niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fsread_annot.py

@@ -0,0 +1,322 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FSREAD_ANNOT_METADATA = Metadata(
+    id="1aee44cf7efa00cb2630f7f3d7fb84af69eadb4f.boutiques",
+    name="FSread_annot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FsreadAnnotParameters = typing.TypedDict('FsreadAnnotParameters', {
+    "__STYX_TYPE__": typing.Literal["FSread_annot"],
+    "infile": InputPathType,
+    "hemi": typing.NotRequired[str | None],
+    "fscmap": typing.NotRequired[InputPathType | None],
+    "fscmap_range": typing.NotRequired[list[float] | None],
+    "fsversion": typing.NotRequired[str | None],
+    "col_1d": typing.NotRequired[str | None],
+    "roi_1d": typing.NotRequired[str | None],
+    "cmap_1d": typing.NotRequired[str | None],
+    "show_fscmap": bool,
+    "dset": typing.NotRequired[str | None],
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "FSread_annot": fsread_annot_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 {
+        "FSread_annot": fsread_annot_outputs,
+    }.get(t)
+
+
+class FsreadAnnotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fsread_annot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_col_1d: OutputPathType
+    """Output 4-column 1D color file."""
+    out_roi_1d: OutputPathType
+    """Output 5-column 1D ROI file."""
+    out_niml_dset: OutputPathType
+    """Output niml formatted label dataset."""
+    out_cmap_1d: OutputPathType
+    """Output 4-column 1D color map file."""
+
+
+def fsread_annot_params(
+    infile: InputPathType,
+    hemi: str | None = None,
+    fscmap: InputPathType | None = None,
+    fscmap_range: list[float] | None = None,
+    fsversion: str | None = None,
+    col_1d: str | None = None,
+    roi_1d: str | None = None,
+    cmap_1d: str | None = None,
+    show_fscmap: bool = False,
+    dset: str | None = None,
+    help_: bool = False,
+) -> FsreadAnnotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Binary formatted FreeSurfer annotation file.
+        hemi: Specify hemisphere. HEMI is one of lh or rh. Program guesses by\
+            default.
+        fscmap: Get the colormap from the Freesurfer colormap file CMAPFILE.\
+            Colormaps inside the ANNOTFILE would be ignored.
+        fscmap_range: CMAPFILE contains multiple types of labels. The\
+            annotation values in ANNOTFILE can map to multiple labels if you do not\
+            restrict the range with iMin and iMax.
+        fsversion: VER is the annotation file vintage. Choose from 2009 or\
+            2005.
+        col_1d: Write a 4-column 1D color file.
+        roi_1d: Write a 5-column 1D roi file.
+        cmap_1d: Write a 4-column 1D color map file.
+        show_fscmap: Show the info of the colormap in the ANNOT file.
+        dset: Write the annotation and colormap as a niml formatted Label Dset.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "FSread_annot",
+        "infile": infile,
+        "show_fscmap": show_fscmap,
+        "help": help_,
+    }
+    if hemi is not None:
+        params["hemi"] = hemi
+    if fscmap is not None:
+        params["fscmap"] = fscmap
+    if fscmap_range is not None:
+        params["fscmap_range"] = fscmap_range
+    if fsversion is not None:
+        params["fsversion"] = fsversion
+    if col_1d is not None:
+        params["col_1d"] = col_1d
+    if roi_1d is not None:
+        params["roi_1d"] = roi_1d
+    if cmap_1d is not None:
+        params["cmap_1d"] = cmap_1d
+    if dset is not None:
+        params["dset"] = dset
+    return params
+
+
+def fsread_annot_cargs(
+    params: FsreadAnnotParameters,
+    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("FSread_annot")
+    cargs.extend([
+        "-input",
+        "-" + execution.input_file(params.get("infile"))
+    ])
+    if params.get("hemi") is not None:
+        cargs.extend([
+            "-hemi",
+            params.get("hemi")
+        ])
+    if params.get("fscmap") is not None:
+        cargs.extend([
+            "-FScmap",
+            execution.input_file(params.get("fscmap"))
+        ])
+    if params.get("fscmap_range") is not None:
+        cargs.extend([
+            "-FScmaprange",
+            *map(str, params.get("fscmap_range"))
+        ])
+    if params.get("fsversion") is not None:
+        cargs.extend([
+            "-FSversion",
+            params.get("fsversion")
+        ])
+    if params.get("col_1d") is not None:
+        cargs.extend([
+            "-col_1D",
+            params.get("col_1d")
+        ])
+    if params.get("roi_1d") is not None:
+        cargs.extend([
+            "-roi_1D",
+            params.get("roi_1d")
+        ])
+    if params.get("cmap_1d") is not None:
+        cargs.extend([
+            "-cmap_1D",
+            params.get("cmap_1d")
+        ])
+    if params.get("show_fscmap"):
+        cargs.append("-show_FScmap")
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset",
+            params.get("dset")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def fsread_annot_outputs(
+    params: FsreadAnnotParameters,
+    execution: Execution,
+) -> FsreadAnnotOutputs:
+    """
+    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 = FsreadAnnotOutputs(
+        root=execution.output_file("."),
+        out_col_1d=execution.output_file("annot.1D.col"),
+        out_roi_1d=execution.output_file("annot.1D.roi"),
+        out_niml_dset=execution.output_file("annot.niml.dset"),
+        out_cmap_1d=execution.output_file("annot.1D.cmap"),
+    )
+    return ret
+
+
+def fsread_annot_execute(
+    params: FsreadAnnotParameters,
+    execution: Execution,
+) -> FsreadAnnotOutputs:
+    """
+    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or a
+    colormap file for use with SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FsreadAnnotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fsread_annot_cargs(params, execution)
+    ret = fsread_annot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fsread_annot(
+    infile: InputPathType,
+    hemi: str | None = None,
+    fscmap: InputPathType | None = None,
+    fscmap_range: list[float] | None = None,
+    fsversion: str | None = None,
+    col_1d: str | None = None,
+    roi_1d: str | None = None,
+    cmap_1d: str | None = None,
+    show_fscmap: bool = False,
+    dset: str | None = None,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> FsreadAnnotOutputs:
+    """
+    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or a
+    colormap file for use with SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Binary formatted FreeSurfer annotation file.
