niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__noisy_skull_strip.py

@@ -0,0 +1,212 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__NOISY_SKULL_STRIP_METADATA = Metadata(
+    id="a95b392481360cc4893886c77cddfcea221759d0.boutiques",
+    name="@NoisySkullStrip",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VNoisySkullStripParameters = typing.TypedDict('VNoisySkullStripParameters', {
+    "__STYX_TYPE__": typing.Literal["@NoisySkullStrip"],
+    "input_file": InputPathType,
+    "keep_tmp": bool,
+    "3dskullstrip_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 {
+        "@NoisySkullStrip": v__noisy_skull_strip_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 {
+        "@NoisySkullStrip": v__noisy_skull_strip_outputs,
+    }.get(t)
+
+
+class VNoisySkullStripOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__noisy_skull_strip(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    anat_ns: OutputPathType
+    """Skull stripped version of ANAT"""
+    anat_air: OutputPathType
+    """Special mask output - air"""
+    anat_skl: OutputPathType
+    """Special mask output - skull"""
+    anat_lsp: OutputPathType
+    """Volume used to threshold 'air' out of the volume to be stripped"""
+
+
+def v__noisy_skull_strip_params(
+    input_file: InputPathType,
+    keep_tmp: bool = False,
+    v_3dskullstrip_opts: str | None = None,
+) -> VNoisySkullStripParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: The anatomical dataset.
+        keep_tmp: Do not erase temporary files at the end.
+        v_3dskullstrip_opts: Anything following this option is passed to\
+            3dSkullStrip.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@NoisySkullStrip",
+        "input_file": input_file,
+        "keep_tmp": keep_tmp,
+    }
+    if v_3dskullstrip_opts is not None:
+        params["3dskullstrip_opts"] = v_3dskullstrip_opts
+    return params
+
+
+def v__noisy_skull_strip_cargs(
+    params: VNoisySkullStripParameters,
+    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("@NoisySkullStrip")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    if params.get("3dskullstrip_opts") is not None:
+        cargs.extend([
+            "-3dSkullStrip_opts",
+            params.get("3dskullstrip_opts")
+        ])
+    return cargs
+
+
+def v__noisy_skull_strip_outputs(
+    params: VNoisySkullStripParameters,
+    execution: Execution,
+) -> VNoisySkullStripOutputs:
+    """
+    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 = VNoisySkullStripOutputs(
+        root=execution.output_file("."),
+        anat_ns=execution.output_file(pathlib.Path(params.get("input_file")).name + ".ns"),
+        anat_air=execution.output_file(pathlib.Path(params.get("input_file")).name + ".air"),
+        anat_skl=execution.output_file(pathlib.Path(params.get("input_file")).name + ".skl"),
+        anat_lsp=execution.output_file(pathlib.Path(params.get("input_file")).name + ".lsp"),
+    )
+    return ret
+
+
+def v__noisy_skull_strip_execute(
+    params: VNoisySkullStripParameters,
+    execution: Execution,
+) -> VNoisySkullStripOutputs:
+    """
+    Strips the skull of anatomical datasets with low SNR.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VNoisySkullStripOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__noisy_skull_strip_cargs(params, execution)
+    ret = v__noisy_skull_strip_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__noisy_skull_strip(
+    input_file: InputPathType,
+    keep_tmp: bool = False,
+    v_3dskullstrip_opts: str | None = None,
+    runner: Runner | None = None,
+) -> VNoisySkullStripOutputs:
+    """
+    Strips the skull of anatomical datasets with low SNR.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: The anatomical dataset.
+        keep_tmp: Do not erase temporary files at the end.
+        v_3dskullstrip_opts: Anything following this option is passed to\
+            3dSkullStrip.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VNoisySkullStripOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__NOISY_SKULL_STRIP_METADATA)
+    params = v__noisy_skull_strip_params(
+        input_file=input_file,
+        keep_tmp=keep_tmp,
+        v_3dskullstrip_opts=v_3dskullstrip_opts,
+    )
+    return v__noisy_skull_strip_execute(params, execution)
+
+
+__all__ = [
+    "VNoisySkullStripOutputs",
+    "VNoisySkullStripParameters",
+    "V__NOISY_SKULL_STRIP_METADATA",
+    "v__noisy_skull_strip",
+    "v__noisy_skull_strip_params",
+]

