from gdcmPython import *
class gdcmTestCase(unittest.TestCase):
- # The files whose name starts with a modality (e.g. CR-MONO1-10-chest.dcm)
- # come from Sebastien Barre's Dicom2 highly recommendable site
- # http://www.barre.nom.fr/medical/samples/index.html
- BarreFiles = [
- ####################################
- # CR modality examples:
- ####################################
- ["CR-MONO1-10-chest.dcm",
- [ ["Modality", "CR"],
- #"Transfer Syntax UID" is absent.
- ["Rows", "440"],
- ["Columns", "440"],
- ["Bits Stored", "10"],
- ["Bits Allocated", "16"],
- ["High Bit", "9"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "FUJI PHOTO FILM CO. LTD."],
- ["Manufacturer Model Name", "9000"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:776 Length:387200"] ] ],
- ####################################
- # CT modality examples:
- ####################################
- ["CT-MONO2-16-brain.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
- ["Modality", "CT"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "1"],
- ["Manufacturer", "Picker International, Inc."],
- ["Manufacturer Model Name", "PQ5000"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1680 Length:524288"] ] ],
- ["CT-MONO2-16-ort.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
- ["Modality", "CT"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "1"],
- ["Manufacturer", "GE MEDICAL SYSTEMS"],
- ["Manufacturer Model Name", "HiSpeed CT/i"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1674 Length:524288"] ] ],
- ["CT-MONO2-16-ankle.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit, little
- ["Modality", "CT"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "1"],
- ["Manufacturer", "GE MEDICAL SYSTEMS"],
- ["Manufacturer Model Name", "GENESIS_ZEUS"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1148 Length:524288"] ] ],
- ["CT-MONO2-8-abdo.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit, little
- ["Modality", "CT"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "FUJI"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:796 Length:262144"] ] ],
- ["CT-MONO2-12-lomb-an2.acr2",
- [ ["Modality", "CT"],
- #"Transfer Syntax UID" and "Photometric Interpretation" are absent.
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1230 Length:524288"] ] ],
- ["CT-MONO2-16-chest.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"], # jpeg...
- ["Modality", "CT"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "400"],
- ["Columns", "512"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "1"],
- ["Manufacturer", "GE MEDICAL SYSTEMS"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1638 Length:143498"] ] ],
- ####################################
- ### MR modality examples:
- ####################################
- ["MR-MONO2-12-angio-an1.acr1",
- [ ["Recognition Code", "ACR-NEMA 1.0"],
- ["Modality", "MR"],
- #"Transfer Syntax UID" and "Photometric Interpretation" are absent.
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "12"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips"],
- # Note: 256*256*12/8 = 98304
- ["7fe0|0010", "gdcm::NotLoaded. Address:650 Length:98304"] ] ],
- ["MR-MONO2-12-an2.acr2",
- [ ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["Manufacturer Model Name", "MAGNETOM VISION"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1866 Length:131072"] ] ],
- ["MR-MONO2-16-head.dcm",
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Imp VR, LE
- ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "1"],
- ["Manufacturer", "GE MEDICAL SYSTEMS"],
- ["Manufacturer Model Name", "GENESIS_SIGNA"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1804 Length:131072"] ] ],
- # MR-MONO2-12-shoulder example is present in the Jpeg section.
- # MR-MONO2-16-knee is not present in the test suite since it is too
- # closely related to MR-MONO2-16-head.dcm to be of interest.
- ####################################
- # OT modality examples:
- ####################################
- # OT-MONO2-8-hip is not present in the test suite since it is too
- # closely related to OT-MONO2-8-a7 to be of interest.
- ["OT-PAL-8-face.dcm",
- # Interest: has a color palette
- [#"Transfer Syntax UID", and "Manufacturer" are absent.
- ["Modality", "OT"],
- ["Photometric Interpretation", "PALETTE COLOR"],
- ["Rows", "480"],
- ["Columns", "640"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1654 Length:307200"] ] ],
- # OT-MONO2-8-colon is not present in the test suite since it is too
- # closely related to OT-MONO2-8-a7 to be of interest.
- ["OT-MONO2-8-a7.dcm",
- [#"Transfer Syntax UID" is absent.
- ["Modality", "OT"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips Medical Systems"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:438 Length:262144"] ] ],
- ####################################
- # US (Ultra Sound) modality examples:
- ####################################
- ["US-RGB-8-esopecho.dcm",
- # Interest: RGB image
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Exp VR, LE
- ["Modality", "US"],
- ["Photometric Interpretation", "RGB"],
- ["Rows", "120"],
- ["Columns", "256"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Acme Products"],
- # FIXME: 92160 / (120*256) = 3 bytes per pixel NOT 1. Maybe
- # it has something to do with [Samples Per Pixel] = [3] ???
- ["7fe0|0010", "gdcm::NotLoaded. Address:904 Length:92160"] ] ],
- ["US-RGB-8-epicard.dcm",
- # Interest: Big endian transfert syntax
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.2"], # Big endian
- ["Modality", "US"],
- ["Photometric Interpretation", "RGB"],
- ["Rows", "480"],
- ["Columns", "640"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "G.E. Medical Systems"],
- ["Manufacturer Model Name", "LOGIQ 700"],
- # FIXME: 921600/(480*640) = 3 bytes per pixel NOT 1. Maybe
- # it has something to do with [Samples Per Pixel] = [3] ???
- ["Implementation Version Name", "OFFIS-DCMTK-311"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1012 Length:921600"] ] ],
- ]
+ # The files whose name starts with a modality (e.g. CR-MONO1-10-chest.dcm)
+ # come from Sebastien Barre's Dicom2 highly recommendable site
+ # http://www.barre.nom.fr/medical/samples/index.html
+ BarreFiles = [
+ ####################################
+ # CR modality examples:
+ ####################################
+ ["CR-MONO1-10-chest.dcm",
+ [ ["Modality", "CR"],
+ #"Transfer Syntax UID" is absent.
