niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_brain_voyagerto_afni.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_BRAIN_VOYAGERTO_AFNI_METADATA = Metadata(
+    id="6e57612e994ff9fb4392a1ea7a2df2f7bddd8e62.boutiques",
+    name="3dBRAIN_VOYAGERtoAFNI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBrainVoyagertoAfniParameters = typing.TypedDict('V3dBrainVoyagertoAfniParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBRAIN_VOYAGERtoAFNI"],
+    "input_file": InputPathType,
+    "force_byte_swap": bool,
+    "brainvoyager_qx": bool,
+    "tlrc_space": bool,
+    "acpc_space": bool,
+    "orig_space": bool,
+    "prefix": typing.NotRequired[str | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "set_environment": typing.NotRequired[str | None],
+    "trace_debugging": bool,
+    "trace_extreme_debugging": bool,
+    "turn_off_memory_tracing": bool,
+    "turn_on_memory_tracing": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dBRAIN_VOYAGERtoAFNI": v_3d_brain_voyagerto_afni_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 {
+        "3dBRAIN_VOYAGERtoAFNI": v_3d_brain_voyagerto_afni_outputs,
+    }.get(t)
+
+
+class V3dBrainVoyagertoAfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_brain_voyagerto_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik_file: OutputPathType
+    """Output BRIK file"""
+    output_head_file: OutputPathType
+    """Output HEAD file"""
+
+
+def v_3d_brain_voyagerto_afni_params(
+    input_file: InputPathType,
+    force_byte_swap: bool = False,
+    brainvoyager_qx: bool = False,
+    tlrc_space: bool = False,
+    acpc_space: bool = False,
+    orig_space: bool = False,
+    prefix: str | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    set_environment: str | None = None,
+    trace_debugging: bool = False,
+    trace_extreme_debugging: bool = False,
+    turn_off_memory_tracing: bool = False,
+    turn_on_memory_tracing: bool = False,
+) -> V3dBrainVoyagertoAfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input BrainVoyager VMR file.
+        force_byte_swap: Force byte swapping.
+        brainvoyager_qx: .vmr file is from BrainVoyager QX.
+        tlrc_space: Dset in tlrc space.
+        acpc_space: Dset in acpc-aligned space.
+        orig_space: Dset in orig space.
+        prefix: Prefix for output files.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        set_environment: Set environment variable ENVname to be ENVvalue.\
+            Quotes are necessary.
+        trace_debugging: Turns on In/Out debug and Memory tracing.
+        trace_extreme_debugging: Turns on extreme tracing.
+        turn_off_memory_tracing: Turn off memory tracing.
+        turn_on_memory_tracing: Turn on memory tracing (default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBRAIN_VOYAGERtoAFNI",
+        "input_file": input_file,
+        "force_byte_swap": force_byte_swap,
+        "brainvoyager_qx": brainvoyager_qx,
+        "tlrc_space": tlrc_space,
+        "acpc_space": acpc_space,
+        "orig_space": orig_space,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "trace_debugging": trace_debugging,
+        "trace_extreme_debugging": trace_extreme_debugging,
+        "turn_off_memory_tracing": turn_off_memory_tracing,
+        "turn_on_memory_tracing": turn_on_memory_tracing,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if set_environment is not None:
+        params["set_environment"] = set_environment
+    return params
+
+
+def v_3d_brain_voyagerto_afni_cargs(
+    params: V3dBrainVoyagertoAfniParameters,
+    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("3dBRAIN_VOYAGERtoAFNI")
+    cargs.extend([
+        "--input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("force_byte_swap"):
+        cargs.append("-bs")
+    if params.get("brainvoyager_qx"):
+        cargs.append("-qx")
+    if params.get("tlrc_space"):
+        cargs.append("-tlrc")
+    if params.get("acpc_space"):
+        cargs.append("-acpc")
+    if params.get("orig_space"):
