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

niwrap_freesurfer/freesurfer/mri_motion_correct_fsl.py

@@ -1,185 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-MRI_MOTION_CORRECT_FSL_METADATA = Metadata(
-    id="e4429f150e08917f7317e164c448c83b94352eed.boutiques",
-    name="mri_motion_correct.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-MriMotionCorrectFslParameters = typing.TypedDict('MriMotionCorrectFslParameters', {
-    "__STYX_TYPE__": typing.Literal["mri_motion_correct.fsl"],
-    "input_image": InputPathType,
-    "output_image": 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_motion_correct.fsl": mri_motion_correct_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 {
-        "mri_motion_correct.fsl": mri_motion_correct_fsl_outputs,
-    }.get(t)
-
-
-class MriMotionCorrectFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `mri_motion_correct_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    corrected_output: OutputPathType
-    """Motion corrected output MRI image"""
-
-
-def mri_motion_correct_fsl_params(
-    input_image: InputPathType,
-    output_image: str,
-) -> MriMotionCorrectFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        input_image: Input MRI image to be motion corrected.
-        output_image: Output corrected MRI image.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "mri_motion_correct.fsl",
-        "input_image": input_image,
-        "output_image": output_image,
-    }
-    return params
-
-
-def mri_motion_correct_fsl_cargs(
-    params: MriMotionCorrectFslParameters,
-    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_motion_correct.fsl")
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_image"))
-    cargs.append("[OPTIONS]")
-    return cargs
-
-
-def mri_motion_correct_fsl_outputs(
-    params: MriMotionCorrectFslParameters,
-    execution: Execution,
-) -> MriMotionCorrectFslOutputs:
-    """
-    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 = MriMotionCorrectFslOutputs(
-        root=execution.output_file("."),
-        corrected_output=execution.output_file(params.get("output_image") + ".nii.gz"),
-    )
-    return ret
-
-
-def mri_motion_correct_fsl_execute(
-    params: MriMotionCorrectFslParameters,
-    execution: Execution,
-) -> MriMotionCorrectFslOutputs:
-    """
-    Tool for motion correction of MRI images using FSL.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `MriMotionCorrectFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = mri_motion_correct_fsl_cargs(params, execution)
-    ret = mri_motion_correct_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def mri_motion_correct_fsl(
-    input_image: InputPathType,
-    output_image: str,
-    runner: Runner | None = None,
-) -> MriMotionCorrectFslOutputs:
-    """
-    Tool for motion correction of MRI images using FSL.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        input_image: Input MRI image to be motion corrected.
-        output_image: Output corrected MRI image.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `MriMotionCorrectFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MOTION_CORRECT_FSL_METADATA)
-    params = mri_motion_correct_fsl_params(
-        input_image=input_image,
-        output_image=output_image,
-    )
-    return mri_motion_correct_fsl_execute(params, execution)
-
-
-__all__ = [
-    "MRI_MOTION_CORRECT_FSL_METADATA",
-    "MriMotionCorrectFslOutputs",
-    "MriMotionCorrectFslParameters",
-    "mri_motion_correct_fsl",
-    "mri_motion_correct_fsl_params",
-]

