GDCM: several improvements
- fixed width and height order - removed unused methods - simplified signature matching - rewrote pixel format matching in more compact form - added dimensions number check (only 2 is allowed) - added target buffer size check - added debug messages in all failing points
This commit is contained in:
Maksim Shabunin
parent
0fd0acf2e3
commit
f3bd508e6d
@ -45,8 +45,19 @@
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#ifdef HAVE_GDCM
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//#define DBG(...) printf(__VA_ARGS__)
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#define DBG(...)
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#include <gdcmImageReader.h>
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static const size_t preamble_skip = 128;
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static const size_t magic_len = 4;
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inline cv::String getMagic()
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{
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return cv::String("\x44\x49\x43\x4D", 4);
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}
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namespace cv
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{
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@ -54,45 +65,22 @@ namespace cv
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DICOMDecoder::DICOMDecoder()
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{
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/// DICOM preable is 128 bytes (can have any vale, defaults to x00) + 4 bytes magic number (DICM)
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m_signature = "";
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for(int iSize=0; iSize<128; iSize++)
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{
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m_signature = m_signature + "\xFF";
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}
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m_signature = m_signature + "\x44\x49\x43\x4D";
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// DICOM preamble is 128 bytes (can have any value, defaults to 0) + 4 bytes magic number (DICM)
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m_signature = String(preamble_skip, (char)'\x0') + getMagic();
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m_buf_supported = false;
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}
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DICOMDecoder::~DICOMDecoder()
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{
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}
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bool DICOMDecoder::checkSignature( const String& signature ) const
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{
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size_t len = signatureLength();
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bool bOK = signature.size() >= len;
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for(int iIndex = 128; iIndex < len; iIndex++)
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if (signature.size() >= preamble_skip + magic_len)
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{
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if(signature[iIndex] == m_signature[iIndex])
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if (signature.substr(preamble_skip, magic_len) == getMagic())
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{
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continue;
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}
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else
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{
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bOK = false;
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break;
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return true;
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}
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}
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return(bOK);
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}
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void DICOMDecoder::close()
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{
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DBG("GDCM | Signature does not match\n");
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return false;
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}
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ImageDecoder DICOMDecoder::newDecoder() const
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@ -106,90 +94,66 @@ bool DICOMDecoder::readHeader()
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csImageReader.SetFileName(m_filename.c_str());
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if(!csImageReader.Read())
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{
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DBG("GDCM | Failed to open DICOM file\n");
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return(false);
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}
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bool bOK = true;
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const gdcm::Image &csImage = csImageReader.GetImage();
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if( ( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 )
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|| ( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2 )
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)
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bool bOK = true;
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switch (csImage.GetPhotometricInterpretation().GetType())
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{
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gdcm::PixelFormat ePixelFormat = csImage.GetPixelFormat();
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if( ePixelFormat == gdcm::PixelFormat::INT8)
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case gdcm::PhotometricInterpretation::MONOCHROME1:
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case gdcm::PhotometricInterpretation::MONOCHROME2:
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{
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m_type = CV_8SC1;
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switch (csImage.GetPixelFormat().GetScalarType())
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{
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case gdcm::PixelFormat::INT8: m_type = CV_8SC1; break;
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case gdcm::PixelFormat::UINT8: m_type = CV_8UC1; break;
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case gdcm::PixelFormat::INT16: m_type = CV_16SC1; break;
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case gdcm::PixelFormat::UINT16: m_type = CV_16UC1; break;
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case gdcm::PixelFormat::INT32: m_type = CV_32SC1; break;
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case gdcm::PixelFormat::FLOAT32: m_type = CV_32FC1; break;
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case gdcm::PixelFormat::FLOAT64: m_type = CV_64FC1; break;
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default: bOK = false; DBG("GDCM | Monochrome scalar type not supported\n"); break;
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}
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break;
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}
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else if( ePixelFormat == gdcm::PixelFormat::UINT8)
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case gdcm::PhotometricInterpretation::RGB:
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{
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m_type = CV_8UC1;
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switch (csImage.GetPixelFormat().GetScalarType())
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{
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case gdcm::PixelFormat::UINT8: m_type = CV_8UC3; break;
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default: bOK = false; DBG("GDCM | RGB scalar type not supported\n"); break;
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}
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break;
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}
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else if( ePixelFormat == gdcm::PixelFormat::INT16)
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{
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m_type = CV_16SC1;
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}
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else if( ePixelFormat == gdcm::PixelFormat::UINT16)
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{