+ ["Rows", "440"],
+ ["Columns", "440"],
+ ["Bits Stored", "10"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "9"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "FUJI PHOTO FILM CO. LTD."],
+ ["Manufacturer Model Name", "9000"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:776 Length:387200"] ] ],
+ ####################################
+ # CT modality examples:
+ ####################################
+ ["CT-MONO2-16-brain.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
+ ["Modality", "CT"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "1"],
+ ["Manufacturer", "Picker International, Inc."],
+ ["Manufacturer Model Name", "PQ5000"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1680 Length:524288"] ] ],
+ ["CT-MONO2-16-ort.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
+ ["Modality", "CT"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "1"],
+ ["Manufacturer", "GE MEDICAL SYSTEMS"],
+ ["Manufacturer Model Name", "HiSpeed CT/i"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1674 Length:524288"] ] ],
+ ["CT-MONO2-16-ankle.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit, little
+ ["Modality", "CT"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "1"],
+ ["Manufacturer", "GE MEDICAL SYSTEMS"],
+ ["Manufacturer Model Name", "GENESIS_ZEUS"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1148 Length:524288"] ] ],
+ ["CT-MONO2-8-abdo.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit, little
+ ["Modality", "CT"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "FUJI"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:796 Length:262144"] ] ],
+ ["CT-MONO2-12-lomb-an2.acr2",
+ [ ["Modality", "CT"],
+ #"Transfer Syntax UID" and "Photometric Interpretation" are absent.
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1230 Length:524288"] ] ],
+ ["CT-MONO2-16-chest.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"], # jpeg...
+ ["Modality", "CT"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "400"],
+ ["Columns", "512"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "1"],
+ ["Manufacturer", "GE MEDICAL SYSTEMS"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1638 Length:143498"] ] ],
+ ####################################
+ ### MR modality examples:
+ ####################################
+ ["MR-MONO2-12-angio-an1.acr1",
+ [ ["Recognition Code", "ACR-NEMA 1.0"],
+ ["Modality", "MR"],
+ #"Transfer Syntax UID" and "Photometric Interpretation" are absent.
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "12"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips"],
+ # Note: 256*256*12/8 = 98304
+ ["7fe0|0010", "gdcm::NotLoaded. Address:650 Length:98304"] ] ],
+ ["MR-MONO2-12-an2.acr2",
+ [ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["Manufacturer Model Name", "MAGNETOM VISION"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1866 Length:131072"] ] ],
+ ["MR-MONO2-16-head.dcm",
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Imp VR, LE
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "1"],
+ ["Manufacturer", "GE MEDICAL SYSTEMS"],
+ ["Manufacturer Model Name", "GENESIS_SIGNA"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1804 Length:131072"] ] ],
+ # MR-MONO2-12-shoulder example is present in the Jpeg section.
+ # MR-MONO2-16-knee is not present in the test suite since it is too
+ # closely related to MR-MONO2-16-head.dcm to be of interest.
+ ####################################
+ # OT modality examples:
+ ####################################
+ # OT-MONO2-8-hip is not present in the test suite since it is too
+ # closely related to OT-MONO2-8-a7 to be of interest.
+ ["OT-PAL-8-face.dcm",
+ # Interest: has a color palette
+ [#"Transfer Syntax UID", and "Manufacturer" are absent.
+ ["Modality", "OT"],
+ ["Photometric Interpretation", "PALETTE COLOR"],
+ ["Rows", "480"],
+ ["Columns", "640"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1654 Length:307200"] ] ],
+ # OT-MONO2-8-colon is not present in the test suite since it is too
+ # closely related to OT-MONO2-8-a7 to be of interest.
+ ["OT-MONO2-8-a7.dcm",
+ [#"Transfer Syntax UID" is absent.
+ ["Modality", "OT"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:438 Length:262144"] ] ],
+ ####################################
+ # US (Ultra Sound) modality examples:
+ ####################################
+ ["US-RGB-8-esopecho.dcm",
+ # Interest: RGB image
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Exp VR, LE
+ ["Modality", "US"],
+ ["Photometric Interpretation", "RGB"],
+ ["Rows", "120"],
+ ["Columns", "256"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Acme Products"],
+ # FIXME: 92160 / (120*256) = 3 bytes per pixel NOT 1. Maybe
+ # it has something to do with [Samples Per Pixel] = [3] ???
+ ["7fe0|0010", "gdcm::NotLoaded. Address:904 Length:92160"] ] ],
+ ["US-RGB-8-epicard.dcm",
+ # Interest: Big endian transfert syntax
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.2"], # Big endian
+ ["Modality", "US"],
+ ["Photometric Interpretation", "RGB"],
+ ["Rows", "480"],
+ ["Columns", "640"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "G.E. Medical Systems"],
+ ["Manufacturer Model Name", "LOGIQ 700"],
+ # FIXME: 921600/(480*640) = 3 bytes per pixel NOT 1. Maybe
+ # it has something to do with [Samples Per Pixel] = [3] ???
+ ["Implementation Version Name", "OFFIS-DCMTK-311"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1012 Length:921600"] ] ],
+ ]
- MultiFrameFiles = [
- # The number of images is contained in the "Number of Frames" element
- ["MR-MONO2-8-16x-heart.dcm",
- # Interest: multi-frame
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
- ["Number of Frames", "16"],
- ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips"],
- # Note: 256*256*16=1048576 (16 is the number of Frames)
- ["7fe0|0010", "gdcm::NotLoaded. Address:920 Length:1048576"] ] ],
- ["NM-MONO2-16-13x-heart.dcm",
- # Interest: NM modality, multi-frame
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
- ["Number of Frames", "13"],
- ["Modality", "NM"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "64"],
- ["Columns", "64"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "ACME Products"],
- # Note: 64*64*13*2=106496
- ["7fe0|0010", "gdcm::NotLoaded. Address:1234 Length:106496"] ] ],
- ["US-MONO2-8-8x-execho.dcm",
- # Interest: multi-frame
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
- ["Number of Frames", "8"],
- ["Modality", "US"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "120"],
- ["Columns", "128"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Acme Products"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:976 Length:122880"] ] ],
- ["US-PAL-8-10x-echo.dcm",
- # Interest: RLE (Run Length Encoded) compression, multiframe
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.5"], # RLE
- ["Number of Frames", "10"],
- ["Modality", "US"],
- ["Photometric Interpretation", "PALETTE COLOR"],
- ["Rows", "430"],
- ["Columns", "600"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "ACME Products"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:2428 Length:481182"] ] ],
