niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/niccc.py

@@ -0,0 +1,307 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NICCC_METADATA = Metadata(
+    id="ecc865fc2143792b2c5c1c0adc6ffbd967c02c7f.boutiques",
+    name="niccc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NicccParameters = typing.TypedDict('NicccParameters', {
+    "__STYX_TYPE__": typing.Literal["niccc"],
+    "streamspec": str,
+    "duplicate": bool,
+    "nodata": bool,
+    "attribute": typing.NotRequired[str | None],
+    "match": typing.NotRequired[str | None],
+    "file": bool,
+    "string": bool,
+    "stdout": bool,
+    "hash": bool,
+    "quiet": bool,
+    "find_attr": typing.NotRequired[list[str] | None],
+    "skip_attr": typing.NotRequired[list[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 {
+        "niccc": niccc_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 {
+        "niccc": niccc_outputs,
+    }.get(t)
+
+
+class NicccOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `niccc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stderr_output: OutputPathType
+    """Results output to stderr"""
+
+
+def niccc_params(
+    streamspec: str,
+    duplicate: bool = False,
+    nodata: bool = False,
+    attribute: str | None = None,
+    match: str | None = None,
+    file: bool = False,
+    string_: bool = False,
+    stdout: bool = False,
+    hash_: bool = False,
+    quiet: bool = False,
+    find_attr: list[str] | None = None,
+    skip_attr: list[str] | None = None,
+) -> NicccParameters:
+    """
+    Build parameters.
+    
+    Args:
+        streamspec: A string defining a NIML stream.
+        duplicate: Duplicate the element before showing it. This is to test\
+            NI_duplicate function.
+        nodata: Show header parts only in output.
+        attribute: Dump the value of attribute ATTR.
+        match: Match attribute: If MATCH is exact, then attribute name is\
+            matched exactly. If MATCH is partial, then a match of all the\
+            characters in ATTR is enough.
+        file: Streamspec is a filename.
+        string_: Streamspec is an element string like: '<T font=9 coords="2.3\
+            23 2"/>'.
+        stdout: Write elements to stdout, instead of stderr.
+        hash_: Put the # at the beginning of lines with no data.
+        quiet: Quiet stderr messages, and don't echo attribute name with\
+            -attribute option.
+        find_attr: Only output elements that have an attribute ATTR of value\
+            ATTRVAL.
+        skip_attr: Do not output elements that have an attribute ATTR of value\
+            ATTRVAL.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "niccc",
+        "streamspec": streamspec,
+        "duplicate": duplicate,
+        "nodata": nodata,
+        "file": file,
+        "string": string_,
+        "stdout": stdout,
+        "hash": hash_,
+        "quiet": quiet,
+    }
+    if attribute is not None:
+        params["attribute"] = attribute
+    if match is not None:
+        params["match"] = match
+    if find_attr is not None:
+        params["find_attr"] = find_attr
+    if skip_attr is not None:
+        params["skip_attr"] = skip_attr
+    return params
+
+
+def niccc_cargs(
+    params: NicccParameters,
+    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("niccc")
+    cargs.append(params.get("streamspec"))
+    if params.get("duplicate"):
+        cargs.append("-dup")
+    if params.get("nodata"):
+        cargs.append("-nodata")
+    if params.get("attribute") is not None:
+        cargs.extend([
+            "-attribute",
+            params.get("attribute")
+        ])
+    if params.get("match") is not None:
+        cargs.extend([
+            "-match",
+            params.get("match")
+        ])
+    if params.get("file"):
+        cargs.append("-f")
+    if params.get("string"):
+        cargs.append("-s")
+    if params.get("stdout"):
+        cargs.append("-stdout")
+    if params.get("hash"):
+        cargs.append("-#")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("find_attr") is not None:
+        cargs.extend([
+            "-find_nel_with_attr",
+            *params.get("find_attr")
+        ])
+    if params.get("skip_attr") is not None:
+        cargs.extend([
+            "-skip_nel_with_attr",
+            *params.get("skip_attr")
+        ])
+    return cargs
+
+
+def niccc_outputs(
+    params: NicccParameters,
+    execution: Execution,
+) -> NicccOutputs:
+    """
+    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 = NicccOutputs(
+        root=execution.output_file("."),
+        stderr_output=execution.output_file("stderr"),
+    )
+    return ret
+
+
+def niccc_execute(
+    params: NicccParameters,
+    execution: Execution,
+) -> NicccOutputs:
+    """
+    A program for conducting certain NIML tests on input from streamspec and write
+    the results to stderr.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NicccOutputs`).
