niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/file_tool.py

@@ -0,0 +1,580 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FILE_TOOL_METADATA = Metadata(
+    id="a338b51bc00f0441446c6ca843266cef70008a68.boutiques",
+    name="file_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FileToolParameters = typing.TypedDict('FileToolParameters', {
+    "__STYX_TYPE__": typing.Literal["file_tool"],
+    "help": bool,
+    "version": bool,
+    "hist": bool,
+    "debug": typing.NotRequired[float | None],
+    "infiles": list[InputPathType],
+    "ge_all": bool,
+    "ge_header": bool,
+    "ge_extras": bool,
+    "ge_uv17": bool,
+    "ge_run": bool,
+    "ge_off": bool,
+    "ge4_all": bool,
+    "ge4_image": bool,
+    "ge4_series": bool,
+    "ge4_study": bool,
+    "def_ana_hdr": bool,
+    "diff_ana_hdrs": bool,
+    "disp_ana_hdr": bool,
+    "hex": bool,
+    "mod_ana_hdr": bool,
+    "mod_field": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "show_bad_all": bool,
+    "show_bad_backslash": bool,
+    "show_bad_char": bool,
+    "show_file_type": bool,
+    "fix_rich_quotes": typing.NotRequired[str | None],
+    "test": bool,
+    "length": typing.NotRequired[float | None],
+    "mod_data": typing.NotRequired[str | None],
+    "mod_type": typing.NotRequired[str | None],
+    "offset": typing.NotRequired[float | None],
+    "quiet": bool,
+    "disp_hex": bool,
+    "disp_hex1": bool,
+    "disp_hex2": bool,
+    "disp_hex4": bool,
+    "disp_int2": bool,
+    "disp_int4": bool,
+    "disp_real4": bool,
+    "swap_bytes": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "file_tool": file_tool_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 {
+        "file_tool": file_tool_outputs,
+    }.get(t)
+
+
+class FileToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `file_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    modified_file: OutputPathType | None
+    """The modified output file"""
+
+
+def file_tool_params(
+    infiles: list[InputPathType],
+    help_: bool = False,
+    version: bool = False,
+    hist: bool = False,
+    debug: float | None = None,
+    ge_all: bool = False,
+    ge_header: bool = False,
+    ge_extras: bool = False,
+    ge_uv17: bool = False,
+    ge_run: bool = False,
+    ge_off: bool = False,
+    ge4_all: bool = False,
+    ge4_image: bool = False,
+    ge4_series: bool = False,
+    ge4_study: bool = False,
+    def_ana_hdr: bool = False,
+    diff_ana_hdrs: bool = False,
+    disp_ana_hdr: bool = False,
+    hex_: bool = False,
+    mod_ana_hdr: bool = False,
+    mod_field: str | None = None,
+    prefix: str | None = None,
+    overwrite: bool = False,
+    show_bad_all: bool = False,
+    show_bad_backslash: bool = False,
+    show_bad_char: bool = False,
+    show_file_type: bool = False,
+    fix_rich_quotes: str | None = None,
+    test: bool = False,
+    length: float | None = None,
+    mod_data: str | None = None,
+    mod_type: str | None = None,
+    offset: float | None = None,
+    quiet: bool = False,
+    disp_hex: bool = False,
+    disp_hex1: bool = False,
+    disp_hex2: bool = False,
+    disp_hex4: bool = False,
+    disp_int2: bool = False,
+    disp_int4: bool = False,
+    disp_real4: bool = False,
+    swap_bytes: bool = False,
+) -> FileToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infiles: Specify input files to display or modify.
+        help_: Show help information.
+        version: Show version information.
+        hist: Show the program's modification history.
+        debug: Print extra info along the way, default is 0, max is 2.
+        ge_all: Display GE header and extras info.
+        ge_header: Display GE header info.
+        ge_extras: Display extra GE image info.
+        ge_uv17: Display the value of uv17 (the run #).
+        ge_run: Display the value of uv17 (the run #).
+        ge_off: Display file offsets for various fields.
+        ge4_all: Display GEMS 4.x series and image headers.
+        ge4_image: Display GEMS 4.x image header.
+        ge4_series: Display GEMS 4.x series header.
+        ge4_study: Display GEMS 4.x study header.
