monai.deploy.operators.DICOMSegmentationWriterOperator¶

class monai.deploy.operators.DICOMSegmentationWriterOperator(fragment, *args, segment_descriptions, output_folder, model_info=None, custom_tags=None, omit_empty_frames=True, **kwargs)[source]¶

Bases: holoscan.core.Operator

This operator writes out a DICOM Segmentation Part 10 file to disk

Named inputs:: seg_image: The Image object of the segment. study_selected_series_list: The DICOM series from which the segment was derived. output_folder: Optional, folder for file output, overriding what is set on the object.
Named output:: None
File output:: Generated DICOM instance file in the output folder set on this object or optional input.

Instantiates the DICOM Seg Writer instance with optional list of segment label strings.

Each unique, non-zero integer value in the segmentation image represents a segment that must be described by an item of the segment descriptions list with the corresponding segment number. Items in the list must be arranged starting at segment number 1 and increasing by 1.

For example, in the CT Spleen Segmentation application, the whole image background has a value of 0, and the Spleen segment of value 1. This then only requires the caller to pass in a list containing a segment description, which is used as label for the Spleen in the DICOM Seg instance.

Note: this interface is subject to change. It is planned that a new object will encapsulate the segment label information, including label value, name, description etc.

Parameters

fragment (Fragment) – An instance of the Application class which is derived from Fragment.
segment_descriptions (List[SegmentDescription]) – List[SegmentDescription] Object encapsulating the description of each segment present in the segmentation.
output_folder (Path) – Folder for file output, overridden by named input on compute. Defaults to current working dir’s child folder, output.
model_info (ModelInfo, optional) – Object encapsulating model creator, name, version and UID.
custom_tags (Optional[Dict[str, str]]) – Optional[Dict[str, str]], optional Dictionary for setting custom DICOM tags using Keywords and str values only
omit_empty_frames (bool) – bool, optional Whether to omit frames that contain no segmented pixels from the output segmentation. Defaults to True, same as the underlying lib API.

Methods

`__init__`(fragment, *args, …[, model_info, …])	Instantiates the DICOM Seg Writer instance with optional list of segment label strings.
`add_arg`(args, *kwargs)	Overloaded function.
`add_dynamic_flow`(args, *kwargs)	Overloaded function.
`compute`(op_input, op_output, context)	Performs computation for this operator and handles I/O.
`create_dicom_seg`(image, dicom_series, output_dir)
`enable_metadata`(self, enable)	Configure whether or not the metadata feature is enabled for this operator.
`find_all_flow_info`(self, predicate, bool])	Find all flow info objects in the operator’s next flows that match a given condition.
`find_flow_info`(self, predicate, bool])	Find a flow info in the operator’s next flows based on a given predicate.
`initialize`()	Default implementation of initialize
`process_images`(image, …)
`queue_policy`(self, port_name, port_type, policy)	Set the queue policy to be used by an input (or output) port’s receiver (or transmitter).
`receiver`(self, port_name)	Get the receiver used by an input port.
`resource`(self, name)	Resources associated with the operator.
`select_input_file`(input_folder[, extensions])	Select the input files based on supported extensions.
`setup`(spec)	Set up the named input(s), and output(s) if applicable, aka ports.
`start`()	Default implementation of start
`stop`()	Default implementation of stop
`stop_execution`(self)	Stop the execution of the operator.
`transmitter`(self, port_name)	Get the transmitter used by an output port.