- ["XA-MONO2-8-12x-catheter.dcm",
- # Interest: XA modality, multi-frame
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"], # jpeg
- ["Number of Frames", "12"], # 12 images
- ["Modality", "XA"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Acme Products"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1006 Length:920072"] ] ],
- ]
+ MultiFrameFiles = [
+ # The number of images is contained in the "Number of Frames" element
+ ["MR-MONO2-8-16x-heart.dcm",
+ # Interest: multi-frame
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
+ ["Number of Frames", "16"],
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips"],
+ # Note: 256*256*16=1048576 (16 is the number of Frames)
+ ["7fe0|0010", "gdcm::NotLoaded. Address:920 Length:1048576"] ] ],
+ ["NM-MONO2-16-13x-heart.dcm",
+ # Interest: NM modality, multi-frame
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
+ ["Number of Frames", "13"],
+ ["Modality", "NM"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "64"],
+ ["Columns", "64"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "ACME Products"],
+ # Note: 64*64*13*2=106496
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1234 Length:106496"] ] ],
+ ["US-MONO2-8-8x-execho.dcm",
+ # Interest: multi-frame
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # ExpVR, LE
+ ["Number of Frames", "8"],
+ ["Modality", "US"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "120"],
+ ["Columns", "128"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Acme Products"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:976 Length:122880"] ] ],
+ ["US-PAL-8-10x-echo.dcm",
+ # Interest: RLE (Run Length Encoded) compression, multiframe
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.5"], # RLE
+ ["Number of Frames", "10"],
+ ["Modality", "US"],
+ ["Photometric Interpretation", "PALETTE COLOR"],
+ ["Rows", "430"],
+ ["Columns", "600"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "ACME Products"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:2428 Length:481182"] ] ],
+ ["XA-MONO2-8-12x-catheter.dcm",
+ # Interest: XA modality, multi-frame
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"], # jpeg
+ ["Number of Frames", "12"], # 12 images
+ ["Modality", "XA"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Acme Products"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1006 Length:920072"] ] ],
+ ]
- GdcmFiles = [
- ["gdcm-MR-SIEMENS-16.acr1",
- # Interest: good old Acr-Nema Version 1, see also Oddities below
- [ ["Recognition Code", "ACR-NEMA 1.0"],
- ["Modality", "MR"],
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["Manufacturer Model Name", "GBS III"],
- # FIXME: this image looks padded at the end. The length of the file
- # is 140288. Notice that, 256*256*2 + 1024 = 131072 + 1024 = 132096
- ["7fe0|0010", "gdcm::NotLoaded. Address:8192 Length:132096"],
- # Oddities: "Study ID" and "Series Number" are empty
- ["Study ID", ""],
- ["Series Number", ""] ] ],
- # Oddities: "Study" and "Serie Instance UID" are not present
- ["gdcm-MR-SIEMENS-16.acr2",
- # Interest: Acr-Nema Version 2
- [ ["Recognition Code", "ACR-NEMA 2.0"],
- ["Modality", "MR"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["Manufacturer Model Name", "MAGNETOM VISION"],
- ["Study Instance UID",
- "1.3.12.2.1107.5.2.4.7630.20000918174641000"],
- ["Study ID", "1"],
- ["Series Instance UID",
- "1.3.12.2.1107.5.2.4.7630.20000918175714000007"],
- ["Series Number", "7"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:6052 Length:524288"] ] ],
- ["gdcm-US-ALOKA-16.dcm",
- # Interest: - possesses 3 LUTS: a Green (checked), a Red and BLue.
- # - announced as implicit VR, but really explicit VR.
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
- ["Modality", "US"],
- ["Photometric Interpretation", "PALETTE COLOR"],
- ["Segmented Green Palette Color LUT Data",
- "gdcm::NotLoaded. Address:89576 Length:113784"],
- ["Rows", "480"],
- ["Columns", "640"],
- ["Bits Stored", "16"],
- ["Bits Allocated", "16"],
- ["High Bit", "15"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "ALOKA CO., LTD."],
- ["Manufacturer Model Name", "SSD-4000"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:258740 Length:614400"] ] ],
- ["gdcm-MR-PHILIPS-16.dcm",
- # Interest: - possesses a sequence
- # - dicom file, with a recognition code of ACR-NEMA1
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
- ["Recognition Code", "ACR-NEMA 1.0"],
- ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "256"],
- ["Columns", "256"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "16"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips Medical Systems"],
- ["Manufacturer Model Name", "Gyroscan Intera"],
- ["Sequence Variant", "OTHER"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:6584 Length:131072"] ] ],
- ["gdcm-MR-PHILIPS-16-NonRectPix.dcm",
- # Interest: - pixels are non rectangular
- # - private elements are in explicit VR (which is normal)
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
- ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "64"],
- ["Columns", "160"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips Medical Systems"],
- ["Manufacturer Model Name", "Gyroscan Intera"],
- ["Pixel Spacing", "0.487416\\0.194966"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:5010 Length:20480"] ] ],
- ["gdcm-CR-DCMTK-16-NonSamplePerPix.dcm",
- # Interest: - Misses the "Samples Per Pixel" element which prevents
- # e-film from reading it.
- # - Misses the Manufacturer related info
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
- ["Modality", "CR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "750"],
- ["Columns", "750"],
- ["Bits Stored", "8"],
- ["Bits Allocated", "8"],
- ["High Bit", "7"],
- ["Pixel Representation", "0"],
- ["Implementation Version Name", "OFFIS_DCMTK_341"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:740 Length:562500"] ] ],
- ]
+ GdcmFiles = [
+ ["gdcm-MR-SIEMENS-16.acr1",
+ # Interest: good old Acr-Nema Version 1, see also Oddities below
+ [ ["Recognition Code", "ACR-NEMA 1.0"],
+ ["Modality", "MR"],
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["Manufacturer Model Name", "GBS III"],
+ # FIXME: this image looks padded at the end. The length of the file
+ # is 140288. Notice that, 256*256*2 + 1024 = 131072 + 1024 = 132096
+ ["7fe0|0010", "gdcm::NotLoaded. Address:8192 Length:132096"],
+ # Oddities: "Study ID" and "Series Number" are empty
+ ["Study ID", ""],
+ ["Series Number", ""] ] ],
+ # Oddities: "Study" and "Serie Instance UID" are not present
+ ["gdcm-MR-SIEMENS-16.acr2",
+ # Interest: Acr-Nema Version 2
+ [ ["Recognition Code", "ACR-NEMA 2.0"],
+ ["Modality", "MR"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["Manufacturer Model Name", "MAGNETOM VISION"],
+ ["Study Instance UID",
+ "1.3.12.2.1107.5.2.4.7630.20000918174641000"],
+ ["Study ID", "1"],
+ ["Series Instance UID",
+ "1.3.12.2.1107.5.2.4.7630.20000918175714000007"],
+ ["Series Number", "7"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:6052 Length:524288"] ] ],
+ ["gdcm-US-ALOKA-16.dcm",
+ # Interest: - possesses 3 LUTS: a Green (checked), a Red and BLue.
