niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwigradcheck.py

@@ -0,0 +1,534 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWIGRADCHECK_METADATA = Metadata(
+    id="bb74671ccd6fa59a51829fa34812108f525873cb.boutiques",
+    name="dwigradcheck",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+DwigradcheckFslgradParameters = typing.TypedDict('DwigradcheckFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+DwigradcheckExportGradFslParameters = typing.TypedDict('DwigradcheckExportGradFslParameters', {
+    "__STYX_TYPE__": typing.Literal["export_grad_fsl"],
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+
+
+DwigradcheckParameters = typing.TypedDict('DwigradcheckParameters', {
+    "__STYX_TYPE__": typing.Literal["dwigradcheck"],
+    "input_image": InputPathType,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DwigradcheckFslgradParameters | None],
+    "mask_image": typing.NotRequired[InputPathType | None],
+    "number": typing.NotRequired[int | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[DwigradcheckExportGradFslParameters | 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],
+    "config": typing.NotRequired[list[str] | None],
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dwigradcheck": dwigradcheck_cargs,
+        "fslgrad": dwigradcheck_fslgrad_cargs,
+        "export_grad_fsl": dwigradcheck_export_grad_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 {
+        "dwigradcheck": dwigradcheck_outputs,
+        "export_grad_fsl": dwigradcheck_export_grad_fsl_outputs,
+    }.get(t)
+
+
+def dwigradcheck_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> DwigradcheckFslgradParameters:
+    """
+    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 dwigradcheck_fslgrad_cargs(
+    params: DwigradcheckFslgradParameters,
+    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 DwigradcheckExportGradFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DwigradcheckExportGradFslParameters | None(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    bvecs_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+    bvals_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+
+
+def dwigradcheck_export_grad_fsl_params(
+    bvecs_path: str,
+    bvals_path: str,
+) -> DwigradcheckExportGradFslParameters:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+        bvals_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "export_grad_fsl",
+        "bvecs_path": bvecs_path,
+        "bvals_path": bvals_path,
+    }
+    return params
+
+
+def dwigradcheck_export_grad_fsl_cargs(
+    params: DwigradcheckExportGradFslParameters,
+    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("-export_grad_fsl")
+    cargs.append(params.get("bvecs_path"))
+    cargs.append(params.get("bvals_path"))
+    return cargs
+
+
+def dwigradcheck_export_grad_fsl_outputs(
+    params: DwigradcheckExportGradFslParameters,
+    execution: Execution,
+) -> DwigradcheckExportGradFslOutputs:
+    """
+    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 = DwigradcheckExportGradFslOutputs(
+        root=execution.output_file("."),
+        bvecs_path=execution.output_file(params.get("bvecs_path")),
+        bvals_path=execution.output_file(params.get("bvals_path")),
+    )
+    return ret
+
+
+class DwigradcheckOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dwigradcheck(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    export_grad_mrtrix: OutputPathType | None
+    """export the diffusion-weighted gradient table to file in MRtrix format """
+    export_grad_fsl: OutputPathType | None
+    """export the diffusion-weighted gradient table to file in FSL format """
+    export_grad_fsl_: DwigradcheckExportGradFslOutputs | None
+    """Outputs from `dwigradcheck_export_grad_fsl_outputs`."""
+
+
+def dwigradcheck_params(
+    input_image: InputPathType,
+    grad: InputPathType | None = None,
+    fslgrad: DwigradcheckFslgradParameters | None = None,
+    mask_image: InputPathType | None = None,
+    number: int | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: DwigradcheckExportGradFslParameters | 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,
+    config: list[str] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DwigradcheckParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: The input DWI series to be checked.
+        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: Provide a brain mask image.
+        number: Set the number of tracks to generate for each test.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        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).
+        config: Temporarily set the value of an MRtrix config file entry.
+        help_: Display help information and exit.
+        version: Display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dwigradcheck",
+        "input_image": input_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 number is not None:
+        params["number"] = number
+    if export_grad_mrtrix is not None:
+        params["export_grad_mrtrix"] = export_grad_mrtrix
+    if export_grad_fsl is not None:
+        params["export_grad_fsl"] = export_grad_fsl
+    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 config is not None:
+        params["config"] = config
+    return params
+
+
+def dwigradcheck_cargs(
+    params: DwigradcheckParameters,
+    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("dwigradcheck")
+    cargs.append(execution.input_file(params.get("input_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("number") is not None:
+        cargs.extend([
+            "-number",
+            str(params.get("number"))
+        ])
+    if params.get("export_grad_mrtrix") is not None:
+        cargs.extend([
+            "-export_grad_mrtrix",
+            params.get("export_grad_mrtrix")
+        ])
+    if params.get("export_grad_fsl") is not None:
+        cargs.extend(dyn_cargs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution))
+    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"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([
+            "-config",
+            *params.get("config")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    return cargs
+
+
+def dwigradcheck_outputs(
+    params: DwigradcheckParameters,
+    execution: Execution,
+) -> DwigradcheckOutputs:
+    """
+    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 = DwigradcheckOutputs(
+        root=execution.output_file("."),
+        export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix")) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_grad_fsl=execution.output_file(params.get("export_grad_mrtrix")) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_grad_fsl_=dyn_outputs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
+    )
+    return ret
+
+
+def dwigradcheck_execute(
+    params: DwigradcheckParameters,
+    execution: Execution,
+) -> DwigradcheckOutputs:
+    """
+    Check the orientation of the diffusion gradient table.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DwigradcheckOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dwigradcheck_cargs(params, execution)
+    ret = dwigradcheck_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwigradcheck(
+    input_image: InputPathType,
+    grad: InputPathType | None = None,
+    fslgrad: DwigradcheckFslgradParameters | None = None,
+    mask_image: InputPathType | None = None,
+    number: int | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: DwigradcheckExportGradFslParameters | 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,
+    config: list[str] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DwigradcheckOutputs:
+    """
+    Check the orientation of the diffusion gradient table.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_image: The input DWI series to be checked.
+        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: Provide a brain mask image.
+        number: Set the number of tracks to generate for each test.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        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).
+        config: Temporarily set the value of an MRtrix config file entry.
+        help_: Display help information and exit.
+        version: Display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DwigradcheckOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWIGRADCHECK_METADATA)
+    params = dwigradcheck_params(
+        input_image=input_image,
+        grad=grad,
+        fslgrad=fslgrad,
+        mask_image=mask_image,
+        number=number,
+        export_grad_mrtrix=export_grad_mrtrix,
+        export_grad_fsl=export_grad_fsl,
+        nocleanup=nocleanup,
+        scratch_dir=scratch_dir,
+        continue_scratch_dir=continue_scratch_dir,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+    )
+    return dwigradcheck_execute(params, execution)
+
+
+__all__ = [
+    "DWIGRADCHECK_METADATA",
+    "DwigradcheckExportGradFslOutputs",
+    "DwigradcheckExportGradFslParameters",
+    "DwigradcheckFslgradParameters",
+    "DwigradcheckOutputs",
+    "DwigradcheckParameters",
+    "dwigradcheck",
+    "dwigradcheck_export_grad_fsl_params",
+    "dwigradcheck_fslgrad_params",
+    "dwigradcheck_params",
+]