niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__djunct_modal_smoothing_with_rep.py

@@ -0,0 +1,249 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA = Metadata(
+    id="3dfe64fe4b416974b4aa2cc3b180143c7a5ada1d.boutiques",
+    name="@djunct_modal_smoothing_with_rep",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDjunctModalSmoothingWithRepParameters = typing.TypedDict('VDjunctModalSmoothingWithRepParameters', {
+    "__STYX_TYPE__": typing.Literal["@djunct_modal_smoothing_with_rep"],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "modesmooth": typing.NotRequired[float | None],
+    "help_view": bool,
+    "help": bool,
+    "version": bool,
+    "overwrite": bool,
+    "no_clean": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@djunct_modal_smoothing_with_rep": v__djunct_modal_smoothing_with_rep_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 {
+        "@djunct_modal_smoothing_with_rep": v__djunct_modal_smoothing_with_rep_outputs,
+    }.get(t)
+
+
+class VDjunctModalSmoothingWithRepOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__djunct_modal_smoothing_with_rep(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file_head: OutputPathType
+    """Output dataset after modal smoothing"""
+    output_file_brik: OutputPathType
+    """Output dataset after modal smoothing"""
+
+
+def v__djunct_modal_smoothing_with_rep_params(
+    input_file: InputPathType,
+    output_prefix: str,
+    modesmooth: float | None = None,
+    help_view: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    overwrite: bool = False,
+    no_clean: bool = False,
+) -> VDjunctModalSmoothingWithRepParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input dataset (assumes < 10^5 subbricks).
+        output_prefix: Prefix for output dataset.
+        modesmooth: Fill in X in: 3dLocalstat -nbhd "SPHERE(-X)" ...
+        help_view: Display help in a viewable format.
+        help_: Display help information.
+        version: Display version information.
+        overwrite: Overwrite existing output files.
+        no_clean: Do not clean up intermediate files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@djunct_modal_smoothing_with_rep",
+        "input_file": input_file,
+        "output_prefix": output_prefix,
+        "help_view": help_view,
+        "help": help_,
+        "version": version,
+        "overwrite": overwrite,
+        "no_clean": no_clean,
+    }
+    if modesmooth is not None:
+        params["modesmooth"] = modesmooth
+    return params
+
+
+def v__djunct_modal_smoothing_with_rep_cargs(
+    params: VDjunctModalSmoothingWithRepParameters,
+    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("@djunct_modal_smoothing_with_rep")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(params.get("output_prefix"))
+    if params.get("modesmooth") is not None:
+        cargs.extend([
+            "-modesmooth",
+            str(params.get("modesmooth"))
+        ])
+    if params.get("help_view"):
+        cargs.append("-hview")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-ver")
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    return cargs
+
+
+def v__djunct_modal_smoothing_with_rep_outputs(
+    params: VDjunctModalSmoothingWithRepParameters,
+    execution: Execution,
+) -> VDjunctModalSmoothingWithRepOutputs:
+    """
+    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 = VDjunctModalSmoothingWithRepOutputs(
+        root=execution.output_file("."),
+        output_file_head=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD"),
+        output_file_brik=execution.output_file(params.get("output_prefix") + "+tlrc.BRIK"),
+    )
+    return ret
+
+
+def v__djunct_modal_smoothing_with_rep_execute(
+    params: VDjunctModalSmoothingWithRepParameters,
+    execution: Execution,
+) -> VDjunctModalSmoothingWithRepOutputs:
+    """
+    A script to perform modal smoothing of ROI maps and check for eliminated ROIs.
+    If any ROIs are eliminated during smoothing, they are restored, potentially in a
+    degraded form.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctModalSmoothingWithRepOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__djunct_modal_smoothing_with_rep_cargs(params, execution)
+    ret = v__djunct_modal_smoothing_with_rep_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__djunct_modal_smoothing_with_rep(
+    input_file: InputPathType,
+    output_prefix: str,
+    modesmooth: float | None = None,
+    help_view: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    overwrite: bool = False,
+    no_clean: bool = False,
+    runner: Runner | None = None,
+) -> VDjunctModalSmoothingWithRepOutputs:
+    """
+    A script to perform modal smoothing of ROI maps and check for eliminated ROIs.
+    If any ROIs are eliminated during smoothing, they are restored, potentially in a
+    degraded form.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input dataset (assumes < 10^5 subbricks).
+        output_prefix: Prefix for output dataset.
+        modesmooth: Fill in X in: 3dLocalstat -nbhd "SPHERE(-X)" ...
+        help_view: Display help in a viewable format.
+        help_: Display help information.
+        version: Display version information.
+        overwrite: Overwrite existing output files.
+        no_clean: Do not clean up intermediate files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctModalSmoothingWithRepOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA)
+    params = v__djunct_modal_smoothing_with_rep_params(
+        input_file=input_file,
+        output_prefix=output_prefix,
+        modesmooth=modesmooth,
+        help_view=help_view,
+        help_=help_,
+        version=version,
+        overwrite=overwrite,
+        no_clean=no_clean,
+    )
+    return v__djunct_modal_smoothing_with_rep_execute(params, execution)
+
+
+__all__ = [
+    "VDjunctModalSmoothingWithRepOutputs",
+    "VDjunctModalSmoothingWithRepParameters",
+    "V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA",
+    "v__djunct_modal_smoothing_with_rep",
+    "v__djunct_modal_smoothing_with_rep_params",
+]