+        def_ana_hdr: Display the definition of an ANALYZE header.
+        diff_ana_hdrs: Display field differences between 2 headers.
+        disp_ana_hdr: Display ANALYZE headers.
+        hex_: Display field values in hexadecimal.
+        mod_ana_hdr: Modify ANALYZE headers.
+        mod_field: Specify a field and value(s) to modify.
+        prefix: Specify an output filename.
+        overwrite: Specify to overwrite the input file(s).
+        show_bad_all: Show lines with whitespace after '\\'.
+        show_bad_backslash: Show lines with whitespace after '\\'.
+        show_bad_char: Show any non-printable characters.
+        show_file_type: Print file type of UNIX, Mac or DOS.
+        fix_rich_quotes: Replace rich-text quotes with ASCII.
+        test: Short for -show_bad_all. Check script files for known issues.
+        length: Specify the number of bytes to print/modify.
+        mod_data: Specify a string to modify the data to.
+        mod_type: Specify the data type to write to the file.
+        offset: Specify the offset into each file.
+        quiet: Do not output header information.
+        disp_hex: Display bytes in hex.
+        disp_hex1: Display bytes in hex.
+        disp_hex2: Display 2-byte integers in hex.
+        disp_hex4: Display 4-byte integers in hex.
+        disp_int2: Display 2-byte integers.
+        disp_int4: Display 4-byte integers.
+        disp_real4: Display 4-byte real numbers.
+        swap_bytes: Use byte-swapping on numbers.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "file_tool",
+        "help": help_,
+        "version": version,
+        "hist": hist,
+        "infiles": infiles,
+        "ge_all": ge_all,
+        "ge_header": ge_header,
+        "ge_extras": ge_extras,
+        "ge_uv17": ge_uv17,
+        "ge_run": ge_run,
+        "ge_off": ge_off,
+        "ge4_all": ge4_all,
+        "ge4_image": ge4_image,
+        "ge4_series": ge4_series,
+        "ge4_study": ge4_study,
+        "def_ana_hdr": def_ana_hdr,
+        "diff_ana_hdrs": diff_ana_hdrs,
+        "disp_ana_hdr": disp_ana_hdr,
+        "hex": hex_,
+        "mod_ana_hdr": mod_ana_hdr,
+        "overwrite": overwrite,
+        "show_bad_all": show_bad_all,
+        "show_bad_backslash": show_bad_backslash,
+        "show_bad_char": show_bad_char,
+        "show_file_type": show_file_type,
+        "test": test,
+        "quiet": quiet,
+        "disp_hex": disp_hex,
+        "disp_hex1": disp_hex1,
+        "disp_hex2": disp_hex2,
+        "disp_hex4": disp_hex4,
+        "disp_int2": disp_int2,
+        "disp_int4": disp_int4,
+        "disp_real4": disp_real4,
+        "swap_bytes": swap_bytes,
+    }
+    if debug is not None:
+        params["debug"] = debug
+    if mod_field is not None:
+        params["mod_field"] = mod_field
+    if prefix is not None:
+        params["prefix"] = prefix
+    if fix_rich_quotes is not None:
+        params["fix_rich_quotes"] = fix_rich_quotes
+    if length is not None:
+        params["length"] = length
+    if mod_data is not None:
+        params["mod_data"] = mod_data
+    if mod_type is not None:
+        params["mod_type"] = mod_type
+    if offset is not None:
+        params["offset"] = offset
+    return params
+
+
+def file_tool_cargs(
+    params: FileToolParameters,
+    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("file_tool")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    cargs.extend([
+        "-infiles",
+        *[execution.input_file(f) for f in params.get("infiles")]
+    ])
+    if params.get("ge_all"):
+        cargs.append("-ge_all")
+    if params.get("ge_header"):
+        cargs.append("-ge_header")
+    if params.get("ge_extras"):
+        cargs.append("-ge_extras")
+    if params.get("ge_uv17"):
+        cargs.append("-ge_uv17")
+    if params.get("ge_run"):
+        cargs.append("-ge_run")
+    if params.get("ge_off"):
+        cargs.append("-ge_off")
+    if params.get("ge4_all"):
+        cargs.append("-ge4_all")
+    if params.get("ge4_image"):
+        cargs.append("-ge4_image")
+    if params.get("ge4_series"):
+        cargs.append("-ge4_series")
+    if params.get("ge4_study"):
+        cargs.append("-ge4_study")
+    if params.get("def_ana_hdr"):
+        cargs.append("-def_ana_hdr")
+    if params.get("diff_ana_hdrs"):