+        cargs.append("-orig")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "--prefix",
+            params.get("prefix")
+        ])
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("set_environment") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("set_environment")
+        ])
+    if params.get("trace_debugging"):
+        cargs.append("-trace")
+    if params.get("trace_extreme_debugging"):
+        cargs.append("-TRACE")
+    if params.get("turn_off_memory_tracing"):
+        cargs.append("-nomall")
+    if params.get("turn_on_memory_tracing"):
+        cargs.append("-yesmall")
+    return cargs
+
+
+def v_3d_brain_voyagerto_afni_outputs(
+    params: V3dBrainVoyagertoAfniParameters,
+    execution: Execution,
+) -> V3dBrainVoyagertoAfniOutputs:
+    """
+    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 = V3dBrainVoyagertoAfniOutputs(
+        root=execution.output_file("."),
+        output_brik_file=execution.output_file("output.BRIK"),
+        output_head_file=execution.output_file("output.HEAD"),
+    )
+    return ret
+
+
+def v_3d_brain_voyagerto_afni_execute(
+    params: V3dBrainVoyagertoAfniParameters,
+    execution: Execution,
+) -> V3dBrainVoyagertoAfniOutputs:
+    """
+    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on information
+    from BrainVoyager's website.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrainVoyagertoAfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_brain_voyagerto_afni_cargs(params, execution)
+    ret = v_3d_brain_voyagerto_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_brain_voyagerto_afni(
+    input_file: InputPathType,
+    force_byte_swap: bool = False,
+    brainvoyager_qx: bool = False,
+    tlrc_space: bool = False,
+    acpc_space: bool = False,
+    orig_space: bool = False,
+    prefix: str | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    set_environment: str | None = None,
+    trace_debugging: bool = False,
+    trace_extreme_debugging: bool = False,
+    turn_off_memory_tracing: bool = False,
+    turn_on_memory_tracing: bool = False,
+    runner: Runner | None = None,
+) -> V3dBrainVoyagertoAfniOutputs:
+    """
+    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on information
+    from BrainVoyager's website.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input BrainVoyager VMR file.
+        force_byte_swap: Force byte swapping.
+        brainvoyager_qx: .vmr file is from BrainVoyager QX.
+        tlrc_space: Dset in tlrc space.
+        acpc_space: Dset in acpc-aligned space.
+        orig_space: Dset in orig space.
+        prefix: Prefix for output files.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        set_environment: Set environment variable ENVname to be ENVvalue.\
+            Quotes are necessary.
+        trace_debugging: Turns on In/Out debug and Memory tracing.
+        trace_extreme_debugging: Turns on extreme tracing.
+        turn_off_memory_tracing: Turn off memory tracing.
+        turn_on_memory_tracing: Turn on memory tracing (default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrainVoyagertoAfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRAIN_VOYAGERTO_AFNI_METADATA)
+    params = v_3d_brain_voyagerto_afni_params(
+        input_file=input_file,
+        force_byte_swap=force_byte_swap,
+        brainvoyager_qx=brainvoyager_qx,
+        tlrc_space=tlrc_space,
+        acpc_space=acpc_space,
+        orig_space=orig_space,
+        prefix=prefix,
+        novolreg=novolreg,
+        noxform=noxform,
+        set_environment=set_environment,
+        trace_debugging=trace_debugging,
+        trace_extreme_debugging=trace_extreme_debugging,
+        turn_off_memory_tracing=turn_off_memory_tracing,
+        turn_on_memory_tracing=turn_on_memory_tracing,
+    )
+    return v_3d_brain_voyagerto_afni_execute(params, execution)
+
+
+__all__ = [
+    "V3dBrainVoyagertoAfniOutputs",
+    "V3dBrainVoyagertoAfniParameters",
+    "V_3D_BRAIN_VOYAGERTO_AFNI_METADATA",
+    "v_3d_brain_voyagerto_afni",
+    "v_3d_brain_voyagerto_afni_params",
+]