niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_rprog_demo.py

@@ -0,0 +1,282 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_RPROG_DEMO_METADATA = Metadata(
+    id="9ea0856bd790ad5ea87b3e458b8bf8d36950ad92.boutiques",
+    name="3dRprogDemo",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRprogDemoParameters = typing.TypedDict('V3dRprogDemoParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRprogDemo"],
+    "input_dsets": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "scale": float,
+    "prefix": str,
+    "help_aspx": bool,
+    "help_raw": bool,
+    "help_spx": bool,
+    "help_txt": bool,
+    "help": bool,
+    "show_allowed_options": bool,
+    "verbosity_level": 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 {
+        "3dRprogDemo": v_3d_rprog_demo_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 {
+        "3dRprogDemo": v_3d_rprog_demo_outputs,
+    }.get(t)
+
+
+class V3dRprogDemoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_rprog_demo(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file with the specified prefix."""
+
+
+def v_3d_rprog_demo_params(
+    input_dsets: list[InputPathType],
+    scale: float,
+    prefix: str,
+    mask: InputPathType | None = None,
+    help_aspx: bool = False,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_txt: bool = False,
+    help_: bool = False,
+    show_allowed_options: bool = False,
+    verbosity_level: float | None = None,
+) -> V3dRprogDemoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dsets: Input dataset(s) to be scaled.
+        scale: Multiply each voxel by SS.
+        prefix: Output prefix (just prefix, no view+suffix needed).
+        mask: Process voxels inside this mask only. Default is no masking.
+        help_aspx: Display help message with autolabeling.
+        help_raw: Display raw help message as in the code.
+        help_spx: Display help message in sphinx format.
+        help_txt: Display help message in simple text.
+        help_: Display help message in simple text.
+        show_allowed_options: List of allowed options.
+        verbosity_level: Verbosity level. 0 for quiet (Default). 1 or more:\
+            talkative.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRprogDemo",
+        "input_dsets": input_dsets,
+        "scale": scale,
+        "prefix": prefix,
+        "help_aspx": help_aspx,
+        "help_raw": help_raw,
+        "help_spx": help_spx,
+        "help_txt": help_txt,
+        "help": help_,
+        "show_allowed_options": show_allowed_options,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if verbosity_level is not None:
+        params["verbosity_level"] = verbosity_level
+    return params
+
+
+def v_3d_rprog_demo_cargs(
+    params: V3dRprogDemoParameters,
+    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("3dRprogDemo")
+    cargs.extend([execution.input_file(f) for f in params.get("input_dsets")])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.extend([
+        "-scale",
+        str(params.get("scale"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("help_aspx"):
+        cargs.append("-h_aspx")
+    if params.get("help_raw"):
+        cargs.append("-h_raw")
+    if params.get("help_spx"):
+        cargs.append("-h_spx")
+    if params.get("help_txt"):
+        cargs.append("-h_txt")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("show_allowed_options"):
+        cargs.append("-show_allowed_options")
+    if params.get("verbosity_level") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity_level"))
+        ])
+    return cargs
+
+
+def v_3d_rprog_demo_outputs(
+    params: V3dRprogDemoParameters,
+    execution: Execution,
+) -> V3dRprogDemoOutputs:
+    """
+    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 = V3dRprogDemoOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii"),
+    )
+    return ret
+
+
+def v_3d_rprog_demo_execute(
+    params: V3dRprogDemoParameters,
+    execution: Execution,
+) -> V3dRprogDemoOutputs:
+    """
+    Template program to help users write their own R processing routines on MRI
+    volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRprogDemoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_rprog_demo_cargs(params, execution)
+    ret = v_3d_rprog_demo_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_rprog_demo(
+    input_dsets: list[InputPathType],
+    scale: float,
+    prefix: str,
+    mask: InputPathType | None = None,
+    help_aspx: bool = False,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_txt: bool = False,
+    help_: bool = False,
+    show_allowed_options: bool = False,
+    verbosity_level: float | None = None,
+    runner: Runner | None = None,
+) -> V3dRprogDemoOutputs:
+    """
+    Template program to help users write their own R processing routines on MRI
+    volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dsets: Input dataset(s) to be scaled.
+        scale: Multiply each voxel by SS.
+        prefix: Output prefix (just prefix, no view+suffix needed).
+        mask: Process voxels inside this mask only. Default is no masking.
+        help_aspx: Display help message with autolabeling.
+        help_raw: Display raw help message as in the code.
+        help_spx: Display help message in sphinx format.
+        help_txt: Display help message in simple text.
+        help_: Display help message in simple text.
+        show_allowed_options: List of allowed options.
+        verbosity_level: Verbosity level. 0 for quiet (Default). 1 or more:\
+            talkative.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRprogDemoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RPROG_DEMO_METADATA)
+    params = v_3d_rprog_demo_params(
+        input_dsets=input_dsets,
+        mask=mask,
+        scale=scale,
+        prefix=prefix,
+        help_aspx=help_aspx,
+        help_raw=help_raw,
+        help_spx=help_spx,
+        help_txt=help_txt,
+        help_=help_,
+        show_allowed_options=show_allowed_options,
+        verbosity_level=verbosity_level,
+    )
+    return v_3d_rprog_demo_execute(params, execution)
+
+
+__all__ = [
+    "V3dRprogDemoOutputs",
+    "V3dRprogDemoParameters",
+    "V_3D_RPROG_DEMO_METADATA",
+    "v_3d_rprog_demo",
+    "v_3d_rprog_demo_params",
+]

