niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dcmedit.py

@@ -0,0 +1,552 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DCMEDIT_METADATA = Metadata(
+    id="8755d3035d88c63d3618eea7e9e40463fa8a47ee.boutiques",
+    name="dcmedit",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_DcmeditTagParamsDictNoTag = typing.TypedDict('_DcmeditTagParamsDictNoTag', {
+    "group": str,
+    "element": str,
+    "newvalue": str,
+})
+DcmeditTagParamsDictTagged = typing.TypedDict('DcmeditTagParamsDictTagged', {
+    "@type": typing.Literal["tag"],
+    "group": str,
+    "element": str,
+    "newvalue": str,
+})
+DcmeditTagParamsDict = _DcmeditTagParamsDictNoTag | DcmeditTagParamsDictTagged
+
+
+_DcmeditConfigParamsDictNoTag = typing.TypedDict('_DcmeditConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+DcmeditConfigParamsDictTagged = typing.TypedDict('DcmeditConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+DcmeditConfigParamsDict = _DcmeditConfigParamsDictNoTag | DcmeditConfigParamsDictTagged
+
+
+_DcmeditParamsDictNoTag = typing.TypedDict('_DcmeditParamsDictNoTag', {
+    "anonymise": bool,
+    "id": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[list[DcmeditTagParamsDict] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DcmeditConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "file": InputPathType,
+})
+DcmeditParamsDictTagged = typing.TypedDict('DcmeditParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dcmedit"],
+    "anonymise": bool,
+    "id": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[list[DcmeditTagParamsDict] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DcmeditConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "file": InputPathType,
+})
+DcmeditParamsDict = _DcmeditParamsDictNoTag | DcmeditParamsDictTagged
+
+
+def dcmedit_tag(
+    group: str,
+    element: str,
+    newvalue: str,
+) -> DcmeditTagParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        group: replace specific tag.
+        element: replace specific tag.
+        newvalue: replace specific tag.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "tag",
+        "group": group,
+        "element": element,
+        "newvalue": newvalue,
+    }
+    return params
+
+
+def dcmedit_tag_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DcmeditTagParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("group", None) is None:
+        raise StyxValidationError("`group` must not be None")
+    if not isinstance(params["group"], str):
+        raise StyxValidationError(f'`group` has the wrong type: Received `{type(params.get("group", None))}` expected `str`')
+    if params.get("element", None) is None:
+        raise StyxValidationError("`element` must not be None")
+    if not isinstance(params["element"], str):
+        raise StyxValidationError(f'`element` has the wrong type: Received `{type(params.get("element", None))}` expected `str`')
+    if params.get("newvalue", None) is None:
+        raise StyxValidationError("`newvalue` must not be None")
+    if not isinstance(params["newvalue"], str):
+        raise StyxValidationError(f'`newvalue` has the wrong type: Received `{type(params.get("newvalue", None))}` expected `str`')
+
+
+def dcmedit_tag_cargs(
+    params: DcmeditTagParamsDict,
+    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("-tag")
+    cargs.append(params.get("group", None))
+    cargs.append(params.get("element", None))
+    cargs.append(params.get("newvalue", None))
+    return cargs
+
+
+def dcmedit_config(
+    key: str,
+    value: str,
+) -> DcmeditConfigParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def dcmedit_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DcmeditConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def dcmedit_config_cargs(
+    params: DcmeditConfigParamsDict,
+    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("-config")
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class DcmeditOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DcmeditParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dcmedit_params(
+    file: InputPathType,
+    anonymise: bool = False,
+    id_: str | None = None,
+    tag: list[DcmeditTagParamsDict] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DcmeditConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DcmeditParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        file: the DICOM file to be edited.
+        anonymise: remove any identifiable information, by replacing the\
+            following tags:\
+            - any tag with Value Representation PN will be replaced with\
+            'anonymous'\
+            - tag (0010,0030) PatientBirthDate will be replaced with an empty\
+            string\
+            WARNING: there is no guarantee that this command will remove all\
+            identiable information, since such information may be contained in\
+            any number of private vendor-specific tags. You will need to\
+            double-check the results independently if you need to ensure\
+            anonymity.
+        id_: replace all ID tags with string supplied. This consists of tags\
+            (0010, 0020) PatientID and (0010, 1000) OtherPatientIDs.
