niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surface_metrics.py

@@ -0,0 +1,377 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURFACE_METRICS_METADATA = Metadata(
+    id="5e58dccd9bd1540ac2ae342efc61a7a9fc45c4c2.boutiques",
+    name="SurfaceMetrics",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfaceMetricsParameters = typing.TypedDict('SurfaceMetricsParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfaceMetrics"],
+    "internal_nodes": bool,
+    "internal_nodes_1": bool,
+    "internal_nodes_2": bool,
+    "internal_nodes_3": bool,
+    "internal_nodes_4": bool,
+    "internal_nodes_5": bool,
+    "internal_nodes_6": bool,
+    "internal_nodes_7": bool,
+    "internal_nodes_8": bool,
+    "internal_nodes_9": bool,
+    "internal_nodes_10": bool,
+    "internal_nodes_11": bool,
+    "internal_nodes_12": bool,
+    "internal_nodes_13": bool,
+    "internal_nodes_14": bool,
+    "internal_nodes_15": bool,
+    "internal_nodes_16": bool,
+    "internal_nodes_17": bool,
+    "internal_nodes_18": bool,
+    "internal_nodes_19": bool,
+    "surf1": str,
+    "tlrc": bool,
+    "prefix": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfaceMetrics": surface_metrics_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 SurfaceMetricsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surface_metrics(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def surface_metrics_params(
+    surf1: str,
+    internal_nodes: bool = False,
+    internal_nodes_1: bool = False,
+    internal_nodes_2: bool = False,
+    internal_nodes_3: bool = False,
+    internal_nodes_4: bool = False,
+    internal_nodes_5: bool = False,
+    internal_nodes_6: bool = False,
+    internal_nodes_7: bool = False,
+    internal_nodes_8: bool = False,
+    internal_nodes_9: bool = False,
+    internal_nodes_10: bool = False,
+    internal_nodes_11: bool = False,
+    internal_nodes_12: bool = False,
+    internal_nodes_13: bool = False,
+    internal_nodes_14: bool = False,
+    internal_nodes_15: bool = False,
+    internal_nodes_16: bool = False,
+    internal_nodes_17: bool = False,
+    internal_nodes_18: bool = False,
+    internal_nodes_19: bool = False,
+    tlrc: bool = False,
+    prefix: str | None = None,
+) -> SurfaceMetricsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surf1: Specifies the input surface.
+        internal_nodes: Output nodes that are not a boundary.
+        internal_nodes_1: Output nodes that are not a boundary.
+        internal_nodes_2: Output nodes that are not a boundary.
+        internal_nodes_3: Output nodes that are not a boundary.
+        internal_nodes_4: Output nodes that are not a boundary.
+        internal_nodes_5: Output nodes that are not a boundary.
+        internal_nodes_6: Output nodes that are not a boundary.
+        internal_nodes_7: Output nodes that are not a boundary.
+        internal_nodes_8: Output nodes that are not a boundary.
+        internal_nodes_9: Output nodes that are not a boundary.
+        internal_nodes_10: Output nodes that are not a boundary.
+        internal_nodes_11: Output nodes that are not a boundary.
+        internal_nodes_12: Output nodes that are not a boundary.
+        internal_nodes_13: Output nodes that are not a boundary.
+        internal_nodes_14: Output nodes that are not a boundary.
+        internal_nodes_15: Output nodes that are not a boundary.
+        internal_nodes_16: Output nodes that are not a boundary.
+        internal_nodes_17: Output nodes that are not a boundary.
+        internal_nodes_18: Output nodes that are not a boundary.
+        internal_nodes_19: Output nodes that are not a boundary.
+        tlrc: Apply Talairach transform to surface.
