PixelData issue

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gzhang
Posts: 50
Joined: Wed, 2015-09-02, 09:24

PixelData issue

#1 Post by gzhang »

Hello, we have some dicom files from optical examination, where the encoding is LittleEndian normal but "PixelData" format is somehow different than usual. Dcmdump shows this:
(7fe0,0010) OB (PixelSequence #=3) # u/l, 1 PixelData
(fffe,e000) pi (no value available) # 0, 1 Item
(fffe,e000) pi 00\00\0c\13\0c\00\00\04\03\00\00\00\01\05\00\03\06\00\00\00\00\00... # 768000, 1 Item
(fffe,e000) pi 00\00\01\10\15\11\03\00\00\00\00\00\0b\13\11\0b\03\00\00\00\00\00... # 768000, 1 Item
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
How should such data be read? The normal "DicomImage" approach does not seem to work. Thanks!

J. Riesmeier
DCMTK Developer
Posts: 2501
Joined: Tue, 2011-05-03, 14:38
Location: Oldenburg, Germany
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Re: PixelData issue

#2 Post by J. Riesmeier »

Could you post the entire dump of the DICOM image, at least the data elements from group (0028,xxxx)?

gzhang
Posts: 50
Joined: Wed, 2015-09-02, 09:24

Re: PixelData issue

#3 Post by gzhang »

