niwrap-freesurfer 0.5.3__tar.gz → 0.6.0__tar.gz

niwrap_freesurfer-0.6.0/PKG-INFO

@@ -0,0 +1,8 @@
+Metadata-Version: 2.4
+Name: niwrap_freesurfer
+Version: 0.6.0
+Summary: NiWrap wrappers for FreeSurfer.
+Author-email: CMI DAIR <dair@childmind.org>
+License-Expression: LGPL-2.1
+Requires-Python: >=3.10
+Requires-Dist: styxdefs~=0.5.0

niwrap_freesurfer-0.6.0/pyproject.toml

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+[project]
+name = "niwrap_freesurfer"
+version = "0.6.0"
+description = "NiWrap wrappers for FreeSurfer."
+license = "LGPL-2.1"
+authors = [{ name = "CMI DAIR", email = "dair@childmind.org" }]
+requires-python = ">=3.10"
+dependencies = [
+    "styxdefs~=0.5.0"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/niwrap_freesurfer"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

niwrap_freesurfer-0.6.0/src/niwrap_freesurfer/freesurfer/analyzeto4dfp.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 *
+
+ANALYZETO4DFP_METADATA = Metadata(
+    id="991ffef88bef8e5d81444f5958c1c7d3e22644f0.boutiques",
+    name="analyzeto4dfp",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Analyzeto4dfpParameters = typing.TypedDict('Analyzeto4dfpParameters', {
+    "__STYX_TYPE__": typing.Literal["analyzeto4dfp"],
+    "analyze_image": InputPathType,
+    "rois_scale": bool,
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "endian": typing.NotRequired[str | None],
+    "orientation": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "analyzeto4dfp": analyzeto4dfp_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 Analyzeto4dfpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `analyzeto4dfp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def analyzeto4dfp_params(
+    analyze_image: InputPathType,
+    rois_scale: bool = False,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    endian: str | None = None,
+    orientation: int | None = None,
+) -> Analyzeto4dfpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        analyze_image: Input ANALYZE image file.
+        rois_scale: Apply ROIScaleFactor.
+        flip_x: Flip first axis.
+        flip_y: Flip second axis.
+        flip_z: Flip third axis.
+        endian: Output big or little endian (default CPU endian).
+        orientation: Supply orientation code (in range [0-5]).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "analyzeto4dfp",
+        "analyze_image": analyze_image,
+        "rois_scale": rois_scale,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+    }
+    if endian is not None:
+        params["endian"] = endian
+    if orientation is not None:
+        params["orientation"] = orientation
+    return params
+
+
+def analyzeto4dfp_cargs(
+    params: Analyzeto4dfpParameters,
+    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("analyzeto4dfp")
+    cargs.append(execution.input_file(params.get("analyze_image")))
+    if params.get("rois_scale"):
+        cargs.append("-s")
+    if params.get("flip_x"):
+        cargs.append("-x")
+    if params.get("flip_y"):
+        cargs.append("-y")
+    if params.get("flip_z"):
+        cargs.append("-z")
+    if params.get("endian") is not None:
+        cargs.extend([
+            "-@",
+            params.get("endian")
+        ])
+    if params.get("orientation") is not None:
+        cargs.extend([
+            "-O",
+            str(params.get("orientation"))
+        ])
+    return cargs
+
+
+def analyzeto4dfp_outputs(
+    params: Analyzeto4dfpParameters,
+    execution: Execution,
+) -> Analyzeto4dfpOutputs:
+    """
+    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 = Analyzeto4dfpOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def analyzeto4dfp_execute(
+    params: Analyzeto4dfpParameters,
+    execution: Execution,
+) -> Analyzeto4dfpOutputs:
+    """
+    Convert ANALYZE image format to 4dfp format with various options.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Analyzeto4dfpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = analyzeto4dfp_cargs(params, execution)
+    ret = analyzeto4dfp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def analyzeto4dfp(
+    analyze_image: InputPathType,
+    rois_scale: bool = False,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    endian: str | None = None,
+    orientation: int | None = None,
+    runner: Runner | None = None,
+) -> Analyzeto4dfpOutputs:
+    """
+    Convert ANALYZE image format to 4dfp format with various options.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        analyze_image: Input ANALYZE image file.
+        rois_scale: Apply ROIScaleFactor.
+        flip_x: Flip first axis.
+        flip_y: Flip second axis.
+        flip_z: Flip third axis.
+        endian: Output big or little endian (default CPU endian).
+        orientation: Supply orientation code (in range [0-5]).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Analyzeto4dfpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANALYZETO4DFP_METADATA)
+    params = analyzeto4dfp_params(
+        analyze_image=analyze_image,
+        rois_scale=rois_scale,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+        endian=endian,
+        orientation=orientation,
+    )
+    return analyzeto4dfp_execute(params, execution)
+
+
+__all__ = [
+    "ANALYZETO4DFP_METADATA",
+    "Analyzeto4dfpOutputs",
+    "Analyzeto4dfpParameters",
+    "analyzeto4dfp",
+    "analyzeto4dfp_params",
+]