+ # - announced as implicit VR, but really explicit VR.
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
+ ["Modality", "US"],
+ ["Photometric Interpretation", "PALETTE COLOR"],
+ ["Segmented Green Palette Color LUT Data",
+ "gdcm::NotLoaded. Address:89576 Length:113784"],
+ ["Rows", "480"],
+ ["Columns", "640"],
+ ["Bits Stored", "16"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "15"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "ALOKA CO., LTD."],
+ ["Manufacturer Model Name", "SSD-4000"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:258740 Length:614400"] ] ],
+ ["gdcm-MR-PHILIPS-16.dcm",
+ # Interest: - possesses a sequence
+ # - dicom file, with a recognition code of ACR-NEMA1
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
+ ["Recognition Code", "ACR-NEMA 1.0"],
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "256"],
+ ["Columns", "256"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["Manufacturer Model Name", "Gyroscan Intera"],
+ ["Sequence Variant", "OTHER"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:6584 Length:131072"] ] ],
+ ["gdcm-MR-PHILIPS-16-Multi-Seq.dcm",
+ # Interest: - possesses many sequences in group 0x0029
+ # - Big sequence 28808 bytes at (0x0029, 0x263d)
+ # - dicom file, with a recognition code of ACR-NEMA1
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"],
+ ["Recognition Code", "ACR-NEMA 1.0"],
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "128"],
+ ["Columns", "128"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["Manufacturer Model Name", "Gyroscan Intera"],
+ ["Sequence Variant", "OTHER"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:35846 Length:32768"] ] ],
+ ["gdcm-MR-PHILIPS-16-NonRectPix.dcm",
+ # Interest: - pixels are non rectangular
+ # - private elements are in explicit VR (which is normal)
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "64"],
+ ["Columns", "160"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["Manufacturer Model Name", "Gyroscan Intera"],
+ ["Pixel Spacing", "0.487416\\0.194966"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:5010 Length:20480"] ] ],
+ ["gdcm-CR-DCMTK-16-NonSamplePerPix.dcm",
+ # Interest: - Misses the "Samples Per Pixel" element which prevents
+ # e-film from reading it.
+ # - Misses the Manufacturer related info
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.1"], # Explicit VR, LE
+ ["Modality", "CR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "750"],
+ ["Columns", "750"],
+ ["Bits Stored", "8"],
+ ["Bits Allocated", "8"],
+ ["High Bit", "7"],
+ ["Pixel Representation", "0"],
+ ["Implementation Version Name", "OFFIS_DCMTK_341"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:740 Length:562500"] ] ],
+ ]
- GdcmJpegFiles = [
- ["gdcm-JPEG-Extended.dcm",
- # Interest: Jpeg compression [Extended (2,4)]
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.51"],
- ["Modality", "CT"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["Manufacturer Model Name", "Volume Zoom"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:2946 Length:192218"] ] ],
- ["MR-MONO2-12-shoulder.dcm",
- # Interest: Jpeg compression [Lossless, non-hierar. (14)]
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.57"],
- ["Modality", "MR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "1024"],
- ["Columns", "1024"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips Medical Systems"],
- ["Manufacturer Model Name", "Gyroscan NT"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:1580 Length:718948"] ] ],
- ["gdcm-JPEG-LossLess3a.dcm",
- # Interest: - Jpeg compression [Lossless, hierar., first-order
- # pred. 14, Select. Val. 1]
- # - contains a sequence [circa (0008,2112)]
- # - contains additional data after the pixels ???
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"],
- ["Modality", "CT"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "512"],
- ["Columns", "512"],
- ["Bits Stored", "12"],
- ["Bits Allocated", "16"],
- ["High Bit", "11"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "SIEMENS"],
- ["Manufacturer Model Name", "Volume Zoom"] ] ],
- # FIXME: the pixel data looks like corrupted. As stated by "od -A d -c"
- # 0002528 à 177 020 \0 O B \0 \0 ÿ ÿ ÿ ÿ þ ÿ \0 à
- # 0002544 \0 \0 \0 \0 þ ÿ \0 à 202 ? 003 \0 ÿ Ø ÿ Ã
- # which we interpret as follows:
- # - 2528: (à 177, 020 \0) = (0x7fe0, 0x0010) i.e. Pixel Data tag,
- # - 2532: OB i.e. encapsulated encoded Pixel Data,
- # - 2534: Two bytes reserved,
- # - 2536: ÿ ÿ ÿ ÿ = 0xffffffff i.e. data element length is undefined.
- # - 2540: (þ ÿ, \0 à) = (0xfffe, 0xe000) i.e. basic offset table
- # item tag
- # - 2544: \0 \0 \0 \0 i.e. offset table as length zero, i.e. no
- # item value for offset table.
- # - 2548: (þ ÿ, \0 à) = (0xfffe, 0xe000) i.e. item tag of first
- # fragment of (encoded) pixel data.
- # - 2552: 202 ? 003 \0 = 212866 bytes i.e. length of first fragment
- # of (encoded) pixel data.
- # and so the next item tag should be found at the 2556+212866 th
- # octet i.e. at address 215422. But, as stated by od, we find:
- # 0215408 E u Ö 026 Î É 7 ¬ Ã ¸ ó ¿ ÿ Ù \f °
- # 0215424 ¶ 016 P Ñ 002 016
- # and (\f °, ¶ 016) is NOT an OB item TAG which is required to be
- # present (at least there should be a sequence delimiter), refer to
- # PS 3.5-2001 page 50.
- ["gdcm-JPEG-LossLess3b.dcm",
- # Interest: - Jpeg compression [Lossless, hierar., first-order
- # pred. 14, Select. Val. 1]
- # - encoding is sligthly different from LossLess3a.dcm ???
