ImFusion::Dicom Namespace Reference

Low-level and intermediate-level interfaces for working with DICOM data. More...

Detailed Description

Low-level and intermediate-level interfaces for working with DICOM data.

Namespaces
namespace	ModalityWorklist
	Basic implementation of a Service Class User (SCU) for the DICOM Modality Worklist standard.
namespace	Utils
	Collection of utility functions to handle DICOM data.
namespace	VolumeReconstruction
	Namespace containing helper functions to reconstruct potential volumes from a set of individual DICOM frames.

Classes
struct	Base
class	ClinicalTrialSubjectDataComponent
	Represents the Clinical Trial Subject Module https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.html#table_C.7-2b. More...
class	ClinicalTrialSubjectExtension
	Extension that loads and saves the ClinicalTrialSubjectDataComponent. More...
class	CommonModule
	Collection of the essential tags describing a Dicom data set combining. More...
class	ConfigurableSequence
class	ConfigurableSequenceItem
class	DatasetCache
	The DatasetCache class provides caching of DcmDataset loaded from different locations. More...
class	DatasetHandler
	Read access handler for proprietary / non-standard DICOM image formats, or non-image datasets. More...
struct	DatasetIodPair
	Named pair of a DcmDataset and the corresponding IOD. More...
class	DatasetModuleList
	A stub that allows to use a Module with a DcmItem alone (without deriving some class from ModuleList). More...
class	DatasetPreviewLabel
	A widget that shows a preview image of a DICOM dataset. More...
class	DicomGeSignaExciteIOD
	Extra IOD specialization for basic support of loading 4D MRI sequences created by GE Signa Excite devices. More...
class	DicomParameter
	A specialized Parameter<T> class that can additionally serialize from and to DICOM. More...
class	DicomParameterBase
	Internal type-erased base class for DicomParameter<T>. More...
class	DicomParameterHelper
	Helper functions to load and save all DicomParameters of a Configurable. More...
class	DicomSegIoAlgorithm
struct	DimensionsInfo
	Describes with which dimensions a series will be loaded. More...
class	Element
	Dicom Element with a concrete value type. More...
class	ElementBase
	Abstract base class for DICOM Elements. More...
class	ElementList
	Interface for classes that consist of Elements. More...
class	EncryptedAttributesExtension
class	EnhancedMultiFrameImageIOD
	Class representing Enhanced CT Image IOD (PS 3.3 A.38) More...
struct	Error
	Structure for storing errors occurring during loading/saving DICOM data. More...
class	ErrorRecorder
	Error handling interface for the Dicom module. More...
class	Extension
	Interface for adding custom functionality to DicomLoader and DicomWriter An Extension might be called in a thread that is not the main thread. More...
struct	FrameDescriptor
	Descriptor for a single DICOM frame that is used during the loading process as intermediate representation before eventually converting the image data to a SharedImageSet. More...
class	GeneralEquipmentExtension
	General Equipment Module (PS 3.3 C.7.5) Only considers tags that are part of the GeneralEquipmentModuleDataComponent. More...
class	GeneralEquipmentModuleDataComponent
	DataComponent mirroring the DICOM General Equipment Module. More...
struct	Image
class	ImagePixel
	Image Pixel Module (PS 3.3 C.7.6.3) More...
class	ImagePlane
	Image Plane Module (PS 3.3 C.7.6.2) More...
class	IOD
	Base class of a Dicom Information Object Definition (IOD). More...
class	IOD_Registry
	A registry that assigns a IOD implementation to a SOP class UID. More...
class	ModalityLUT
	Modality LUT Module (PS 3.3 C.11.1) More...
class	Module
	Base class for Dicom Modules. More...
class	ModuleList
	Interface for classes that consist of modules. More...
class	MultiFrameImageIOD
	Base IOD for classic DICOM files. More...
class	OverlayAnnotation
	The OverlayAnnotation displays any DICOM overlay stored in a OverlayDataComponent. More...
class	OverlayDataComponent
	DataComponent providing DICOM overlays. More...
struct	PacsSeriesProxy
	Proxy item to represent Series that exist on the PACS but have not yet been downloaded completely. More...
struct	Patient
class	PixelSpacingCalibration
	Basic Pixel Spacing Calibration Macro (PS 3.3 Table 10.7) Pixel Measures Macro (PS 3.3 Table C.7.6.16-2) More...
class	RealWorldValueMappingExtension
	Real World Value Mapping Macro (PS 3.3 C.7.6.16.2.11) More...
class	ReferencedInstancesComponent
	DataComponent to store DICOM instances that are referenced by the dataset. More...
class	RTStructureDataComponent
	DataComponent for PointClouds loaded from a DICOM RTStructureSet. More...
class	RTStructureDataController
	A DataController for PointClouds that contain a RTStructureDataComponent. More...
class	RTStructureDataDisplayHandler
	DataDisplayHandler for PointClouds that represent DICOM RT Structs. More...
class	RTStructureDatasetHandler
	A DatasetHandler for loading DICOM RTStructureSet. More...
class	RTStructureRenderingDataComponent
	Internal rendering data that represent a RT Structure. More...
class	Scanner
	Scan different locations for DICOM files. More...
class	ScannerQt
	A scanner with Qt interop. More...
class	SegmentationStorageIOD
	Class representing Segmentation IOD. More...
class	SegmentItem
	Element in the (0062,0002) SegmentSequence. More...
class	Sequence
	Concrete sequence of items of type T, which must be derived from SequenceItem. More...
class	SequenceBase
	Abstract base class for a sequence of elements. More...
class	SequenceItem
	Base class for sequence items. More...
struct	Series
class	SettingsWidget
	Simple Qt widget to configure the DicomPluginSettings. More...
class	SourceInfoComponent
	DataComponent to store the mapping of SharedImage to the DICOM URIs (such as file names) used for loading. More...
struct	Study
struct	TagProxy
class	TagsWidget
	The TagsWidget class provides a widget to display dicom tags. More...
class	value_error
	Exception specialization for DICOM element retrieval. More...
class	VOILUTExtension
	VOI LUT Module (PS 3.3 C.11.2) Loads and saves windowing related values to and from DisplayOptions2d. More...
class	VolumetricImageIOD
	The VolumetricImageIOD is a generic IOD for volumetric data that is stored slice by slice. More...
class	WebClient
	Interface for querying and retrieving objects from a DicomWeb compliant server. More...

