_cutoff") is not None:
+        cargs.extend([
+            "-cormat_cutoff",
+            str(params.get("cormat_cutoff"))
+        ])
+    if params.get("cosmat_cutoff") is not None:
+        cargs.extend([
+            "-cosmat_cutoff",
+            str(params.get("cosmat_cutoff"))
+        ])
+    if params.get("cosmat_motion"):
+        cargs.append("-cosmat_motion")
+    if params.get("verb") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb"))
+        ])
+    if params.get("show_col_types"):
+        cargs.append("-show_col_types")
+    if params.get("show_conds"):
+        cargs.append("-show_conds")
+    if params.get("show_cormat"):
+        cargs.append("-show_cormat")
+    if params.get("show_cormat_warnings"):
+        cargs.append("-show_cormat_warnings")
+    if params.get("show_cosmat"):
+        cargs.append("-show_cosmat")
+    if params.get("show_cosmat_warnings"):
+        cargs.append("-show_cosmat_warnings")
+    if params.get("show_fit_betas"):
+        cargs.append("-show_fit_betas")
+    if params.get("show_fit_ts"):
+        cargs.append("-show_fit_ts")
+    if params.get("show_xmat"):
+        cargs.append("-show_xmat")
+    if params.get("show_1d"):
+        cargs.append("-show_1D")
+    if params.get("gui_plot_xmat_as_one"):
+        cargs.append("-gui_plot_xmat_as_one")
+    return cargs
+
+
+def xmat_tool_py_outputs(
+    params: XmatToolPyParameters,
+    execution: Execution,
+) -> XmatToolPyOutputs:
+    """
+    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 = XmatToolPyOutputs(
+        root=execution.output_file("."),
+        output_fitts=execution.output_file("fitts.1D"),
+    )
+    return ret
+
+
+def xmat_tool_py_execute(
+    params: XmatToolPyParameters,
+    execution: Execution,
+) -> XmatToolPyOutputs:
+    """
+    A tool for evaluating an AFNI X-matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `XmatToolPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = xmat_tool_py_cargs(params, execution)
+    ret = xmat_tool_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def xmat_tool_py(
+    no_gui: bool = False,
+    load_xmat: InputPathType | None = None,
+    load_1d: InputPathType | None = None,
+    choose_cols: str | None = None,
+    choose_nonzero_cols: bool = False,
+    chrono: bool = False,
+    cormat_cutoff: float | None = None,
+    cosmat_cutoff: float | None = None,
+    cosmat_motion: bool = False,
+    verb: float | None = None,
+    show_col_types: bool = False,
+    show_conds: bool = False,
+    show_cormat: bool = False,
+    show_cormat_warnings: bool = False,
+    show_cosmat: bool = False,
+    show_cosmat_warnings: bool = False,
+    show_fit_betas: bool = False,
+    show_fit_ts: bool = False,
+    show_xmat: bool = False,
+    show_1d: bool = False,
+    gui_plot_xmat_as_one: bool = False,
+    runner: Runner | None = None,
+) -> XmatToolPyOutputs:
+    """
+    A tool for evaluating an AFNI X-matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        no_gui: Do not start the GUI.
+        load_xmat: Load the AFNI X-matrix.
+        load_1d: Load the 1D time series.
+        choose_cols: Select columns to fit against.
+        choose_nonzero_cols: Select only non-zero columns.
+        chrono: Apply options chronologically.
+        cormat_cutoff: Set min cutoff for correlation matrix warnings.
+        cosmat_cutoff: Set min cutoff for cosine matrix warnings.
+        cosmat_motion: Include motion in cosine matrix warnings.
+        verb: Set the verbose level. Valid levels are currently 0..5.
+        show_col_types: Display columns by regressor types.
+        show_conds: Display a list of condition numbers.
+        show_cormat: Display the correlation matrix.
+        show_cormat_warnings: Show correlation matrix warnings.
+        show_cosmat: Display the cosine matrix.
+        show_cosmat_warnings: Show cosine matrix warnings.
+        show_fit_betas: Show fit betas.
+        show_fit_ts: Show fit time series.
+        show_xmat: Display general X-matrix information.
+        show_1d: Display general 1D information.
+        gui_plot_xmat_as_one: Plot Xmat columns on single axis.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `XmatToolPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XMAT_TOOL_PY_METADATA)
+    params = xmat_tool_py_params(
+        no_gui=no_gui,
+        load_xmat=load_xmat,
+        load_1d=load_1d,
+        choose_cols=choose_cols,
+        choose_nonzero_cols=choose_nonzero_cols,
+        chrono=chrono,
+        cormat_cutoff=cormat_cutoff,
+        cosmat_cutoff=cosmat_cutoff,
+        cosmat_motion=cosmat_motion,
+        verb=verb,
+        show_col_types=show_col_types,
+        show_conds=show_conds,
+        show_cormat=show_cormat,
+        show_cormat_warnings=show_cormat_warnings,
+        show_cosmat=show_cosmat,
+        show_cosmat_warnings=show_cosmat_warnings,
+        show_fit_betas=show_fit_betas,
+        show_fit_ts=show_fit_ts,
+        show_xmat=show_xmat,
+        show_1d=show_1d,
+        gui_plot_xmat_as_one=gui_plot_xmat_as_one,
+    )
+    return xmat_tool_py_execute(params, execution)
+
+
+__all__ = [
+    "XMAT_TOOL_PY_METADATA",
+    "XmatToolPyOutputs",
+    "XmatToolPyParameters",
+    "xmat_tool_py",
+    "xmat_tool_py_params",
+]

niwrap_afni-0.5.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: niwrap_afni
+Version: 0.5.0
+Summary: NiWrap wrappers for AFNI.
+Author-email: CMI DAIR <dair@childmind.org>
+License-Expression: LGPL-2.1
+Requires-Python: >=3.10
+Requires-Dist: styxdefs~=0.5.0