- [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"],
- ["Modality", "CR"],
- ["Photometric Interpretation", "MONOCHROME2"],
- ["Rows", "2076"],
- ["Columns", "1876"],
- ["Bits Stored", "15"],
- ["Bits Allocated", "16"],
- ["High Bit", "14"],
- ["Pixel Representation", "0"],
- ["Manufacturer", "Philips Medical Systems"],
- ["Manufacturer Model Name", "Cassette Holder Type 9840 500 35201"],
- ["7fe0|0010", "gdcm::NotLoaded. Address:3144 Length:4795668"] ] ],
- ]
+ GdcmJpegFiles = [
+ ["gdcm-JPEG-Extended.dcm",
+ # Interest: Jpeg compression [Extended (2,4)]
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.51"],
+ ["Modality", "CT"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["Manufacturer Model Name", "Volume Zoom"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:2946 Length:192218"] ] ],
+ ["MR-MONO2-12-shoulder.dcm",
+ # Interest: Jpeg compression [Lossless, non-hierar. (14)]
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.57"],
+ ["Modality", "MR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "1024"],
+ ["Columns", "1024"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["Manufacturer Model Name", "Gyroscan NT"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:1580 Length:718948"] ] ],
+ ["gdcm-JPEG-LossLess3a.dcm",
+ # Interest: - Jpeg compression [Lossless, hierar., first-order
+ # pred. 14, Select. Val. 1]
+ # - contains a sequence [circa (0008,2112)]
+ # - contains additional data after the pixels ???
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"],
+ ["Modality", "CT"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "512"],
+ ["Columns", "512"],
+ ["Bits Stored", "12"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "11"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "SIEMENS"],
+ ["Manufacturer Model Name", "Volume Zoom"] ] ],
+ # FIXME: the pixel data looks like corrupted. As stated by "od -A d -c"
+ # 0002528 à 177 020 \0 O B \0 \0 ÿ ÿ ÿ ÿ þ ÿ \0 à
+ # 0002544 \0 \0 \0 \0 þ ÿ \0 à 202 ? 003 \0 ÿ Ø ÿ Ã
+ # which we interpret as follows:
+ # - 2528: (à 177, 020 \0) = (0x7fe0, 0x0010) i.e. Pixel Data tag,
+ # - 2532: OB i.e. encapsulated encoded Pixel Data,
+ # - 2534: Two bytes reserved,
+ # - 2536: ÿ ÿ ÿ ÿ = 0xffffffff i.e. data element length is undefined.
+ # - 2540: (þ ÿ, \0 à) = (0xfffe, 0xe000) i.e. basic offset table
+ # item tag
+ # - 2544: \0 \0 \0 \0 i.e. offset table as length zero, i.e. no
+ # item value for offset table.
+ # - 2548: (þ ÿ, \0 à) = (0xfffe, 0xe000) i.e. item tag of first
+ # fragment of (encoded) pixel data.
+ # - 2552: 202 ? 003 \0 = 212866 bytes i.e. length of first fragment
+ # of (encoded) pixel data.
+ # and so the next item tag should be found at the 2556+212866 th
+ # octet i.e. at address 215422. But, as stated by od, we find:
+ # 0215408 E u Ö 026 Î É 7 ¬ Ã ¸ ó ¿ ÿ Ù \f °
+ # 0215424 ¶ 016 P Ñ 002 016
+ # and (\f °, ¶ 016) is NOT an OB item TAG which is required to be
+ # present (at least there should be a sequence delimiter), refer to
+ # PS 3.5-2001 page 50.
+ ["gdcm-JPEG-LossLess3b.dcm",
+ # Interest: - Jpeg compression [Lossless, hierar., first-order
+ # pred. 14, Select. Val. 1]
+ # - encoding is sligthly different from LossLess3a.dcm ???
+ [ ["Transfer Syntax UID", "1.2.840.10008.1.2.4.70"],
+ ["Modality", "CR"],
+ ["Photometric Interpretation", "MONOCHROME2"],
+ ["Rows", "2076"],
+ ["Columns", "1876"],
+ ["Bits Stored", "15"],
+ ["Bits Allocated", "16"],
+ ["High Bit", "14"],
+ ["Pixel Representation", "0"],
+ ["Manufacturer", "Philips Medical Systems"],
+ ["Manufacturer Model Name", "Cassette Holder Type 9840 500 35201"],
+ ["7fe0|0010", "gdcm::NotLoaded. Address:3144 Length:4795668"] ] ],
+ ]
- def _BaseTest(self, FileSet):
- for entry in FileSet:
- fileName = os.path.join(GDCM_DATA_PATH, entry[0])
- toRead = gdcmHeader(fileName)
- valDict = toRead.GetPubElVal()
- for subEntry in entry[1]:
- element = subEntry[0]
- value = subEntry[1]
- self.assertEqual(valDict[element], value,
- ("Wrong %s for file %s (got %s, shoud be %s)"
- % (element,fileName, valDict[element], value)) )
+ def _BaseTest(self, FileSet):
+ for entry in FileSet:
+ fileName = os.path.join(GDCM_DATA_PATH, entry[0])
+ toRead = gdcmHeader(fileName)
+ valDict = toRead.GetPubElVal()
+ for subEntry in entry[1]:
+ element = subEntry[0]
+ value = subEntry[1]
+ self.assertEqual(valDict[element], value,
+ ("Wrong %s for file %s (got %s, shoud be %s)"
+ % (element,fileName, valDict[element], value)) )
- def testBarre(self):
- gdcmTestCase._BaseTest(self, gdcmTestCase.BarreFiles)
+ def testBarre(self):
+ gdcmTestCase._BaseTest(self, gdcmTestCase.BarreFiles)
- def testMultiFram(self):
- gdcmTestCase._BaseTest(self, gdcmTestCase.MultiFrameFiles)
+ def testMultiFram(self):
+ gdcmTestCase._BaseTest(self, gdcmTestCase.MultiFrameFiles)
- def testFiles(self):
- gdcmTestCase._BaseTest(self, gdcmTestCase.GdcmFiles)
+ def testFiles(self):
+ gdcmTestCase._BaseTest(self, gdcmTestCase.GdcmFiles)
- def testJpeg(self):
- gdcmTestCase._BaseTest(self, gdcmTestCase.GdcmJpegFiles)
+ def testJpeg(self):
+ gdcmTestCase._BaseTest(self, gdcmTestCase.GdcmJpegFiles)
+
+ def testWrite(self):
+ import md5
+ SourceFileName = os.path.join(GDCM_DATA_PATH,
+ 'gdcm-MR-PHILIPS-16-Multi-Seq.dcm')
