niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/dcm2niix_afni.py

@@ -0,0 +1,550 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DCM2NIIX_AFNI_METADATA = Metadata(
+    id="2b048e6ed8405f5110cc5399162aab212faa5c72.boutiques",
+    name="dcm2niix_afni",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+Dcm2niixAfniParameters = typing.TypedDict('Dcm2niixAfniParameters', {
+    "__STYX_TYPE__": typing.Literal["dcm2niix_afni"],
+    "input_folder": str,
+    "compression_level": typing.NotRequired[int | None],
+    "adjacent_dicoms": typing.NotRequired[str | None],
+    "bids_sidecar": typing.NotRequired[str | None],
+    "anonymize_bids": typing.NotRequired[str | None],
+    "comment": typing.NotRequired[str | None],
+    "directory_search_depth": typing.NotRequired[int | None],
+    "export_format": typing.NotRequired[str | None],
+    "filename_template": typing.NotRequired[str | None],
+    "generate_defaults": typing.NotRequired[str | None],
+    "ignore_images": typing.NotRequired[str | None],
+    "lossless_scale": typing.NotRequired[str | None],
+    "merge_slices": typing.NotRequired[str | None],
+    "series_crc_number": typing.NotRequired[list[str] | None],
+    "output_directory": typing.NotRequired[str | None],
+    "phillips_scaling": typing.NotRequired[str | None],
+    "rename_dicoms": typing.NotRequired[str | None],
+    "single_file_mode": typing.NotRequired[str | None],
+    "up_to_date": bool,
+    "verbose": typing.NotRequired[str | None],
+    "write_behavior": typing.NotRequired[int | None],
+    "crop_3d": typing.NotRequired[str | None],
+    "gz_compress": typing.NotRequired[str | None],
+    "big_endian": typing.NotRequired[str | None],
+    "progress": typing.NotRequired[str | None],
+    "ignore_trigger_times": bool,
+    "terse": bool,
+    "version": bool,
+    "xml": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dcm2niix_afni": dcm2niix_afni_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 {
+        "dcm2niix_afni": dcm2niix_afni_outputs,
+    }.get(t)
+
+
+class Dcm2niixAfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dcm2niix_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    nifti_files: OutputPathType
+    """The main output NIfTI files"""
+
+
+def dcm2niix_afni_params(
+    input_folder: str,
+    compression_level: int | None = None,
+    adjacent_dicoms: str | None = None,
+    bids_sidecar: str | None = None,
+    anonymize_bids: str | None = None,
+    comment: str | None = None,
+    directory_search_depth: int | None = None,
+    export_format: str | None = None,
+    filename_template: str | None = None,
+    generate_defaults: str | None = None,
+    ignore_images: str | None = None,
+    lossless_scale: str | None = None,
+    merge_slices: str | None = None,
+    series_crc_number: list[str] | None = None,
+    output_directory: str | None = None,
+    phillips_scaling: str | None = None,
+    rename_dicoms: str | None = None,
+    single_file_mode: str | None = None,
+    up_to_date: bool = False,
+    verbose: str | None = None,
+    write_behavior: int | None = None,
+    crop_3d: str | None = None,
+    gz_compress: str | None = None,
+    big_endian: str | None = None,
+    progress: str | None = None,
+    ignore_trigger_times: bool = False,
+    terse: bool = False,
+    version: bool = False,
+    xml_: bool = False,
+) -> Dcm2niixAfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_folder: Folder containing DICOM files.
+        compression_level: GZ compression level (1=fastest..9=smallest, default\
+            6).
+        adjacent_dicoms: Adjacent DICOMs (images from same series always in\
+            same folder) for faster conversion (n/y, default n).
+        bids_sidecar: BIDS sidecar (y/n/o [o=only: no NIfTI], default y).
+        anonymize_bids: Anonymize BIDS (y/n, default y).
+        comment: Comment stored in NIfTI aux_file (provide up to 24 characters\
+            e.g. '-c first_visit').
+        directory_search_depth: Directory search depth. Convert DICOMs in\
+            sub-folders of in_folder? (0..9, default 5).
+        export_format: Export as NRRD (y) or MGH (o) instead of NIfTI (y/n/o,\
+            default n).
+        filename_template: Filename template for output (default '%f_%p_%t_%s').
+        generate_defaults: Generate defaults file (y/n/o/i [o=only: reset and\
+            write defaults; i=ignore: reset defaults], default n).
+        ignore_images: Ignore derived, localizer and 2D images (y/n, default n).
