niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/examine_xmat.py

@@ -0,0 +1,280 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+EXAMINE_XMAT_METADATA = Metadata(
+    id="5dc4f1bb85e99556ff1ac2fbae72bb95c00b5ac2.boutiques",
+    name="ExamineXmat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ExamineXmatParameters = typing.TypedDict('ExamineXmatParameters', {
+    "__STYX_TYPE__": typing.Literal["ExamineXmat"],
+    "input_file": typing.NotRequired[InputPathType | None],
+    "interactive": bool,
+    "prefix": typing.NotRequired[str | None],
+    "cprefix": typing.NotRequired[str | None],
+    "pprefix": typing.NotRequired[str | None],
+    "select": typing.NotRequired[str | None],
+    "msg_trace": bool,
+    "verbosity": 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 {
+        "ExamineXmat": examine_xmat_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 {
+        "ExamineXmat": examine_xmat_outputs,
+    }.get(t)
+
+
+class ExamineXmatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `examine_xmat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    plot_image: OutputPathType | None
+    """Output plot image"""
+    plot_image_png: OutputPathType | None
+    """Output plot image"""
+    plot_image_pdf: OutputPathType | None
+    """Output plot image"""
+    cor_image: OutputPathType | None
+    """Output cor image"""
+    plot_image_prefix: OutputPathType | None
+    """Output plot image"""
+
+
+def examine_xmat_params(
+    input_file: InputPathType | None = None,
+    interactive: bool = False,
+    prefix: str | None = None,
+    cprefix: str | None = None,
+    pprefix: str | None = None,
+    select_: str | None = None,
+    msg_trace: bool = False,
+    verbosity: float | None = None,
+) -> ExamineXmatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: xmat file to plot.
+        interactive: Run ExamineXmat in interactive mode. This is the default\
+            if -prefix is not given. If -interactive is used with -prefix, the last\
+            plot you see is the plot saved to file.
+        prefix: Prefix of plot image and cor image.
+        cprefix: Prefix of cor image only.
+        pprefix: Prefix of plot image only.
+        select_: What to plot. Selection strings to specify regressors.
+        msg_trace: Output trace information along with errors and notices.
+        verbosity: Verbosity level. 0 for quiet, 1 or more for talkative.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ExamineXmat",
+        "interactive": interactive,
+        "msg_trace": msg_trace,
+    }
+    if input_file is not None:
+        params["input_file"] = input_file
+    if prefix is not None:
+        params["prefix"] = prefix
+    if cprefix is not None:
+        params["cprefix"] = cprefix
+    if pprefix is not None:
+        params["pprefix"] = pprefix
+    if select_ is not None:
+        params["select"] = select_
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def examine_xmat_cargs(
+    params: ExamineXmatParameters,
+    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("ExamineXmat")
+    if params.get("input_file") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_file"))
+        ])
+    if params.get("interactive"):
+        cargs.append("-interactive")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("cprefix") is not None:
+        cargs.extend([
+            "-cprefix",
+            params.get("cprefix")
+        ])
+    if params.get("pprefix") is not None:
+        cargs.extend([
+            "-pprefix",
+            params.get("pprefix")
+        ])
+    if params.get("select") is not None:
+        cargs.extend([
+            "-select",
+            params.get("select")
+        ])
+    if params.get("msg_trace"):
+        cargs.append("-msg.trace")
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def examine_xmat_outputs(
+    params: ExamineXmatParameters,
+    execution: Execution,
+) -> ExamineXmatOutputs:
+    """
+    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 = ExamineXmatOutputs(
+        root=execution.output_file("."),
+        plot_image=execution.output_file(params.get("prefix") + ".jpg") if (params.get("prefix") is not None) else None,
+        plot_image_png=execution.output_file(params.get("prefix") + ".png") if (params.get("prefix") is not None) else None,
+        plot_image_pdf=execution.output_file(params.get("prefix") + ".pdf") if (params.get("prefix") is not None) else None,
+        cor_image=execution.output_file(params.get("cprefix") + ".jpg") if (params.get("cprefix") is not None) else None,
+        plot_image_prefix=execution.output_file(params.get("pprefix") + ".jpg") if (params.get("pprefix") is not None) else None,
+    )
+    return ret
+
+
+def examine_xmat_execute(
+    params: ExamineXmatParameters,
+    execution: Execution,
+) -> ExamineXmatOutputs:
+    """
+    A program for examining the design matrix generated by 3dDeconvolve.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ExamineXmatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = examine_xmat_cargs(params, execution)
+    ret = examine_xmat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def examine_xmat(
+    input_file: InputPathType | None = None,
+    interactive: bool = False,
+    prefix: str | None = None,
+    cprefix: str | None = None,
+    pprefix: str | None = None,
+    select_: str | None = None,
+    msg_trace: bool = False,
+    verbosity: float | None = None,
+    runner: Runner | None = None,
+) -> ExamineXmatOutputs:
+    """
+    A program for examining the design matrix generated by 3dDeconvolve.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: xmat file to plot.
