niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mrisp_paint.py

@@ -0,0 +1,348 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRISP_PAINT_METADATA = Metadata(
+    id="ee10714d3437e3ff63bdc4e23471b26ed9cb9121.boutiques",
+    name="mrisp_paint",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrispPaintParameters = typing.TypedDict('MrispPaintParameters', {
+    "__STYX_TYPE__": typing.Literal["mrisp_paint"],
+    "template_file": InputPathType,
+    "input_surface": InputPathType,
+    "output_name": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "vertex_coords": typing.NotRequired[str | None],
+    "average_flag": typing.NotRequired[float | None],
+    "normalize_flag": bool,
+    "frame_number": typing.NotRequired[float | None],
+    "square_root_flag": bool,
+    "variance_params": typing.NotRequired[str | None],
+    "usage_flag": bool,
+    "birn_info_flag": bool,
+    "help_flag": bool,
+    "diag_vertex": typing.NotRequired[float | None],
+    "version_flag": bool,
+    "diag_write_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrisp_paint": mrisp_paint_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 {
+        "mrisp_paint": mrisp_paint_outputs,
+    }.get(t)
+
+
+class MrispPaintOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrisp_paint(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file containing a surface-worth of per-vertex values in
+    'curvature' format."""
+
+
+def mrisp_paint_params(
+    template_file: InputPathType,
+    input_surface: InputPathType,
+    output_name: str,
+    subjects_dir: str | None = None,
+    vertex_coords: str | None = None,
+    average_flag: float | None = None,
+    normalize_flag: bool = False,
+    frame_number: float | None = None,
+    square_root_flag: bool = False,
+    variance_params: str | None = None,
+    usage_flag: bool = False,
+    birn_info_flag: bool = False,
+    help_flag: bool = False,
+    diag_vertex: float | None = None,
+    version_flag: bool = False,
+    diag_write_flag: bool = False,
+) -> MrispPaintParameters:
+    """
+    Build parameters.
+    
+    Args:
+        template_file: Full path to the template file. Template may contain\
+            multiple parameters. Example: 'somepath/mytemplate.tif#1'.
+        input_surface: Full path to the input surface file, which provides the\
+            grid onto which the template data is sampled.
+        output_name: Output file name. Saves the surface-worth of per-vertex\
+            values.
+        subjects_dir: Set the SUBJECTS_DIR. Default: use environment variable.
+        vertex_coords: Treat overlay as a surface and write it into a 3 frame\
+            parameterization.
+        average_flag: Average curvature patterns a given number of times.
+        normalize_flag: Normalize curvature by variance.
+        frame_number: Paint the specified frame number to the output file.\
+            Default: 0.
+        square_root_flag: Take the square-root of the output variable.
+        variance_params: Generate variance map. Requires subject name,\
+            hemisphere, and field number.
+        usage_flag: Print usage.
+        birn_info_flag: Print BIRN-standard program information.
+        help_flag: Print help message.
+        diag_vertex: Invoke diagnostics for a specific vertex number.
+        version_flag: Print version information.
