niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dcmedit.py

@@ -0,0 +1,440 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DCMEDIT_METADATA = Metadata(
+    id="01158fce9a81a53a1cc2f81c6577cb2f6210d5a8.boutiques",
+    name="dcmedit",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+DcmeditTagParameters = typing.TypedDict('DcmeditTagParameters', {
+    "__STYX_TYPE__": typing.Literal["tag"],
+    "group": str,
+    "element": str,
+    "newvalue": str,
+})
+
+
+DcmeditConfigParameters = typing.TypedDict('DcmeditConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+DcmeditParameters = typing.TypedDict('DcmeditParameters', {
+    "__STYX_TYPE__": typing.Literal["dcmedit"],
+    "anonymise": bool,
+    "id": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[list[DcmeditTagParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DcmeditConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dcmedit": dcmedit_cargs,
+        "tag": dcmedit_tag_cargs,
+        "config": dcmedit_config_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)
+
+
+def dcmedit_tag_params(
+    group: str,
+    element: str,
+    newvalue: str,
+) -> DcmeditTagParameters:
+    """
+    Build parameters.
+    
+    Args:
+        group: replace specific tag.
+        element: replace specific tag.
+        newvalue: replace specific tag.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tag",
+        "group": group,
+        "element": element,
+        "newvalue": newvalue,
+    }
+    return params
+
+
+def dcmedit_tag_cargs(
+    params: DcmeditTagParameters,
+    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"))
+    cargs.append(params.get("element"))
+    cargs.append(params.get("newvalue"))
+    return cargs
+
+
+def dcmedit_config_params(
+    key: str,
+    value: str,
+) -> DcmeditConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def dcmedit_config_cargs(
+    params: DcmeditConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class DcmeditOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dcmedit(...)`.
+    """
+    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[DcmeditTagParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DcmeditConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DcmeditParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: DcmeditParameters,
+    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"):
+        cargs.append("-anonymise")
+    if params.get("id") is not None:
+        cargs.extend([
+            "-id",
+            params.get("id")
+        ])
+    if params.get("tag") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("tag")] for a in c])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("file")))
+    return cargs
+
+
+def dcmedit_outputs(
+    params: DcmeditParameters,
+    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: DcmeditParameters,
+    execution: Execution,
+) -> DcmeditOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DcmeditOutputs`).
+    """
+    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[DcmeditTagParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DcmeditConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DcmeditOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMEDIT_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "DCMEDIT_METADATA",
+    "DcmeditConfigParameters",
+    "DcmeditOutputs",
+    "DcmeditParameters",
+    "DcmeditTagParameters",
+    "dcmedit",
+    "dcmedit_config_params",
+    "dcmedit_params",
+    "dcmedit_tag_params",
+]