Attributes

`DCM_EXTENSION`
`DEFAULT_OUTPUT_FOLDER`
`INPUT_EXEC_PORT_NAME`
`OUTPUT_EXEC_PORT_NAME`
`SUPPORTED_EXTENSIONS`
`args`	The list of arguments associated with the component.
`async_condition`	The internal asynchronous condition for the operator.
`conditions`	Conditions associated with the operator.
`description`	YAML formatted string describing the operator.
`execution_context`	The execution context for the operator.
`fragment`	The fragment (`holoscan.core.Fragment`) that the operator belongs to.
`id`	The identifier of the component.
`is_metadata_enabled`	Boolean indicating whether the fragment this operator belongs to has metadata transmission enabled.
`metadata`	The metadata dictionary (`holoscan.core.MetadataDictionary`) associated with the operator.
`metadata_policy`	The metadata policy (`holoscan.core.MetadataPolicy`) associated with the operator.
`name`	The name of the operator.
`next_flows`	Get the list of flow information for connections to downstream operators.
`operator_type`	The operator type.
`resources`	Resources associated with the operator.
`spec`	The operator spec (`holoscan.core.OperatorSpec`) associated with the operator.

class OperatorType(self: holoscan.core._core.Operator.OperatorType, value: int) → None¶

Bases: pybind11_builtins.pybind11_object

Enum class for operator types used by the executor.

NATIVE: Native operator.
GXF: GXF operator.
VIRTUAL: Virtual operator. (for internal use, not intended for use by application authors)

Members:

NATIVE

GXF

VIRTUAL

property name¶

__init__(fragment, *args, segment_descriptions, output_folder, model_info=None, custom_tags=None, omit_empty_frames=True, **kwargs)[source]¶

Instantiates the DICOM Seg Writer instance with optional list of segment label strings.

Note: this interface is subject to change. It is planned that a new object will encapsulate the segment label information, including label value, name, description etc.

Parameters

fragment (Fragment) – An instance of the Application class which is derived from Fragment.
segment_descriptions (List[SegmentDescription]) – List[SegmentDescription] Object encapsulating the description of each segment present in the segmentation.
output_folder (Path) – Folder for file output, overridden by named input on compute. Defaults to current working dir’s child folder, output.
model_info (ModelInfo, optional) – Object encapsulating model creator, name, version and UID.
custom_tags (Optional[Dict[str, str]]) – Optional[Dict[str, str]], optional Dictionary for setting custom DICOM tags using Keywords and str values only
omit_empty_frames (bool) – bool, optional Whether to omit frames that contain no segmented pixels from the output segmentation. Defaults to True, same as the underlying lib API.

add_arg(*args, **kwargs)¶

Overloaded function.

add_arg(self: holoscan.core._core.Operator, arg: holoscan.core._core.Arg) -> None

Add an argument to the component.

add_arg(self: holoscan.core._core.Operator, arg: holoscan.core._core.ArgList) -> None

Add a list of arguments to the component.

add_arg(self: holoscan.core._core.Operator, **kwargs) -> None

Add arguments to the component via Python kwargs.

add_arg(self: holoscan.core._core.Operator, arg: holoscan.core._core.Condition) -> None
add_arg(self: holoscan.core._core.Operator, arg: holoscan.core._core.Resource) -> None

Add a condition or resource to the Operator.

This can be used to add a condition or resource to an operator after it has already been constructed.

argholoscan.core.Condition or holoscan.core.Resource: The condition or resource to add.

add_dynamic_flow(*args, **kwargs)¶

Overloaded function.

add_dynamic_flow(self: holoscan.core._core.Operator, flow: holoscan.core._core.FlowInfo) -> None
add_dynamic_flow(self: holoscan.core._core.Operator, flows: list[holoscan.core._core.FlowInfo]) -> None
add_dynamic_flow(self: holoscan.core._core.Operator, next_op: holoscan.core._core.Operator, next_input_port_name: str = ‘’) -> None

Add a dynamic flow from this operator to another operator.

next_opholoscan.core.Operator: The downstream operator to connect to.
next_input_port_namestr, optional: The name of the input port on the downstream operator to connect to. If not specified, the first available input port will be used.