niwrap_afni/afni/v_3d_rsfc.py

@@ -0,0 +1,198 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_RSFC_METADATA = Metadata(
+    id="b5c2a121f1ca24f0166e661caec651b36aec44bd.boutiques",
+    name="3dRSFC",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRsfcParameters = typing.TypedDict('V3dRsfcParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRSFC"],
+    "fbot": float,
+    "ftop": float,
+    "input_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dRSFC": v_3d_rsfc_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 {
+        "3dRSFC": v_3d_rsfc_outputs,
+    }.get(t)
+
+
+class V3dRsfcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_rsfc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    filtered_time_series: OutputPathType
+    """Filtered time series output"""
+    un_bandpassed_series: OutputPathType
+    """Un-bandpassed series output"""
+
+
+def v_3d_rsfc_params(
+    fbot: float,
+    ftop: float,
+    input_dataset: InputPathType,
+) -> V3dRsfcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fbot: Lowest frequency in the passband, in Hz.
+        ftop: Highest frequency in the passband (must be > fbot).
+        input_dataset: Input dataset (3D+time sequence of volumes).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRSFC",
+        "fbot": fbot,
+        "ftop": ftop,
+        "input_dataset": input_dataset,
+    }
+    return params
+
+
+def v_3d_rsfc_cargs(
+    params: V3dRsfcParameters,
+    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("3dRSFC")
+    cargs.append("[OPTIONS]")
+    cargs.append(str(params.get("fbot")))
+    cargs.append(str(params.get("ftop")))
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v_3d_rsfc_outputs(
+    params: V3dRsfcParameters,
+    execution: Execution,
+) -> V3dRsfcOutputs:
+    """
+    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 = V3dRsfcOutputs(
+        root=execution.output_file("."),
+        filtered_time_series=execution.output_file("[PREFIX]_LFF+orig.*"),
+        un_bandpassed_series=execution.output_file("[PREFIX]_unBP+orig.*"),
+    )
+    return ret
+
+
+def v_3d_rsfc_execute(
+    params: V3dRsfcParameters,
+    execution: Execution,
+) -> V3dRsfcOutputs:
+    """
+    Program to calculate common resting state functional connectivity (RSFC)
+    parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRsfcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_rsfc_cargs(params, execution)
+    ret = v_3d_rsfc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_rsfc(
+    fbot: float,
+    ftop: float,
+    input_dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dRsfcOutputs:
+    """
+    Program to calculate common resting state functional connectivity (RSFC)
+    parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        fbot: Lowest frequency in the passband, in Hz.
+        ftop: Highest frequency in the passband (must be > fbot).
+        input_dataset: Input dataset (3D+time sequence of volumes).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRsfcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RSFC_METADATA)
+    params = v_3d_rsfc_params(
+        fbot=fbot,
+        ftop=ftop,
+        input_dataset=input_dataset,
+    )
+    return v_3d_rsfc_execute(params, execution)
+
+
+__all__ = [
+    "V3dRsfcOutputs",
+    "V3dRsfcParameters",
+    "V_3D_RSFC_METADATA",
+    "v_3d_rsfc",
+    "v_3d_rsfc_params",
+]