monai.deploy.operators.DICOMSeriesSelectorOperator

class monai.deploy.operators.DICOMSeriesSelectorOperator(fragment, *args, rules='', all_matched=False, sort_by_sop_instance_count=False, **kwargs)

Bases: holoscan.core.Operator

This operator selects a list of DICOM Series in a DICOM Study for a given set of selection rules.

Named input:

dicom_study_list: A list of DICOMStudy objects.

Named output:

study_selected_series_list: A list of StudySelectedSeries objects. Downstream receiver optional.

This class can be considered a base class, and a derived class can override the ‘filter’ function to with custom logics.

In its default implementation, this class

1. selects a series or all matched series within the scope of a study in a list of studies

2. uses rules defined in JSON string, see below for details

3. supports DICOM Study and Series module attribute matching

4. supports multiple named selections, in the scope of each DICOM study

5. outputs a list of SutdySelectedSeries objects, as well as a flat list of SelectedSeries (to be deprecated)

The selection rules are defined in JSON,

1. attribute “selections” value is a list of selections

2. each selection has a “name”, and its “conditions” value is a list of matching criteria

3. each condition uses the implicit equal operator; in addition, the following are supported:

   • regex and range matching for float and int types

   • regex matching for str type

   • union matching for set type

4. DICOM attribute keywords are used, and only for those defined as DICOMStudy and DICOMSeries properties

An example selection rules: {

“selections”: [

{

“name”: “CT Series 1”, “conditions”: {

“StudyDescription”: “(?i)^Spleen”, “Modality”: “(?i)CT”, “SeriesDescription”: “(?i)^No series description|(.*?)”

}

}, {

“name”: “CT Series 2”, “conditions”: {

“Modality”: “CT”, “BodyPartExamined”: “Abdomen”, “SeriesDescription” : “Not to be matched. For illustration only.”

}

}, {

“name”: “CT Series 3”, “conditions”: {

“StudyDescription”: “(.*?)”, “Modality”: “(?i)CT”, “ImageType”: [“PRIMARY”, “ORIGINAL”, “AXIAL”], “SliceThickness”: [3, 5]

}

}

]

}

Instantiate an instance.

Parameters

• fragment (Fragment) – An instance of the Application class which is derived from Fragment.

• rules (Text) – Selection rules in JSON string.

• all_matched (bool) – Gets all matched series in a study. Defaults to False for first match only.

• sort_by_sop_instance_count (bool) – If all_matched = True and multiple series are matched, sorts the matched series in

• # (descending SOP instance count (i.e. the first Series in the returned List[StudySelectedSeries] will have the highest) –

• sorting. (of DICOM images); Defaults to False for no) –

Methods

__init__(fragment, *args[, rules, …])	Instantiate an instance.
add_arg(*args, **kwargs)	Overloaded function.
compute(op_input, op_output, context)	Performs computation for this operator.
filter(selection_rules, dicom_study_list[, …])	Selects the series with the given matching rules.
initialize()	Default implementation of initialize
resource(self, name)	Resources associated with the operator.
setup(spec)	Default implementation of setup method.
start()	Default implementation of start
stop()	Default implementation of stop

Attributes

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, rules='', all_matched=False, sort_by_sop_instance_count=False, **kwargs)

Instantiate an instance.

Parameters

• fragment (Fragment) – An instance of the Application class which is derived from Fragment.

• rules (Text) – Selection rules in JSON string.

• all_matched (bool) – Gets all matched series in a study. Defaults to False for first match only.

• sort_by_sop_instance_count (bool) – If all_matched = True and multiple series are matched, sorts the matched series in

• # (descending SOP instance count (i.e. the first Series in the returned List[StudySelectedSeries] will have the highest) –

• sorting. (of DICOM images); Defaults to False for no) –

add_arg(*args, **kwargs)

Overloaded function.

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

Add an argument to the component.

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

Add a list of arguments to the component.

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

Add arguments to the component via Python kwargs.

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

5. 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)

Performs computation for this operator.

property conditions

Conditions associated with the operator.

property description

YAML formatted string describing the operator.

filter(selection_rules, dicom_study_list, all_matched=False, sort_by_sop_instance_count=False)

Selects the series with the given matching rules.

If rules object is None, all series will be returned with series instance UID as the selection name.

Supported matching logic:

Float + Int: exact matching, range matching (if a list with two numerical elements is provided), and regex matching String: matches case insensitive, if fails then tries RegEx search String array (set): matches as subset, case insensitive

Parameters

• selection_rules (object) – JSON object containing the matching rules.

• dicom_study_list (list) – A list of DICOMStudy objects.

• all_matched (bool) – Gets all matched series in a study. Defaults to False for first match only.

• sort_by_sop_instance_count (bool) – If all_matched = True and multiple series are matched, sorts the matched series in

• # (descending SOP instance count (i.e. the first Series in the returned List[StudySelectedSeries] will have the highest) –

• sorting. (of DICOM images); Defaults to False for no) –

Returns

A list of objects of type StudySelectedSeries.

Return type

list

Raises

ValueError – If the selection_rules object does not contain “selections” attribute.

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.

setup(spec)

Default implementation of setup method.

property spec

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

start()

Default implementation of start

stop()

Default implementation of stop

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