Typedefs
typedef std::vector< FrameDescriptor >	FrameDescriptorSet
	This typedef indicates a semantic difference compared to std::vector<FrameDescriptor>: A FrameDescriptorSet indicates that the frames resemble a (potential) volume, while a std::vector<FrameDescriptor> is just a list of (potential) unrelated frames.
typedef std::shared_ptr< DatasetCache >	SharedDatasetCache
using	DcmItemsResult = ImFusion::Utils::Expected<std::vector<DcmItem>, Network::HttpError>
using	DcmDatasetsResult = ImFusion::Utils::Expected<std::vector<std::shared_ptr<DcmDataset>>, Network::HttpError>

Enumerations
enum class	AnonymizationProfile : int { None = 0 , Relaxed = 1 , Strict = 2 }
enum class	ExportFileType { File , Folder , Auto }
enum class	Compression {   LittleEndianImplicit , LittleEndianExplicit , DeflatedLittleEndianExplicit , BigEndianExplicit ,   JPEG , JPEG_lossless , JPEGLS_lossless , JPEGLS_lossy ,   JPEG2000 , JPEG2000_lossless }
	Enumeration of supported compression/transfer syntax when writing DICOM.
enum class	ReferenceModules { None = 0 , CommonInstanceReference = 1 , ClinicalTrialSubject = 2 , All = CommonInstanceReference | ClinicalTrialSubject }
enum class	PhotometricInterpretation {   Invalid , Monochrome1 , Monochrome2 , Palette ,   RGB , YbrFull , YbrFull422 }
	Enumeration describing the DICOM photometeric interpetration type.
enum class	WritePolicy { Always , NonEmpty }
enum class	ROIGenerationAlgorithm { Unknown = 0 , Automatic = 1 , SemiAutomatic = 2 , Manual = 3 }
enum class	SeriesDimensions {   Unknown , Image , Volume , ImageSet ,   VolumeSet , Other }
	Dimensions of this series. More...

