niwrap-freesurfer 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_freesurfer/freesurfer/fslorient_fsl.py

@@ -1,207 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSLORIENT_FSL_METADATA = Metadata(
-    id="91c87d301655f1a487272843a72c1efbca6dd79a.boutiques",
-    name="fslorient.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FslorientFslParameters = typing.TypedDict('FslorientFslParameters', {
-    "__STYX_TYPE__": typing.Literal["fslorient.fsl"],
-    "swap_orient": bool,
-    "filename": InputPathType,
-    "set_qform": typing.NotRequired[list[float] | None],
-    "set_qform_code": typing.NotRequired[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 {
-        "fslorient.fsl": fslorient_fsl_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 FslorientFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fslorient_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-
-
-def fslorient_fsl_params(
-    filename: InputPathType,
-    swap_orient: bool = False,
-    set_qform: list[float] | None = None,
-    set_qform_code: str | None = None,
-) -> FslorientFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        filename: Input image filename.
-        swap_orient: Swaps FSL radiological and FSL neurological.
-        set_qform: Sets the 16 elements of the qform matrix.
-        set_qform_code: Sets qform integer code.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fslorient.fsl",
-        "swap_orient": swap_orient,
-        "filename": filename,
-    }
-    if set_qform is not None:
-        params["set_qform"] = set_qform
-    if set_qform_code is not None:
-        params["set_qform_code"] = set_qform_code
-    return params
-
-
-def fslorient_fsl_cargs(
-    params: FslorientFslParameters,
-    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("fslorient")
-    if params.get("swap_orient"):
-        cargs.append("-swaporient")
-    cargs.append(execution.input_file(params.get("filename")))
-    if params.get("set_qform") is not None:
-        cargs.extend([
-            "-setqform",
-            *map(str, params.get("set_qform"))
-        ])
-    if params.get("set_qform_code") is not None:
-        cargs.extend([
-            "-setqformcode",
-            params.get("set_qform_code")
-        ])
-    return cargs
-
-
-def fslorient_fsl_outputs(
-    params: FslorientFslParameters,
-    execution: Execution,
-) -> FslorientFslOutputs:
-    """
-    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 = FslorientFslOutputs(
-        root=execution.output_file("."),
-    )
-    return ret
-
-
-def fslorient_fsl_execute(
-    params: FslorientFslParameters,
-    execution: Execution,
-) -> FslorientFslOutputs:
-    """
-    A tool for managing the orientations and orientation headers of NIFTI images.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FslorientFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fslorient_fsl_cargs(params, execution)
-    ret = fslorient_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fslorient_fsl(
-    filename: InputPathType,
-    swap_orient: bool = False,
-    set_qform: list[float] | None = None,
-    set_qform_code: str | None = None,
-    runner: Runner | None = None,
-) -> FslorientFslOutputs:
-    """
-    A tool for managing the orientations and orientation headers of NIFTI images.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        filename: Input image filename.
-        swap_orient: Swaps FSL radiological and FSL neurological.
-        set_qform: Sets the 16 elements of the qform matrix.
-        set_qform_code: Sets qform integer code.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FslorientFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSLORIENT_FSL_METADATA)
-    params = fslorient_fsl_params(
-        swap_orient=swap_orient,
-        filename=filename,
-        set_qform=set_qform,
-        set_qform_code=set_qform_code,
-    )
-    return fslorient_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FSLORIENT_FSL_METADATA",
-    "FslorientFslOutputs",
-    "FslorientFslParameters",
-    "fslorient_fsl",
-    "fslorient_fsl_params",
-]