+        cargs.append("-diff_ana_hdrs")
+    if params.get("disp_ana_hdr"):
+        cargs.append("-disp_ana_hdr")
+    if params.get("hex"):
+        cargs.append("-hex")
+    if params.get("mod_ana_hdr"):
+        cargs.append("-mod_ana_hdr")
+    if params.get("mod_field") is not None:
+        cargs.extend([
+            "-mod_field",
+            params.get("mod_field")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("show_bad_all"):
+        cargs.append("-show_bad_all")
+    if params.get("show_bad_backslash"):
+        cargs.append("-show_bad_backslash")
+    if params.get("show_bad_char"):
+        cargs.append("-show_bad_char")
+    if params.get("show_file_type"):
+        cargs.append("-show_file_type")
+    if params.get("fix_rich_quotes") is not None:
+        cargs.extend([
+            "-fix_rich_quotes",
+            params.get("fix_rich_quotes")
+        ])
+    if params.get("test"):
+        cargs.append("-test")
+    if params.get("length") is not None:
+        cargs.extend([
+            "-length",
+            str(params.get("length"))
+        ])
+    if params.get("mod_data") is not None:
+        cargs.extend([
+            "-mod_data",
+            params.get("mod_data")
+        ])
+    if params.get("mod_type") is not None:
+        cargs.extend([
+            "-mod_type",
+            params.get("mod_type")
+        ])
+    if params.get("offset") is not None:
+        cargs.extend([
+            "-offset",
+            str(params.get("offset"))
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("disp_hex"):
+        cargs.append("-disp_hex")
+    if params.get("disp_hex1"):
+        cargs.append("-disp_hex1")
+    if params.get("disp_hex2"):
+        cargs.append("-disp_hex2")
+    if params.get("disp_hex4"):
+        cargs.append("-disp_hex4")
+    if params.get("disp_int2"):
+        cargs.append("-disp_int2")
+    if params.get("disp_int4"):
+        cargs.append("-disp_int4")
+    if params.get("disp_real4"):
+        cargs.append("-disp_real4")
+    if params.get("swap_bytes"):
+        cargs.append("-swap_bytes")
+    return cargs
+
+
+def file_tool_outputs(
+    params: FileToolParameters,
+    execution: Execution,
+) -> FileToolOutputs:
+    """
+    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 = FileToolOutputs(
+        root=execution.output_file("."),
+        modified_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def file_tool_execute(
+    params: FileToolParameters,
+    execution: Execution,
+) -> FileToolOutputs:
+    """
+    Program to display or modify sections of a file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FileToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = file_tool_cargs(params, execution)
+    ret = file_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def file_tool(
+    infiles: list[InputPathType],
+    help_: bool = False,
+    version: bool = False,
+    hist: bool = False,
+    debug: float | None = None,
+    ge_all: bool = False,
+    ge_header: bool = False,
+    ge_extras: bool = False,
+    ge_uv17: bool = False,
+    ge_run: bool = False,
+    ge_off: bool = False,
+    ge4_all: bool = False,
+    ge4_image: bool = False,
+    ge4_series: bool = False,
+    ge4_study: bool = False,
+    def_ana_hdr: bool = False,
+    diff_ana_hdrs: bool = False,
+    disp_ana_hdr: bool = False,
+    hex_: bool = False,
+    mod_ana_hdr: bool = False,
+    mod_field: str | None = None,
+    prefix: str | None = None,
+    overwrite: bool = False,
+    show_bad_all: bool = False,
+    show_bad_backslash: bool = False,
+    show_bad_char: bool = False,
+    show_file_type: bool = False,
+    fix_rich_quotes: str | None = None,
+    test: bool = False,
+    length: float | None = None,
+    mod_data: str | None = None,
+    mod_type: str | None = None,
+    offset: float | None = None,
+    quiet: bool = False,
+    disp_hex: bool = False,
+    disp_hex1: bool = False,
+    disp_hex2: bool = False,
+    disp_hex4: bool = False,
+    disp_int2: bool = False,
+    disp_int4: bool = False,
+    disp_real4: bool = False,
+    swap_bytes: bool = False,
+    runner: Runner | None = None,
+) -> FileToolOutputs:
+    """
+    Program to display or modify sections of a file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infiles: Specify input files to display or modify.