+        diag_write_flag: Write some diagnostics (DIAG_WRITE).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mrisp_paint",
+        "template_file": template_file,
+        "input_surface": input_surface,
+        "output_name": output_name,
+        "normalize_flag": normalize_flag,
+        "square_root_flag": square_root_flag,
+        "usage_flag": usage_flag,
+        "birn_info_flag": birn_info_flag,
+        "help_flag": help_flag,
+        "version_flag": version_flag,
+        "diag_write_flag": diag_write_flag,
+    }
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if vertex_coords is not None:
+        params["vertex_coords"] = vertex_coords
+    if average_flag is not None:
+        params["average_flag"] = average_flag
+    if frame_number is not None:
+        params["frame_number"] = frame_number
+    if variance_params is not None:
+        params["variance_params"] = variance_params
+    if diag_vertex is not None:
+        params["diag_vertex"] = diag_vertex
+    return params
+
+
+def mrisp_paint_cargs(
+    params: MrispPaintParameters,
+    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("mrisp_paint")
+    cargs.append(execution.input_file(params.get("template_file")))
+    cargs.append(execution.input_file(params.get("input_surface")))
+    cargs.append(params.get("output_name"))
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-SDIR",
+            params.get("subjects_dir")
+        ])
+    if params.get("vertex_coords") is not None:
+        cargs.extend([
+            "-coords",
+            params.get("vertex_coords")
+        ])
+    if params.get("average_flag") is not None:
+        cargs.extend([
+            "-A",
+            str(params.get("average_flag"))
+        ])
+    if params.get("normalize_flag"):
+        cargs.append("-N")
+    if params.get("frame_number") is not None:
+        cargs.extend([
+            "-f",
+            str(params.get("frame_number"))
+        ])
+    if params.get("square_root_flag"):
+        cargs.append("-S")
+    if params.get("variance_params") is not None:
+        cargs.extend([
+            "-variance",
+            params.get("variance_params")
+        ])
+    if params.get("usage_flag"):
+        cargs.append("-?")
+    if params.get("birn_info_flag"):
+        cargs.append("--all-info")
+    if params.get("help_flag"):
+        cargs.append("--help")
+    if params.get("diag_vertex") is not None:
+        cargs.extend([
+            "-V",
+            str(params.get("diag_vertex"))
+        ])
+    if params.get("version_flag"):
+        cargs.append("--version")
+    if params.get("diag_write_flag"):
+        cargs.append("-W")
+    return cargs
+
+
+def mrisp_paint_outputs(
+    params: MrispPaintParameters,
+    execution: Execution,
+) -> MrispPaintOutputs:
+    """
+    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 = MrispPaintOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_name")),
+    )
+    return ret
+
+
+def mrisp_paint_execute(
+    params: MrispPaintParameters,
+    execution: Execution,
+) -> MrispPaintOutputs:
+    """
+    A tool for extracting arrays from a surface-registration template file and
+    sampling them onto a surface mesh.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrispPaintOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrisp_paint_cargs(params, execution)
+    ret = mrisp_paint_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrisp_paint(
+    template_file: InputPathType,
+    input_surface: InputPathType,
+    output_name: str,
+    subjects_dir: str | None = None,
+    vertex_coords: str | None = None,
+    average_flag: float | None = None,
+    normalize_flag: bool = False,
+    frame_number: float | None = None,
+    square_root_flag: bool = False,
+    variance_params: str | None = None,
+    usage_flag: bool = False,
+    birn_info_flag: bool = False,
+    help_flag: bool = False,
+    diag_vertex: float | None = None,
+    version_flag: bool = False,
+    diag_write_flag: bool = False,
+    runner: Runner | None = None,
+) -> MrispPaintOutputs:
+    """
+    A tool for extracting arrays from a surface-registration template file and
+    sampling them onto a surface mesh.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        template_file: Full path to the template file. Template may contain\
+            multiple parameters. Example: 'somepath/mytemplate.tif#1'.
+        input_surface: Full path to the input surface file, which provides the\
+            grid onto which the template data is sampled.
+        output_name: Output file name. Saves the surface-worth of per-vertex\
+            values.
+        subjects_dir: Set the SUBJECTS_DIR. Default: use environment variable.
+        vertex_coords: Treat overlay as a surface and write it into a 3 frame\
+            parameterization.
+        average_flag: Average curvature patterns a given number of times.
+        normalize_flag: Normalize curvature by variance.
+        frame_number: Paint the specified frame number to the output file.\
+            Default: 0.
+        square_root_flag: Take the square-root of the output variable.
+        variance_params: Generate variance map. Requires subject name,\
+            hemisphere, and field number.
+        usage_flag: Print usage.
+        birn_info_flag: Print BIRN-standard program information.
+        help_flag: Print help message.
+        diag_vertex: Invoke diagnostics for a specific vertex number.
+        version_flag: Print version information.