Functions
const std::map< TagProxy, std::string > &	tagDeidentificationActionBasicProfile ()
	Dicom De-identification Action Codes according to PS3.15 Annex E Table E.1-1 (http://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_E.html)
const std::map< TagProxy, std::string > &	tagDeidentificationActionRelaxedProfile ()
	Like Basic, but keeps certains tags and all UIDs.
std::string	toDecimalString (double value, int maxChars=16)
std::vector< std::unique_ptr< DcmDataset > >	exportToDataset (SharedImageSet &input, ErrorRecorder &errors, ExportFileType filetype=ExportFileType::Auto, IOD_Registry *registry=nullptr, Progress *progress=nullptr)
	Exports the given image to a DcmDatasets.
void	addReference (Flags< ReferenceModules > modules, const std::vector< DcmDataset * > &datasets, const SharedImageSet &reference, ErrorRecorder &errors)
	Adds a reference to the given image to all datasets.
void	addReference (Flags< ReferenceModules > modules, const std::vector< DcmDataset * > &datasets, const std::vector< DcmDataset * > &reference, ErrorRecorder &errors)
	Similar to the function above but add a reference to the given datasets.
bool	saveDatasets (const std::vector< DcmDataset * > &datasets, const Filesystem::Url &url, ErrorRecorder &errors, Compression compression=Compression::LittleEndianImplicit, int compressionQuality=90, const std::string &filenameFormat="", Progress *progress=nullptr)
	Saves the given datasets to the url.
bool	isLosslessCompression (Compression compression)
	Returns whether the compression is lossless or lossy.
template<typename T>
bool	operator== (const DicomParameter< T > &param, const T &value)
template<typename T>
bool	operator== (const T &value, const DicomParameter< T > &param)
template<typename T>
bool	operator!= (const DicomParameter< T > &param, const T &value)
template<typename T>
bool	operator!= (const T &value, const DicomParameter< T > &param)
std::unique_ptr< DcmDataset >	exportSegmentationsToDataset (const std::vector< SharedImageSet * > &labelmapLayers, ErrorRecorder &errors, bool cropToContent=false, Progress *progress=nullptr)
	Exports one or multiple segmentation layers as a single DICOM Segmentation object.
std::unique_ptr< DcmDataset >	exportRTStructToDataset (const std::vector< PointCloud * > &pointClouds, ErrorRecorder &errors, Progress *progress=nullptr)
	Exports a PointCloud with a Dicom::RTStructureDataComponent as a DICOM RT Structure Set.

Enumeration Type Documentation

ExportFileType

enum class ExportFileType

strong

Enumerator
File	If possible, write all image data to a single file.
Folder	Write each frame as separate DICOM file to a folder.
Auto	Automatically determine storage type based on the image.

ReferenceModules

enum class ReferenceModules

strong

Enumerator
CommonInstanceReference	Requires the ImageInfoDataComponent and the SourceDataComponent.
ClinicalTrialSubject	Requires the Dicom::ClinicalTrialSubjectDataComponent.

ROIGenerationAlgorithm

enum class ROIGenerationAlgorithm

strong

Enumerator
Unknown	Unknown.
Automatic	Calculated ROI.
SemiAutomatic	ROI calculated with user assistance.
Manual	User-entered ROI.

SeriesDimensions

enum class SeriesDimensions

strong

Dimensions of this series.

This corresponds to the Kind of a SharedImageSet but with only the values we expect from DICOM.

Function Documentation

exportToDataset()

std::vector< std::unique_ptr< DcmDataset > > exportToDataset	(	SharedImageSet &	input,
		ErrorRecorder &	errors,
		ExportFileType	filetype = ExportFileType::Auto,
		IOD_Registry *	registry = nullptr,
		Progress *	progress = nullptr )

Exports the given image to a DcmDatasets.

Depending on the filetype, this result contains a single dataset (File) or multiple (Folder). If no registry is provided, the default one is created.

This function cannot export images with modality LABEL! Use DicomSegIoAlgorithm instead.

The transfer syntax of the returned datasets is always Little Endian (Implicit).

addReference() [1/2]

void addReference	(	Flags< ReferenceModules >	modules,
		const std::vector< DcmDataset * > &	datasets,
		const SharedImageSet &	reference,
		ErrorRecorder &	errors )

Adds a reference to the given image to all datasets.

