niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_fix_topology.py

@@ -0,0 +1,446 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_FIX_TOPOLOGY_METADATA = Metadata(
+    id="5d7620635b54b49eefdf920890334e0223158089.boutiques",
+    name="mris_fix_topology",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisFixTopologyParameters = typing.TypedDict('MrisFixTopologyParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_fix_topology"],
+    "subject_name": str,
+    "hemisphere": str,
+    "orig_name": typing.NotRequired[str | None],
+    "sphere_name": typing.NotRequired[str | None],
+    "inflated_name": typing.NotRequired[str | None],
+    "output_name": typing.NotRequired[str | None],
+    "defect_base_name": typing.NotRequired[str | None],
+    "write_fixed_inflated": bool,
+    "verbose": bool,
+    "verbose_low": bool,
+    "warnings": bool,
+    "errors": bool,
+    "movies": bool,
+    "intersect": bool,
+    "mappings": bool,
+    "correct_defect": typing.NotRequired[float | None],
+    "niters": typing.NotRequired[float | None],
+    "genetic": bool,
+    "optimize": bool,
+    "random": typing.NotRequired[float | None],
+    "seed": typing.NotRequired[float | None],
+    "diag": bool,
+    "mgz": bool,
+    "smooth": typing.NotRequired[float | None],
+    "diagnostic_level": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_fix_topology": mris_fix_topology_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 {
+    }.get(t)
+
+
+class MrisFixTopologyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_fix_topology(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_fix_topology_params(
+    subject_name: str,
+    hemisphere: str,
+    orig_name: str | None = "orig.nofix",
+    sphere_name: str | None = "qsphere.nofix",
+    inflated_name: str | None = "inflated.nofix",
+    output_name: str | None = "orig",
+    defect_base_name: str | None = "defect",
+    write_fixed_inflated: bool = False,
+    verbose: bool = False,
+    verbose_low: bool = False,
+    warnings_: bool = False,
+    errors: bool = False,
+    movies: bool = False,
+    intersect: bool = False,
+    mappings: bool = False,
+    correct_defect: float | None = None,
+    niters: float | None = None,
+    genetic: bool = False,
+    optimize: bool = False,
+    random_: float | None = None,
+    seed: float | None = None,
+    diag: bool = False,
+    mgz: bool = False,
+    smooth: float | None = None,
+    diagnostic_level: float | None = None,
+    threads: float | None = None,
+) -> MrisFixTopologyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_name: Subject name.
+        hemisphere: Hemisphere.
+        orig_name: Input orig name (default is orig.nofix).
+        sphere_name: Sphere name (default is qsphere.nofix).
+        inflated_name: Inflated name (default is inflated.nofix).
+        output_name: Output name (default is orig).
+        defect_base_name: Defect basename (default is defect).
+        write_fixed_inflated: Write fixed inflated.
+        verbose: Increase verbosity.
+        verbose_low: Low verbosity.
+        warnings_: Show warnings.
+        errors: Show errors.
+        movies: Generate movies.
+        intersect: Check if the final surface self-intersects.
+        mappings: Generate several different mappings.
+        correct_defect: Correct specific defect number.
+        niters: Number of iterations for genetic algorithm.
+        genetic: Use genetic search.
+        optimize: Optimize genetic search.
+        random_: Use random search with specified iterations.
+        seed: Set random number generator seed.
+        diag: Sets DIAG_SAVE_DIAGS.
+        mgz: Assume volumes are in mgz format.
+        smooth: Smooth corrected surface by N iterations.
+        diagnostic_level: Set diagnostic level.