+        prefix: Use prefix for output files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfaceMetrics",
+        "internal_nodes": internal_nodes,
+        "internal_nodes_1": internal_nodes_1,
+        "internal_nodes_2": internal_nodes_2,
+        "internal_nodes_3": internal_nodes_3,
+        "internal_nodes_4": internal_nodes_4,
+        "internal_nodes_5": internal_nodes_5,
+        "internal_nodes_6": internal_nodes_6,
+        "internal_nodes_7": internal_nodes_7,
+        "internal_nodes_8": internal_nodes_8,
+        "internal_nodes_9": internal_nodes_9,
+        "internal_nodes_10": internal_nodes_10,
+        "internal_nodes_11": internal_nodes_11,
+        "internal_nodes_12": internal_nodes_12,
+        "internal_nodes_13": internal_nodes_13,
+        "internal_nodes_14": internal_nodes_14,
+        "internal_nodes_15": internal_nodes_15,
+        "internal_nodes_16": internal_nodes_16,
+        "internal_nodes_17": internal_nodes_17,
+        "internal_nodes_18": internal_nodes_18,
+        "internal_nodes_19": internal_nodes_19,
+        "surf1": surf1,
+        "tlrc": tlrc,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def surface_metrics_cargs(
+    params: SurfaceMetricsParameters,
+    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("SurfaceMetrics")
+    if params.get("internal_nodes"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_1"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_2"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_3"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_4"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_5"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_6"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_7"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_8"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_9"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_10"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_11"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_12"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_13"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_14"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_15"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_16"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_17"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_18"):
+        cargs.append("-internal_nodes")
+    if params.get("internal_nodes_19"):
+        cargs.append("-internal_nodes")
+    cargs.extend([
+        "-SURF_1",
+        params.get("surf1")
+    ])
+    if params.get("tlrc"):
+        cargs.append("-tlrc")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def surface_metrics_outputs(
+    params: SurfaceMetricsParameters,
+    execution: Execution,
+) -> SurfaceMetricsOutputs:
+    """
+    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 = SurfaceMetricsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def surface_metrics_execute(
+    params: SurfaceMetricsParameters,
+    execution: Execution,
+) -> SurfaceMetricsOutputs:
+    """
+    Outputs information about a surface's mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfaceMetricsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surface_metrics_cargs(params, execution)
+    ret = surface_metrics_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surface_metrics(
+    surf1: str,
+    internal_nodes: bool = False,
+    internal_nodes_1: bool = False,
+    internal_nodes_2: bool = False,
+    internal_nodes_3: bool = False,
+    internal_nodes_4: bool = False,
+    internal_nodes_5: bool = False,
+    internal_nodes_6: bool = False,
+    internal_nodes_7: bool = False,
+    internal_nodes_8: bool = False,
+    internal_nodes_9: bool = False,
+    internal_nodes_10: bool = False,
+    internal_nodes_11: bool = False,
+    internal_nodes_12: bool = False,
+    internal_nodes_13: bool = False,
+    internal_nodes_14: bool = False,
+    internal_nodes_15: bool = False,
+    internal_nodes_16: bool = False,
+    internal_nodes_17: bool = False,
+    internal_nodes_18: bool = False,
+    internal_nodes_19: bool = False,
+    tlrc: bool = False,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> SurfaceMetricsOutputs:
+    """
+    Outputs information about a surface's mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surf1: Specifies the input surface.
+        internal_nodes: Output nodes that are not a boundary.
+        internal_nodes_1: Output nodes that are not a boundary.
+        internal_nodes_2: Output nodes that are not a boundary.
+        internal_nodes_3: Output nodes that are not a boundary.
+        internal_nodes_4: Output nodes that are not a boundary.
+        internal_nodes_5: Output nodes that are not a boundary.
+        internal_nodes_6: Output nodes that are not a boundary.
+        internal_nodes_7: Output nodes that are not a boundary.
+        internal_nodes_8: Output nodes that are not a boundary.
+        internal_nodes_9: Output nodes that are not a boundary.
+        internal_nodes_10: Output nodes that are not a boundary.
+        internal_nodes_11: Output nodes that are not a boundary.
+        internal_nodes_12: Output nodes that are not a boundary.
+        internal_nodes_13: Output nodes that are not a boundary.
+        internal_nodes_14: Output nodes that are not a boundary.
+        internal_nodes_15: Output nodes that are not a boundary.
+        internal_nodes_16: Output nodes that are not a boundary.
+        internal_nodes_17: Output nodes that are not a boundary.
+        internal_nodes_18: Output nodes that are not a boundary.
+        internal_nodes_19: Output nodes that are not a boundary.
+        tlrc: Apply Talairach transform to surface.