+        lossless_scale: Losslessly scale 16-bit integers to use dynamic range\
+            (y/n/o, default o).
+        merge_slices: Merge 2D slices from same series regardless of echo,\
+            exposure, etc. (n/y or 0/1/2, default 2).
+        series_crc_number: Only convert this series CRC number - can be used up\
+            to 16 times (default convert all).
+        output_directory: Output directory (omit to save to input folder).
+        phillips_scaling: Philips precise float (not display) scaling (y/n,\
+            default y).
+        rename_dicoms: Rename instead of convert DICOMs (y/n, default n).
+        single_file_mode: Single file mode, do not convert other images in\
+            folder (y/n, default n).
+        up_to_date: Up-to-date check.
+        verbose: Verbose (n/y or 0/1/2, default 0).
+        write_behavior: Write behavior for name conflicts (0=skip duplicates,\
+            1=overwrite, 2=add suffix).
+        crop_3d: Crop 3D acquisitions (y/n/i, default n, use 'i'gnore to\
+            neither crop nor rotate 3D acquisitions).
+        gz_compress: GZ compress images (y/o/i/n/3, default n) [y=pigz,\
+            o=optimal pigz, i=internal:miniz, n=no, 3=no,3D].
+        big_endian: Byte order (y/n/o, default o) [y=big-endian,\
+            n=little-endian, o=optimal/native].
+        progress: Slicer format progress information (y/n, default n).
+        ignore_trigger_times: Disregard values in 0018, 1060 and 0020, 9153.
+        terse: Omit filename post-fixes (can cause overwrites).
+        version: Report version.
+        xml_: Slicer format features.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dcm2niix_afni",
+        "input_folder": input_folder,
+        "up_to_date": up_to_date,
+        "ignore_trigger_times": ignore_trigger_times,
+        "terse": terse,
+        "version": version,
+        "xml": xml_,
+    }
+    if compression_level is not None:
+        params["compression_level"] = compression_level
+    if adjacent_dicoms is not None:
+        params["adjacent_dicoms"] = adjacent_dicoms
+    if bids_sidecar is not None:
+        params["bids_sidecar"] = bids_sidecar
+    if anonymize_bids is not None:
+        params["anonymize_bids"] = anonymize_bids
+    if comment is not None:
+        params["comment"] = comment
+    if directory_search_depth is not None:
+        params["directory_search_depth"] = directory_search_depth
+    if export_format is not None:
+        params["export_format"] = export_format
+    if filename_template is not None:
+        params["filename_template"] = filename_template
+    if generate_defaults is not None:
+        params["generate_defaults"] = generate_defaults
+    if ignore_images is not None:
+        params["ignore_images"] = ignore_images
+    if lossless_scale is not None:
+        params["lossless_scale"] = lossless_scale
+    if merge_slices is not None:
+        params["merge_slices"] = merge_slices
+    if series_crc_number is not None:
+        params["series_crc_number"] = series_crc_number
+    if output_directory is not None:
+        params["output_directory"] = output_directory
+    if phillips_scaling is not None:
+        params["phillips_scaling"] = phillips_scaling
+    if rename_dicoms is not None:
+        params["rename_dicoms"] = rename_dicoms
+    if single_file_mode is not None:
+        params["single_file_mode"] = single_file_mode
+    if verbose is not None:
+        params["verbose"] = verbose
+    if write_behavior is not None:
+        params["write_behavior"] = write_behavior
+    if crop_3d is not None:
+        params["crop_3d"] = crop_3d
+    if gz_compress is not None:
+        params["gz_compress"] = gz_compress
+    if big_endian is not None:
+        params["big_endian"] = big_endian
+    if progress is not None:
+        params["progress"] = progress
+    return params
+
+
+def dcm2niix_afni_cargs(
+    params: Dcm2niixAfniParameters,
+    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("dcm2niix_afni")
+    cargs.append(params.get("input_folder"))
+    if params.get("compression_level") is not None:
+        cargs.extend([
+            "-1..-9",
+            str(params.get("compression_level"))
+        ])
+    if params.get("adjacent_dicoms") is not None:
+        cargs.extend([
+            "-a",
+            params.get("adjacent_dicoms")
+        ])
+    if params.get("bids_sidecar") is not None:
+        cargs.extend([
+            "-b",
+            params.get("bids_sidecar")
+        ])
+    if params.get("anonymize_bids") is not None:
+        cargs.extend([
+            "-ba",
+            params.get("anonymize_bids")
+        ])
+    if params.get("comment") is not None:
+        cargs.extend([
+            "-c",
+            params.get("comment")
+        ])
+    if params.get("directory_search_depth") is not None:
+        cargs.extend([
+            "-d",
+            str(params.get("directory_search_depth"))
+        ])
+    if params.get("export_format") is not None:
+        cargs.extend([
+            "-e",
+            params.get("export_format")
+        ])
+    if params.get("filename_template") is not None:
+        cargs.extend([
+            "-f",
+            params.get("filename_template")
+        ])
+    if params.get("generate_defaults") is not None:
+        cargs.extend([
+            "-g",
+            params.get("generate_defaults")
+        ])
+    if params.get("ignore_images") is not None:
+        cargs.extend([
+            "-i",
+            params.get("ignore_images")
+        ])
+    if params.get("lossless_scale") is not None:
+        cargs.extend([
+            "-l",
+            params.get("lossless_scale")
+        ])
+    if params.get("merge_slices") is not None:
+        cargs.extend([
+            "-m",
+            params.get("merge_slices")
+        ])
+    if params.get("series_crc_number") is not None:
+        cargs.extend([
+            "-n",
+            *params.get("series_crc_number")
+        ])
+    if params.get("output_directory") is not None:
+        cargs.extend([
+            "-o",
+            params.get("output_directory")
+        ])
+    if params.get("phillips_scaling") is not None:
+        cargs.extend([
+            "-p",
+            params.get("phillips_scaling")
+        ])
+    if params.get("rename_dicoms") is not None:
+        cargs.extend([
+            "-r",
+            params.get("rename_dicoms")
+        ])
+    if params.get("single_file_mode") is not None:
+        cargs.extend([
+            "-s",
+            params.get("single_file_mode")
+        ])
+    if params.get("up_to_date"):
+        cargs.append("-u")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-v",
+            params.get("verbose")
+        ])
+    if params.get("write_behavior") is not None:
+        cargs.extend([
+            "-w",
+            str(params.get("write_behavior"))
+        ])
+    if params.get("crop_3d") is not None:
+        cargs.extend([
+            "-x",
+            params.get("crop_3d")
+        ])
+    if params.get("gz_compress") is not None:
+        cargs.extend([
+            "-z",
+            params.get("gz_compress")
+        ])
+    if params.get("big_endian") is not None:
+        cargs.extend([
+            "--big-endian",
+            params.get("big_endian")
+        ])
+    if params.get("progress") is not None:
+        cargs.extend([
+            "--progress",
+            params.get("progress")
+        ])
+    if params.get("ignore_trigger_times"):
+        cargs.append("--ignore_trigger_times")
+    if params.get("terse"):
+        cargs.append("--terse")
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("xml"):
+        cargs.append("--xml")
+    return cargs
+
+
+def dcm2niix_afni_outputs(
+    params: Dcm2niixAfniParameters,
+    execution: Execution,
+) -> Dcm2niixAfniOutputs:
+    """
+    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 = Dcm2niixAfniOutputs(
+        root=execution.output_file("."),
+        nifti_files=execution.output_file("<OUTPUT_DIRECTORY>/*.nii"),
+    )
+    return ret
+
+
+def dcm2niix_afni_execute(
+    params: Dcm2niixAfniParameters,
+    execution: Execution,
+) -> Dcm2niixAfniOutputs:
+    """
+    DICOM to NIfTI converter optimized for AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Dcm2niixAfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dcm2niix_afni_cargs(params, execution)
+    ret = dcm2niix_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dcm2niix_afni(
+    input_folder: str,
+    compression_level: int | None = None,
+    adjacent_dicoms: str | None = None,
+    bids_sidecar: str | None = None,
+    anonymize_bids: str | None = None,
+    comment: str | None = None,
+    directory_search_depth: int | None = None,
+    export_format: str | None = None,
+    filename_template: str | None = None,
+    generate_defaults: str | None = None,
+    ignore_images: str | None = None,
+    lossless_scale: str | None = None,
+    merge_slices: str | None = None,
+    series_crc_number: list[str] | None = None,
+    output_directory: str | None = None,
+    phillips_scaling: str | None = None,
+    rename_dicoms: str | None = None,
+    single_file_mode: str | None = None,
+    up_to_date: bool = False,
+    verbose: str | None = None,
+    write_behavior: int | None = None,
+    crop_3d: str | None = None,
+    gz_compress: str | None = None,
+    big_endian: str | None = None,
+    progress: str | None = None,
+    ignore_trigger_times: bool = False,
+    terse: bool = False,
+    version: bool = False,
+    xml_: bool = False,
+    runner: Runner | None = None,
+) -> Dcm2niixAfniOutputs:
+    """
+    DICOM to NIfTI converter optimized for AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_folder: Folder containing DICOM files.
+        compression_level: GZ compression level (1=fastest..9=smallest, default\
+            6).
+        adjacent_dicoms: Adjacent DICOMs (images from same series always in\
+            same folder) for faster conversion (n/y, default n).
+        bids_sidecar: BIDS sidecar (y/n/o [o=only: no NIfTI], default y).
+        anonymize_bids: Anonymize BIDS (y/n, default y).
+        comment: Comment stored in NIfTI aux_file (provide up to 24 characters\
+            e.g. '-c first_visit').
+        directory_search_depth: Directory search depth. Convert DICOMs in\
+            sub-folders of in_folder? (0..9, default 5).
+        export_format: Export as NRRD (y) or MGH (o) instead of NIfTI (y/n/o,\
+            default n).
+        filename_template: Filename template for output (default '%f_%p_%t_%s').
+        generate_defaults: Generate defaults file (y/n/o/i [o=only: reset and\
+            write defaults; i=ignore: reset defaults], default n).
+        ignore_images: Ignore derived, localizer and 2D images (y/n, default n).
+        lossless_scale: Losslessly scale 16-bit integers to use dynamic range\
+            (y/n/o, default o).
+        merge_slices: Merge 2D slices from same series regardless of echo,\
+            exposure, etc. (n/y or 0/1/2, default 2).
+        series_crc_number: Only convert this series CRC number - can be used up\
+            to 16 times (default convert all).
+        output_directory: Output directory (omit to save to input folder).
+        phillips_scaling: Philips precise float (not display) scaling (y/n,\
+            default y).
+        rename_dicoms: Rename instead of convert DICOMs (y/n, default n).
+        single_file_mode: Single file mode, do not convert other images in\
+            folder (y/n, default n).
+        up_to_date: Up-to-date check.
+        verbose: Verbose (n/y or 0/1/2, default 0).
+        write_behavior: Write behavior for name conflicts (0=skip duplicates,\
+            1=overwrite, 2=add suffix).
+        crop_3d: Crop 3D acquisitions (y/n/i, default n, use 'i'gnore to\
+            neither crop nor rotate 3D acquisitions).
+        gz_compress: GZ compress images (y/o/i/n/3, default n) [y=pigz,\
+            o=optimal pigz, i=internal:miniz, n=no, 3=no,3D].
+        big_endian: Byte order (y/n/o, default o) [y=big-endian,\
+            n=little-endian, o=optimal/native].
+        progress: Slicer format progress information (y/n, default n).
+        ignore_trigger_times: Disregard values in 0018, 1060 and 0020, 9153.
+        terse: Omit filename post-fixes (can cause overwrites).
+        version: Report version.
+        xml_: Slicer format features.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dcm2niixAfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCM2NIIX_AFNI_METADATA)
+    params = dcm2niix_afni_params(
+        input_folder=input_folder,
+        compression_level=compression_level,
+        adjacent_dicoms=adjacent_dicoms,
+        bids_sidecar=bids_sidecar,
+        anonymize_bids=anonymize_bids,
+        comment=comment,
+        directory_search_depth=directory_search_depth,
+        export_format=export_format,
+        filename_template=filename_template,
+        generate_defaults=generate_defaults,
+        ignore_images=ignore_images,
+        lossless_scale=lossless_scale,
+        merge_slices=merge_slices,
+        series_crc_number=series_crc_number,
+        output_directory=output_directory,
+        phillips_scaling=phillips_scaling,
+        rename_dicoms=rename_dicoms,
+        single_file_mode=single_file_mode,
+        up_to_date=up_to_date,
+        verbose=verbose,
+        write_behavior=write_behavior,
+        crop_3d=crop_3d,
+        gz_compress=gz_compress,
+        big_endian=big_endian,
+        progress=progress,
+        ignore_trigger_times=ignore_trigger_times,
+        terse=terse,
+        version=version,
+        xml_=xml_,
+    )
+    return dcm2niix_afni_execute(params, execution)
+
+
+__all__ = [
+    "DCM2NIIX_AFNI_METADATA",
+    "Dcm2niixAfniOutputs",
+    "Dcm2niixAfniParameters",
+    "dcm2niix_afni",
+    "dcm2niix_afni_params",
+]