+        threads: Set number of OpenMP threads.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_fix_topology",
+        "subject_name": subject_name,
+        "hemisphere": hemisphere,
+        "write_fixed_inflated": write_fixed_inflated,
+        "verbose": verbose,
+        "verbose_low": verbose_low,
+        "warnings": warnings_,
+        "errors": errors,
+        "movies": movies,
+        "intersect": intersect,
+        "mappings": mappings,
+        "genetic": genetic,
+        "optimize": optimize,
+        "diag": diag,
+        "mgz": mgz,
+    }
+    if orig_name is not None:
+        params["orig_name"] = orig_name
+    if sphere_name is not None:
+        params["sphere_name"] = sphere_name
+    if inflated_name is not None:
+        params["inflated_name"] = inflated_name
+    if output_name is not None:
+        params["output_name"] = output_name
+    if defect_base_name is not None:
+        params["defect_base_name"] = defect_base_name
+    if correct_defect is not None:
+        params["correct_defect"] = correct_defect
+    if niters is not None:
+        params["niters"] = niters
+    if random_ is not None:
+        params["random"] = random_
+    if seed is not None:
+        params["seed"] = seed
+    if smooth is not None:
+        params["smooth"] = smooth
+    if diagnostic_level is not None:
+        params["diagnostic_level"] = diagnostic_level
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mris_fix_topology_cargs(
+    params: MrisFixTopologyParameters,
+    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("mris_fix_topology")
+    cargs.append(params.get("subject_name"))
+    cargs.append(params.get("hemisphere"))
+    if params.get("orig_name") is not None:
+        cargs.extend([
+            "-orig",
+            params.get("orig_name")
+        ])
+    if params.get("sphere_name") is not None:
+        cargs.extend([
+            "-sphere",
+            params.get("sphere_name")
+        ])
+    if params.get("inflated_name") is not None:
+        cargs.extend([
+            "-inflated",
+            params.get("inflated_name")
+        ])
+    if params.get("output_name") is not None:
+        cargs.extend([
+            "-out",
+            params.get("output_name")
+        ])
+    if params.get("defect_base_name") is not None:
+        cargs.extend([
+            "-defect",
+            params.get("defect_base_name")
+        ])
+    if params.get("write_fixed_inflated"):
+        cargs.append("-wi")
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("verbose_low"):
+        cargs.append("-verbose_low")
+    if params.get("warnings"):
+        cargs.append("-warnings")
+    if params.get("errors"):
+        cargs.append("-errors")
+    if params.get("movies"):
+        cargs.append("-movies")
+    if params.get("intersect"):
+        cargs.append("-intersect")
+    if params.get("mappings"):
+        cargs.append("-mappings")
+    if params.get("correct_defect") is not None:
+        cargs.extend([
+            "-correct_defect",
+            str(params.get("correct_defect"))
+        ])
+    if params.get("niters") is not None:
+        cargs.extend([
+            "-niters",
+            str(params.get("niters"))
+        ])
+    if params.get("genetic"):
+        cargs.append("-genetic")
+    if params.get("optimize"):
+        cargs.append("-optimize")
+    if params.get("random") is not None:
+        cargs.extend([
+            "-random",
+            str(params.get("random"))
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    if params.get("diag"):
+        cargs.append("-diag")
+    if params.get("mgz"):
+        cargs.append("-mgz")
+    if params.get("smooth") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("smooth"))
+        ])
+    if params.get("diagnostic_level") is not None:
+        cargs.extend([
+            "-v",
+            str(params.get("diagnostic_level"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "-threads",
+            str(params.get("threads"))
+        ])
+    return cargs
+
+
+def mris_fix_topology_outputs(
+    params: MrisFixTopologyParameters,
+    execution: Execution,
+) -> MrisFixTopologyOutputs:
+    """
+    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 = MrisFixTopologyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_fix_topology_execute(
+    params: MrisFixTopologyParameters,
+    execution: Execution,
+) -> MrisFixTopologyOutputs:
+    """
+    Computes a mapping from the unit sphere onto the cortical surface, ensuring a
+    topologically correct surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisFixTopologyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_fix_topology_cargs(params, execution)
+    ret = mris_fix_topology_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_fix_topology(
+    subject_name: str,
+    hemisphere: str,
+    orig_name: str | None = "orig.nofix",
+    sphere_name: str | None = "qsphere.nofix",
+    inflated_name: str | None = "inflated.nofix",
+    output_name: str | None = "orig",
+    defect_base_name: str | None = "defect",
+    write_fixed_inflated: bool = False,
+    verbose: bool = False,
+    verbose_low: bool = False,
+    warnings_: bool = False,
+    errors: bool = False,
+    movies: bool = False,
+    intersect: bool = False,
+    mappings: bool = False,
+    correct_defect: float | None = None,
+    niters: float | None = None,
+    genetic: bool = False,
+    optimize: bool = False,
+    random_: float | None = None,
+    seed: float | None = None,
+    diag: bool = False,
+    mgz: bool = False,
+    smooth: float | None = None,
+    diagnostic_level: float | None = None,
+    threads: float | None = None,
+    runner: Runner | None = None,
+) -> MrisFixTopologyOutputs:
+    """
+    Computes a mapping from the unit sphere onto the cortical surface, ensuring a
+    topologically correct surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_name: Subject name.
