niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/dcmunpack.py

@@ -0,0 +1,594 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DCMUNPACK_METADATA = Metadata(
+    id="01d871981fcfe7211d8f4250bbd352a2a097e2e7.boutiques",
+    name="dcmunpack",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DcmunpackParameters = typing.TypedDict('DcmunpackParameters', {
+    "__STYX_TYPE__": typing.Literal["dcmunpack"],
+    "src": str,
+    "targ": typing.NotRequired[str | None],
+    "run": typing.NotRequired[str | None],
+    "auto_runseq": typing.NotRequired[str | None],
+    "keep_scouts": bool,
+    "scanonly": typing.NotRequired[str | None],
+    "one_per_dir": bool,
+    "ext": typing.NotRequired[str | None],
+    "pre": typing.NotRequired[str | None],
+    "pat": typing.NotRequired[str | None],
+    "no_infodump": bool,
+    "generic": bool,
+    "copy_only": bool,
+    "no_convert": bool,
+    "force_update": bool,
+    "max": bool,
+    "base": bool,
+    "key_string": typing.NotRequired[str | None],
+    "index_out": typing.NotRequired[str | None],
+    "index_in": typing.NotRequired[str | None],
+    "it_dicom": bool,
+    "no_exit_on_error": bool,
+    "run_skip": typing.NotRequired[str | None],
+    "no_rescale_dicom": bool,
+    "rescale_dicom": bool,
+    "no_dwi": bool,
+    "iid": typing.NotRequired[list[float] | None],
+    "ijd": typing.NotRequired[list[float] | None],
+    "ikd": typing.NotRequired[list[float] | None],
+    "extra_info": bool,
+    "first_dicom": bool,
+    "no_dcm2niix": bool,
+    "phase": bool,
+    "fips": typing.NotRequired[str | None],
+    "fips_run": typing.NotRequired[str | None],
+    "xml_only": bool,
+    "log": typing.NotRequired[str | None],
+    "debug": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dcmunpack": dcmunpack_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 DcmunpackOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dcmunpack(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dcmunpack_params(
+    src: str,
+    targ: str | None = None,
+    run: str | None = None,
+    auto_runseq: str | None = None,
+    keep_scouts: bool = False,
+    scanonly: str | None = None,
+    one_per_dir: bool = False,
+    ext: str | None = None,
+    pre: str | None = None,
+    pat: str | None = None,
+    no_infodump: bool = False,
+    generic: bool = False,
+    copy_only: bool = False,
+    no_convert: bool = False,
+    force_update: bool = False,
+    max_: bool = False,
+    base: bool = False,
+    key_string: str | None = None,
+    index_out: str | None = None,
+    index_in: str | None = None,
+    it_dicom: bool = False,
+    no_exit_on_error: bool = False,
+    run_skip: str | None = None,
+    no_rescale_dicom: bool = False,
+    rescale_dicom: bool = False,
+    no_dwi: bool = False,
+    iid: list[float] | None = None,
+    ijd: list[float] | None = None,
+    ikd: list[float] | None = None,
+    extra_info: bool = False,
+    first_dicom: bool = False,
+    no_dcm2niix: bool = False,
+    phase: bool = False,
+    fips: str | None = None,
+    fips_run: str | None = None,
+    xml_only: bool = False,
+    log: str | None = None,
+    debug: bool = False,
+) -> DcmunpackParameters:
+    """
+    Build parameters.
+    
+    Args:
+        src: Dicom source directory. You can specify more than one.
+        targ: Output directory. Do not need to include when just getting\
+            information about what is in the directory.
+        run: Specify unpacking rules for a given run (series). Eg, "-run 3 bold\
+            nii f.nii".
+        auto_runseq: Save all scans in the targetdir as runo.seqname.format.
+        keep_scouts: Unpack series with 'scout' or 'setter' in the name.
+        scanonly: Only scan the directory and put result in file.
+        one_per_dir: Assume that there is only one dicom series in each subdir.
+        ext: Input extension (eg, dcm).
+        pre: Input prefix (i.e., input file name init string).
+        pat: Input pattern (i.e., string that occurs in the middle of file\
+            name).
+        no_infodump: Do not create the fname-infodump.dat file.
+        generic: Do not use FSFAST hierarchy.
+        copy_only: Only copy dicom files to output directory (implies\
+            -no-convert).
+        no_convert: Do not convert to output format.
+        force_update: Convert even if output is newer than the input dicom.