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m_type = CV_16UC1;
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}
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else if( ePixelFormat == gdcm::PixelFormat::INT32)
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{
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m_type = CV_32SC1;
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}
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else if( ePixelFormat == gdcm::PixelFormat::FLOAT32)
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{
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m_type = CV_32FC1;
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}
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else if( ePixelFormat == gdcm::PixelFormat::FLOAT64)
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{
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m_type = CV_64FC1;
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}
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else if( ePixelFormat == gdcm::PixelFormat::INT12)
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default:
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{
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bOK = false;
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DBG("GDCM | PI not supported: %s\n", csImage.GetPhotometricInterpretation().GetString());
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break;
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}
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else if( ePixelFormat == gdcm::PixelFormat::UINT12)
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{
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bOK = false;
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}
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else if( ePixelFormat == gdcm::PixelFormat::UINT32)
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{
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bOK = false;
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}
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else if( ePixelFormat == gdcm::PixelFormat::SINGLEBIT)
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{
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bOK = false;
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}
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else
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{
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bOK = false;
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}
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}
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else if( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB )
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{
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gdcm::PixelFormat ePixelFormat = csImage.GetPixelFormat();
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if( ePixelFormat == gdcm::PixelFormat::UINT8)
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{
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m_type = CV_8UC3;
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}
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else
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{
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bOK = false;
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}
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}
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else
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{
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bOK = false;
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}
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if(bOK)
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{
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unsigned int ndim = csImage.GetNumberOfDimensions();
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if (ndim != 2)
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{
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DBG("GDCM | Invalid dimensions number: %d\n", ndim);
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bOK = false;
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}
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}
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if (bOK)
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{
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const unsigned int *piDimension = csImage.GetDimensions();
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m_width = piDimension[0];
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m_height = piDimension[1];
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m_height = piDimension[0];
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m_width = piDimension[1];
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if( ( m_width <=0 ) || ( m_height <=0 ) )
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{
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DBG("GDCM | Invalid dimensions: %d x %d\n", piDimension[0], piDimension[1]);
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bOK = false;
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}
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}
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@ -206,15 +170,28 @@ bool DICOMDecoder::readData( Mat& csImage )
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csImageReader.SetFileName(m_filename.c_str());
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if(!csImageReader.Read())
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{
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return(false);
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DBG("GDCM | Failed to Read\n");
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return false;
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}
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bool bOK = true;
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const gdcm::Image &csGDCMImage = csImageReader.GetImage();
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bOK = csGDCMImage.GetBuffer((char*)csImage.ptr());
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const gdcm::Image &img = csImageReader.GetImage();
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return(bOK);
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}
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unsigned long len = img.GetBufferLength();
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if (len > csImage.elemSize() * csImage.total())
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{
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DBG("GDCM | Buffer is bigger than Mat: %ld > %ld * %ld\n", len, csImage.elemSize(), csImage.total());
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return false;
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}
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if (!img.GetBuffer((char*)csImage.ptr()))
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{
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DBG("GDCM | Failed to GetBuffer\n");
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return false;
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}
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DBG("GDCM | Read OK\n");
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return true;
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}
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#endif
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}
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#endif // HAVE_GDCM
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@ -56,22 +56,15 @@ namespace cv
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class DICOMDecoder : public BaseImageDecoder
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{
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public:
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DICOMDecoder();
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~DICOMDecoder();
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bool readData( Mat& img );
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bool readHeader();
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void close();
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ImageDecoder newDecoder() const;
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virtual bool checkSignature( const String& signature ) const;
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protected:
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};
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}
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#endif
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#endif // HAVE_GDCM
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#endif/*_GDCM_DICOM_H_*/
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