+        prefix: Use prefix for output files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfaceMetricsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURFACE_METRICS_METADATA)
+    params = surface_metrics_params(
+        internal_nodes=internal_nodes,
+        internal_nodes_1=internal_nodes_1,
+        internal_nodes_2=internal_nodes_2,
+        internal_nodes_3=internal_nodes_3,
+        internal_nodes_4=internal_nodes_4,
+        internal_nodes_5=internal_nodes_5,
+        internal_nodes_6=internal_nodes_6,
+        internal_nodes_7=internal_nodes_7,
+        internal_nodes_8=internal_nodes_8,
+        internal_nodes_9=internal_nodes_9,
+        internal_nodes_10=internal_nodes_10,
+        internal_nodes_11=internal_nodes_11,
+        internal_nodes_12=internal_nodes_12,
+        internal_nodes_13=internal_nodes_13,
+        internal_nodes_14=internal_nodes_14,
+        internal_nodes_15=internal_nodes_15,
+        internal_nodes_16=internal_nodes_16,
+        internal_nodes_17=internal_nodes_17,
+        internal_nodes_18=internal_nodes_18,
+        internal_nodes_19=internal_nodes_19,
+        surf1=surf1,
+        tlrc=tlrc,
+        prefix=prefix,
+    )
+    return surface_metrics_execute(params, execution)
+
+
+__all__ = [
+    "SURFACE_METRICS_METADATA",
+    "SurfaceMetricsOutputs",
+    "SurfaceMetricsParameters",
+    "surface_metrics",
+    "surface_metrics_params",
+]

niwrap_afni/afni/tedana_wrapper_py.py

@@ -0,0 +1,306 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TEDANA_WRAPPER_PY_METADATA = Metadata(
+    id="2a5d2d42a60628be534dad0f8a18d103f5db8377.boutiques",
+    name="tedana_wrapper.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+TedanaWrapperPyParameters = typing.TypedDict('TedanaWrapperPyParameters', {
+    "__STYX_TYPE__": typing.Literal["tedana_wrapper.py"],
+    "input_files": list[InputPathType],
+    "echo_times": list[float],
+    "mask": InputPathType,
+    "results_dir": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "save_all": bool,
+    "prep_only": bool,
+    "tedana_prog": typing.NotRequired[str | None],
+    "tedana_is_exec": bool,
+    "ted_label": typing.NotRequired[str | None],
+    "tedana_opts": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tedana_wrapper.py": tedana_wrapper_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 {
+        "tedana_wrapper.py": tedana_wrapper_py_outputs,
+    }.get(t)
+
+
+class TedanaWrapperPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tedana_wrapper_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    tedana_output: OutputPathType | None
+    """Output directory for tedana results."""
+    tedana_report: OutputPathType | None
+    """Tedana report file."""
+
+
+def tedana_wrapper_py_params(
+    input_files: list[InputPathType],
+    echo_times: list[float],
+    mask: InputPathType,
+    results_dir: str | None = None,
+    prefix: str | None = None,
+    save_all: bool = False,
+    prep_only: bool = False,
+    tedana_prog: str | None = None,
+    tedana_is_exec: bool = False,
+    ted_label: str | None = None,
+    tedana_opts: str | None = None,
+) -> TedanaWrapperPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: 4D dataset for each echo.
+        echo_times: Echo time (ms) for each echo.
+        mask: Mask in same space/grid as the input datasets.
+        results_dir: Folder to be created for all outputs. Default\
+            [./Bunnymen].
+        prefix: Prefix for dataset names. Default [Bunnymen].
+        save_all: Save intermediate datasets. Default is to save only the\
+            3dZcat stacked dataset (and tedana stuff).
+        prep_only: Do not run tedana.py, stop at 3dZcat.
+        tedana_prog: Path and name of the version of tedana.py that will be\
+            run. Default is meica.libs/tedana.py in the afni binaries directory.
+        tedana_is_exec: Run 'tedana.py' rather than 'python tedana.py'.
+        ted_label: Suffix for output folder. Adds suffix like TED.LABEL (NOT A\
+            PATH).