+        max_: Print out max in given dicom file.
+        base: Report filename without path.
+        key_string: Put keystring before each run line (good for searching).
+        index_out: Save index of files to index.out.dat (for re-use).
+        index_in: Read index of files (can make things much faster on 2nd run).
+        it_dicom: Add -it dicom to mri_convert cmd line.
+        no_exit_on_error: Continue to unpack data even if there is an error in\
+            conversion.
+        run_skip: Skip a given run (good when using -auto-runseq).
+        no_rescale_dicom: Turn off DICOM rescaling based on tags (0028,1052)\
+            (0028,1053).
+        rescale_dicom: Turn DICOM rescaling on.
+        no_dwi: Turn off trying to read DWI parameters.
+        iid: Set -iid to mri_convert.
+        ijd: Set -ijd to mri_convert.
+        ikd: Set -ikd to mri_convert.
+        extra_info: Add session info to each line of the info file (pat, date,\
+            man, scan, field, serno).
+        first_dicom: Copy first dicom file into output folder.
+        no_dcm2niix: Turn off dcm2niix conversion.
+        phase: Add the string _phase to volumes that are phase images based on\
+            ImageType.
+        fips: Fips parameters: project, site, birnid, visit.
+        fips_run: Fips-run parameters: run paradigm.
+        xml_only: For fips, only create xml file, do not convert to output.
+        log: Log output to a file.
+        debug: Enable debug mode.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dcmunpack",
+        "src": src,
+        "keep_scouts": keep_scouts,
+        "one_per_dir": one_per_dir,
+        "no_infodump": no_infodump,
+        "generic": generic,
+        "copy_only": copy_only,
+        "no_convert": no_convert,
+        "force_update": force_update,
+        "max": max_,
+        "base": base,
+        "it_dicom": it_dicom,
+        "no_exit_on_error": no_exit_on_error,
+        "no_rescale_dicom": no_rescale_dicom,
+        "rescale_dicom": rescale_dicom,
+        "no_dwi": no_dwi,
+        "extra_info": extra_info,
+        "first_dicom": first_dicom,
+        "no_dcm2niix": no_dcm2niix,
+        "phase": phase,
+        "xml_only": xml_only,
+        "debug": debug,
+    }
+    if targ is not None:
+        params["targ"] = targ
+    if run is not None:
+        params["run"] = run
+    if auto_runseq is not None:
+        params["auto_runseq"] = auto_runseq
+    if scanonly is not None:
+        params["scanonly"] = scanonly
+    if ext is not None:
+        params["ext"] = ext
+    if pre is not None:
+        params["pre"] = pre
+    if pat is not None:
+        params["pat"] = pat
+    if key_string is not None:
+        params["key_string"] = key_string
+    if index_out is not None:
+        params["index_out"] = index_out
+    if index_in is not None:
+        params["index_in"] = index_in
+    if run_skip is not None:
+        params["run_skip"] = run_skip
+    if iid is not None:
+        params["iid"] = iid
+    if ijd is not None:
+        params["ijd"] = ijd
+    if ikd is not None:
+        params["ikd"] = ikd
+    if fips is not None:
+        params["fips"] = fips
+    if fips_run is not None:
+        params["fips_run"] = fips_run
+    if log is not None:
+        params["log"] = log
+    return params
+
+
+def dcmunpack_cargs(
+    params: DcmunpackParameters,
+    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("dcmunpack")
+    cargs.extend([
+        "-src",
+        params.get("src")
+    ])
+    if params.get("targ") is not None:
+        cargs.extend([
+            "-targ",
+            params.get("targ")
+        ])
+    if params.get("run") is not None:
+        cargs.extend([
+            "-run",
+            params.get("run")
+        ])
+    if params.get("auto_runseq") is not None:
+        cargs.extend([
+            "-auto-runseq",
+            params.get("auto_runseq")
+        ])
+    if params.get("keep_scouts"):
+        cargs.append("-keep-scouts")
+    if params.get("scanonly") is not None:
+        cargs.extend([
+            "-scanonly",
+            params.get("scanonly")
+        ])
+    if params.get("one_per_dir"):
+        cargs.append("-one-per-dir")
+    if params.get("ext") is not None:
+        cargs.extend([
+            "-ext",
+            params.get("ext")
+        ])
+    if params.get("pre") is not None:
+        cargs.extend([
+            "-pre",
+            params.get("pre")
+        ])
+    if params.get("pat") is not None:
+        cargs.extend([
+            "-pat",
+            params.get("pat")
+        ])
+    if params.get("no_infodump"):
+        cargs.append("-no-infodump")
+    if params.get("generic"):
+        cargs.append("-generic")