+        hemi: Specify hemisphere. HEMI is one of lh or rh. Program guesses by\
+            default.
+        fscmap: Get the colormap from the Freesurfer colormap file CMAPFILE.\
+            Colormaps inside the ANNOTFILE would be ignored.
+        fscmap_range: CMAPFILE contains multiple types of labels. The\
+            annotation values in ANNOTFILE can map to multiple labels if you do not\
+            restrict the range with iMin and iMax.
+        fsversion: VER is the annotation file vintage. Choose from 2009 or\
+            2005.
+        col_1d: Write a 4-column 1D color file.
+        roi_1d: Write a 5-column 1D roi file.
+        cmap_1d: Write a 4-column 1D color map file.
+        show_fscmap: Show the info of the colormap in the ANNOT file.
+        dset: Write the annotation and colormap as a niml formatted Label Dset.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FsreadAnnotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSREAD_ANNOT_METADATA)
+    params = fsread_annot_params(
+        infile=infile,
+        hemi=hemi,
+        fscmap=fscmap,
+        fscmap_range=fscmap_range,
+        fsversion=fsversion,
+        col_1d=col_1d,
+        roi_1d=roi_1d,
+        cmap_1d=cmap_1d,
+        show_fscmap=show_fscmap,
+        dset=dset,
+        help_=help_,
+    )
+    return fsread_annot_execute(params, execution)
+
+
+__all__ = [
+    "FSREAD_ANNOT_METADATA",
+    "FsreadAnnotOutputs",
+    "FsreadAnnotParameters",
+    "fsread_annot",
+    "fsread_annot_params",
+]

niwrap_afni/afni/gen_epi_review_py.py

@@ -0,0 +1,292 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GEN_EPI_REVIEW_PY_METADATA = Metadata(
+    id="d8d2bfa4cbebb23bdbab47bb389c8686d9524ec8.boutiques",
+    name="gen_epi_review.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+GenEpiReviewPyParameters = typing.TypedDict('GenEpiReviewPyParameters', {
+    "__STYX_TYPE__": typing.Literal["gen_epi_review.py"],
+    "datasets": list[str],
+    "script_name": typing.NotRequired[str | None],
+    "windows": typing.NotRequired[list[str] | None],
+    "verbosity": typing.NotRequired[float | None],
+    "image_size": typing.NotRequired[list[float] | None],
+    "image_xoffset": typing.NotRequired[float | None],
+    "image_yoffset": typing.NotRequired[float | None],
+    "graph_size": typing.NotRequired[list[float] | None],
+    "graph_xoffset": typing.NotRequired[float | None],
+    "graph_yoffset": 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 {
+        "gen_epi_review.py": gen_epi_review_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 {
+    }.get(t)
+
+
+class GenEpiReviewPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `gen_epi_review_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def gen_epi_review_py_params(
+    datasets: list[str],
+    script_name: str | None = None,
+    windows: list[str] | None = None,
+    verbosity: float | None = None,
+    image_size: list[float] | None = None,
+    image_xoffset: float | None = None,
+    image_yoffset: float | None = None,
+    graph_size: list[float] | None = None,
+    graph_xoffset: float | None = None,
+    graph_yoffset: float | None = None,
+) -> GenEpiReviewPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: Specify input datasets for processing.
+        script_name: Specify the name of the generated script.
+        windows: Specify the image windows to open.
+        verbosity: Specify a verbosity level.
+        image_size: Set image dimensions, in pixels.