+        diag_write_flag: Write some diagnostics (DIAG_WRITE).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrispPaintOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRISP_PAINT_METADATA)
+    params = mrisp_paint_params(
+        template_file=template_file,
+        input_surface=input_surface,
+        output_name=output_name,
+        subjects_dir=subjects_dir,
+        vertex_coords=vertex_coords,
+        average_flag=average_flag,
+        normalize_flag=normalize_flag,
+        frame_number=frame_number,
+        square_root_flag=square_root_flag,
+        variance_params=variance_params,
+        usage_flag=usage_flag,
+        birn_info_flag=birn_info_flag,
+        help_flag=help_flag,
+        diag_vertex=diag_vertex,
+        version_flag=version_flag,
+        diag_write_flag=diag_write_flag,
+    )
+    return mrisp_paint_execute(params, execution)
+
+
+__all__ = [
+    "MRISP_PAINT_METADATA",
+    "MrispPaintOutputs",
+    "MrispPaintParameters",
+    "mrisp_paint",
+    "mrisp_paint_params",
+]

niwrap_freesurfer/freesurfer/mrisp_write.py

@@ -0,0 +1,293 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRISP_WRITE_METADATA = Metadata(
+    id="7b8fc1540fc76774d461ee491e6eccf087b42779.boutiques",
+    name="mrisp_write",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrispWriteParameters = typing.TypedDict('MrispWriteParameters', {
+    "__STYX_TYPE__": typing.Literal["mrisp_write"],
+    "input_surface": InputPathType,
+    "overlay_filename": InputPathType,
+    "output_name": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "coords": typing.NotRequired[str | None],
+    "average_curvature": typing.NotRequired[float | None],
+    "correlation_matrix": typing.NotRequired[InputPathType | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "normalize_curvature": bool,
+    "verbose_vertex": typing.NotRequired[float | None],
+    "write_diagnostics": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrisp_write": mrisp_write_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 {
+        "mrisp_write": mrisp_write_outputs,
+    }.get(t)
+
+
+class MrispWriteOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrisp_write(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """A file containing a surface-worth of per-vertex values saved in spherical
+    coordinates."""
+
+
+def mrisp_write_params(
+    input_surface: InputPathType,
+    overlay_filename: InputPathType,
+    output_name: str,
+    subjects_dir: str | None = None,
+    coords: str | None = None,
+    average_curvature: float | None = None,
+    correlation_matrix: InputPathType | None = None,
+    scale_factor: float | None = None,
+    normalize_curvature: bool = False,
+    verbose_vertex: float | None = None,
+    write_diagnostics: bool = False,
+) -> MrispWriteParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Full path to input surface.
+        overlay_filename: Full path to the overlay to map.
+        output_name: Output file name. Can be full path to a .tif or .mgz file.
+        subjects_dir: Set SUBJECTS_DIR. Default: uses environment variable.
+        coords: Treat overlay as a surface and write it into a 3 frame\
+            parameterization.
+        average_curvature: Average curvature patterns navgs times.
+        correlation_matrix: Use the overlay to compute the correlation matrix\
+            within the specified label.
+        scale_factor: Scale factor to adjust resolution of the spherical map.
+        normalize_curvature: Normalize curvature by variance.
+        verbose_vertex: Invoke diagnostics for specified vertex number.