+        interactive: Run ExamineXmat in interactive mode. This is the default\
+            if -prefix is not given. If -interactive is used with -prefix, the last\
+            plot you see is the plot saved to file.
+        prefix: Prefix of plot image and cor image.
+        cprefix: Prefix of cor image only.
+        pprefix: Prefix of plot image only.
+        select_: What to plot. Selection strings to specify regressors.
+        msg_trace: Output trace information along with errors and notices.
+        verbosity: Verbosity level. 0 for quiet, 1 or more for talkative.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ExamineXmatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EXAMINE_XMAT_METADATA)
+    params = examine_xmat_params(
+        input_file=input_file,
+        interactive=interactive,
+        prefix=prefix,
+        cprefix=cprefix,
+        pprefix=pprefix,
+        select_=select_,
+        msg_trace=msg_trace,
+        verbosity=verbosity,
+    )
+    return examine_xmat_execute(params, execution)
+
+
+__all__ = [
+    "EXAMINE_XMAT_METADATA",
+    "ExamineXmatOutputs",
+    "ExamineXmatParameters",
+    "examine_xmat",
+    "examine_xmat_params",
+]

niwrap_afni/afni/fat_mat2d_plot_py.py

@@ -0,0 +1,428 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_MAT2D_PLOT_PY_METADATA = Metadata(
+    id="4a1c04bfb1114a4c4dfde20fda4aea87cabad529.boutiques",
+    name="fat_mat2d_plot.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatMat2dPlotPyParameters = typing.TypedDict('FatMat2dPlotPyParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_mat2d_plot.py"],
+    "input_file": InputPathType,
+    "matrices": typing.NotRequired[list[str] | None],
+    "prefix": typing.NotRequired[str | None],
+    "file_type": typing.NotRequired[str | None],
+    "dpi": typing.NotRequired[float | None],
+    "min_colorbar": typing.NotRequired[float | None],
+    "max_colorbar": typing.NotRequired[float | None],
+    "fs_xticks": typing.NotRequired[float | None],
+    "fs_yticks": typing.NotRequired[float | None],
+    "fs_title": typing.NotRequired[float | None],
+    "fs_cbar": typing.NotRequired[float | None],
+    "cbar_n_intervals": typing.NotRequired[float | None],
+    "cbar": typing.NotRequired[str | None],
+    "cbar_width_perc": typing.NotRequired[float | None],
+    "no_colorbar": bool,
+    "figsize_x": typing.NotRequired[float | None],
+    "figsize_y": typing.NotRequired[float | None],
+    "hold_image": bool,
+    "tight_layout": bool,
+    "xticks_off": bool,
+    "yticks_off": bool,
+    "version": bool,
+    "date": bool,
+    "help": bool,
+    "help_view": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_mat2d_plot.py": fat_mat2d_plot_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 {
+        "fat_mat2d_plot.py": fat_mat2d_plot_py_outputs,
+    }.get(t)
+
+
+class FatMat2dPlotPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_mat2d_plot_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType | None
+    """Individual image files of matrices; these can contain colorbars, as
+    well."""