This method has several overloads to support different ways of creating dynamic flows:

add_dynamic_flow(next_op: Operator, next_input_port_name: str = ‘’) - Basic connection using default output port. This is the simplest form for connecting

two operators when you only need to specify the destination.
add_dynamic_flow(curr_output_port_name: str, next_op: Operator, next_input_port_name: str = ‘’) - Connection with explicit output port specification. Use this when the source operator has

multiple output ports and you need to specify which one to use.
add_dynamic_flow(flow: FlowInfo) - Connection using a FlowInfo object, which encapsulates all connection details including:
- Source operator and its output port specification
- Destination operator and its input port specification
- Port names and associated IOSpecs
- This is useful for complex connections or when reusing connection patterns.
add_dynamic_flow(flows: List[FlowInfo]) - Batch connection using multiple FlowInfo objects. Use this to set up multiple

connections in a single call, which is more efficient than making multiple individual connections.

The FlowInfo class provides a complete description of a flow connection between operators, including all port specifications and naming. It’s particularly useful when you need to:

Store and reuse connection patterns
Create complex routing configurations
Handle dynamic port specifications
Manage multiple connections systematically

add_dynamic_flow(self: holoscan.core._core.Operator, curr_output_port_name: str, next_op: holoscan.core._core.Operator, next_input_port_name: str = ‘’) -> None

property args¶

The list of arguments associated with the component.

arglist : holoscan.core.ArgList

property async_condition¶

The internal asynchronous condition for the operator.

This property provides access to the internal asynchronous condition for the operator, which controls the scheduling of the operator’s compute method.

conditionholoscan.conditions.AsynchronousCondition: An instance of holoscan.conditions.AsynchronousCondition that is the internal asynchronous condition for the operator.

compute(op_input, op_output, context)[source]¶

Performs computation for this operator and handles I/O.

For now, only a single segmentation image object or file is supported and the selected DICOM series for inference is required, because the DICOM Seg IOD needs to refer to original instance. When there are multiple selected series in the input, the first series’ containing study will be used for retrieving DICOM Study module attributes, e.g. StudyInstanceUID.

Raises

FileNotFoundError – When image object not in the input, and segmentation image file not found either.
ValueError – Neither image object nor image file’s folder is in the input, or no selected series.

property conditions¶: Conditions associated with the operator.

property description¶: YAML formatted string describing the operator.

enable_metadata(self: holoscan.core._core.Operator, enable: bool) → None¶: Configure whether or not the metadata feature is enabled for this operator. If it is not set, the default value will be determined by the enable_metadata setting from the Fragment that this operator belongs to.

property execution_context¶

The execution context for the operator.

This property provides access to the execution context of the operator, which contains information about the current execution environment including scheduling details.

holoscan.core.ExecutionContext: The execution context object for this operator.

find_all_flow_info(self: holoscan.core._core.Operator, predicate: Callable[[holoscan.core._core.FlowInfo], bool]) → list[holoscan.core._core.FlowInfo]¶

Find all flow info objects in the operator’s next flows that match a given condition.

predicatecallable: A function that takes a FlowInfo object and returns a boolean.

list[holoscan.core.FlowInfo]: List of matching FlowInfo objects.

find_flow_info(self: holoscan.core._core.Operator, predicate: Callable[[holoscan.core._core.FlowInfo], bool]) → holoscan.core._core.FlowInfo¶

Find a flow info in the operator’s next flows based on a given predicate.

predicatecallable: A function that takes a FlowInfo object and returns a boolean.

holoscan.core.FlowInfo or None: The first matching FlowInfo object, or None if not found.

property fragment¶: The fragment (holoscan.core.Fragment) that the operator belongs to.

property id¶

The identifier of the component.

The identifier is initially set to -1, and will become a valid value when the component is initialized.

With the default executor (holoscan.gxf.GXFExecutor), the identifier is set to the GXF component ID.

id : int

initialize()¶: Default implementation of initialize

property is_metadata_enabled¶: Boolean indicating whether the fragment this operator belongs to has metadata transmission enabled.

property metadata¶: The metadata dictionary (holoscan.core.MetadataDictionary) associated with the operator.

property metadata_policy¶

The metadata policy (holoscan.core.MetadataPolicy) associated with the operator.