niwrap_freesurfer-0.6.0/src/niwrap_freesurfer/freesurfer/anatomi_cuts_utils.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 *
+
+ANATOMI_CUTS_UTILS_METADATA = Metadata(
+    id="5b8fc2fbd044825ca8524543fcf4b4b3d56cb1f7.boutiques",
+    name="anatomiCutsUtils",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+AnatomiCutsUtilsParameters = typing.TypedDict('AnatomiCutsUtilsParameters', {
+    "__STYX_TYPE__": typing.Literal["anatomiCutsUtils"],
+    "modules": typing.NotRequired[list[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 {
+        "anatomiCutsUtils": anatomi_cuts_utils_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 AnatomiCutsUtilsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `anatomi_cuts_utils(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def anatomi_cuts_utils_params(
+    modules: list[str] | None = None,
+) -> AnatomiCutsUtilsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        modules: Specify the modules to import for processing. Ensure necessary\
+            modules like 'graph_tools' are installed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "anatomiCutsUtils",
+    }
+    if modules is not None:
+        params["modules"] = modules
+    return params
+
+
+def anatomi_cuts_utils_cargs(
+    params: AnatomiCutsUtilsParameters,
+    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("anatomiCutsUtils")
+    if params.get("modules") is not None:
+        cargs.extend(params.get("modules"))
+    return cargs
+
+
+def anatomi_cuts_utils_outputs(
+    params: AnatomiCutsUtilsParameters,
+    execution: Execution,
+) -> AnatomiCutsUtilsOutputs:
+    """
+    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 = AnatomiCutsUtilsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def anatomi_cuts_utils_execute(
+    params: AnatomiCutsUtilsParameters,
+    execution: Execution,
+) -> AnatomiCutsUtilsOutputs:
+    """
+    A tool for anatomical segmentation using graph-based methods.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AnatomiCutsUtilsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = anatomi_cuts_utils_cargs(params, execution)
+    ret = anatomi_cuts_utils_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def anatomi_cuts_utils(
+    modules: list[str] | None = None,
+    runner: Runner | None = None,
+) -> AnatomiCutsUtilsOutputs:
+    """
+    A tool for anatomical segmentation using graph-based methods.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        modules: Specify the modules to import for processing. Ensure necessary\
+            modules like 'graph_tools' are installed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AnatomiCutsUtilsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANATOMI_CUTS_UTILS_METADATA)
+    params = anatomi_cuts_utils_params(
+        modules=modules,
+    )
+    return anatomi_cuts_utils_execute(params, execution)
+
+
+__all__ = [
+    "ANATOMI_CUTS_UTILS_METADATA",
+    "AnatomiCutsUtilsOutputs",
+    "AnatomiCutsUtilsParameters",
+    "anatomi_cuts_utils",
+    "anatomi_cuts_utils_params",
+]