If enabled, this will add tags according to the Common Instance Reference Module (https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.12.2.html#table_C.12-8) The given SharedImageSet must provide a ImageInfoDataComponent and a SourceInfoComponent for each SharedImage. Both are automatically created when the SharedImageSet was loaded from DICOM. If the image does not provide all necessary information, an error is recorded.

If enabled, the Clinical Trial Subject Module is also copied from the reference image to the datasets.

addReference() [2/2]

void addReference	(	Flags< ReferenceModules >	modules,
		const std::vector< DcmDataset * > &	datasets,
		const std::vector< DcmDataset * > &	reference,
		ErrorRecorder &	errors )

Similar to the function above but add a reference to the given datasets.

This should be used when the reference image was already exported and a reference should be added to the exported dataset and not the original. During exportToDataset, certain UIDs are generated. If you would e.g. export a image and a labelmap together, you need to call this function when the labelmap is supposed to reference the image.

This function requires that all reference datasets have the same SeriesInstanceUID and the same FrameOfReferenceUID. If you want to add references to multiple series, call this method for each series.

saveDatasets()

bool saveDatasets	(	const std::vector< DcmDataset * > &	datasets,
		const Filesystem::Url &	url,
		ErrorRecorder &	errors,
		Compression	compression = Compression::LittleEndianImplicit,
		int	compressionQuality = 90,
		const std::string &	filenameFormat = "",
		Progress *	progress = nullptr )

Saves the given datasets to the url.

For local files, a folder is required if there is more than one dataset. If the path doesn't exist, it is created (including all subfolders).

When exporting to PACS, the client config is determined via the global Settings but the server config is determined from the url.

The compression quality is only used for lossy compressions and goes from 1 to 100, with 1 being the lowest quality and highest compression and 100 being the highest quality and the lowest compression. Values will be clamped to 1 and 100. JPEGLS_lossy currently ignores the quality and uses a hardcoded value.

The input datasets will be converted to the given compression (transfer syntax) inplace.

The filenameFormat defines how files exported to a folder are named. It expects a pattern of 'prefix$0..0$suffix'. The amount of '0' in between the two $ markers specifies the size the filename will be padded to. If no '0' are given, the number depends on the number of files (e.g. 10 files would use 2 digits, 100 would use 3). E.g. 'IMG_$0000$.dcm' would name files 'IMG_0001.dcm', 'IMG_0002.dcm', ... If only one '0' is given, the files are not padded with a 0, e.g. the pattern 'IMG_$0$' produces 'IMG_0', 'IMG_1', ..., 'IMG_9', 'IMG_10', ... If there are more than one '0', but the number of datasets would require more digits, a warning is issued and only the lower files are padded with '0', e.g. a pattern of 'IMG_$00$' and 120 files: 'IMG_00', 'IMG_01', ..., 'IMG_99', 'IMG_100', 'IMG_101'... The default pattern is 'IMG_$$' which results in 'IMG_001', 'IMG_002', ... for 100 to 999 datasets.

Returns true if all datasets could be saved successfully. The first dataset that cannot be exported successfully will abort the export. In this case, any files already written will not be deleted!

exportSegmentationsToDataset()

std::unique_ptr< DcmDataset > exportSegmentationsToDataset	(	const std::vector< SharedImageSet * > &	labelmapLayers,
		ErrorRecorder &	errors,
		bool	cropToContent = false,
		Progress *	progress = nullptr )

Exports one or multiple segmentation layers as a single DICOM Segmentation object.

All labels present in the labelmaps will be exported. Labels that are missing from the LabelDataComponent will be assigned some default values. If multiple layers are passed, all layers must have the same ImageDescriptor. SharedImageSets with multiple images are currently not supported. cropToContent currently doesn't have an effect.

exportRTStructToDataset()

std::unique_ptr< DcmDataset > exportRTStructToDataset	(	const std::vector< PointCloud * > &	pointClouds,
		ErrorRecorder &	errors,
		Progress *	progress = nullptr )

Exports a PointCloud with a Dicom::RTStructureDataComponent as a DICOM RT Structure Set.

To export labelmaps, use the LabelMapToRTStructure before.