+        hemisphere: Hemisphere.
+        orig_name: Input orig name (default is orig.nofix).
+        sphere_name: Sphere name (default is qsphere.nofix).
+        inflated_name: Inflated name (default is inflated.nofix).
+        output_name: Output name (default is orig).
+        defect_base_name: Defect basename (default is defect).
+        write_fixed_inflated: Write fixed inflated.
+        verbose: Increase verbosity.
+        verbose_low: Low verbosity.
+        warnings_: Show warnings.
+        errors: Show errors.
+        movies: Generate movies.
+        intersect: Check if the final surface self-intersects.
+        mappings: Generate several different mappings.
+        correct_defect: Correct specific defect number.
+        niters: Number of iterations for genetic algorithm.
+        genetic: Use genetic search.
+        optimize: Optimize genetic search.
+        random_: Use random search with specified iterations.
+        seed: Set random number generator seed.
+        diag: Sets DIAG_SAVE_DIAGS.
+        mgz: Assume volumes are in mgz format.
+        smooth: Smooth corrected surface by N iterations.
+        diagnostic_level: Set diagnostic level.
+        threads: Set number of OpenMP threads.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisFixTopologyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FIX_TOPOLOGY_METADATA)
+    params = mris_fix_topology_params(
+        subject_name=subject_name,
+        hemisphere=hemisphere,
+        orig_name=orig_name,
+        sphere_name=sphere_name,
+        inflated_name=inflated_name,
+        output_name=output_name,
+        defect_base_name=defect_base_name,
+        write_fixed_inflated=write_fixed_inflated,
+        verbose=verbose,
+        verbose_low=verbose_low,
+        warnings_=warnings_,
+        errors=errors,
+        movies=movies,
+        intersect=intersect,
+        mappings=mappings,
+        correct_defect=correct_defect,
+        niters=niters,
+        genetic=genetic,
+        optimize=optimize,
+        random_=random_,
+        seed=seed,
+        diag=diag,
+        mgz=mgz,
+        smooth=smooth,
+        diagnostic_level=diagnostic_level,
+        threads=threads,
+    )
+    return mris_fix_topology_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_FIX_TOPOLOGY_METADATA",
+    "MrisFixTopologyOutputs",
+    "MrisFixTopologyParameters",
+    "mris_fix_topology",
+    "mris_fix_topology_params",
+]

niwrap_freesurfer/freesurfer/mris_flatten.py

@@ -0,0 +1,264 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_FLATTEN_METADATA = Metadata(
+    id="c7d351c53d00767efc2edd450d96b67b497b34f9.boutiques",
+    name="mris_flatten",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisFlattenParameters = typing.TypedDict('MrisFlattenParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_flatten"],
+    "input_patch": InputPathType,
+    "output_patch": str,
+    "iterations": typing.NotRequired[float | None],
+    "distances": typing.NotRequired[list[float] | None],
+    "dilations": typing.NotRequired[float | None],
+    "random_seed": typing.NotRequired[float | None],
+    "copy_coords": typing.NotRequired[str | None],
+    "norand": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_flatten": mris_flatten_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 {
+        "mris_flatten": mris_flatten_outputs,
+    }.get(t)
+
+
+class MrisFlattenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_flatten(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_patch_file: OutputPathType
+    """Output flattened surface patch"""
+
+
+def mris_flatten_params(
+    input_patch: InputPathType,
+    output_patch: str,
+    iterations: float | None = None,
+    distances: list[float] | None = None,
+    dilations: float | None = None,
+    random_seed: float | None = None,
+    copy_coords: str | None = None,
+    norand: bool = False,
+) -> MrisFlattenParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_patch: Input surface patch.