+        tag: replace specific tag.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        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 this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "mrtrix/dcmedit",
+        "anonymise": anonymise,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "file": file,
+    }
+    if id_ is not None:
+        params["id"] = id_
+    if tag is not None:
+        params["tag"] = tag
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dcmedit_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DcmeditParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("anonymise", False) is None:
+        raise StyxValidationError("`anonymise` must not be None")
+    if not isinstance(params["anonymise"], bool):
+        raise StyxValidationError(f'`anonymise` has the wrong type: Received `{type(params.get("anonymise", False))}` expected `bool`')
+    if params.get("id", None) is not None:
+        if not isinstance(params["id"], str):
+            raise StyxValidationError(f'`id` has the wrong type: Received `{type(params.get("id", None))}` expected `str | None`')
+    if params.get("tag", None) is not None:
+        if not isinstance(params["tag"], list):
+            raise StyxValidationError(f'`tag` has the wrong type: Received `{type(params.get("tag", None))}` expected `list[DcmeditTagParamsDict] | None`')
+        for e in params["tag"]:
+            dcmedit_tag_validate(e)
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[DcmeditConfigParamsDict] | None`')
+        for e in params["config"]:
+            dcmedit_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("file", None) is None:
+        raise StyxValidationError("`file` must not be None")
+    if not isinstance(params["file"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`file` has the wrong type: Received `{type(params.get("file", None))}` expected `InputPathType`')
+
+
+def dcmedit_cargs(
+    params: DcmeditParamsDict,
+    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("dcmedit")
+    if params.get("anonymise", False):
+        cargs.append("-anonymise")
+    if params.get("id", None) is not None:
+        cargs.extend([
+            "-id",
+            params.get("id", None)
+        ])
+    if params.get("tag", None) is not None:
+        cargs.extend([a for c in [dcmedit_tag_cargs(s, execution) for s in params.get("tag", None)] for a in c])
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [dcmedit_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("file", None)))
+    return cargs
+
+
+def dcmedit_outputs(
+    params: DcmeditParamsDict,
+    execution: Execution,
+) -> DcmeditOutputs:
+    """
+    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 = DcmeditOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dcmedit_execute(
+    params: DcmeditParamsDict,
+    runner: Runner | None = None,
+) -> DcmeditOutputs:
+    """
+    dcmedit
+    
+    Edit DICOM file in-place.
+    
+    Note that this command simply replaces the existing values without modifying
+    the DICOM structure in any way. Replacement text will be truncated if it is
+    too long to fit inside the existing tag.
+    
+    WARNING: this command will modify existing data! It is recommended to run
+    this command on a copy of the original data set to avoid loss of data.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DcmeditOutputs`).
+    """
+    dcmedit_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMEDIT_METADATA)
+    params = execution.params(params)
+    cargs = dcmedit_cargs(params, execution)
+    ret = dcmedit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dcmedit(
+    file: InputPathType,
+    anonymise: bool = False,
+    id_: str | None = None,
+    tag: list[DcmeditTagParamsDict] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DcmeditConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DcmeditOutputs:
+    """
+    dcmedit
+    
+    Edit DICOM file in-place.
+    
+    Note that this command simply replaces the existing values without modifying
+    the DICOM structure in any way. Replacement text will be truncated if it is
+    too long to fit inside the existing tag.
+    
+    WARNING: this command will modify existing data! It is recommended to run
+    this command on a copy of the original data set to avoid loss of data.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        file: the DICOM file to be edited.
+        anonymise: remove any identifiable information, by replacing the\
+            following tags:\
+            - any tag with Value Representation PN will be replaced with\
+            'anonymous'\
+            - tag (0010,0030) PatientBirthDate will be replaced with an empty\
+            string\
+            WARNING: there is no guarantee that this command will remove all\
+            identiable information, since such information may be contained in\
+            any number of private vendor-specific tags. You will need to\
+            double-check the results independently if you need to ensure\
+            anonymity.
+        id_: replace all ID tags with string supplied. This consists of tags\
+            (0010, 0020) PatientID and (0010, 1000) OtherPatientIDs.
+        tag: replace specific tag.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        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 this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DcmeditOutputs`).
+    """
+    params = dcmedit_params(
+        anonymise=anonymise,
+        id_=id_,
+        tag=tag,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        file=file,
+    )
+    return dcmedit_execute(params, runner)
+
+
+__all__ = [
+    "DCMEDIT_METADATA",
+    "DcmeditConfigParamsDict",
+    "DcmeditConfigParamsDictTagged",
+    "DcmeditOutputs",
+    "DcmeditParamsDict",
+    "DcmeditParamsDictTagged",
+    "DcmeditTagParamsDict",
+    "DcmeditTagParamsDictTagged",
+    "dcmedit",
+    "dcmedit_config",
+    "dcmedit_execute",
+    "dcmedit_params",
+    "dcmedit_tag",
+]