niwrap_freesurfer/freesurfer/fslswapdim_fsl.py

@@ -1,216 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSLSWAPDIM_FSL_METADATA = Metadata(
-    id="7302b08bc4d86f9914f7a8203cbaf36cc9515b0c.boutiques",
-    name="fslswapdim.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FslswapdimFslParameters = typing.TypedDict('FslswapdimFslParameters', {
-    "__STYX_TYPE__": typing.Literal["fslswapdim.fsl"],
-    "input_file": InputPathType,
-    "axis_a": str,
-    "axis_b": str,
-    "axis_c": str,
-    "output_file": typing.NotRequired[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 {
-        "fslswapdim.fsl": fslswapdim_fsl_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 {
-        "fslswapdim.fsl": fslswapdim_fsl_outputs,
-    }.get(t)
-
-
-class FslswapdimFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fslswapdim_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    output_image: OutputPathType | None
-    """Output image with swapped dimensions"""
-
-
-def fslswapdim_fsl_params(
-    input_file: InputPathType,
-    axis_a: str,
-    axis_b: str,
-    axis_c: str,
-    output_file: str | None = None,
-) -> FslswapdimFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        input_file: Input image file.
-        axis_a: New X-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        axis_b: New Y-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        axis_c: New Z-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        output_file: Output image file.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fslswapdim.fsl",
-        "input_file": input_file,
-        "axis_a": axis_a,
-        "axis_b": axis_b,
-        "axis_c": axis_c,
-    }
-    if output_file is not None:
-        params["output_file"] = output_file
-    return params
-
-
-def fslswapdim_fsl_cargs(
-    params: FslswapdimFslParameters,
-    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("fslswapdim")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("axis_a"))
-    cargs.append(params.get("axis_b"))
-    cargs.append(params.get("axis_c"))
-    if params.get("output_file") is not None:
-        cargs.append(params.get("output_file"))
-    return cargs
-
-
-def fslswapdim_fsl_outputs(
-    params: FslswapdimFslParameters,
-    execution: Execution,
-) -> FslswapdimFslOutputs:
-    """
-    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 = FslswapdimFslOutputs(
-        root=execution.output_file("."),
-        output_image=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
-    )
-    return ret
-
-
-def fslswapdim_fsl_execute(
-    params: FslswapdimFslParameters,
-    execution: Execution,
-) -> FslswapdimFslOutputs:
-    """
-    FSLSwapdim allows swapping and flipping of dimensions of an image.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FslswapdimFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fslswapdim_fsl_cargs(params, execution)
-    ret = fslswapdim_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fslswapdim_fsl(
-    input_file: InputPathType,
-    axis_a: str,
-    axis_b: str,
-    axis_c: str,
-    output_file: str | None = None,
-    runner: Runner | None = None,
-) -> FslswapdimFslOutputs:
-    """
-    FSLSwapdim allows swapping and flipping of dimensions of an image.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        input_file: Input image file.
-        axis_a: New X-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        axis_b: New Y-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        axis_c: New Z-axis in terms of the old axes; can be one of -x, x, y,\
-            -y, z, -z or RL, LR, AP, PA, SI, IS.
-        output_file: Output image file.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FslswapdimFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSLSWAPDIM_FSL_METADATA)
-    params = fslswapdim_fsl_params(
-        input_file=input_file,
-        axis_a=axis_a,
-        axis_b=axis_b,
-        axis_c=axis_c,
-        output_file=output_file,
-    )
-    return fslswapdim_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FSLSWAPDIM_FSL_METADATA",
-    "FslswapdimFslOutputs",
-    "FslswapdimFslParameters",
-    "fslswapdim_fsl",
-    "fslswapdim_fsl_params",
-]

niwrap_freesurfer/freesurfer/fspython.py

@@ -1,175 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSPYTHON_METADATA = Metadata(
-    id="2424f19a382cf96fd7771ce3d7180d81a8324105.boutiques",
-    name="fspython",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FspythonParameters = typing.TypedDict('FspythonParameters', {
-    "__STYX_TYPE__": typing.Literal["fspython"],
-    "args": 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 {
-        "fspython": fspython_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 FspythonOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fspython(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-
-
-def fspython_params(
-    args: list[str] | None = None,
-) -> FspythonParameters:
-    """
-    Build parameters.
-    
-    Args:
-        args: Arguments passed to the program.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fspython",
-    }
-    if args is not None:
-        params["args"] = args
-    return params
-
-
-def fspython_cargs(
-    params: FspythonParameters,
-    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("python3")
-    cargs.append("[OPTION]")
-    if params.get("args") is not None:
-        cargs.extend(params.get("args"))
-    return cargs
-
-
-def fspython_outputs(
-    params: FspythonParameters,
-    execution: Execution,
-) -> FspythonOutputs:
-    """
-    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 = FspythonOutputs(
-        root=execution.output_file("."),
-    )
-    return ret
-
-
-def fspython_execute(
-    params: FspythonParameters,
-    execution: Execution,
-) -> FspythonOutputs:
-    """
-    Freesurfer's embedded Python interpreter.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FspythonOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fspython_cargs(params, execution)
-    ret = fspython_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fspython(
-    args: list[str] | None = None,
-    runner: Runner | None = None,
-) -> FspythonOutputs:
-    """
-    Freesurfer's embedded Python interpreter.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        args: Arguments passed to the program.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FspythonOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSPYTHON_METADATA)
-    params = fspython_params(
-        args=args,
-    )
-    return fspython_execute(params, execution)
-
-
-__all__ = [
-    "FSPYTHON_METADATA",
-    "FspythonOutputs",
-    "FspythonParameters",
-    "fspython",
-    "fspython_params",
-]