Question

我正在使用Ubuntu 14上的Python 2.7来解压缩我要解压缩的DICOM图像。我正在使用gdcm，我在this link之后安装了sudo apt-get install python-gdcm（import gdcm import sys if __name__ == "__main__": file1 = sys.argv[1] file2 = sys.argv[2] r = gdcm.ImageReader() r.SetFileName(cin) if not r.Read(): sys.exit(1) image = gdcm.Image() ir = r.GetImage() image.SetNumberOfDimensions( ir.GetNumberOfDimensions() ); dims = ir.GetDimensions(); print ir.GetDimension(0); print ir.GetDimension(1); print "Dims:",dims image.SetDimension(0, ir.GetDimension(0) ); image.SetDimension(1, ir.GetDimension(1) ); pixeltype = ir.GetPixelFormat(); image.SetPixelFormat( pixeltype ); pi = ir.GetPhotometricInterpretation(); image.SetPhotometricInterpretation( pi ); pixeldata = gdcm.DataElement( gdcm.Tag(0x7fe0,0x0010) ) str1 = ir.GetBuffer() #print ir.GetBufferLength() pixeldata.SetByteValue( str1, gdcm.VL( len(str1) ) ) image.SetDataElement( pixeldata ) w = gdcm.ImageWriter() w.SetFileName(path_save+"uncompressed.png") w.SetFile( r.GetFile() ) w.SetImage( image ) if not w.Write(): sys.exit(1)）

我正在使用this example解压缩图像（当我尝试打开它时，至少ImageJ将其称为“压缩的dicom图像”），但是我得到了一个我无法解决的错误。代码如下（它只是链接中的示例）

print dims

在w.SetImage(image)标记程序中确实打印出正确的图像尺寸。但是当它达到Warning: In /build/gdcm-uIgnvq/gdcm-2.6.3/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx, line 205, function void gdcm::Overlay::Update(const gdcm::DataElement&) Warning: In /build/gdcm-uIgnvq/gdcm-2.6.3/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx, line 544, function bool gdcm::DoOverlays(const gdcm::DataSet&, gdcm::Pixmap&) Bits Allocated are wrong. Correcting. Error: In /build/gdcm-uIgnvq/gdcm-2.6.3/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx, line 265, function bool gdcm::Overlay::GrabOverlayFromPixelData(const gdcm::DataSet&) Could not find Pixel Data. Cannot extract Overlay. Warning: In /build/gdcm-uIgnvq/gdcm-2.6.3/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx, line 550, function bool gdcm::DoOverlays(const gdcm::DataSet&, gdcm::Pixmap&) Could not extract Overlay from Pixel Data Warning: In /build/gdcm-uIgnvq/gdcm-2.6.3/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx, line 575, function bool gdcm::DoOverlays(const gdcm::DataSet&, gdcm::Pixmap&) Invalid BitPosition: 0 for overlay #0 removing it. python2.7: /build/gdcm-uIgnvq/gdcm-2.6.3/Source/Common/gdcmObject.h:58: virtual gdcm::Object::~Object(): Assertion `ReferenceCount == 0' failed.时，我收到一个错误，我也收到了一堆警告：

{{1}}

此示例仅适用于某些类型的图像吗？或者我错过了什么？

Answer 1

由于您尝试使用python简单地解压缩图像，为什么不简单地使用它：

import gdcm
import sys

if __name__ == "__main__":
  file1 = sys.argv[1] # input filename
  file2 = sys.argv[2] # output filename

  reader = gdcm.ImageReader()
  reader.SetFileName( file1 )

  if not reader.Read():
    sys.exit(1)

  change = gdcm.ImageChangeTransferSyntax()
  change.SetTransferSyntax( gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian) )
  change.SetInput( reader.GetImage() )
  if not change.Change():
    sys.exit(1)

  writer = gdcm.ImageWriter()
  writer.SetFileName( file2 )
  writer.SetFile( reader.GetFile() )
  writer.SetImage( change.GetOutput() )

  if not writer.Write():
    sys.exit(1)

使用时：

$ python decompress.py gdcm/Testing/Data/012345.002.050.dcm raw.dcm

这导致：

$ gdcminfo raw.dcm 
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2 [Implicit VR Little Endian: Default Transfer Syntax for DICOM]
NumberOfDimensions: 2
Dimensions: (256,256,1)
SamplesPerPixel    :1
BitsAllocated      :16
BitsStored         :16
HighBit            :15
PixelRepresentation:1
ScalarType found   :INT16
PhotometricInterpretation: MONOCHROME2 
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2
Origin: (-85,21.6,108.7)
Spacing: (0.664062,0.664062,1.5)
DirectionCosines: (1,0,0,0,0,-1)
Rescale Intercept/Slope: (0,1)
Orientation Label: CORONAL

更新，似乎是最初的错误

gdcmObject.h：58：virtual gdcm :: Object :: ~Object（）：断言 `ReferenceCount == 0'失败。

已在上游解决：

Fix an issue with SmartPointer of an Image in Python

如何使用gdcm和Python解压缩压缩的DICOM图像？

1 个答案: