niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/meica_py.py

@@ -0,0 +1,259 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MEICA_PY_METADATA = Metadata(
+    id="4f8853ae256f37ea17513108bcc3c27cb471dc45.boutiques",
+    name="meica.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MeicaPyParameters = typing.TypedDict('MeicaPyParameters', {
+    "__STYX_TYPE__": typing.Literal["meica.py"],
+    "infile": InputPathType,
+    "echo_times": str,
+    "affine": str,
+    "output_directory": str,
+    "components": typing.NotRequired[float | None],
+    "talairach": bool,
+    "threshold": typing.NotRequired[float | None],
+    "debug": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "meica.py": meica_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 {
+        "meica.py": meica_py_outputs,
+    }.get(t)
+
+
+class MeicaPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `meica_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    cleaned_bold: OutputPathType
+    """Cleaned BOLD image after ME-ICA processing"""
+    components_output: OutputPathType
+    """Independent components result of ICA"""
+
+
+def meica_py_params(
+    infile: InputPathType,
+    echo_times: str,
+    affine: str,
+    output_directory: str,
+    components: float | None = None,
+    talairach: bool = False,
+    threshold: float | None = None,
+    debug: bool = False,
+) -> MeicaPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input image dataset (e.g. dataset.nii.gz).
+        echo_times: Echo times (e.g. 15.0,30.0,45.0).
+        affine: Affine registration matrix.
+        output_directory: Output directory.
+        components: Number of components for ICA.
+        talairach: Apply standard Talairach transformation.
+        threshold: Threshold value for masking.
+        debug: Enable debug mode.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "meica.py",
+        "infile": infile,
+        "echo_times": echo_times,
+        "affine": affine,
+        "output_directory": output_directory,
+        "talairach": talairach,
+        "debug": debug,
+    }
+    if components is not None:
+        params["components"] = components
+    if threshold is not None:
+        params["threshold"] = threshold
+    return params
+
+
+def meica_py_cargs(
+    params: MeicaPyParameters,
+    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("meica.py")
+    cargs.extend([
+        "-d",
+        execution.input_file(params.get("infile"))
+    ])
+    cargs.extend([
+        "-e",
+        params.get("echo_times")
+    ])
+    cargs.extend([
+        "-a",
+        params.get("affine")
+    ])
+    cargs.extend([
+        "-o",
+        params.get("output_directory")
+    ])
+    if params.get("components") is not None:
+        cargs.extend([
+            "-c",
+            str(params.get("components"))
+        ])
+    if params.get("talairach"):
+        cargs.append("-t")
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "--thresh",
+            str(params.get("threshold"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    return cargs
+
+
+def meica_py_outputs(
+    params: MeicaPyParameters,
+    execution: Execution,
+) -> MeicaPyOutputs:
+    """
+    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 = MeicaPyOutputs(
+        root=execution.output_file("."),
+        cleaned_bold=execution.output_file(params.get("output_directory") + "/cleaned_bold.nii.gz"),
+        components_output=execution.output_file(params.get("output_directory") + "/components.nii.gz"),
+    )
+    return ret
+
+
+def meica_py_execute(
+    params: MeicaPyParameters,
+    execution: Execution,
+) -> MeicaPyOutputs:
+    """
+    Multi-Echo Independent Component Analysis for fMRI denoising.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MeicaPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = meica_py_cargs(params, execution)
+    ret = meica_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def meica_py(
+    infile: InputPathType,
+    echo_times: str,
+    affine: str,
+    output_directory: str,
+    components: float | None = None,
+    talairach: bool = False,
+    threshold: float | None = None,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> MeicaPyOutputs:
+    """
+    Multi-Echo Independent Component Analysis for fMRI denoising.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input image dataset (e.g. dataset.nii.gz).
+        echo_times: Echo times (e.g. 15.0,30.0,45.0).
+        affine: Affine registration matrix.
+        output_directory: Output directory.
+        components: Number of components for ICA.
+        talairach: Apply standard Talairach transformation.
+        threshold: Threshold value for masking.
+        debug: Enable debug mode.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MeicaPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MEICA_PY_METADATA)
+    params = meica_py_params(
+        infile=infile,
+        echo_times=echo_times,
+        affine=affine,
+        output_directory=output_directory,
+        components=components,
+        talairach=talairach,
+        threshold=threshold,
+        debug=debug,
+    )
+    return meica_py_execute(params, execution)
+
+
+__all__ = [
+    "MEICA_PY_METADATA",
+    "MeicaPyOutputs",
+    "MeicaPyParameters",
+    "meica_py",
+    "meica_py_params",
+]

niwrap_afni/afni/myget.py

@@ -0,0 +1,186 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MYGET_METADATA = Metadata(
+    id="2f6d3f9ad29fa84e230f411a821134ff68c91853.boutiques",
+    name="myget",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MygetParameters = typing.TypedDict('MygetParameters', {
+    "__STYX_TYPE__": typing.Literal["myget"],
+    "protocol_version": typing.NotRequired[typing.Literal["-1", "-1.1"] | None],
+    "url": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "myget": myget_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 {
+        "myget": myget_outputs,
+    }.get(t)
+
+
+class MygetOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `myget(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """The filename to save the downloaded file"""
+
+
+def myget_params(
+    url: str,
+    protocol_version: typing.Literal["-1", "-1.1"] | None = None,
+) -> MygetParameters:
+    """
+    Build parameters.
+    
+    Args:
+        url: The URL to download the file from.
+        protocol_version: Specify protocol version. You can choose between -1\
+            or -1.1.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "myget",
+        "url": url,
+    }
+    if protocol_version is not None:
+        params["protocol_version"] = protocol_version
+    return params
+
+
+def myget_cargs(
+    params: MygetParameters,
+    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 = []
+    if params.get("protocol_version") is not None:
+        cargs.append("myget" + params.get("protocol_version") + params.get("url"))
+    return cargs
+
+
+def myget_outputs(
+    params: MygetParameters,
+    execution: Execution,
+) -> MygetOutputs:
+    """
+    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 = MygetOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("[OUTPUT_FILE]"),
+    )
+    return ret
+
+
+def myget_execute(
+    params: MygetParameters,
+    execution: Execution,
+) -> MygetOutputs:
+    """
+    A simple file downloader from a URL.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MygetOutputs`).
+    """
+    params = execution.params(params)
+    cargs = myget_cargs(params, execution)
+    ret = myget_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def myget(
+    url: str,
+    protocol_version: typing.Literal["-1", "-1.1"] | None = None,
+    runner: Runner | None = None,
+) -> MygetOutputs:
+    """
+    A simple file downloader from a URL.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        url: The URL to download the file from.
+        protocol_version: Specify protocol version. You can choose between -1\
+            or -1.1.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MygetOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MYGET_METADATA)
+    params = myget_params(
+        protocol_version=protocol_version,
+        url=url,
+    )
+    return myget_execute(params, execution)
+
+
+__all__ = [
+    "MYGET_METADATA",
+    "MygetOutputs",
+    "MygetParameters",
+    "myget",
+    "myget_params",
+]