JavaScript implementation of a DICOM P10 converter to Amazon Ion
Project Status: pre-release software, do not use yet
- ION supports two encodings - a human readable format like JSON and a compact binary format. With other codecs, you either get one or the other
- ION is self describing - no external schema required. Self describing codecs are not as space efficient as schema based codecs, but are easier to work with as they are self contained
- ION has a rich type system - can store binary data, high precision data, timestamps, annotations and symbolic expressions. JSON has precision issues with Number types and poor support for binary (must encode in base64).
- ION is optimized for reading/parsing - enables efficient sparse/shallow reads. ION is much faster at decoding than JSON and competitive with other codecs (protobuf, etc)
- ION has libraries for most popular languages. Protobuf and JSON have the largest language support, all others are lacking in several ways
- ION will be supported for a very long time - it used internally at Amazon
- ION has direct support for hashing.
Read more here: https://amzn.github.io/ion-docs/guides/why.html
- Support async iterator as input so we can design for a full streaming implementation
- Make the attribute->value as simple and lightweight as possible (basically TAG=VALUE)
- Preserve the VRs in the original DICOM P10, but only the ones we don't already know (private vrs and multi-vr attributes)
- Use human friendly (Keyword) names for attributes (rather than group/element)
- Order attributes so the most common ones are first
- Must be possible to regenerate DICOM P10 from ION Format. Ideally bit for bit lossless, but semantic equivalence is acceptable
- Store the sha256 digest of the original DICOM P10 so we can very integrity later
- Store the sha256 for each referenced data item so we can verify integrity later
- Stream to source DICOM P10
- Source Info (optional)
- uri to source DICOM P10 file
- creation date
- modification date
- Encoding Algorithm Parameters (optional)
- privateAttributeMaxInlineLength - defaults to 256
- standardAttributeMaxInlineLength - defaults to 256
- data dictionary to use
- Attribute Ordering
- Enables faster parsing/lookups
- Private attributes put at the end
- Uses human readable names vs tags for common attribute groups
- Easier to read/debug
- Stores VRs separately from values
- Easier to read/debug. You rarely need the VR anyway
- Does not parse multi-valude string values into arrays
- Easier to read/debug
- Encodes multi valued numeric types into binary data
- these can be very large (e.g. LUTs) and rarely need to be human readable
{
sourceInfo: {
uri: "file:///workspaces/dicom2ion-js/test/fixtures/CT0012.fragmented_no_bot_jpeg_ls.80.dcm"
},
options: {
maximumInlineDataLength: 256,
dataDictionary: {
description: "Unknown edition",
sha256: "c2e30d6191b63d67a9a0606da204e00968286bfe1f94c2ccd2dcf9b8d33ebf4b"
}
},
fileInfo: {
sha256: "dc3ff8e550c833236bbee92d163762698b7b0b7b68a1af1b060243580741b7a6",
createdAt: 2021-02-03T21:22:54.051Z
},
dataSet: {
StudyInstanceUID: "1.3.6.1.4.1.5962.1.2.10.1166562673.14401",
SeriesInstanceUID: "1.3.6.1.4.1.5962.1.3.10.3.1166562673.14401",
SOPInstanceUID: "1.3.6.1.4.1.5962.1.1.10.3.1.1166562673.14401",
SOPClassUID: "1.2.840.10008.5.1.4.1.1.2.1",
SpecificCharacterSet: "ISO_IR 100",
PatientName: "Perfusion^MCA Stroke",
PatientID: "0010",
PatientBirthDate: "19500704",
PatientSex: "M",
