niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwibiascorrect.py

@@ -0,0 +1,467 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWIBIASCORRECT_METADATA = Metadata(
+    id="9185a0c94cb9a81f571005ce1de2411183c6df3f.boutiques",
+    name="dwibiascorrect",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+DwibiascorrectFslgradParameters = typing.TypedDict('DwibiascorrectFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+DwibiascorrectParameters = typing.TypedDict('DwibiascorrectParameters', {
+    "__STYX_TYPE__": typing.Literal["dwibiascorrect"],
+    "algorithm": str,
+    "input_image": InputPathType,
+    "output_image": str,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DwibiascorrectFslgradParameters | None],
+    "mask_image": typing.NotRequired[InputPathType | None],
+    "bias_image": typing.NotRequired[InputPathType | None],
+    "nocleanup": bool,
+    "scratch_dir": typing.NotRequired[InputPathType | None],
+    "continue_scratch_dir": typing.NotRequired[list[InputPathType] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[float | None],
+    "help": bool,
+    "version": bool,
+    "ants_b": typing.NotRequired[str | None],
+    "ants_c": typing.NotRequired[str | None],
+    "ants_s": 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 {
+        "dwibiascorrect": dwibiascorrect_cargs,
+        "fslgrad": dwibiascorrect_fslgrad_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 {
+        "dwibiascorrect": dwibiascorrect_outputs,
+    }.get(t)
+
+
+def dwibiascorrect_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> DwibiascorrectFslgradParameters:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def dwibiascorrect_fslgrad_cargs(
+    params: DwibiascorrectFslgradParameters,
+    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("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs")))
+    cargs.append(execution.input_file(params.get("bvals")))
+    return cargs
+
+
+class DwibiascorrectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dwibiascorrect(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image_file: OutputPathType
+    """File containing the corrected image series"""
+    bias_image_file: OutputPathType | None
+    """File containing the estimated bias field"""
+
+
+def dwibiascorrect_params(
+    algorithm: str,
+    input_image: InputPathType,
+    output_image: str,
+    grad: InputPathType | None = None,
+    fslgrad: DwibiascorrectFslgradParameters | None = None,
+    mask_image: InputPathType | None = None,
+    bias_image: InputPathType | None = None,
+    nocleanup: bool = False,
+    scratch_dir: InputPathType | None = None,
+    continue_scratch_dir: list[InputPathType] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: float | None = None,
+    help_: bool = False,
+    version: bool = False,
+    ants_b: str | None = None,
+    ants_c: str | None = None,
+    ants_s: str | None = None,
+) -> DwibiascorrectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        algorithm: Select the algorithm to be used for bias correction. Options\
+            are: ants, fsl.
+        input_image: The input image series to be corrected.
+        output_image: The output corrected image series.
+        grad: Provide the diffusion gradient table in MRtrix format.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        mask_image: Manually provide a mask image for bias field estimation.
+        bias_image: Output the estimated bias field.
+        nocleanup: Do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch_dir: Manually specify the path in which to generate the scratch\
+            directory.
+        continue_scratch_dir: Continue the script from a previous execution;\
+            must provide the scratch directory path.
+        info: Display information messages.
+        quiet: Do not display information messages or progress status.
+        debug: Display debugging messages.
+        force: Force overwrite of output files.
+        nthreads: Use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        help_: Display help information and exit.
+        version: Display version information and exit.
+        ants_b: N4BiasFieldCorrection option -b (initial mesh resolution in mm,\
+            spline order).
+        ants_c: N4BiasFieldCorrection option -c (number of iterations,\
+            convergence threshold).