+        tedana_opts: Additional options to pass to tedana.py. (In quotes)\
+            Example: '--initcost=tanh --conv=2.5e-5'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tedana_wrapper.py",
+        "input_files": input_files,
+        "echo_times": echo_times,
+        "mask": mask,
+        "save_all": save_all,
+        "prep_only": prep_only,
+        "tedana_is_exec": tedana_is_exec,
+    }
+    if results_dir is not None:
+        params["results_dir"] = results_dir
+    if prefix is not None:
+        params["prefix"] = prefix
+    if tedana_prog is not None:
+        params["tedana_prog"] = tedana_prog
+    if ted_label is not None:
+        params["ted_label"] = ted_label
+    if tedana_opts is not None:
+        params["tedana_opts"] = tedana_opts
+    return params
+
+
+def tedana_wrapper_py_cargs(
+    params: TedanaWrapperPyParameters,
+    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("tedana_wrapper.py")
+    cargs.extend([
+        "-input",
+        *[execution.input_file(f) for f in params.get("input_files")]
+    ])
+    cargs.extend([
+        "-TE",
+        *map(str, params.get("echo_times"))
+    ])
+    cargs.extend([
+        "-mask",
+        execution.input_file(params.get("mask"))
+    ])
+    if params.get("results_dir") is not None:
+        cargs.extend([
+            "-results_dir",
+            params.get("results_dir")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("save_all"):
+        cargs.append("-save_all")
+    if params.get("prep_only"):
+        cargs.append("-prep_only")
+    if params.get("tedana_prog") is not None:
+        cargs.extend([
+            "-tedana_prog",
+            params.get("tedana_prog")
+        ])
+    if params.get("tedana_is_exec"):
+        cargs.append("-tedana_is_exec")
+    if params.get("ted_label") is not None:
+        cargs.extend([
+            "-ted_label",
+            params.get("ted_label")
+        ])
+    if params.get("tedana_opts") is not None:
+        cargs.extend([
+            "-tedana_opts",
+            params.get("tedana_opts")
+        ])
+    return cargs
+
+
+def tedana_wrapper_py_outputs(
+    params: TedanaWrapperPyParameters,
+    execution: Execution,
+) -> TedanaWrapperPyOutputs:
+    """
+    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 = TedanaWrapperPyOutputs(
+        root=execution.output_file("."),
+        tedana_output=execution.output_file(params.get("results_dir") + "/" + params.get("prefix") + "_ted_output") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
+        tedana_report=execution.output_file(params.get("results_dir") + "/" + params.get("prefix") + "_tedana_report.txt") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def tedana_wrapper_py_execute(
+    params: TedanaWrapperPyParameters,
+    execution: Execution,
+) -> TedanaWrapperPyOutputs:
+    """
+    Internal wrapper to run tedana.py, typically used within afni_proc.py.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TedanaWrapperPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tedana_wrapper_py_cargs(params, execution)
+    ret = tedana_wrapper_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tedana_wrapper_py(
+    input_files: list[InputPathType],
+    echo_times: list[float],
+    mask: InputPathType,
+    results_dir: str | None = None,
+    prefix: str | None = None,
+    save_all: bool = False,
+    prep_only: bool = False,
+    tedana_prog: str | None = None,
+    tedana_is_exec: bool = False,
+    ted_label: str | None = None,
+    tedana_opts: str | None = None,
+    runner: Runner | None = None,
+) -> TedanaWrapperPyOutputs:
+    """
+    Internal wrapper to run tedana.py, typically used within afni_proc.py.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: 4D dataset for each echo.
+        echo_times: Echo time (ms) for each echo.
+        mask: Mask in same space/grid as the input datasets.
+        results_dir: Folder to be created for all outputs. Default\
+            [./Bunnymen].
+        prefix: Prefix for dataset names. Default [Bunnymen].
+        save_all: Save intermediate datasets. Default is to save only the\
+            3dZcat stacked dataset (and tedana stuff).
+        prep_only: Do not run tedana.py, stop at 3dZcat.
+        tedana_prog: Path and name of the version of tedana.py that will be\
+            run. Default is meica.libs/tedana.py in the afni binaries directory.
+        tedana_is_exec: Run 'tedana.py' rather than 'python tedana.py'.
+        ted_label: Suffix for output folder. Adds suffix like TED.LABEL (NOT A\
+            PATH).
+        tedana_opts: Additional options to pass to tedana.py. (In quotes)\
+            Example: '--initcost=tanh --conv=2.5e-5'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TedanaWrapperPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TEDANA_WRAPPER_PY_METADATA)
+    params = tedana_wrapper_py_params(
+        input_files=input_files,
+        echo_times=echo_times,
+        mask=mask,
+        results_dir=results_dir,
+        prefix=prefix,
+        save_all=save_all,
+        prep_only=prep_only,
+        tedana_prog=tedana_prog,
+        tedana_is_exec=tedana_is_exec,
+        ted_label=ted_label,
+        tedana_opts=tedana_opts,
+    )
+    return tedana_wrapper_py_execute(params, execution)
+
+
+__all__ = [
+    "TEDANA_WRAPPER_PY_METADATA",
+    "TedanaWrapperPyOutputs",
+    "TedanaWrapperPyParameters",
+    "tedana_wrapper_py",
+    "tedana_wrapper_py_params",
+]