+        help_: Show help information.
+        version: Show version information.
+        hist: Show the program's modification history.
+        debug: Print extra info along the way, default is 0, max is 2.
+        ge_all: Display GE header and extras info.
+        ge_header: Display GE header info.
+        ge_extras: Display extra GE image info.
+        ge_uv17: Display the value of uv17 (the run #).
+        ge_run: Display the value of uv17 (the run #).
+        ge_off: Display file offsets for various fields.
+        ge4_all: Display GEMS 4.x series and image headers.
+        ge4_image: Display GEMS 4.x image header.
+        ge4_series: Display GEMS 4.x series header.
+        ge4_study: Display GEMS 4.x study header.
+        def_ana_hdr: Display the definition of an ANALYZE header.
+        diff_ana_hdrs: Display field differences between 2 headers.
+        disp_ana_hdr: Display ANALYZE headers.
+        hex_: Display field values in hexadecimal.
+        mod_ana_hdr: Modify ANALYZE headers.
+        mod_field: Specify a field and value(s) to modify.
+        prefix: Specify an output filename.
+        overwrite: Specify to overwrite the input file(s).
+        show_bad_all: Show lines with whitespace after '\\'.
+        show_bad_backslash: Show lines with whitespace after '\\'.
+        show_bad_char: Show any non-printable characters.
+        show_file_type: Print file type of UNIX, Mac or DOS.
+        fix_rich_quotes: Replace rich-text quotes with ASCII.
+        test: Short for -show_bad_all. Check script files for known issues.
+        length: Specify the number of bytes to print/modify.
+        mod_data: Specify a string to modify the data to.
+        mod_type: Specify the data type to write to the file.
+        offset: Specify the offset into each file.
+        quiet: Do not output header information.
+        disp_hex: Display bytes in hex.
+        disp_hex1: Display bytes in hex.
+        disp_hex2: Display 2-byte integers in hex.
+        disp_hex4: Display 4-byte integers in hex.
+        disp_int2: Display 2-byte integers.
+        disp_int4: Display 4-byte integers.
+        disp_real4: Display 4-byte real numbers.
+        swap_bytes: Use byte-swapping on numbers.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FileToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FILE_TOOL_METADATA)
+    params = file_tool_params(
+        help_=help_,
+        version=version,
+        hist=hist,
+        debug=debug,
+        infiles=infiles,
+        ge_all=ge_all,
+        ge_header=ge_header,
+        ge_extras=ge_extras,
+        ge_uv17=ge_uv17,
+        ge_run=ge_run,
+        ge_off=ge_off,
+        ge4_all=ge4_all,
+        ge4_image=ge4_image,
+        ge4_series=ge4_series,
+        ge4_study=ge4_study,
+        def_ana_hdr=def_ana_hdr,
+        diff_ana_hdrs=diff_ana_hdrs,
+        disp_ana_hdr=disp_ana_hdr,
+        hex_=hex_,
+        mod_ana_hdr=mod_ana_hdr,
+        mod_field=mod_field,
+        prefix=prefix,
+        overwrite=overwrite,
+        show_bad_all=show_bad_all,
+        show_bad_backslash=show_bad_backslash,
+        show_bad_char=show_bad_char,
+        show_file_type=show_file_type,
+        fix_rich_quotes=fix_rich_quotes,
+        test=test,
+        length=length,
+        mod_data=mod_data,
+        mod_type=mod_type,
+        offset=offset,
+        quiet=quiet,
+        disp_hex=disp_hex,
+        disp_hex1=disp_hex1,
+        disp_hex2=disp_hex2,
+        disp_hex4=disp_hex4,
+        disp_int2=disp_int2,
+        disp_int4=disp_int4,
+        disp_real4=disp_real4,
+        swap_bytes=swap_bytes,
+    )
+    return file_tool_execute(params, execution)
+
+
+__all__ = [
+    "FILE_TOOL_METADATA",
+    "FileToolOutputs",
+    "FileToolParameters",
+    "file_tool",
+    "file_tool_params",
+]