StudyDescription: null,
AccessionNumber: "0010",
StudyID: "0010",
StudyDate: "20061219",
StudyTime: "111154.812",
SeriesDescription: null,
SeriesNumber: "3",
Modality: "CT",
SeriesDate: "20061219",
SeriesTime: "110929.984",
InstanceNumber: "1",
AcquisitionNumber: "1",
InstanceCreationDate: "20061219",
InstanceCreationTime: "202309",
ContentDate: "20061219",
ContentTime: "110930.671",
ImageType: "DERIVED\\PRIMARY\\PERFUSION\\RCBF",
Rows: 512,
Columns: 512,
BitsAllocated: 16,
BitsStored: 16,
HighBit: 15,
PixelRepresentation: 0,
SamplesPerPixel: 1,
TransferSyntaxUID: "1.2.840.10008.1.2.4.80",
NumberOfFrames: "2",
PixelData: {
dataOffset: 3920,
length: 85672,
sha256: "600138c2a369ce2d25dc0842c0a9f634bd8ad0ec09b208c067d020fc71b659bb",
encapsulatedPixelData: true,
basicOffsetTable: [
],
fragments: [
{
offset: 0,
position: 3936,
length: 8192
},
{
offset: 8200,
position: 12136,
length: 8192
},
{
offset: 16400,
position: 20336,
length: 8192
},
{
offset: 24600,
position: 28536,
length: 8192
},
{
offset: 32800,
position: 36736,
length: 8192
},
{
offset: 41000,
position: 44936,
length: 5448
},
{
offset: 46456,
position: 50392,
length: 8192
},
{
offset: 54656,
position: 58592,
length: 8192
},
{
offset: 62856,
position: 66792,
length: 8192
},
{
offset: 71056,
position: 74992,
length: 8192
},
{
offset: 79256,
position: 83192,
length: 6392
}
]
},
PhotometricInterpretation: "MONOCHROME2",
FrameOfReferenceUID: "1.3.6.1.4.1.5962.1.4.10.1.1166562673.14401",
Manufacturer: "Acme Medical Devices",
ManufacturerModelName: "Super Dooper Scanner",
StationName: "CONSOLE01",
SourceApplicationEntityTitle: "CLUNIE1",
InstitutionName: "St. Nowhere Hospital",
ImplementationVersionName: "OFFIS_DCMTK_361",
FileMetaInformationGroupLength: {{0AAAAA==}},
FileMetaInformationVersion: {{AAE=}},
MediaStorageSOPClassUID: "1.2.840.10008.5.1.4.1.1.2.1",
MediaStorageSOPInstanceUID: "1.3.6.1.4.1.5962.1.1.10.3.1.1166562673.14401",
ImplementationClassUID: "1.2.276.0.7230010.3.0.3.6.1",
InstanceCreatorUID: "1.3.6.1.4.1.5962.3",
ReferringPhysicianName: "Thomas^Albert",
TimezoneOffsetFromUTC: "-0500",
PerformingPhysicianName: "Smith^John",
NameOfPhysiciansReadingStudy: "Smith^John",
OperatorsName: "Jones^Molly",
ReferencedRawDataSequence: [
{
StudyInstanceUID: "1.3.6.1.4.1.5962.1.2.10.1166562673.14401",
ReferencedSeriesSequence: [
{
SeriesInstanceUID: "1.3.6.1.4.1.5962.1.3.10.3.1166562673.14401",
ReferencedSOPSequence: [
{
ReferencedSOPClassUID: "1.2.840.10008.5.1.4.1.1.66",
ReferencedSOPInstanceUID: "1.3.6.1.4.1.5962.1.9.10.1.1166562673.14401"
}
]
}
]
}
],
PixelPresentation: "COLOR",
VolumetricProperties: "VOLUME",
VolumeBasedCalculationTechnique: "NONE",
PatientAge: "052Y",
PatientSize: "1.6",
PatientWeight: "75",
ContrastBolusAgentSequence: [
{
CodeValue: "C-B0322",
CodingSchemeDesignator: "SRT",
CodeMeaning: "Iohexol",
ContrastBolusAdministrationRouteSequence: [
{
CodeValue: "G-D101",
CodingSchemeDesignator: "SNM3",
CodeMeaning: "Intravenous route"
}
],
ContrastBolusVolume: "150",
ContrastBolusIngredientConcentration: "300",
ContrastBolusAgentNumber: 1,
ContrastBolusIngredientCodeSequence: [
{
CodeValue: "C-11400",
CodingSchemeDesignator: "SRT",
CodeMeaning: "Iodine"
}
]
}
],
DeviceSerialNumber: "123456",
SoftwareVersions: "1.00",
PatientPosition: "HFS",
ContentQualification: "PRODUCT",
PositionReferenceIndicator: null,
DimensionOrganizationSequence: [
{
DimensionOrganizationUID: "1.3.6.1.4.1.5962.1.6.10.3.0.1166562673.14401"
}
],