+
+
+def fat_mat2d_plot_py_params(
+    input_file: InputPathType,
+    matrices: list[str] | None = None,
+    prefix: str | None = None,
+    file_type: str | None = None,
+    dpi: float | None = None,
+    min_colorbar: float | None = None,
+    max_colorbar: float | None = None,
+    fs_xticks: float | None = None,
+    fs_yticks: float | None = None,
+    fs_title: float | None = None,
+    fs_cbar: float | None = None,
+    cbar_n_intervals: float | None = None,
+    cbar: str | None = None,
+    cbar_width_perc: float | None = None,
+    no_colorbar: bool = False,
+    figsize_x: float | None = None,
+    figsize_y: float | None = None,
+    hold_image: bool = False,
+    tight_layout: bool = False,
+    xticks_off: bool = False,
+    yticks_off: bool = False,
+    version: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    help_view: bool = False,
+) -> FatMat2dPlotPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Name of *.netcc or *.grid file with matrices to be plotted.
+        matrices: List of matrices to be plotted, identified by their parameter\
+            name. If no list is provided, then all matrices in the input file will\
+            be plotted.
+        prefix: Output basename for image(s). Note that this can include path\
+            information, but the name of each matrix and the file extension will be\
+            appended to it.
+        file_type: Filetype, given as extension (e.g., png, jpg). Available\
+            filetypes depend slightly on your OS and setup.
+        dpi: Spatial resolution (dots per inch) of output images.
+        min_colorbar: Minimum value of the colorbar.
+        max_colorbar: Maximum value of the colorbar.
+        fs_xticks: Font size of ticks along the x-axis.
+        fs_yticks: Font size of ticks along the y-axis.
+        fs_title: Font size of the title.
+        fs_cbar: Font size of the colorbar.
+        cbar_n_intervals: Number of intervals on colorbars for enumeration\
+            purposes. This controls how many numbers appear along the colorbar\
+            (which would be NI +1).
+        cbar: Name of the colorbar to use. The available colormaps can be found\
+            online.
+        cbar_width_perc: Width of the colorbar as a percentage of the image.
+        no_colorbar: Disable the colorbar in the image.
+        figsize_x: Width of the created image in inches.
+        figsize_y: Height of the created image in inches.
+        hold_image: In addition to saving an image file, open the image and\
+            keep displaying it until a key is pressed in the terminal.
+        tight_layout: Use matplotlib's tight layout functionality in arranging\
+            the plot.
+        xticks_off: Don't display labels along the x-axis.
+        yticks_off: Don't display labels along the y-axis.
+        version: Display the version number of the program.
+        date: Display the release/editing date of the current version.
+        help_: Display help in the terminal.