Here is the entire dump. Skipped parts are marked with "...". Thanks for helping!
# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 270 # 4, 1 FileMetaInformationGroupLength
(0002,0002) UI [1.2.840.10008.5.1.4.1.1.12.77] # 58, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.276.0.75.2.2.44.88623634820587.20190628121611239.336028027] # 124, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit # 20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.721.2233.11] # 16, 1 ImplementationClassUID
(0002,0013) SH [Baycor DICOM] # 12, 1 ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0008) CS [ORIGINAL] # 16, 1 ImageType
(0008,0016) UI [1.2.840.10008.5.1.4.1.1.12.77] # 58, 1 SOPClassUID
(0008,0018) UI [1.2.276.0.75.2.2.44.88623634820587.20190628121611239.336028027] # 124, 1 SOPInstanceUID
(0008,0020) DA [20190628] # 16, 1 StudyDate
(0008,0021) DA [20190628] # 16, 1 SeriesDate
(0008,0022) DA [20190628] # 16, 1 AcquisitionDate
(0008,002a) DT [20190628121541] # 28, 1 AcquisitionDateTime
(0008,0030) TM [121608] # 12, 1 StudyTime
(0008,0031) TM [121541] # 12, 1 SeriesTime
(0008,0032) TM [121541] # 12, 1 AcquisitionTime
(0008,0050) SH (no value available) # 0, 0 AccessionNumber
(0008,0060) CS (no value available) # 0, 0 Modality
...
(0020,000d) UI [1.2.276.0.75.2.2.44.88623634820587.20190628121608915.336085801] # 124, 1 StudyInstanceUID
(0020,000e) UI [1.2.276.0.75.2.2.44.88623634820587.20190628121608993.336040506] # 124, 1 SeriesInstanceUID
(0020,0010) SH [2019062812160891] # 32, 1 StudyID
(0020,0011) IS [1] # 2, 1 SeriesNumber
(0020,0012) IS [0] # 2, 1 AcquisitionNumber
(0020,0013) IS [1] # 2, 1 InstanceNumber
(0020,0052) UI [1.2.276.0.75.2.2.44.88623634820587.20190628121608993.336040506] # 124, 1 FrameOfReferenceUID
(0020,0060) CS [OS] # 4, 1 Laterality
(0020,0200) UI [1.2.276.0.75.2.2.44.88623634820587.20190320175953349.347622423] # 124, 1 SynchronizationFrameOfReferenceUID
(0020,4000) LT (no value available) # 0, 0 ImageComments
(0028,0002) US 1 # 2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2] # 22, 1 PhotometricInterpretation
(0028,0008) IS [2] # 2, 1 NumberOfFrames
(0028,0010) US 500 # 2, 1 Rows
(0028,0011) US 1536 # 2, 1 Columns
(0028,0030) DS [0.01202405,0.001954397] # 44, 1 PixelSpacing
(0028,0100) US 8 # 2, 1 BitsAllocated
(0028,0101) US 8 # 2, 1 BitsStored
(0028,0102) US 7 # 2, 1 HighBit
(0028,0103) US 1 # 2, 1 PixelRepresentation
(0028,1050) DS [10] # 4, 1 WindowCenter
(0028,1051) DS [250] # 6, 1 WindowWidth
(0028,2110) CS [00] # 4, 1 LossyImageCompression
(0028,2112) DS [1] # 2, 1 LossyImageCompressionRatio
(0032,1060) LO (no value available) # 0, 0 RequestedProcedureDescription
(0040,0008) SQ (Sequence with undefined length #=1) # u/l, 1 ScheduledProtocolCodeSequence
(fffe,e000) na (Item with undefined length #=12) # u/l, 1 Item
(0008,0100) SH [SD-E1] # 10, 1 CodeValue
(0008,0102) SH [99CZM] # 10, 1 CodingSchemeDesignator
(0008,0103) SH [1.0] # 6, 1 CodingSchemeVersion
(0008,0104) LO [ALL SCANS] # 18, 1 CodeMeaning
(0008,010d) UI [CZM] # 6, 1 ContextGroupExtensionCreatorUID
(0061,0111) UL 1 # 4, 1 Unknown Tag & Data
(0061,0113) LO [1] # 2, 1 Unknown Tag & Data
(0061,0115) LO (no value available) # 0, 0 Unknown Tag & Data
(0061,0117) LO [SD-E1.xml] # 18, 1 Unknown Tag & Data
(0061,0119) LO [False] # 10, 1 Unknown Tag & Data
(0061,011b) LO (no value available) # 0, 0 Unknown Tag & Data
(0061,011d) LO [True] # 8, 1 Unknown Tag & Data
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0040,0244) DA [20190628] # 16, 1 PerformedProcedureStepStartDate
(0040,0245) TM [121608] # 12, 1 PerformedProcedureStepStartTime
(0040,0260) SQ (Sequence with undefined length #=1) # u/l, 1 PerformedProtocolCodeSequence
(fffe,e000) na (Item with undefined length #=12) # u/l, 1 Item
(0008,0100) SH [SS-S28] # 12, 1 CodeValue
(0008,0102) SH [99CZM] # 10, 1 CodingSchemeDesignator
(0008,0103) SH [1.0] # 6, 1 CodingSchemeVersion
(0008,0104) LO [Angio (6mmx6mm)] # 30, 1 CodeMeaning
(0008,010d) UI [CZM] # 6, 1 ContextGroupExtensionCreatorUID
(0061,0111) UL 2 # 4, 1 Unknown Tag & Data
