niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_ribbon.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 *
+
+MRI_RIBBON_METADATA = Metadata(
+    id="63d995760cf07991e31c0b77f7e67dbab7a6b9bb.boutiques",
+    name="mri_ribbon",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriRibbonParameters = typing.TypedDict('MriRibbonParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_ribbon"],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "inner_surface": InputPathType,
+    "outer_surface": InputPathType,
+    "input_volume": str,
+    "output_volume": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_ribbon": mri_ribbon_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 {
+        "mri_ribbon": mri_ribbon_outputs,
+    }.get(t)
+
+
+class MriRibbonOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_ribbon(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    ribbon_output: OutputPathType
+    """Output ribbon volume"""
+
+
+def mri_ribbon_params(
+    inner_surface: InputPathType,
+    outer_surface: InputPathType,
+    input_volume: str,
+    output_volume: str,
+    label_file: InputPathType | None = None,
+) -> MriRibbonParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inner_surface: File name of the inner surface.
+        outer_surface: File name of the outer surface.
+        input_volume: Prefix for the input volume file.
+        output_volume: Prefix for the output volume file.
+        label_file: Label file specifying regions of interest (optional).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_ribbon",
+        "inner_surface": inner_surface,
+        "outer_surface": outer_surface,
+        "input_volume": input_volume,
+        "output_volume": output_volume,
+    }
+    if label_file is not None:
+        params["label_file"] = label_file
+    return params
+
+
+def mri_ribbon_cargs(
+    params: MriRibbonParameters,
+    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("mri_ribbon")
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "-l",
+            execution.input_file(params.get("label_file"))
+        ])
+    cargs.append(execution.input_file(params.get("inner_surface")))
+    cargs.append(execution.input_file(params.get("outer_surface")))
+    cargs.append(params.get("input_volume"))
+    cargs.append(params.get("output_volume"))
+    return cargs
+
+
+def mri_ribbon_outputs(
+    params: MriRibbonParameters,
+    execution: Execution,
+) -> MriRibbonOutputs:
+    """
+    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 = MriRibbonOutputs(
+        root=execution.output_file("."),
+        ribbon_output=execution.output_file(params.get("output_volume") + "_ribbon.nii.gz"),
+    )
+    return ret
+
+
+def mri_ribbon_execute(
+    params: MriRibbonParameters,
+    execution: Execution,
+) -> MriRibbonOutputs:
+    """
+    MRI Ribbon tool to create ribbon volumes from surface files.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriRibbonOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_ribbon_cargs(params, execution)
+    ret = mri_ribbon_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_ribbon(
+    inner_surface: InputPathType,
+    outer_surface: InputPathType,
+    input_volume: str,
+    output_volume: str,
+    label_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriRibbonOutputs:
+    """
+    MRI Ribbon tool to create ribbon volumes from surface files.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        inner_surface: File name of the inner surface.
+        outer_surface: File name of the outer surface.
+        input_volume: Prefix for the input volume file.
+        output_volume: Prefix for the output volume file.
+        label_file: Label file specifying regions of interest (optional).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriRibbonOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RIBBON_METADATA)
+    params = mri_ribbon_params(
+        label_file=label_file,
+        inner_surface=inner_surface,
+        outer_surface=outer_surface,
+        input_volume=input_volume,
+        output_volume=output_volume,
+    )
+    return mri_ribbon_execute(params, execution)
+
+
+__all__ = [
+    "MRI_RIBBON_METADATA",
+    "MriRibbonOutputs",
+    "MriRibbonParameters",
+    "mri_ribbon",
+    "mri_ribbon_params",
+]

niwrap_freesurfer/freesurfer/mri_rigid_register.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_RIGID_REGISTER_METADATA = Metadata(
+    id="3a621587bc05ee701fd4feb941dda84ba58c25da.boutiques",
+    name="mri_rigid_register",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriRigidRegisterParameters = typing.TypedDict('MriRigidRegisterParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_rigid_register"],
+    "source_volume": InputPathType,
+    "target_volume": InputPathType,
+    "transform_output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_rigid_register": mri_rigid_register_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 {
+        "mri_rigid_register": mri_rigid_register_outputs,
+    }.get(t)
+
+
+class MriRigidRegisterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_rigid_register(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    transform_file: OutputPathType
+    """Output file for transform matrix"""
+
+
+def mri_rigid_register_params(
+    source_volume: InputPathType,
+    target_volume: InputPathType,
+    transform_output: str,
+) -> MriRigidRegisterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        source_volume: Source volume file for registration.
+        target_volume: Target volume file for registration.
+        transform_output: Output file name for the transform.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_rigid_register",
+        "source_volume": source_volume,
+        "target_volume": target_volume,
+        "transform_output": transform_output,
+    }
+    return params
+
+
+def mri_rigid_register_cargs(
+    params: MriRigidRegisterParameters,
+    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("mri_rigid_register")
+    cargs.append(execution.input_file(params.get("source_volume")))
+    cargs.append(execution.input_file(params.get("target_volume")))
+    cargs.append(params.get("transform_output"))
+    return cargs
+
+
+def mri_rigid_register_outputs(
+    params: MriRigidRegisterParameters,
+    execution: Execution,
+) -> MriRigidRegisterOutputs:
+    """
+    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 = MriRigidRegisterOutputs(
+        root=execution.output_file("."),
+        transform_file=execution.output_file(params.get("transform_output")),
+    )
+    return ret
+
+
+def mri_rigid_register_execute(
+    params: MriRigidRegisterParameters,
+    execution: Execution,
+) -> MriRigidRegisterOutputs:
+    """
+    Rigid registration tool for MRI volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriRigidRegisterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_rigid_register_cargs(params, execution)
+    ret = mri_rigid_register_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_rigid_register(
+    source_volume: InputPathType,
+    target_volume: InputPathType,
+    transform_output: str,
+    runner: Runner | None = None,
+) -> MriRigidRegisterOutputs:
+    """
+    Rigid registration tool for MRI volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        source_volume: Source volume file for registration.
+        target_volume: Target volume file for registration.
+        transform_output: Output file name for the transform.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriRigidRegisterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RIGID_REGISTER_METADATA)
+    params = mri_rigid_register_params(
+        source_volume=source_volume,
+        target_volume=target_volume,
+        transform_output=transform_output,
+    )
+    return mri_rigid_register_execute(params, execution)
+
+
+__all__ = [
+    "MRI_RIGID_REGISTER_METADATA",
+    "MriRigidRegisterOutputs",
+    "MriRigidRegisterParameters",
+    "mri_rigid_register",
+    "mri_rigid_register_params",
+]