+ Source = gdcmFile(SourceFileName);
+ Source.GetImageData()
+ TargetFileName = "junk"
+ Target = Source.WriteDcm(TargetFileName)
+ Sign = 'c7d6bedae1bef3851f35b29952fbbd4b'
+ ComputeSign = md5.new(open(TargetFileName).read()).hexdigest()
+ #print ComputeSign
+ self.assertEqual(ComputeSign, Sign,
+ ("Wrong signature for file %s (got %s, shoud be %s)"
+ % (SourceFileName, ComputeSign, Sign)) )
if __name__ == '__main__':
- unittest.main()
+ unittest.main()
}
}
-gdcmElValue* gdcmElValSet::GetElementByNumber(guint32 group, guint32 element) {
+gdcmElValue* gdcmElValSet::GetElementByNumber(guint16 group, guint16 element) {
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHt.count(key))
return (gdcmElValue*)0;
- if (tagHt.count(key) > 1)
- dbg.Verbose(0, "gdcmElValSet::GetElementByNumber",
- "multiple entries for this key (FIXME) !");
return tagHt.find(key)->second;
}
gdcmElValue* gdcmElValSet::GetElementByName(string TagName) {
if ( ! NameHt.count(TagName))
return (gdcmElValue*)0;
- if (NameHt.count(TagName) > 1)
- dbg.Verbose(0, "gdcmElValSet::GetElement",
- "multipe entries for this key (FIXME) !");
return NameHt.find(TagName)->second;
}
-string gdcmElValSet::GetElValueByNumber(guint32 group, guint32 element) {
+string gdcmElValSet::GetElValueByNumber(guint16 group, guint16 element) {
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHt.count(key))
return "gdcm::Unfound";
- if (tagHt.count(key) > 1)
- dbg.Verbose(0, "gdcmElValSet::GetElValueByNumber",
- "multiple entries for this key (FIXME) !");
return tagHt.find(key)->second->GetValue();
}
string gdcmElValSet::GetElValueByName(string TagName) {
if ( ! NameHt.count(TagName))
return "gdcm::Unfound";
- if (NameHt.count(TagName) > 1)
- dbg.Verbose(0, "gdcmElValSet::GetElValue",
- "multipe entries for this key (FIXME) !");
return NameHt.find(TagName)->second->GetValue();
}
int gdcmElValSet::SetElValueByNumber(string content,
- guint32 group, guint32 element) {
-
-// TODO : comprendre pourquoi ils sont déclares comme des guint32, alors que c'est des guint16
-
+ guint16 group, guint16 element) {
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHt.count(key))
return 0;
- if (tagHt.count(key) > 1) {
- dbg.Verbose(0, "gdcmElValSet::SetElValueByNumber",
- "multiple entries for this key (FIXME) !");
- return (0);
- }
-
tagHt[key]->SetValue(content);
-
- // Question : m à j LgrElem ?
- tagHt[key]->SetLength(strlen(content.c_str()));
-
- // FIXME should we really update the element length ?
tagHt[key]->SetLength(content.length());
-
- return(1);
+ return 1;
}
int gdcmElValSet::SetElValueByName(string content, string TagName) {
if ( ! NameHt.count(TagName))
return 0;
- if (NameHt.count(TagName) > 1) {
- dbg.Verbose(0, "gdcmElValSet::SetElValueByName",
- "multipe entries for this key (FIXME) !");
- return 0;
- }
- NameHt.find(TagName)->second->SetValue(content);
- NameHt.find(TagName)->second->SetLength(strlen(content.c_str()));
- return(1);
+ NameHt[TagName]->SetValue(content);
+ NameHt[TagName]->SetLength(content.length());
+ return 1;
}
/**
- * \ingroup gdcmElValSet
- * \brief Generate a free TagKey i.e. a TagKey that is not present
- * in the TagHt dictionary. One of the potential usage is
- * to add gdcm generated additional informartion to the ElValSet
- * (see gdcmHeader::AddAndDefaultElements).
- * @param group The generated tag must belong to this group.
- * @return The element of tag with given group which is fee.
+ * \ingroup gdcmElValSet
+ * \brief Generate a free TagKey i.e. a TagKey that is not present
+ * in the TagHt dictionary.
+ * @param group The generated tag must belong to this group.
+ * @return The element of tag with given group which is fee.
*/
-guint32 gdcmElValSet::GenerateFreeTagKeyInGroup(guint32 group) {
+guint32 gdcmElValSet::GenerateFreeTagKeyInGroup(guint16 group) {
for (guint32 elem = 0; elem < UINT32_MAX; elem++) {
TagKey key = gdcmDictEntry::TranslateToKey(group, elem);
if (tagHt.count(key) == 0)
return UINT32_MAX;
}
-int gdcmElValSet::SetElValueLengthByNumber(guint32 l,
- guint32 group, guint32 element) {
+int gdcmElValSet::SetElValueLengthByNumber(guint32 length,
+ guint16 group, guint16 element) {
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHt.count(key))
return 0;
- tagHt[key]->SetLength(l);
+ tagHt[key]->SetLength(length);
return 1 ;
}
-int gdcmElValSet::SetElValueLengthByName(guint32 l, string TagName) {
+int gdcmElValSet::SetElValueLengthByName(guint32 length, string TagName) {
if ( ! NameHt.count(TagName))
return 0;
- NameHt.find(TagName)->second->SetLength(l);
+ NameHt.find(TagName)->second->SetLength(length);
return 1 ;
}
-// Sorry for the DEBUG's, but tomorow is gonna be hoter than today
-
-int gdcmElValSet::Write(FILE * _fp) {
-
- guint16 gr, el;
- guint32 lgr;
- const char * val;
- string vr;
- guint32 val_uint32;
- guint16 val_uint16;
-
- vector<string> tokens;
-
- void *ptr;
-
- string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
-
- // Utilisées pour le calcul Group Length
- guint32 lgrCalcGroupe=0;
- gdcmElValue *elem, *elemZ, *elemZPrec;
- guint16 grCourant = 0;
-
- // Question :
- // Comment pourrait-on tester si on est TrueDicom ou non ,
- // (FileType est un champ de gdcmHeader ...)