(0061,0113) LO [1] # 2, 1 Unknown Tag & Data
(0061,0115) LO (no value available) # 0, 0 Unknown Tag & Data
(0061,0117) LO [SS-S28.xml] # 20, 1 Unknown Tag & Data
(0061,0119) LO [False] # 10, 1 Unknown Tag & Data
(0061,011b) LO [HD Angio (6mmx6mm)] # 36, 1 Unknown Tag & Data
(0061,011d) LO [False] # 10, 1 Unknown Tag & Data
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0040,0280) ST [Sample Procedure Step] # 42, 1 CommentsOnThePerformedProcedureStep
(0040,1001) SH (no value available) # 0, 0 RequestedProcedureID
(0057,0001) UI [1.2.276.0.75.2.2.44.4] # 42, 1 Unknown Tag & Data
(0057,1003) UL 1 # 4, 1 Unknown Tag & Data
(0057,1015) LO [CZMI] # 8, 1 Unknown Tag & Data
(0057,1021) LO (no value available) # 0, 0 Unknown Tag & Data
(0057,1023) LO [88623634820587] # 28, 1 Unknown Tag & Data
(0059,1000) LO [DATAFILES/E404/1DXP3G9VZN29YOKLLYZAUQBVYIE8USXPB27IOLS4X2ZU.EX.DCM] # 132, 1 Unknown Tag & Data
(0059,1005) SL 0 # 4, 1 Unknown Tag & Data
(0059,3500) SL 0 # 4, 1 Unknown Tag & Data
...
(0073,1135) FL 0.60000002 # 4, 1 Unknown Tag & Data
(0075,1015) SQ (Sequence with undefined length #=554) # u/l, 1 Unknown Tag & Data
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0075,1004) FL 0.00056730589 # 4, 1 Unknown Tag & Data
(0075,1005) FL 2.4080067 # 4, 1 Unknown Tag & Data
(0075,1010) FL 15.0628576 # 4, 1 Unknown Tag & Data
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0075,1004) FL 0.00015451595 # 4, 1 Unknown Tag & Data
(0075,1005) FL 0.13143417 # 4, 1 Unknown Tag & Data
(0075,1010) FL 21.517481 # 4, 1 Unknown Tag & Data
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0075,1004) FL 9.0977737e-05 # 4, 1 Unknown Tag & Data
(0075,1005) FL -1.7393855 # 4, 1 Unknown Tag & Data
(0075,1010) FL 18.228857 # 4, 1 Unknown Tag & Data
...
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0075,1004) FL -0.0099568889 # 4, 1 Unknown Tag & Data
(0075,1005) FL -809.37701 # 4, 1 Unknown Tag & Data
(0075,1010) FL -644.49408 # 4, 1 Unknown Tag & Data
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0075,1020) SL 1 # 4, 1 Unknown Tag & Data
(0075,1021) SL 1 # 4, 1 Unknown Tag & Data
(0075,1030) SL 37560\50080\62600\75120\87640\100160\287962\300482\313002\325522... # 2000,500 Unknown Tag & Data
(0075,1035) FL 12.40971 # 4, 1 Unknown Tag & Data
(0075,1065) FL 0 # 4, 1 Unknown Tag & Data
(0075,1070) FL 0 # 4, 1 Unknown Tag & Data
(0075,1075) FL 0 # 4, 1 Unknown Tag & Data
(0075,1080) FL 0.75100243 # 4, 1 Unknown Tag & Data
(0075,1085) SL 0 # 4, 1 Unknown Tag & Data
(0075,1210) UL 0 # 4, 1 Unknown Tag & Data
(0075,1215) FL -inf # 4, 1 Unknown Tag & Data
(0075,1220) FL -inf # 4, 1 Unknown Tag & Data
(0075,1225) SL 0 # 4, 1 Unknown Tag & Data
(0405,0046) LO [UNKNOWN] # 14, 1 PrivateCreator
(7fe0,0010) OB (PixelSequence #=3) # u/l, 1 PixelData
(fffe,e000) pi (no value available) # 0, 1 Item
(fffe,e000) pi 00\00\0c\13\0c\00\00\04\03\00\00\00\01\05\00\03\06\00\00\00\00\00... # 768000, 1 Item
(fffe,e000) pi 00\00\01\10\15\11\03\00\00\00\00\00\0b\13\11\0b\03\00\00\00\00\00... # 768000, 1 Item
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem

J. Riesmeier
DCMTK Developer
Posts: 2501
Joined: Tue, 2011-05-03, 14:38
Location: Oldenburg, Germany
Contact:

Re: PixelData issue

#4 Post by J. Riesmeier »

This "DICOM image" has numerous issues, some of them seem to be discussed here: https://groups.google.com/forum/#!topic ... vx2IpKa0BM

The SOP Class UID refers to an unnamed retired SOP Class that apparently was never really defined in the DICOM standard.
The Pixel data of the two frames seem to be uncompressed (Rows * Columns * 1 Byte/Pixel = 768,000 Bytes) but the encapsulated structure (pixel sequence with items) is used, which is only defined for compressed pixel data...

If you want to process this invalid "DICOM image", you should correct the most serious violations first, i.e. extract the data from the pixel items and store them in an uncompressed way.

gzhang
Posts: 50
Joined: Wed, 2015-09-02, 09:24

Re: PixelData issue

#5 Post by gzhang »

Thanks!

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