The supported policies are:

MetadataPolicy.REJECT: Reject the new value if the key already exists
MetadataPolicy.UPDATE: Replace existing value with the new one if the key already exists
MetadataPolicy.INPLACE_UPDATE: Update the value stored within an existing MetadataObject in-place if the key already exists (in contrast to UPDATE which always replaces the existing MetadataObject with a new one).
MetadataPolicy.RAISE: Raise an exception if the key already exists

property name¶: The name of the operator.

property next_flows¶

Get the list of flow information for connections to downstream operators.

list[holoscan.core.FlowInfo]: List of flow information objects describing connections to downstream operators.

property operator_type¶

The operator type.

holoscan.core.Operator.OperatorType enum representing the type of the operator. The two types currently implemented are native and GXF.

queue_policy(self: holoscan.core._core.Operator, port_name: str, port_type: holoscan.core._core.IOSpec.IOType = <IOType.INPUT: 0>, policy: holoscan.core._core.IOSpec.QueuePolicy = <QueuePolicy.FAULT: 2>) → None¶

Set the queue policy to be used by an input (or output) port’s receiver (or transmitter).

port_namestr

The name of the port.

port_typeIOSpec.IOType, optional

Enum indicating whether port_name corresponds to an input port or output port.

policyIOSpec.QueuePolicy, optional

The queue policy to set. Valid values are:

QueuePolicy.POP : If the queue is full, pop the oldest item, then add the new one.
QueuePolicy.REJECT : If the queue is full, reject (discard) the new item.
QueuePolicy.FAULT : If the queue is full, log a warning and reject the new item.

transmitterholoscan.resources.Transmitter or None: The transmitter used by this output port. Will be None if the port does not exist.

receiver(self: holoscan.core._core.Operator, port_name: str) → Optional[holoscan::Receiver]¶

Get the receiver used by an input port.

port_namestr: The name of the input port.

receiverholoscan.resources.Receiver: The receiver used by this input port. Will be None if the port does not exist.

resource(self: holoscan.core._core.Operator, name: str) → Optional[object]¶

Resources associated with the operator.

namestr: The name of the resource to retrieve

holoscan.core.Resource or None: The resource with the given name. If no resource with the given name is found, None is returned.

property resources¶: Resources associated with the operator.

select_input_file(input_folder, extensions=['.nii', '.nii.gz', '.mhd'])[source]¶

Select the input files based on supported extensions.

Parameters

input_folder (string) – the path of the folder containing the input file(s)
extensions (array) – the supported file formats identified by the extensions.

Returns

The path of the selected file ext (string): The extension of the selected file

Return type

file_path (string)

setup(spec)[source]¶

Set up the named input(s), and output(s) if applicable, aka ports.

Parameters: spec (OperatorSpec) – The Operator specification for inputs and outputs etc.

property spec¶: The operator spec (holoscan.core.OperatorSpec) associated with the operator.

start()¶: Default implementation of start

stop()¶: Default implementation of stop

stop_execution(self: holoscan.core._core.Operator) → None¶

Stop the execution of the operator.

This method is used to stop the execution of the operator by setting the internal async condition to EVENT_NEVER state, which sets the scheduling condition to NEVER. Once stopped, the operator will not be scheduled for execution (the compute() method will not be called).

Note that executing this method does not trigger the operator’s stop() method. The stop() method is called only when the scheduler deactivates all operators together.

transmitter(self: holoscan.core._core.Operator, port_name: str) → Optional[holoscan::Transmitter]¶

Get the transmitter used by an output port.

port_namestr: The name of the output port.

transmitterholoscan.resources.Transmitter or None: The transmitter used by this output port. Will be None if the port does not exist.

monai.deploy.operators.DICOMEncapsulatedPDFWriterOperator monai.deploy.operators.DICOMSeriesSelectorOperator