+        image_xoffset: Set the X-offset for the image, in pixels.
+        image_yoffset: Set the Y-offset for the image, in pixels.
+        graph_size: Set graph dimensions, in pixels.
+        graph_xoffset: Set the X-offset for the graph, in pixels.
+        graph_yoffset: Set the Y-offset for the graph, in pixels.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "gen_epi_review.py",
+        "datasets": datasets,
+    }
+    if script_name is not None:
+        params["script_name"] = script_name
+    if windows is not None:
+        params["windows"] = windows
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    if image_size is not None:
+        params["image_size"] = image_size
+    if image_xoffset is not None:
+        params["image_xoffset"] = image_xoffset
+    if image_yoffset is not None:
+        params["image_yoffset"] = image_yoffset
+    if graph_size is not None:
+        params["graph_size"] = graph_size
+    if graph_xoffset is not None:
+        params["graph_xoffset"] = graph_xoffset
+    if graph_yoffset is not None:
+        params["graph_yoffset"] = graph_yoffset
+    return params
+
+
+def gen_epi_review_py_cargs(
+    params: GenEpiReviewPyParameters,
+    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("gen_epi_review.py")
+    cargs.extend([
+        "-dsets",
+        *params.get("datasets")
+    ])
+    if params.get("script_name") is not None:
+        cargs.extend([
+            "-script",
+            params.get("script_name")
+        ])
+    if params.get("windows") is not None:
+        cargs.extend([
+            "-windows",
+            *params.get("windows")
+        ])
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    if params.get("image_size") is not None:
+        cargs.extend([
+            "-im_size",
+            *map(str, params.get("image_size"))
+        ])
+    if params.get("image_xoffset") is not None:
+        cargs.extend([
+            "-im_xoff",
+            str(params.get("image_xoffset"))
+        ])
+    if params.get("image_yoffset") is not None:
+        cargs.extend([
+            "-im_yoff",
+            str(params.get("image_yoffset"))
+        ])
+    if params.get("graph_size") is not None:
+        cargs.extend([
+            "-gr_size",
+            *map(str, params.get("graph_size"))
+        ])
+    if params.get("graph_xoffset") is not None:
+        cargs.extend([
+            "-gr_xoff",
+            str(params.get("graph_xoffset"))
+        ])
+    if params.get("graph_yoffset") is not None:
+        cargs.extend([
+            "-gr_yoff",
+            str(params.get("graph_yoffset"))
+        ])
+    return cargs
+
+
+def gen_epi_review_py_outputs(
+    params: GenEpiReviewPyParameters,
+    execution: Execution,
+) -> GenEpiReviewPyOutputs:
+    """
+    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 = GenEpiReviewPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def gen_epi_review_py_execute(
+    params: GenEpiReviewPyParameters,
+    execution: Execution,
+) -> GenEpiReviewPyOutputs:
+    """
+    Generate an AFNI processing script to review EPI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GenEpiReviewPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = gen_epi_review_py_cargs(params, execution)
+    ret = gen_epi_review_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def gen_epi_review_py(
+    datasets: list[str],
+    script_name: str | None = None,
+    windows: list[str] | None = None,
+    verbosity: float | None = None,
+    image_size: list[float] | None = None,
+    image_xoffset: float | None = None,
+    image_yoffset: float | None = None,
+    graph_size: list[float] | None = None,
+    graph_xoffset: float | None = None,
+    graph_yoffset: float | None = None,
+    runner: Runner | None = None,
+) -> GenEpiReviewPyOutputs:
+    """
+    Generate an AFNI processing script to review EPI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: Specify input datasets for processing.
+        script_name: Specify the name of the generated script.
+        windows: Specify the image windows to open.
+        verbosity: Specify a verbosity level.
+        image_size: Set image dimensions, in pixels.
+        image_xoffset: Set the X-offset for the image, in pixels.
+        image_yoffset: Set the Y-offset for the image, in pixels.
+        graph_size: Set graph dimensions, in pixels.
+        graph_xoffset: Set the X-offset for the graph, in pixels.
+        graph_yoffset: Set the Y-offset for the graph, in pixels.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GenEpiReviewPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEN_EPI_REVIEW_PY_METADATA)
+    params = gen_epi_review_py_params(
+        datasets=datasets,
+        script_name=script_name,
+        windows=windows,
+        verbosity=verbosity,
+        image_size=image_size,
+        image_xoffset=image_xoffset,
+        image_yoffset=image_yoffset,
+        graph_size=graph_size,
+        graph_xoffset=graph_xoffset,
+        graph_yoffset=graph_yoffset,
+    )
+    return gen_epi_review_py_execute(params, execution)
+
+
+__all__ = [
+    "GEN_EPI_REVIEW_PY_METADATA",
+    "GenEpiReviewPyOutputs",
+    "GenEpiReviewPyParameters",
+    "gen_epi_review_py",
+    "gen_epi_review_py_params",
+]