niwrap_afni/afni/v__djunct_montage_coordinator.py

@@ -0,0 +1,234 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DJUNCT_MONTAGE_COORDINATOR_METADATA = Metadata(
+    id="9c2cbb473d95421a680be52f18d9f90f2ec86dfb.boutiques",
+    name="@djunct_montage_coordinator",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDjunctMontageCoordinatorParameters = typing.TypedDict('VDjunctMontageCoordinatorParameters', {
+    "__STYX_TYPE__": typing.Literal["@djunct_montage_coordinator"],
+    "input_file": InputPathType,
+    "montx": float,
+    "monty": float,
+    "out_xyz": bool,
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@djunct_montage_coordinator": v__djunct_montage_coordinator_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 {
+        "@djunct_montage_coordinator": v__djunct_montage_coordinator_outputs,
+    }.get(t)
+
+
+class VDjunctMontageCoordinatorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__djunct_montage_coordinator(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_coords: OutputPathType
+    """Output coordinates (IJK or XYZ) for the montage setup."""
+
+
+def v__djunct_montage_coordinator_params(
+    input_file: InputPathType,
+    montx: float,
+    monty: float,
+    out_xyz: bool = False,
+    help_: bool = False,
+    version: bool = False,
+) -> VDjunctMontageCoordinatorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Name of input dataset.
+        montx: Montage dimension: number of panels along x-axis (i.e., number\
+            of cols).
+        monty: Montage dimension: number of panels along y-axis (i.e., number\
+            of rows).
+        out_xyz: Make program output 'X Y Z' values.
+        help_: See helpfile.
+        version: See version number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@djunct_montage_coordinator",
+        "input_file": input_file,
+        "montx": montx,
+        "monty": monty,
+        "out_xyz": out_xyz,
+        "help": help_,
+        "version": version,
+    }
+    return params
+
+
+def v__djunct_montage_coordinator_cargs(
+    params: VDjunctMontageCoordinatorParameters,
+    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("@djunct_montage_coordinator")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-montx",
+        str(params.get("montx"))
+    ])
+    cargs.extend([
+        "-monty",
+        str(params.get("monty"))
+    ])
+    if params.get("out_xyz"):
+        cargs.append("-out_xyz")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def v__djunct_montage_coordinator_outputs(
+    params: VDjunctMontageCoordinatorParameters,
+    execution: Execution,
+) -> VDjunctMontageCoordinatorOutputs:
+    """
+    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 = VDjunctMontageCoordinatorOutputs(
+        root=execution.output_file("."),
+        output_coords=execution.output_file("output.txt"),
+    )
+    return ret
+
+
+def v__djunct_montage_coordinator_execute(
+    params: VDjunctMontageCoordinatorParameters,
+    execution: Execution,
+) -> VDjunctMontageCoordinatorOutputs:
+    """
+    Small program to calculate how to evenly space a certain number of slices within
+    each view plane of a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctMontageCoordinatorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__djunct_montage_coordinator_cargs(params, execution)
+    ret = v__djunct_montage_coordinator_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__djunct_montage_coordinator(
+    input_file: InputPathType,
+    montx: float,
+    monty: float,
+    out_xyz: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> VDjunctMontageCoordinatorOutputs:
+    """
+    Small program to calculate how to evenly space a certain number of slices within
+    each view plane of a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Name of input dataset.
+        montx: Montage dimension: number of panels along x-axis (i.e., number\
+            of cols).
+        monty: Montage dimension: number of panels along y-axis (i.e., number\
+            of rows).
+        out_xyz: Make program output 'X Y Z' values.
+        help_: See helpfile.
+        version: See version number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctMontageCoordinatorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DJUNCT_MONTAGE_COORDINATOR_METADATA)
+    params = v__djunct_montage_coordinator_params(
+        input_file=input_file,
+        montx=montx,
+        monty=monty,
+        out_xyz=out_xyz,
+        help_=help_,
+        version=version,
+    )
+    return v__djunct_montage_coordinator_execute(params, execution)
+
+
+__all__ = [
+    "VDjunctMontageCoordinatorOutputs",
+    "VDjunctMontageCoordinatorParameters",
+    "V__DJUNCT_MONTAGE_COORDINATOR_METADATA",
+    "v__djunct_montage_coordinator",
+    "v__djunct_montage_coordinator_params",
+]