DimensionIndexSequence: [
{
DimensionOrganizationUID: "1.3.6.1.4.1.5962.1.6.10.3.0.1166562673.14401",
DimensionIndexPointer: "00209056",
FunctionalGroupPointer: "00209111"
},
{
DimensionOrganizationUID: "1.3.6.1.4.1.5962.1.6.10.3.0.1166562673.14401",
DimensionIndexPointer: "00209057",
FunctionalGroupPointer: "00209111"
}
],
BurnedInAnnotation: "NO",
RedPaletteColorLookupTableDescriptor: {{ZAAABBAA}},
GreenPaletteColorLookupTableDescriptor: {{ZAAABBAA}},
BluePaletteColorLookupTableDescriptor: {{ZAAABBAA}},
RedPaletteColorLookupTableData: {{AAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEAAQABAAEBAgIDAwRTB+MKcw4EEpQVJBm1HEUg1SNmJ/YqhS0WMaY0NzhUPHE/6EJ4RghKmU0CUR9USVfZWnZelWO0aNJtMnTge4+CPYrqkJiYR6D1p6OvUbf/vq3GW86i1bbcZOQS7MDzbfr+/j////////////8=}},
GreenPaletteColorLookupTableData: {{AAEAAQABAAEAAQABAAEAAQABAAGAAQ8EBQZUCL4MUBGuFcsZ6h6VIycoRCxiMIE1njm9PttC+UcXTDZRVFVxWZBermLLZulqCHAldEN4Yn2AgJ+Fvordj/uUGpqHoDSn4a2btLu73MKWyUPQ8Nad3X7k9+qk8dz1+fkY//////////////////////////////////////////////////////////////////////////////////////////////////////8=}},
BluePaletteColorLookupTableData: {{AAE9C3kUtx6VMENEvFc2a3wXN5Cjox23/sqd3bXo8/Mx/v////////////////////////////////////////////////////////////////////////////////////8L/3397/uR91Tuy+Qb22zSY8kmwF63rq5ypTac+ZLwiUGBRHkIcMtmj11TVBZL2kHEOBUwqCmJJGsfAx6SICIjWSeUL9E4DEGISTdSv1r9ZDtw+Xq4hPWONJpxpK+v7bnRxGjOpNc=}},
LossyImageCompression: "00",
AcquisitionContextSequence: [
],
PresentationLUTShape: "IDENTITY",
SharedFunctionalGroupsSequence: [
{
CTImageFrameTypeSequence: [
{
FrameType: "DERIVED\\PRIMARY\\PERFUSION\\RCBF",
PixelPresentation: "COLOR",
VolumetricProperties: "VOLUME",
VolumeBasedCalculationTechnique: "NONE"
}
],
ContrastBolusUsageSequence: [
{
ContrastBolusAgentNumber: 1,
ContrastBolusAgentAdministered: "YES",
ContrastBolusAgentDetected: "YES",
ContrastBolusAgentPhase: "DYNAMIC"
}
],
IrradiationEventIdentificationSequence: [
{
IrradiationEventUID: "1.3.6.1.4.1.5962.1.10.10.3.1.1166562673.14401"
}
],
FrameAnatomySequence: [
{
AnatomicRegionSequence: [
{
CodeValue: "T-A0100",
CodingSchemeDesignator: "SNM3",
CodeMeaning: "Brain"
}
],
FrameLaterality: "U"
}
],
PlaneOrientationSequence: [
{
ImageOrientationPatient: "-1.00000\\0.00000\\0.00000\\0.00000\\1.00000\\0.00000"
}
],
PixelMeasuresSequence: [
{
PixelSpacing: "0.388672\\0.388672",
SliceThickness: "10.0000"
}
],
FrameVOILUTSequence: [
{
WindowCenter: "49.0000",
WindowWidth: "102.000"
}
],
PixelValueTransformationSequence: [
{
RescaleSlope: "1.00000",
RescaleIntercept: "-1024.00",
RescaleType: "US"
}
],
RealWorldValueMappingSequence: [
{
LUTExplanation: "Regional Cerebral Blood Flow",
MeasurementUnitsCodeSequence: [
{
CodeValue: "ml/100ml/s",
CodingSchemeDesignator: "UCUM",
CodingSchemeVersion: "1.4",
CodeMeaning: "ml/100ml/s"
}
],
LUTLabel: "RCBF",
RealWorldValueLastValueMapped: 4095,
RealWorldValueFirstValueMapped: 0,
RealWorldValueIntercept: -1024,
RealWorldValueSlope: 1
}
]
}
],
PerFrameFunctionalGroupsSequence: [
{
FrameContentSequence: [
{
StackID: "1",
InStackPositionNumber: {{AgAAAA==}},
FrameAcquisitionNumber: 1,
DimensionIndexValues: {{AQAAAAIAAAA=}}
}
],
PlanePositionSequence: [
{
ImagePositionPatient: "99.5000\\-301.500\\-159.000"
}
]
},
{
FrameContentSequence: [
{
StackID: "1",
InStackPositionNumber: {{AQAAAA==}},
FrameAcquisitionNumber: 1,
DimensionIndexValues: {{AQAAAAEAAAA=}}
}
],
PlanePositionSequence: [
{
ImagePositionPatient: "99.5000\\-301.500\\-149.000"
}
]
}
]
}
}