+        help_view: Display help in a separate text editor.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_mat2d_plot.py",
+        "input_file": input_file,
+        "no_colorbar": no_colorbar,
+        "hold_image": hold_image,
+        "tight_layout": tight_layout,
+        "xticks_off": xticks_off,
+        "yticks_off": yticks_off,
+        "version": version,
+        "date": date,
+        "help": help_,
+        "help_view": help_view,
+    }
+    if matrices is not None:
+        params["matrices"] = matrices
+    if prefix is not None:
+        params["prefix"] = prefix
+    if file_type is not None:
+        params["file_type"] = file_type
+    if dpi is not None:
+        params["dpi"] = dpi
+    if min_colorbar is not None:
+        params["min_colorbar"] = min_colorbar
+    if max_colorbar is not None:
+        params["max_colorbar"] = max_colorbar
+    if fs_xticks is not None:
+        params["fs_xticks"] = fs_xticks
+    if fs_yticks is not None:
+        params["fs_yticks"] = fs_yticks
+    if fs_title is not None:
+        params["fs_title"] = fs_title
+    if fs_cbar is not None:
+        params["fs_cbar"] = fs_cbar
+    if cbar_n_intervals is not None:
+        params["cbar_n_intervals"] = cbar_n_intervals
+    if cbar is not None:
+        params["cbar"] = cbar
+    if cbar_width_perc is not None:
+        params["cbar_width_perc"] = cbar_width_perc
+    if figsize_x is not None:
+        params["figsize_x"] = figsize_x
+    if figsize_y is not None:
+        params["figsize_y"] = figsize_y
+    return params
+
+
+def fat_mat2d_plot_py_cargs(
+    params: FatMat2dPlotPyParameters,
+    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("fat_mat2d_plot.py")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("matrices") is not None:
+        cargs.extend(params.get("matrices"))
+    if params.get("prefix") is not None:
+        cargs.append(params.get("prefix"))
+    if params.get("file_type") is not None:
+        cargs.append(params.get("file_type"))
+    if params.get("dpi") is not None:
+        cargs.append(str(params.get("dpi")))
+    if params.get("min_colorbar") is not None:
+        cargs.append(str(params.get("min_colorbar")))
+    if params.get("max_colorbar") is not None:
+        cargs.append(str(params.get("max_colorbar")))
+    if params.get("fs_xticks") is not None:
+        cargs.append(str(params.get("fs_xticks")))
+    if params.get("fs_yticks") is not None:
+        cargs.append(str(params.get("fs_yticks")))
+    if params.get("fs_title") is not None:
+        cargs.append(str(params.get("fs_title")))
+    if params.get("fs_cbar") is not None:
+        cargs.append(str(params.get("fs_cbar")))
+    if params.get("cbar_n_intervals") is not None:
+        cargs.append(str(params.get("cbar_n_intervals")))
+    if params.get("cbar") is not None:
+        cargs.append(params.get("cbar"))
+    if params.get("cbar_width_perc") is not None:
+        cargs.append(str(params.get("cbar_width_perc")))
+    if params.get("no_colorbar"):
+        cargs.append("-cbar_off")
+    if params.get("figsize_x") is not None:
+        cargs.append(str(params.get("figsize_x")))
+    if params.get("figsize_y") is not None:
+        cargs.append(str(params.get("figsize_y")))
+    if params.get("hold_image"):
+        cargs.append("-hold_image")
+    if params.get("tight_layout"):
+        cargs.append("-tight_layout")
+    if params.get("xticks_off"):
+        cargs.append("-xticks_off")
+    if params.get("yticks_off"):
+        cargs.append("-yticks_off")
+    if params.get("version"):
+        cargs.append("-ver")
+    if params.get("date"):
+        cargs.append("-date")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("help_view"):
+        cargs.append("-hview")
+    return cargs
+
+
+def fat_mat2d_plot_py_outputs(
+    params: FatMat2dPlotPyParameters,
+    execution: Execution,
+) -> FatMat2dPlotPyOutputs:
+    """
+    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 = FatMat2dPlotPyOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("prefix") + "_[MATRIX_NAME]." + params.get("file_type")) if (params.get("prefix") is not None and params.get("file_type") is not None) else None,
+    )
+    return ret
+
+
+def fat_mat2d_plot_py_execute(
+    params: FatMat2dPlotPyParameters,
+    execution: Execution,
+) -> FatMat2dPlotPyOutputs:
+    """
+    Plots simple matrices output from 3dNetCorr (*.netcc) and 3dTrackID (*.grid).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatMat2dPlotPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_mat2d_plot_py_cargs(params, execution)
+    ret = fat_mat2d_plot_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_mat2d_plot_py(
+    input_file: InputPathType,
+    matrices: list[str] | None = None,
+    prefix: str | None = None,
+    file_type: str | None = None,
+    dpi: float | None = None,
+    min_colorbar: float | None = None,
+    max_colorbar: float | None = None,
+    fs_xticks: float | None = None,
+    fs_yticks: float | None = None,
+    fs_title: float | None = None,
+    fs_cbar: float | None = None,
+    cbar_n_intervals: float | None = None,
+    cbar: str | None = None,
+    cbar_width_perc: float | None = None,
+    no_colorbar: bool = False,
+    figsize_x: float | None = None,
+    figsize_y: float | None = None,
+    hold_image: bool = False,
+    tight_layout: bool = False,
+    xticks_off: bool = False,
+    yticks_off: bool = False,
+    version: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    help_view: bool = False,
+    runner: Runner | None = None,
+) -> FatMat2dPlotPyOutputs:
+    """
+    Plots simple matrices output from 3dNetCorr (*.netcc) and 3dTrackID (*.grid).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Name of *.netcc or *.grid file with matrices to be plotted.