niwrap_freesurfer/freesurfer/slicetimer_fsl.py

@@ -1,291 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-SLICETIMER_FSL_METADATA = Metadata(
-    id="27673c86089b795cd88a005218734e798ec23211.boutiques",
-    name="slicetimer.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-SlicetimerFslParameters = typing.TypedDict('SlicetimerFslParameters', {
-    "__STYX_TYPE__": typing.Literal["slicetimer.fsl"],
-    "infile": InputPathType,
-    "outfile": typing.NotRequired[str | None],
-    "tr": typing.NotRequired[float | None],
-    "direction": typing.NotRequired[typing.Literal["x", "y", "z"] | None],
-    "interleaved": bool,
-    "reverse": bool,
-    "custom_timings": typing.NotRequired[InputPathType | None],
-    "global_shift": typing.NotRequired[float | None],
-    "custom_interleave_order": typing.NotRequired[InputPathType | None],
-    "verbose": bool,
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "slicetimer.fsl": slicetimer_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 {
-        "slicetimer.fsl": slicetimer_fsl_outputs,
-    }.get(t)
-
-
-class SlicetimerFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `slicetimer_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    corrected_timeseries: OutputPathType | None
-    """Corrected output timeseries"""
-
-
-def slicetimer_fsl_params(
-    infile: InputPathType,
-    outfile: str | None = None,
-    tr: float | None = None,
-    direction: typing.Literal["x", "y", "z"] | None = None,
-    interleaved: bool = False,
-    reverse: bool = False,
-    custom_timings: InputPathType | None = None,
-    global_shift: float | None = None,
-    custom_interleave_order: InputPathType | None = None,
-    verbose: bool = False,
-) -> SlicetimerFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        infile: Filename of input timeseries.
-        outfile: Filename of output corrected timeseries.
-        tr: Specify TR of data, default is 3s.
-        direction: Direction of slice acquisition (x=1, y=2, z=3); default is z.
-        interleaved: Use interleaved acquisition.
-        reverse: Reverse slice indexing (default is slices were acquired\
-            bottom-up).
-        custom_timings: Filename of single-column slice timings in fractions of\
-            TR, positive values shift slices forwards in time.
-        global_shift: Global shift in fraction of TR, default is 0.
-        custom_interleave_order: Filename of single-column custom interleave\
-            order file (first slice is referred to as 1 not 0).
-        verbose: Switch on diagnostic messages.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "slicetimer.fsl",
-        "infile": infile,
-        "interleaved": interleaved,
-        "reverse": reverse,
-        "verbose": verbose,
-    }
-    if outfile is not None:
-        params["outfile"] = outfile
-    if tr is not None:
-        params["tr"] = tr
-    if direction is not None:
-        params["direction"] = direction
-    if custom_timings is not None:
-        params["custom_timings"] = custom_timings
-    if global_shift is not None:
-        params["global_shift"] = global_shift
-    if custom_interleave_order is not None:
-        params["custom_interleave_order"] = custom_interleave_order
-    return params
-
-
-def slicetimer_fsl_cargs(
-    params: SlicetimerFslParameters,
-    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("slicetimer")
-    cargs.append("--in")
-    cargs.extend([
-        "-i",
-        execution.input_file(params.get("infile"))
-    ])
-    if params.get("outfile") is not None:
-        cargs.extend([
-            "-o",
-            params.get("outfile")
-        ])
-    if params.get("tr") is not None:
-        cargs.extend([
-            "-r",
-            str(params.get("tr"))
-        ])
-    if params.get("direction") is not None:
-        cargs.extend([
-            "-d",
-            params.get("direction")
-        ])
-    if params.get("interleaved"):
-        cargs.append("--odd")
-    if params.get("reverse"):
-        cargs.append("--down")
-    if params.get("custom_timings") is not None:
-        cargs.extend([
-            "--tcustom",
-            execution.input_file(params.get("custom_timings"))
-        ])
-    if params.get("global_shift") is not None:
-        cargs.extend([
-            "--tglobal",
-            str(params.get("global_shift"))
-        ])
-    if params.get("custom_interleave_order") is not None:
-        cargs.extend([
-            "--ocustom",
-            execution.input_file(params.get("custom_interleave_order"))
-        ])
-    if params.get("verbose"):
-        cargs.append("-v")
-    return cargs
-
-
-def slicetimer_fsl_outputs(
-    params: SlicetimerFslParameters,
-    execution: Execution,
-) -> SlicetimerFslOutputs:
-    """
-    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 = SlicetimerFslOutputs(
-        root=execution.output_file("."),
-        corrected_timeseries=execution.output_file(params.get("outfile")) if (params.get("outfile") is not None) else None,
-    )
-    return ret
-
-
-def slicetimer_fsl_execute(
-    params: SlicetimerFslParameters,
-    execution: Execution,
-) -> SlicetimerFslOutputs:
-    """
-    FMRIB's Interpolation for Slice Timing correction in FMRI data.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `SlicetimerFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = slicetimer_fsl_cargs(params, execution)
-    ret = slicetimer_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def slicetimer_fsl(
-    infile: InputPathType,
-    outfile: str | None = None,
-    tr: float | None = None,
-    direction: typing.Literal["x", "y", "z"] | None = None,
-    interleaved: bool = False,
-    reverse: bool = False,
-    custom_timings: InputPathType | None = None,
-    global_shift: float | None = None,
-    custom_interleave_order: InputPathType | None = None,
-    verbose: bool = False,
-    runner: Runner | None = None,
-) -> SlicetimerFslOutputs:
-    """
-    FMRIB's Interpolation for Slice Timing correction in FMRI data.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        infile: Filename of input timeseries.
-        outfile: Filename of output corrected timeseries.
-        tr: Specify TR of data, default is 3s.
-        direction: Direction of slice acquisition (x=1, y=2, z=3); default is z.
-        interleaved: Use interleaved acquisition.
-        reverse: Reverse slice indexing (default is slices were acquired\
-            bottom-up).
-        custom_timings: Filename of single-column slice timings in fractions of\
-            TR, positive values shift slices forwards in time.
-        global_shift: Global shift in fraction of TR, default is 0.
-        custom_interleave_order: Filename of single-column custom interleave\
-            order file (first slice is referred to as 1 not 0).
-        verbose: Switch on diagnostic messages.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `SlicetimerFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SLICETIMER_FSL_METADATA)
-    params = slicetimer_fsl_params(
-        infile=infile,
-        outfile=outfile,
-        tr=tr,
-        direction=direction,
-        interleaved=interleaved,
-        reverse=reverse,
-        custom_timings=custom_timings,
-        global_shift=global_shift,
-        custom_interleave_order=custom_interleave_order,
-        verbose=verbose,
-    )
-    return slicetimer_fsl_execute(params, execution)
-
-
-__all__ = [
-    "SLICETIMER_FSL_METADATA",
-    "SlicetimerFslOutputs",
-    "SlicetimerFslParameters",
-    "slicetimer_fsl",
-    "slicetimer_fsl_params",
-]