- //
-
+void gdcmElValSet::UpdateGroupLength(bool SkipSequence) {
// On parcourt la table pour recalculer la longueur des 'elements 0x0000'
// au cas ou un tag ai été ajouté par rapport à ce qui a été lu
// dans l'image native
// On fait de l'implicit VR little Endian
// (pour moins se fairche sur processeur INTEL)
// On force le TRANSFERT SYNTAX UID
+ guint16 gr, el;
+ string vr;
+ guint32 lgrCalcGroupe=0;
+ gdcmElValue *elem, *elemZ, *elemZPrec;
+ guint16 grCourant = 0;
- SetElValueByNumber(implicitVRTransfertSyntax, 0x0002, 0x0010);
- SetElValueLengthByNumber(18, 0x0002, 0x0010); // Le 0 de fin de chaine doit etre stocké, dans ce cas
-
TagElValueHT::iterator tag = tagHt.begin();
elem = tag->second;
elem = tag->second;
gr = elem->GetGroup();
el = elem->GetElement();
-
+ vr = elem->GetVR();
+
+ if (SkipSequence && vr == "SQ")
+ // pas SEQUENCE en ACR-NEMA
+ // WARNING : risque de pb
+ // si on est descendu 'a l'interieur' des SQ
+ continue;
+ //
+ //
if ( (gr != grCourant) /*&& // On arrive sur un nv Groupe
(el != 0xfffe) */ ) {
elem->GetLength(), el, lgrCalcGroupe, gr);
}
}
+}
+
+void gdcmElValSet::WriteElements(FileType type, FILE * _fp) {
+ guint16 gr, el;
+ guint32 lgr;
+ const char * val;
+ string vr;
+ guint32 val_uint32;
+ guint16 val_uint16;
+
+ vector<string> tokens;
+
+ void *ptr;
+
+ for (TagElValueHT::iterator tag2 = tagHt.begin();
+ tag2 != tagHt.end();
+ ++tag2){
+
+ gr = tag2->second->GetGroup();
+ el = tag2->second->GetElement();
+ lgr = tag2->second->GetLength();
+ val = tag2->second->GetValue().c_str();
+ vr = tag2->second->GetVR();
+ if(DEBUG)printf ("%04x %04x [%s] : [%s]\n",gr, el, vr.c_str(), val);
+
+ if ( type == ACR ) {
+ if (gr < 0x0008) continue;
+ if (gr %2) continue;
+ if (vr == "SQ" ) continue;
+ }
+
+
+ fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
+ fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
+
+ if ( (type == ExplicitVR) && (gr <= 0x0002) ) {
+ // On est en EXPLICIT VR
+ guint16 z=0, shortLgr;
+ fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
+
+ if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) {
+ fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
+ fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
+
+ } else {
+ shortLgr=lgr;
+ fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
+ }
+ } else {
+ fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
+ }
+
+ tokens.erase(tokens.begin(),tokens.end());
+ Tokenize (tag2->second->GetValue(), tokens, "\\");
+
+ if (vr == "US" || vr == "SS") {
+ for (unsigned int i=0; i<tokens.size();i++) {
+ val_uint16 = atoi(tokens[i].c_str());
+ ptr = &val_uint16;
+ fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
+ }
+ continue;
+ }
+ if (vr == "UL" || vr == "SL") {
+ for (unsigned int i=0; i<tokens.size();i++) {
+ val_uint32 = atoi(tokens[i].c_str());
+ ptr = &val_uint32;
+ fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
+ }
+ continue;
+ }
+
+ // Les pixels ne sont pas chargés dans l'element !
+ if ((gr == 0x7fe0) && (el == 0x0010) ) break;
+
+ fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); //valeur Elem
+ }
+}
+
+// Sorry for the DEBUG's, but tomorow is gonna be hoter than today
+
+int gdcmElValSet::Write(FILE * _fp) {
+
+ guint16 gr, el;
+ guint32 lgr;
+ const char * val;
+ string vr;
+ guint32 val_uint32;
+ guint16 val_uint16;
+ vector<string> tokens;
+
+ void *ptr;
+
+ string implicitVRTransfertSyntax = "1.2.840.10008.1.2";
+ SetElValueByNumber(implicitVRTransfertSyntax, 0x0002, 0x0010);
+ //FIXME Refer to standards on page 21, chapter 6.2 "Value representation":
+ // values with a VR of UI shall be padded with a single trailing null
+ // Dans le cas suivant on doit pader manuellement avec un 0.
+ SetElValueLengthByNumber(18, 0x0002, 0x0010);
+
+ // Question :
+ // Comment pourrait-on tester si on est TrueDicom ou non ,
+ // (FileType est un champ de gdcmHeader ...)
+ //
+ UpdateGroupLength();
+
// restent à tester les echecs en écriture (apres chaque fwrite)
for (TagElValueHT::iterator tag2 = tagHt.begin();
fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
- //fwrite ( vr,(size_t)2 ,(size_t)1 ,_fp); //VR
-
// si on n'est pas en IMPLICIT VR voir pb (lgr + VR)
fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); //lgr
tokens.erase(tokens.begin(),tokens.end());
Tokenize (tag2->second->GetValue(), tokens, "\\");
- //if (tokens.size() > 1) { printf ("size : %d\n",tokens.size());}
-
if (vr == "US" || vr == "SS") {
for (unsigned int i=0; i<tokens.size();i++) {
val_uint16 = atoi(tokens[i].c_str());
void *ptr;
//string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; // supprime par rapport à Write
-
- // Utilisées pour le calcul Group Length
+ //CLEANME Utilisées pour le calcul Group Length
+ //CLEANMEguint32 lgrCalcGroupe=0;
+ //CLEANMEgdcmElValue *elem, *elemZ, *elemZPrec;
+ //CLEANMEguint16 grCourant = 0;
+
+ // Question :
+ // Comment pourrait-on tester si on est TrueDicom ou non ,
+ // (FileType est un champ de gdcmHeader ...)