+        ants_s: N4BiasFieldCorrection option -s (shrink-factor applied to\
+            spatial dimensions).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dwibiascorrect",
+        "algorithm": algorithm,
+        "input_image": input_image,
+        "output_image": output_image,
+        "nocleanup": nocleanup,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+    }
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if mask_image is not None:
+        params["mask_image"] = mask_image
+    if bias_image is not None:
+        params["bias_image"] = bias_image
+    if scratch_dir is not None:
+        params["scratch_dir"] = scratch_dir
+    if continue_scratch_dir is not None:
+        params["continue_scratch_dir"] = continue_scratch_dir
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if ants_b is not None:
+        params["ants_b"] = ants_b
+    if ants_c is not None:
+        params["ants_c"] = ants_c
+    if ants_s is not None:
+        params["ants_s"] = ants_s
+    return params
+
+
+def dwibiascorrect_cargs(
+    params: DwibiascorrectParameters,
+    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("dwibiascorrect")
+    cargs.append(params.get("algorithm"))
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(params.get("output_image"))
+    if params.get("grad") is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad"))
+        ])
+    if params.get("fslgrad") is not None:
+        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
+    if params.get("mask_image") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_image"))
+        ])
+    if params.get("bias_image") is not None:
+        cargs.extend([
+            "-bias",
+            execution.input_file(params.get("bias_image"))
+        ])
+    if params.get("nocleanup"):
+        cargs.append("-nocleanup")
+    if params.get("scratch_dir") is not None:
+        cargs.extend([
+            "-scratch",
+            execution.input_file(params.get("scratch_dir"))
+        ])
+    if params.get("continue_scratch_dir") is not None:
+        cargs.extend([
+            "-continue",
+            *[execution.input_file(f) for f in params.get("continue_scratch_dir")]
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    cargs.append("[CONFIG]")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("ants_b") is not None:
+        cargs.extend([
+            "-ants.b",
+            params.get("ants_b")
+        ])
+    if params.get("ants_c") is not None:
+        cargs.extend([
+            "-ants.c",
+            params.get("ants_c")
+        ])
+    if params.get("ants_s") is not None:
+        cargs.extend([
+            "-ants.s",
+            params.get("ants_s")
+        ])
+    return cargs
+
+
+def dwibiascorrect_outputs(
+    params: DwibiascorrectParameters,
+    execution: Execution,
+) -> DwibiascorrectOutputs:
+    """
+    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 = DwibiascorrectOutputs(
+        root=execution.output_file("."),
+        output_image_file=execution.output_file(params.get("output_image")),
+        bias_image_file=execution.output_file(pathlib.Path(params.get("bias_image")).name) if (params.get("bias_image") is not None) else None,
+    )
+    return ret
+
+
+def dwibiascorrect_execute(
+    params: DwibiascorrectParameters,
+    execution: Execution,
+) -> DwibiascorrectOutputs:
+    """
+    Perform B1 field inhomogeneity correction for a DWI volume series using either
+    ANTs or FSL.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DwibiascorrectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dwibiascorrect_cargs(params, execution)
+    ret = dwibiascorrect_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwibiascorrect(
+    algorithm: str,
+    input_image: InputPathType,
+    output_image: str,
+    grad: InputPathType | None = None,
+    fslgrad: DwibiascorrectFslgradParameters | None = None,
+    mask_image: InputPathType | None = None,
+    bias_image: InputPathType | None = None,
+    nocleanup: bool = False,
+    scratch_dir: InputPathType | None = None,
+    continue_scratch_dir: list[InputPathType] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: float | None = None,
+    help_: bool = False,
+    version: bool = False,
+    ants_b: str | None = None,
+    ants_c: str | None = None,
+    ants_s: str | None = None,
+    runner: Runner | None = None,
+) -> DwibiascorrectOutputs:
+    """
+    Perform B1 field inhomogeneity correction for a DWI volume series using either
+    ANTs or FSL.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        algorithm: Select the algorithm to be used for bias correction. Options\
+            are: ants, fsl.
+        input_image: The input image series to be corrected.
+        output_image: The output corrected image series.
+        grad: Provide the diffusion gradient table in MRtrix format.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        mask_image: Manually provide a mask image for bias field estimation.
+        bias_image: Output the estimated bias field.
+        nocleanup: Do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch_dir: Manually specify the path in which to generate the scratch\
+            directory.
+        continue_scratch_dir: Continue the script from a previous execution;\
+            must provide the scratch directory path.
+        info: Display information messages.
+        quiet: Do not display information messages or progress status.
+        debug: Display debugging messages.
+        force: Force overwrite of output files.
+        nthreads: Use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        help_: Display help information and exit.
+        version: Display version information and exit.
+        ants_b: N4BiasFieldCorrection option -b (initial mesh resolution in mm,\
+            spline order).
+        ants_c: N4BiasFieldCorrection option -c (number of iterations,\
+            convergence threshold).
+        ants_s: N4BiasFieldCorrection option -s (shrink-factor applied to\
+            spatial dimensions).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DwibiascorrectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWIBIASCORRECT_METADATA)
+    params = dwibiascorrect_params(
+        algorithm=algorithm,
+        input_image=input_image,
+        output_image=output_image,
+        grad=grad,
+        fslgrad=fslgrad,
+        mask_image=mask_image,
+        bias_image=bias_image,
+        nocleanup=nocleanup,
+        scratch_dir=scratch_dir,
+        continue_scratch_dir=continue_scratch_dir,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        help_=help_,
+        version=version,
+        ants_b=ants_b,
+        ants_c=ants_c,
+        ants_s=ants_s,
+    )
+    return dwibiascorrect_execute(params, execution)
+
+
+__all__ = [
+    "DWIBIASCORRECT_METADATA",
+    "DwibiascorrectFslgradParameters",
+    "DwibiascorrectOutputs",
+    "DwibiascorrectParameters",
+    "dwibiascorrect",
+    "dwibiascorrect_fslgrad_params",
+    "dwibiascorrect_params",
+]