+        write_diagnostics: Write some diagnostics.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mrisp_write",
+        "input_surface": input_surface,
+        "overlay_filename": overlay_filename,
+        "output_name": output_name,
+        "normalize_curvature": normalize_curvature,
+        "write_diagnostics": write_diagnostics,
+    }
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if coords is not None:
+        params["coords"] = coords
+    if average_curvature is not None:
+        params["average_curvature"] = average_curvature
+    if correlation_matrix is not None:
+        params["correlation_matrix"] = correlation_matrix
+    if scale_factor is not None:
+        params["scale_factor"] = scale_factor
+    if verbose_vertex is not None:
+        params["verbose_vertex"] = verbose_vertex
+    return params
+
+
+def mrisp_write_cargs(
+    params: MrispWriteParameters,
+    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("mrisp_write")
+    cargs.append(execution.input_file(params.get("input_surface")))
+    cargs.append(execution.input_file(params.get("overlay_filename")))
+    cargs.append(params.get("output_name"))
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-SDIR",
+            params.get("subjects_dir")
+        ])
+    if params.get("coords") is not None:
+        cargs.extend([
+            "-coords",
+            params.get("coords")
+        ])
+    if params.get("average_curvature") is not None:
+        cargs.extend([
+            "-A",
+            str(params.get("average_curvature"))
+        ])
+    if params.get("correlation_matrix") is not None:
+        cargs.extend([
+            "-CORR",
+            execution.input_file(params.get("correlation_matrix"))
+        ])
+    if params.get("scale_factor") is not None:
+        cargs.extend([
+            "-SCALE",
+            str(params.get("scale_factor"))
+        ])
+    if params.get("normalize_curvature"):
+        cargs.append("-N")
+    if params.get("verbose_vertex") is not None:
+        cargs.extend([
+            "-V",
+            str(params.get("verbose_vertex"))
+        ])
+    if params.get("write_diagnostics"):
+        cargs.append("-W")
+    return cargs
+
+
+def mrisp_write_outputs(
+    params: MrispWriteParameters,
+    execution: Execution,
+) -> MrispWriteOutputs:
+    """
+    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 = MrispWriteOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_name")),
+    )
+    return ret
+
+
+def mrisp_write_execute(
+    params: MrispWriteParameters,
+    execution: Execution,
+) -> MrispWriteOutputs:
+    """
+    This tool converts a surface overlay on a sphere into spherical coordinates.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrispWriteOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrisp_write_cargs(params, execution)
+    ret = mrisp_write_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrisp_write(
+    input_surface: InputPathType,
+    overlay_filename: InputPathType,
+    output_name: str,
+    subjects_dir: str | None = None,
+    coords: str | None = None,
+    average_curvature: float | None = None,
+    correlation_matrix: InputPathType | None = None,
+    scale_factor: float | None = None,
+    normalize_curvature: bool = False,
+    verbose_vertex: float | None = None,
+    write_diagnostics: bool = False,
+    runner: Runner | None = None,
+) -> MrispWriteOutputs:
+    """
+    This tool converts a surface overlay on a sphere into spherical coordinates.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_surface: Full path to input surface.
+        overlay_filename: Full path to the overlay to map.
+        output_name: Output file name. Can be full path to a .tif or .mgz file.
+        subjects_dir: Set SUBJECTS_DIR. Default: uses environment variable.
+        coords: Treat overlay as a surface and write it into a 3 frame\
+            parameterization.
+        average_curvature: Average curvature patterns navgs times.
+        correlation_matrix: Use the overlay to compute the correlation matrix\
+            within the specified label.
+        scale_factor: Scale factor to adjust resolution of the spherical map.
+        normalize_curvature: Normalize curvature by variance.
+        verbose_vertex: Invoke diagnostics for specified vertex number.
+        write_diagnostics: Write some diagnostics.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrispWriteOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRISP_WRITE_METADATA)
+    params = mrisp_write_params(
+        input_surface=input_surface,
+        overlay_filename=overlay_filename,
+        output_name=output_name,
+        subjects_dir=subjects_dir,
+        coords=coords,
+        average_curvature=average_curvature,
+        correlation_matrix=correlation_matrix,
+        scale_factor=scale_factor,
+        normalize_curvature=normalize_curvature,
+        verbose_vertex=verbose_vertex,
+        write_diagnostics=write_diagnostics,
+    )
+    return mrisp_write_execute(params, execution)
+
+
+__all__ = [
+    "MRISP_WRITE_METADATA",
+    "MrispWriteOutputs",
+    "MrispWriteParameters",
+    "mrisp_write",
+    "mrisp_write_params",
+]