+ //
+ UpdateGroupLength(true);
- guint32 lgrCalcGroupe=0;
- gdcmElValue *elem, *elemZ, *elemZPrec;
- guint16 grCourant = 0;
-
- // On parcourt la table pour recalculer la longueur des 'elements 0x0000'
- // au cas ou un tag ai été ajouté par rapport à ce qui a été lu
- // dans l'image native
- //
- // cf : code IdDcmWriteFile dans libido/src/dcmwrite.c
-
- TagElValueHT::iterator tag = tagHt.begin();
-
- elem = tag->second;
- gr = elem->GetGroup();
- el = elem->GetElement();
-
- if (el != 0x0000) {
- if(DEBUG)printf("ajout elem OOOO premiere fois\n");
- gdcmDictEntry * tagZ = new gdcmDictEntry(gr, 0x0000, "UL");
- elemZPrec = new gdcmElValue(tagZ); // on le cree
- elemZPrec->SetLength(4);
- Add(elemZPrec); // On l'accroche à sa place
- } else {
- elemZPrec = elem;
- if(DEBUG)printf("Pas d'ajout elem OOOO premiere fois\n");
- }
- lgrCalcGroupe = 0;
- if(DEBUG)printf("init-1 lgr (%d) pour gr %04x\n",lgrCalcGroupe, gr);
- grCourant = gr;
-
- for (tag = ++tagHt.begin();
- tag != tagHt.end();
- ++tag){
-
- elem = tag->second;
- gr = elem->GetGroup();
- el = elem->GetElement();
- vr = elem->GetVR();
-
- if (vr == "SQ") continue; // pas SEQUENCE en ACR-NEMA
- // WARNING : risque de pb
- // si on est descendu 'a l'interieur' des SQ
-
- if ( (gr != grCourant) /*&& // On arrive sur un nv Groupe
- (el != 0xfffe) */ ) {
-
- if (el != 0x0000) {
- gdcmDictEntry * tagZ = new gdcmDictEntry(gr, 0x0000, "UL");
- elemZ = new gdcmElValue(tagZ); // on le cree
- elemZ->SetLength(4);
- Add(elemZ); // On l'accroche à sa place
- if(DEBUG)printf("ajout elem OOOO pour gr %04x\n",gr);
- } else {
- elemZ=elem;
- if(DEBUG)printf("maj elmeZ\n");
- }
-
- ostringstream f;
- f << lgrCalcGroupe;
- elemZPrec->SetValue(f.str());
- if(DEBUG)printf("ecriture lgr (%d, %s) pour gr %04x\n",lgrCalcGroupe, f.str().c_str(), grCourant);
- if(DEBUG)printf ("%04x %04x [%s]\n",elemZPrec->GetGroup(), elemZPrec->GetElement(),
- elemZPrec->GetValue().c_str());
- if(DEBUG)cout << "Addresse elemZPrec " << elemZPrec<< endl;
- elemZPrec=elemZ;
- lgrCalcGroupe = 0;
- grCourant = gr;
- if(DEBUG)printf("init-2 lgr (%d) pour gr %04x\n",lgrCalcGroupe, gr);
- } else { // On n'EST PAS sur un nv Groupe
- lgrCalcGroupe += 2 + 2 + 4 + elem->GetLength(); // Gr + Num + Lgr + LgrElem
- if(DEBUG)printf("increment (%d) el %04x-->lgr (%d) pour gr %04x\n",elem->GetLength(), el,
- lgrCalcGroupe, gr);
- }
- }
-
// Si on fait de l'implicit VR little Endian
// (pour moins se fairche sur processeur INTEL)
// penser a forcer le TRANSFERT SYNTAX UID
string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
- // Utilisées pour le calcul Group Length
- guint32 lgrCalcGroupe=0;
- gdcmElValue *elem, *elemZ, *elemZPrec;
- guint16 grCourant = 0;
// Question :
// Comment pourrait-on tester si on est TrueDicom ou non ,
// (FileType est un champ de gdcmHeader ...)
//
- // On parcourt la table pour recalculer la longueur des 'elements 0x0000'
- // au cas ou un tag ai été ajouté par rapport à ce qui a été lu
- // dans l'image native
- //
- // cf : code IdDcmWriteFile dans libido/src/dcmwrite.c
-
-
// On fait de l'Explicit VR little Endian
SetElValueByNumber(explicitVRTransfertSyntax, 0x0002, 0x0010);
SetElValueLengthByNumber(20, 0x0002, 0x0010); // Le 0 de fin de chaine doit etre stocké, dans ce cas // ???
- TagElValueHT::iterator tag = tagHt.begin();
-
- elem = tag->second;
- gr = elem->GetGroup();
- el = elem->GetElement();
-
- if (el != 0x0000) {
- if(DEBUG)printf("ajout elem OOOO premiere fois\n");
- gdcmDictEntry * tagZ = new gdcmDictEntry(gr, 0x0000, "UL");
- elemZPrec = new gdcmElValue(tagZ); // on le cree
- elemZPrec->SetLength(4);
- Add(elemZPrec); // On l'accroche à sa place
- } else {
- elemZPrec = elem;
- if(DEBUG)printf("Pas d'ajout elem OOOO premiere fois\n");
- }
- lgrCalcGroupe = 0;
- if(DEBUG)printf("init-1 lgr (%d) pour gr %04x\n",lgrCalcGroupe, gr);
- grCourant = gr;
-
- for (tag = ++tagHt.begin();
- tag != tagHt.end();
- ++tag){
-
- elem = tag->second;
- gr = elem->GetGroup();
- el = elem->GetElement();
+ // Question :
+ // Comment pourrait-on tester si on est TrueDicom ou non ,
+ // (FileType est un champ de gdcmHeader ...)
+ //
+ UpdateGroupLength();
- if ( (gr != grCourant) /*&& // On arrive sur un nv Groupe
- (el != 0xfffe) */ ) {
-
- if (el != 0x0000) {
- gdcmDictEntry * tagZ = new gdcmDictEntry(gr, 0x0000, "UL");
- elemZ = new gdcmElValue(tagZ); // on le cree
- elemZ->SetLength(4);
- Add(elemZ); // On l'accroche à sa place
- if(DEBUG)printf("ajout elem OOOO pour gr %04x\n",gr);
- } else {
- elemZ=elem;
- if(DEBUG)printf("maj elemZ\n");
- }
-
- ostringstream f;
- f << lgrCalcGroupe;
- //sprintf(str_lgrCalcGroupe,"%d",lgrCalcGroupe);
- elemZPrec->SetValue(f.str());
- if(DEBUG)printf("ecriture lgr (%d, %s) pour gr %04x\n",lgrCalcGroupe, f.str().c_str(), grCourant);
- if(DEBUG)printf ("%04x %04x [%s]\n",elemZPrec->GetGroup(), elemZPrec->GetElement(),
- elemZPrec->GetValue().c_str());
- if(DEBUG)cout << "Addresse elemZPrec " << elemZPrec<< endl;
- elemZPrec=elemZ;
- lgrCalcGroupe = 0;
- grCourant = gr;
- if(DEBUG)printf("init-2 lgr (%d) pour gr %04x\n",lgrCalcGroupe, gr);
- } else { // On n'EST PAS sur un nv Groupe
- lgrCalcGroupe += 2 + 2 + 4 + elem->GetLength(); // Gr + Num + Lgr + LgrElem
- if(DEBUG)printf("increment (%d) el %04x-->lgr (%d) pour gr %04x\n",elem->GetLength(),
- el, lgrCalcGroupe, gr);
- }
- }
// restent à tester les echecs en écriture (apres chaque fwrite)
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff