monai.deploy.operators.DICOMSegmentationWriterOperator¶

class monai.deploy.operators.DICOMSegmentationWriterOperator(fragment, *args, segment_descriptions, output_folder, 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.
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, …[, …])	Instantiates the DICOM Seg Writer instance with optional list of segment label strings.
`add_arg`(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)
`initialize`()	Default implementation of initialize
`process_images`(image, …)
`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

Attributes

`DCM_EXTENSION`
`DEFAULT_OUTPUT_FOLDER`
`SUPPORTED_EXTENSIONS`
`args`	The list of arguments associated with the component.
`conditions`	Conditions associated with the operator.
`description`	YAML formatted string describing 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 dictionary (`holoscan.core.MetadataPolicy`) associated with the operator.
`name`	The name of the operator.
`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, 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.
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.

property args¶

The list of arguments associated with the component.

arglist : holoscan.core.ArgList

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.

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 dictionary (holoscan.core.MetadataPolicy) associated with the operator.

property name¶: The name of the operator.

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.

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

Resources associated with the operator.

name : str 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

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