+    if params.get("copy_only"):
+        cargs.append("-copy-only")
+    if params.get("no_convert"):
+        cargs.append("-no-convert")
+    if params.get("force_update"):
+        cargs.append("-force-update")
+    if params.get("max"):
+        cargs.append("-max")
+    if params.get("base"):
+        cargs.append("-base")
+    if params.get("key_string") is not None:
+        cargs.extend([
+            "-key",
+            params.get("key_string")
+        ])
+    if params.get("index_out") is not None:
+        cargs.extend([
+            "-index-out",
+            params.get("index_out")
+        ])
+    if params.get("index_in") is not None:
+        cargs.extend([
+            "-index-in",
+            params.get("index_in")
+        ])
+    if params.get("it_dicom"):
+        cargs.append("-itdicom")
+    if params.get("no_exit_on_error"):
+        cargs.append("-no-exit-on-error")
+    if params.get("run_skip") is not None:
+        cargs.extend([
+            "-run-skip",
+            params.get("run_skip")
+        ])
+    if params.get("no_rescale_dicom"):
+        cargs.append("-no-rescale-dicom")
+    if params.get("rescale_dicom"):
+        cargs.append("-rescale-dicom")
+    if params.get("no_dwi"):
+        cargs.append("-no-dwi")
+    if params.get("iid") is not None:
+        cargs.extend([
+            "-iid",
+            *map(str, params.get("iid"))
+        ])
+    if params.get("ijd") is not None:
+        cargs.extend([
+            "-ijd",
+            *map(str, params.get("ijd"))
+        ])
+    if params.get("ikd") is not None:
+        cargs.extend([
+            "-ikd",
+            *map(str, params.get("ikd"))
+        ])
+    if params.get("extra_info"):
+        cargs.append("-extra-info")
+    if params.get("first_dicom"):
+        cargs.append("-first-dicom")
+    if params.get("no_dcm2niix"):
+        cargs.append("-no-dcm2niix")
+    if params.get("phase"):
+        cargs.append("-phase")
+    if params.get("fips") is not None:
+        cargs.extend([
+            "-fips",
+            params.get("fips")
+        ])
+    if params.get("fips_run") is not None:
+        cargs.extend([
+            "-fips-run",
+            params.get("fips_run")
+        ])
+    if params.get("xml_only"):
+        cargs.append("-xml-only")
+    if params.get("log") is not None:
+        cargs.extend([
+            "-log",
+            params.get("log")
+        ])
+    if params.get("debug"):
+        cargs.append("-debug")
+    return cargs
+
+
+def dcmunpack_outputs(
+    params: DcmunpackParameters,
+    execution: Execution,
+) -> DcmunpackOutputs:
+    """
+    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 = DcmunpackOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dcmunpack_execute(
+    params: DcmunpackParameters,
+    execution: Execution,
+) -> DcmunpackOutputs:
+    """
+    Sorts and converts a directory of DICOM files (Siemens, GE, Philips) into an
+    output hierarchy with nifti (nii), mgh, mgz, or analyze output formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DcmunpackOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dcmunpack_cargs(params, execution)
+    ret = dcmunpack_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dcmunpack(
+    src: str,
+    targ: str | None = None,
+    run: str | None = None,
+    auto_runseq: str | None = None,
+    keep_scouts: bool = False,
+    scanonly: str | None = None,
+    one_per_dir: bool = False,
+    ext: str | None = None,
+    pre: str | None = None,
+    pat: str | None = None,
+    no_infodump: bool = False,
+    generic: bool = False,
+    copy_only: bool = False,
+    no_convert: bool = False,
+    force_update: bool = False,
+    max_: bool = False,
+    base: bool = False,
+    key_string: str | None = None,
+    index_out: str | None = None,
+    index_in: str | None = None,
+    it_dicom: bool = False,
+    no_exit_on_error: bool = False,
+    run_skip: str | None = None,
+    no_rescale_dicom: bool = False,
+    rescale_dicom: bool = False,
+    no_dwi: bool = False,
+    iid: list[float] | None = None,
+    ijd: list[float] | None = None,
+    ikd: list[float] | None = None,
+    extra_info: bool = False,
+    first_dicom: bool = False,
+    no_dcm2niix: bool = False,
+    phase: bool = False,
+    fips: str | None = None,
+    fips_run: str | None = None,
+    xml_only: bool = False,
+    log: str | None = None,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> DcmunpackOutputs:
+    """
+    Sorts and converts a directory of DICOM files (Siemens, GE, Philips) into an
+    output hierarchy with nifti (nii), mgh, mgz, or analyze output formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        src: Dicom source directory. You can specify more than one.
+        targ: Output directory. Do not need to include when just getting\
+            information about what is in the directory.
+        run: Specify unpacking rules for a given run (series). Eg, "-run 3 bold\
+            nii f.nii".
+        auto_runseq: Save all scans in the targetdir as runo.seqname.format.
+        keep_scouts: Unpack series with 'scout' or 'setter' in the name.
+        scanonly: Only scan the directory and put result in file.
+        one_per_dir: Assume that there is only one dicom series in each subdir.
+        ext: Input extension (eg, dcm).
+        pre: Input prefix (i.e., input file name init string).
+        pat: Input pattern (i.e., string that occurs in the middle of file\
+            name).
+        no_infodump: Do not create the fname-infodump.dat file.
+        generic: Do not use FSFAST hierarchy.
+        copy_only: Only copy dicom files to output directory (implies\
+            -no-convert).
+        no_convert: Do not convert to output format.
+        force_update: Convert even if output is newer than the input dicom.
+        max_: Print out max in given dicom file.
+        base: Report filename without path.
+        key_string: Put keystring before each run line (good for searching).
+        index_out: Save index of files to index.out.dat (for re-use).
+        index_in: Read index of files (can make things much faster on 2nd run).
+        it_dicom: Add -it dicom to mri_convert cmd line.
+        no_exit_on_error: Continue to unpack data even if there is an error in\
+            conversion.
+        run_skip: Skip a given run (good when using -auto-runseq).
+        no_rescale_dicom: Turn off DICOM rescaling based on tags (0028,1052)\
+            (0028,1053).
+        rescale_dicom: Turn DICOM rescaling on.
+        no_dwi: Turn off trying to read DWI parameters.
+        iid: Set -iid to mri_convert.
+        ijd: Set -ijd to mri_convert.
+        ikd: Set -ikd to mri_convert.
+        extra_info: Add session info to each line of the info file (pat, date,\
+            man, scan, field, serno).
+        first_dicom: Copy first dicom file into output folder.
+        no_dcm2niix: Turn off dcm2niix conversion.
+        phase: Add the string _phase to volumes that are phase images based on\
+            ImageType.
+        fips: Fips parameters: project, site, birnid, visit.
+        fips_run: Fips-run parameters: run paradigm.
+        xml_only: For fips, only create xml file, do not convert to output.
+        log: Log output to a file.
+        debug: Enable debug mode.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DcmunpackOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMUNPACK_METADATA)
+    params = dcmunpack_params(
+        src=src,
+        targ=targ,
+        run=run,
+        auto_runseq=auto_runseq,
+        keep_scouts=keep_scouts,
+        scanonly=scanonly,
+        one_per_dir=one_per_dir,
+        ext=ext,
+        pre=pre,
+        pat=pat,
+        no_infodump=no_infodump,
+        generic=generic,
+        copy_only=copy_only,
+        no_convert=no_convert,
+        force_update=force_update,
+        max_=max_,
+        base=base,
+        key_string=key_string,
+        index_out=index_out,
+        index_in=index_in,
+        it_dicom=it_dicom,
+        no_exit_on_error=no_exit_on_error,
+        run_skip=run_skip,
+        no_rescale_dicom=no_rescale_dicom,
+        rescale_dicom=rescale_dicom,
+        no_dwi=no_dwi,
+        iid=iid,
+        ijd=ijd,
+        ikd=ikd,
+        extra_info=extra_info,
+        first_dicom=first_dicom,
+        no_dcm2niix=no_dcm2niix,
+        phase=phase,
+        fips=fips,
+        fips_run=fips_run,
+        xml_only=xml_only,
+        log=log,
+        debug=debug,
+    )
+    return dcmunpack_execute(params, execution)
+
+
+__all__ = [
+    "DCMUNPACK_METADATA",
+    "DcmunpackOutputs",
+    "DcmunpackParameters",
+    "dcmunpack",
+    "dcmunpack_params",
+]