+    """
+    params = execution.params(params)
+    cargs = niccc_cargs(params, execution)
+    ret = niccc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def niccc(
+    streamspec: str,
+    duplicate: bool = False,
+    nodata: bool = False,
+    attribute: str | None = None,
+    match: str | None = None,
+    file: bool = False,
+    string_: bool = False,
+    stdout: bool = False,
+    hash_: bool = False,
+    quiet: bool = False,
+    find_attr: list[str] | None = None,
+    skip_attr: list[str] | None = None,
+    runner: Runner | None = None,
+) -> NicccOutputs:
+    """
+    A program for conducting certain NIML tests on input from streamspec and write
+    the results to stderr.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        streamspec: A string defining a NIML stream.
+        duplicate: Duplicate the element before showing it. This is to test\
+            NI_duplicate function.
+        nodata: Show header parts only in output.
+        attribute: Dump the value of attribute ATTR.
+        match: Match attribute: If MATCH is exact, then attribute name is\
+            matched exactly. If MATCH is partial, then a match of all the\
+            characters in ATTR is enough.
+        file: Streamspec is a filename.
+        string_: Streamspec is an element string like: '<T font=9 coords="2.3\
+            23 2"/>'.
+        stdout: Write elements to stdout, instead of stderr.
+        hash_: Put the # at the beginning of lines with no data.
+        quiet: Quiet stderr messages, and don't echo attribute name with\
+            -attribute option.
+        find_attr: Only output elements that have an attribute ATTR of value\
+            ATTRVAL.
+        skip_attr: Do not output elements that have an attribute ATTR of value\
+            ATTRVAL.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NicccOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NICCC_METADATA)
+    params = niccc_params(
+        streamspec=streamspec,
+        duplicate=duplicate,
+        nodata=nodata,
+        attribute=attribute,
+        match=match,
+        file=file,
+        string_=string_,
+        stdout=stdout,
+        hash_=hash_,
+        quiet=quiet,
+        find_attr=find_attr,
+        skip_attr=skip_attr,
+    )
+    return niccc_execute(params, execution)
+
+
+__all__ = [
+    "NICCC_METADATA",
+    "NicccOutputs",
+    "NicccParameters",
+    "niccc",
+    "niccc_params",
+]

niwrap_afni/afni/nifti_tool.py

@@ -0,0 +1,310 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NIFTI_TOOL_METADATA = Metadata(
+    id="3d62871ad5a6df5a56027e145232bf726b83d960.boutiques",
+    name="nifti_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NiftiToolParameters = typing.TypedDict('NiftiToolParameters', {
+    "__STYX_TYPE__": typing.Literal["nifti_tool"],
+    "action": str,
+    "input_files": typing.NotRequired[list[InputPathType] | None],
+    "field": typing.NotRequired[str | None],
+    "mod_field": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[float | None],
+    "overwrite": bool,
+    "convert2dtype": typing.NotRequired[str | None],
+    "convert_fail_choice": typing.NotRequired[str | None],
+    "convert_verify": bool,
+    "add_comment_ext": typing.NotRequired[str | None],
+    "rm_ext": 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 {
+        "nifti_tool": nifti_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 {
+        "nifti_tool": nifti_tool_outputs,
+    }.get(t)
+
+
+class NiftiToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `nifti_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """The nifti file generated as output."""
+
+
+def nifti_tool_params(
+    action: str,
+    input_files: list[InputPathType] | None = None,
+    field: str | None = None,
+    mod_field: str | None = None,
+    prefix: str | None = None,
+    debug: float | None = None,
+    overwrite: bool = False,
+    convert2dtype: str | None = None,
+    convert_fail_choice: str | None = None,
+    convert_verify: bool = False,
+    add_comment_ext: str | None = None,
+    rm_ext: str | None = None,
+) -> NiftiToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        action: Action type that defines what nifti_tool will do.
+        input_files: One or more input nifti files.
+        field: Field name to display, modify, or compare.
+        mod_field: Field name and new value to modify.
+        prefix: Prefix for the output file.
+        debug: Debugging level (0-3).
+        overwrite: Overwrite input files with modifications.
+        convert2dtype: Convert data to a new datatype.
+        convert_fail_choice: Action on conversion failure (ignore, warn, fail).
+        convert_verify: Verify datatype conversion exactness.