+        matrices: List of matrices to be plotted, identified by their parameter\
+            name. If no list is provided, then all matrices in the input file will\
+            be plotted.
+        prefix: Output basename for image(s). Note that this can include path\
+            information, but the name of each matrix and the file extension will be\
+            appended to it.
+        file_type: Filetype, given as extension (e.g., png, jpg). Available\
+            filetypes depend slightly on your OS and setup.
+        dpi: Spatial resolution (dots per inch) of output images.
+        min_colorbar: Minimum value of the colorbar.
+        max_colorbar: Maximum value of the colorbar.
+        fs_xticks: Font size of ticks along the x-axis.
+        fs_yticks: Font size of ticks along the y-axis.
+        fs_title: Font size of the title.
+        fs_cbar: Font size of the colorbar.
+        cbar_n_intervals: Number of intervals on colorbars for enumeration\
+            purposes. This controls how many numbers appear along the colorbar\
+            (which would be NI +1).
+        cbar: Name of the colorbar to use. The available colormaps can be found\
+            online.
+        cbar_width_perc: Width of the colorbar as a percentage of the image.
+        no_colorbar: Disable the colorbar in the image.
+        figsize_x: Width of the created image in inches.
+        figsize_y: Height of the created image in inches.
+        hold_image: In addition to saving an image file, open the image and\
+            keep displaying it until a key is pressed in the terminal.
+        tight_layout: Use matplotlib's tight layout functionality in arranging\
+            the plot.
+        xticks_off: Don't display labels along the x-axis.
+        yticks_off: Don't display labels along the y-axis.
+        version: Display the version number of the program.
+        date: Display the release/editing date of the current version.
+        help_: Display help in the terminal.
+        help_view: Display help in a separate text editor.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatMat2dPlotPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MAT2D_PLOT_PY_METADATA)
+    params = fat_mat2d_plot_py_params(
+        input_file=input_file,
+        matrices=matrices,
+        prefix=prefix,
+        file_type=file_type,
+        dpi=dpi,
+        min_colorbar=min_colorbar,
+        max_colorbar=max_colorbar,
+        fs_xticks=fs_xticks,
+        fs_yticks=fs_yticks,
+        fs_title=fs_title,
+        fs_cbar=fs_cbar,
+        cbar_n_intervals=cbar_n_intervals,
+        cbar=cbar,
+        cbar_width_perc=cbar_width_perc,
+        no_colorbar=no_colorbar,
+        figsize_x=figsize_x,
+        figsize_y=figsize_y,
+        hold_image=hold_image,
+        tight_layout=tight_layout,
+        xticks_off=xticks_off,
+        yticks_off=yticks_off,
+        version=version,
+        date=date,
+        help_=help_,
+        help_view=help_view,
+    )
+    return fat_mat2d_plot_py_execute(params, execution)
+
+
+__all__ = [
+    "FAT_MAT2D_PLOT_PY_METADATA",
+    "FatMat2dPlotPyOutputs",
+    "FatMat2dPlotPyParameters",
+    "fat_mat2d_plot_py",
+    "fat_mat2d_plot_py_params",
+]