niwrap_afni/afni/v__np.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__NP_METADATA = Metadata(
+    id="19475e309cca046197768d1ade01d7e521898bd3.boutiques",
+    name="@np",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VNpParameters = typing.TypedDict('VNpParameters', {
+    "__STYX_TYPE__": typing.Literal["@np"],
+    "prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@np": v__np_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 {
+        "@np": v__np_outputs,
+    }.get(t)
+
+
+class VNpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__np(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output text file with the appropriate new prefix."""
+
+
+def v__np_params(
+    prefix: str,
+) -> VNpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: The prefix to be checked.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@np",
+        "prefix": prefix,
+    }
+    return params
+
+
+def v__np_cargs(
+    params: VNpParameters,
+    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("@np")
+    cargs.append(params.get("prefix"))
+    return cargs
+
+
+def v__np_outputs(
+    params: VNpParameters,
+    execution: Execution,
+) -> VNpOutputs:
+    """
+    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 = VNpOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("appropriate_prefix.txt"),
+    )
+    return ret
+
+
+def v__np_execute(
+    params: VNpParameters,
+    execution: Execution,
+) -> VNpOutputs:
+    """
+    Finds an appropriate new prefix to use, given the files you already have in your
+    directory. It automatically creates a valid prefix when you are repeatedly
+    running similar commands but do not want to delete previous output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VNpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__np_cargs(params, execution)
+    ret = v__np_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__np(
+    prefix: str,
+    runner: Runner | None = None,
+) -> VNpOutputs:
+    """
+    Finds an appropriate new prefix to use, given the files you already have in your
+    directory. It automatically creates a valid prefix when you are repeatedly
+    running similar commands but do not want to delete previous output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: The prefix to be checked.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VNpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__NP_METADATA)
+    params = v__np_params(
+        prefix=prefix,
+    )
+    return v__np_execute(params, execution)
+
+
+__all__ = [
+    "VNpOutputs",
+    "VNpParameters",
+    "V__NP_METADATA",
+    "v__np",
+    "v__np_params",
+]

niwrap_afni/afni/v__parse_afni_name.py

@@ -0,0 +1,187 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__PARSE_AFNI_NAME_METADATA = Metadata(
+    id="6b460b863377f6ef2cf8dd2bc95819c049ae8246.boutiques",
+    name="@parse_afni_name",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VParseAfniNameParameters = typing.TypedDict('VParseAfniNameParameters', {
+    "__STYX_TYPE__": typing.Literal["@parse_afni_name"],
+    "afni_name": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@parse_afni_name": v__parse_afni_name_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 {
+        "@parse_afni_name": v__parse_afni_name_outputs,
+    }.get(t)
+
+
+class VParseAfniNameOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__parse_afni_name(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_path: OutputPathType
+    """Output path parsed from the AFNI name"""
+    output_prefix: OutputPathType
+    """Output prefix parsed from the AFNI name"""
+    output_view: OutputPathType
+    """Output view parsed from the AFNI name"""
+    output_subbrick: OutputPathType
+    """Output sub-brick selection string parsed from the AFNI name"""
+
+
+def v__parse_afni_name_params(
+    afni_name: str,
+) -> VParseAfniNameParameters:
+    """
+    Build parameters.
+    
+    Args:
+        afni_name: The AFNI name to be parsed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@parse_afni_name",
+        "afni_name": afni_name,
+    }
+    return params
+
+
+def v__parse_afni_name_cargs(
+    params: VParseAfniNameParameters,
+    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("@parse_afni_name")
+    cargs.append(params.get("afni_name"))
+    return cargs
+
+
+def v__parse_afni_name_outputs(
+    params: VParseAfniNameParameters,
+    execution: Execution,
+) -> VParseAfniNameOutputs:
+    """
+    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 = VParseAfniNameOutputs(
+        root=execution.output_file("."),
+        output_path=execution.output_file("parsed_name_path.txt"),
+        output_prefix=execution.output_file("parsed_name_prefix.txt"),
+        output_view=execution.output_file("parsed_name_view.txt"),
+        output_subbrick=execution.output_file("parsed_name_subbrick.txt"),
+    )
+    return ret
+
+
+def v__parse_afni_name_execute(
+    params: VParseAfniNameParameters,
+    execution: Execution,
+) -> VParseAfniNameOutputs:
+    """
+    A script to parse an AFNI name, outputting the path, prefix, view, and sub-brick
+    selection string.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VParseAfniNameOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__parse_afni_name_cargs(params, execution)
+    ret = v__parse_afni_name_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__parse_afni_name(
+    afni_name: str,
+    runner: Runner | None = None,
+) -> VParseAfniNameOutputs:
+    """
+    A script to parse an AFNI name, outputting the path, prefix, view, and sub-brick
+    selection string.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        afni_name: The AFNI name to be parsed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VParseAfniNameOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__PARSE_AFNI_NAME_METADATA)
+    params = v__parse_afni_name_params(
+        afni_name=afni_name,
+    )
+    return v__parse_afni_name_execute(params, execution)
+
+
+__all__ = [
+    "VParseAfniNameOutputs",
+    "VParseAfniNameParameters",
+    "V__PARSE_AFNI_NAME_METADATA",
+    "v__parse_afni_name",
+    "v__parse_afni_name_params",
+]