+        add_comment_ext: Add COMMENT-type extension to dataset.
+        rm_ext: Remove extension by index or ALL.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "nifti_tool",
+        "action": action,
+        "overwrite": overwrite,
+        "convert_verify": convert_verify,
+    }
+    if input_files is not None:
+        params["input_files"] = input_files
+    if field is not None:
+        params["field"] = field
+    if mod_field is not None:
+        params["mod_field"] = mod_field
+    if prefix is not None:
+        params["prefix"] = prefix
+    if debug is not None:
+        params["debug"] = debug
+    if convert2dtype is not None:
+        params["convert2dtype"] = convert2dtype
+    if convert_fail_choice is not None:
+        params["convert_fail_choice"] = convert_fail_choice
+    if add_comment_ext is not None:
+        params["add_comment_ext"] = add_comment_ext
+    if rm_ext is not None:
+        params["rm_ext"] = rm_ext
+    return params
+
+
+def nifti_tool_cargs(
+    params: NiftiToolParameters,
+    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("nifti_tool" + params.get("action"))
+    if params.get("input_files") is not None:
+        cargs.extend([
+            "-infiles",
+            *[execution.input_file(f) for f in params.get("input_files")]
+        ])
+    if params.get("field") is not None:
+        cargs.extend([
+            "-field",
+            params.get("field")
+        ])
+    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("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("convert2dtype") is not None:
+        cargs.extend([
+            "-convert2dtype",
+            params.get("convert2dtype")
+        ])
+    if params.get("convert_fail_choice") is not None:
+        cargs.extend([
+            "-convert_fail_choice",
+            params.get("convert_fail_choice")
+        ])
+    if params.get("convert_verify"):
+        cargs.append("-convert_verify")
+    if params.get("add_comment_ext") is not None:
+        cargs.extend([
+            "-add_comment_ext",
+            params.get("add_comment_ext")
+        ])
+    if params.get("rm_ext") is not None:
+        cargs.extend([
+            "-rm_ext",
+            params.get("rm_ext")
+        ])
+    return cargs
+
+
+def nifti_tool_outputs(
+    params: NiftiToolParameters,
+    execution: Execution,
+) -> NiftiToolOutputs:
+    """
+    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 = NiftiToolOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def nifti_tool_execute(
+    params: NiftiToolParameters,
+    execution: Execution,
+) -> NiftiToolOutputs:
+    """
+    Display, modify, or compare nifti headers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NiftiToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = nifti_tool_cargs(params, execution)
+    ret = nifti_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def nifti_tool(
+    action: str,
+    input_files: list[InputPathType] | None = None,
+    field: str | None = None,
+    mod_field: str | None = None,
+    prefix: str | None = None,
+    debug: float | None = None,
+    overwrite: bool = False,
+    convert2dtype: str | None = None,
+    convert_fail_choice: str | None = None,
+    convert_verify: bool = False,
+    add_comment_ext: str | None = None,
+    rm_ext: str | None = None,
+    runner: Runner | None = None,
+) -> NiftiToolOutputs:
+    """
+    Display, modify, or compare nifti headers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        action: Action type that defines what nifti_tool will do.
+        input_files: One or more input nifti files.
+        field: Field name to display, modify, or compare.
+        mod_field: Field name and new value to modify.
+        prefix: Prefix for the output file.
+        debug: Debugging level (0-3).
+        overwrite: Overwrite input files with modifications.
+        convert2dtype: Convert data to a new datatype.
+        convert_fail_choice: Action on conversion failure (ignore, warn, fail).
+        convert_verify: Verify datatype conversion exactness.
+        add_comment_ext: Add COMMENT-type extension to dataset.
+        rm_ext: Remove extension by index or ALL.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NiftiToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NIFTI_TOOL_METADATA)
+    params = nifti_tool_params(
+        action=action,
+        input_files=input_files,
+        field=field,
+        mod_field=mod_field,
+        prefix=prefix,
+        debug=debug,
+        overwrite=overwrite,
+        convert2dtype=convert2dtype,
+        convert_fail_choice=convert_fail_choice,
+        convert_verify=convert_verify,
+        add_comment_ext=add_comment_ext,
+        rm_ext=rm_ext,
+    )
+    return nifti_tool_execute(params, execution)
+
+
+__all__ = [
+    "NIFTI_TOOL_METADATA",
+    "NiftiToolOutputs",
+    "NiftiToolParameters",
+    "nifti_tool",
+    "nifti_tool_params",
+]