+        output_patch: Output flattened surface patch.
+        iterations: Write out the surface every # of iterations.
+        distances: Specify size of neighborhood and number of vertices at each\
+            distance to be used in the optimization.
+        dilations: Specify the number of times to dilate the ripped edges to\
+            ensure a clean cut.
+        random_seed: Set the random seed to a specific value so that flattening\
+            is repeatable.
+        copy_coords: Copy xyz coords from surface before flattening.
+        norand: Set the random seed to 0 so that flattening is repeatable.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_flatten",
+        "input_patch": input_patch,
+        "output_patch": output_patch,
+        "norand": norand,
+    }
+    if iterations is not None:
+        params["iterations"] = iterations
+    if distances is not None:
+        params["distances"] = distances
+    if dilations is not None:
+        params["dilations"] = dilations
+    if random_seed is not None:
+        params["random_seed"] = random_seed
+    if copy_coords is not None:
+        params["copy_coords"] = copy_coords
+    return params
+
+
+def mris_flatten_cargs(
+    params: MrisFlattenParameters,
+    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("mris_flatten")
+    cargs.append(execution.input_file(params.get("input_patch")))
+    cargs.append(params.get("output_patch"))
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-w",
+            str(params.get("iterations"))
+        ])
+    if params.get("distances") is not None:
+        cargs.extend([
+            "-distances",
+            *map(str, params.get("distances"))
+        ])
+    if params.get("dilations") is not None:
+        cargs.extend([
+            "-dilate",
+            str(params.get("dilations"))
+        ])
+    if params.get("random_seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("random_seed"))
+        ])
+    if params.get("copy_coords") is not None:
+        cargs.extend([
+            "-copy-coords",
+            params.get("copy_coords")
+        ])
+    if params.get("norand"):
+        cargs.append("-norand")
+    return cargs
+
+
+def mris_flatten_outputs(
+    params: MrisFlattenParameters,
+    execution: Execution,
+) -> MrisFlattenOutputs:
+    """
+    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 = MrisFlattenOutputs(
+        root=execution.output_file("."),
+        output_patch_file=execution.output_file(params.get("output_patch")),
+    )
+    return ret
+
+
+def mris_flatten_execute(
+    params: MrisFlattenParameters,
+    execution: Execution,
+) -> MrisFlattenOutputs:
+    """
+    This program will flatten a surface patch.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisFlattenOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_flatten_cargs(params, execution)
+    ret = mris_flatten_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_flatten(
+    input_patch: InputPathType,
+    output_patch: str,
+    iterations: float | None = None,
+    distances: list[float] | None = None,
+    dilations: float | None = None,
+    random_seed: float | None = None,
+    copy_coords: str | None = None,
+    norand: bool = False,
+    runner: Runner | None = None,
+) -> MrisFlattenOutputs:
+    """
+    This program will flatten a surface patch.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_patch: Input surface patch.
+        output_patch: Output flattened surface patch.
+        iterations: Write out the surface every # of iterations.
+        distances: Specify size of neighborhood and number of vertices at each\
+            distance to be used in the optimization.
+        dilations: Specify the number of times to dilate the ripped edges to\
+            ensure a clean cut.
+        random_seed: Set the random seed to a specific value so that flattening\
+            is repeatable.
+        copy_coords: Copy xyz coords from surface before flattening.
+        norand: Set the random seed to 0 so that flattening is repeatable.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisFlattenOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FLATTEN_METADATA)
+    params = mris_flatten_params(
+        input_patch=input_patch,
+        output_patch=output_patch,
+        iterations=iterations,
+        distances=distances,
+        dilations=dilations,
+        random_seed=random_seed,
+        copy_coords=copy_coords,
+        norand=norand,
+    )
+    return mris_flatten_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_FLATTEN_METADATA",
+    "MrisFlattenOutputs",
+    "MrisFlattenParameters",
+    "mris_flatten",
+    "mris_flatten_params",
+]