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itkGDCMImageIO.cxx
1660 lines (1515 loc) · 53 KB
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itkGDCMImageIO.cxx
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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
/*=========================================================================
*
* Portions of this file are subject to the VTK Toolkit Version 3 copyright.
*
* Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
*
* For complete copyright, license and disclaimer of warranty information
* please refer to the NOTICE file at the top of the ITK source tree.
*
*=========================================================================*/
#include "itkVersion.h"
#include "itkGDCMImageIO.h"
#include "itkIOCommon.h"
#include "itkArray.h"
#include "itkByteSwapper.h"
#include "vnl/vnl_cross.h"
#include "itkMetaDataObject.h"
#include "itksys/SystemTools.hxx"
#include "itksys/Base64.h"
#include "itkMakeUniqueForOverwrite.h"
#include "gdcmImageHelper.h"
#include "gdcmFileExplicitFilter.h"
#include "gdcmImageChangeTransferSyntax.h"
#include "gdcmImageChangePhotometricInterpretation.h"
#include "gdcmDataSetHelper.h"
#include "gdcmStringFilter.h"
#include "gdcmImageApplyLookupTable.h"
#include "gdcmImageChangePlanarConfiguration.h"
#include "gdcmRescaler.h"
#include "gdcmImageReader.h"
#include "gdcmImageWriter.h"
#include "gdcmUIDGenerator.h"
#include "gdcmAttribute.h"
#include "gdcmGlobal.h"
#include "gdcmMediaStorage.h"
#include "gdcmDirectionCosines.h"
#include <fstream>
#include <sstream>
namespace itk
{
class InternalHeader
{
public:
InternalHeader() = default;
~InternalHeader() { delete m_Header; }
gdcm::File * m_Header{ nullptr };
};
GDCMImageIO::GDCMImageIO()
{
this->m_DICOMHeader = new InternalHeader;
this->SetNumberOfDimensions(3); // needed for getting the 3 coordinates of
// the origin, even if it is a 2D slice.
m_ByteOrder = IOByteOrderEnum::LittleEndian; // default
m_FileType = IOFileEnum::Binary; // default...always true
m_RescaleSlope = 1.0;
m_RescaleIntercept = 0.0;
// UIDPrefix is the ITK root id tacked with a ".1"
// allowing to designate a subspace of the id space for ITK generated DICOM
m_UIDPrefix = "1.2.826.0.1.3680043.2.1125."
"1";
// Purely internal use, no user access:
m_StudyInstanceUID = "";
m_SeriesInstanceUID = "";
m_FrameOfReferenceInstanceUID = "";
m_KeepOriginalUID = false;
m_LoadPrivateTags = false;
m_ReadYBRtoRGB = true;
m_InternalComponentType = IOComponentEnum::UNKNOWNCOMPONENTTYPE;
// by default assume that images will be 2D.
// This number is updated according the information
// received through the MetaDataDictionary
m_GlobalNumberOfDimensions = 2;
m_SingleBit = false;
// By default use JPEG2000. For legacy system, one should prefer JPEG since
// JPEG2000 was only recently added to the DICOM standard
this->Self::SetCompressor("");
const char * extensions[] = { ".dcm", ".DCM", ".dicom", ".DICOM" };
for (auto ext : extensions)
{
this->AddSupportedWriteExtension(ext);
this->AddSupportedReadExtension(ext);
}
}
GDCMImageIO::~GDCMImageIO()
{
delete this->m_DICOMHeader;
}
/**
* Helper function to test for some dicom like formatting.
* @param file A stream to test if the file is dicom like
* @return true if the structure of the file is dicom like
*/
static bool
readNoPreambleDicom(std::ifstream & file) // NOTE: This file is duplicated in itkDCMTKImageIO.cxx
{
// Adapted from https://stackoverflow.com/questions/2381983/c-how-to-read-parts-of-a-file-dicom
/* This heuristic tries to determine if the file follows the basic structure of a dicom file organization.
* Any file that begins with the a byte sequence
* where groupNo matches below will be then read several SOP Instance sections.
*/
unsigned short groupNo = 0xFFFF;
unsigned short tagElementNo = 0xFFFF;
do
{
file.read(reinterpret_cast<char *>(&groupNo), sizeof(unsigned short));
ByteSwapper<unsigned short>::SwapFromSystemToLittleEndian(&groupNo);
file.read(reinterpret_cast<char *>(&tagElementNo), sizeof(unsigned short));
ByteSwapper<unsigned short>::SwapFromSystemToLittleEndian(&tagElementNo);
if (groupNo != 0x0002 && groupNo != 0x0008) // Only groupNo 2 & 8 are supported without preambles
{
return false;
}
char vrcode[3] = { '\0', '\0', '\0' };
file.read(vrcode, 2);
long length = std::numeric_limits<long>::max();
const std::string vr{ vrcode };
if (vr == "AE" || vr == "AS" || vr == "AT" || vr == "CS" || vr == "DA" || vr == "DS" || vr == "DT" || vr == "FL" ||
vr == "FD" || vr == "IS" || vr == "LO" || vr == "PN" || vr == "SH" || vr == "SL" || vr == "SS" || vr == "ST" ||
vr == "TM" || vr == "UI" || vr == "UL" || vr == "US")
{
// Explicit VR (value representation stored in the file)
unsigned short uslength = 0;
file.read(reinterpret_cast<char *>(&uslength), sizeof(unsigned short));
ByteSwapper<unsigned short>::SwapFromSystemToLittleEndian(&uslength);
length = uslength;
}
else
{
// Implicit VR (value representation not stored in the file)
char lengthChars[4] = { vrcode[0], vrcode[1], '\0', '\0' };
file.read(lengthChars + 2, 2);
auto * uilength = reinterpret_cast<unsigned int *>(lengthChars);
ByteSwapper<unsigned int>::SwapFromSystemToLittleEndian(uilength);
length = (*uilength);
}
if (length <= 0)
{
return false;
}
file.ignore(length);
if (file.eof())
{
return false;
}
} while (groupNo == 2);
#if defined(NDEBUG)
std::ostringstream itkmsg;
itkmsg << "No DICOM magic number found, but the file appears to be DICOM without a preamble.\n"
<< "Proceeding without caution.";
itk::OutputWindowDisplayDebugText(itkmsg.str().c_str());
#endif
return true;
}
static void
YCbCr_to_RGB(unsigned char * p, const size_t len)
{
for (size_t x = 0; x < len; x += 3)
{
const unsigned char in[] = { p[x], p[x + 1], p[x + 2] };
gdcm::ImageChangePhotometricInterpretation::YBR2RGB<unsigned char>(&p[x], in);
}
}
// This method will only test if the header looks like a
// GDCM image file.
bool
GDCMImageIO::CanReadFile(const char * filename)
{
std::ifstream file;
try
{
this->OpenFileForReading(file, filename);
}
catch (const ExceptionObject &)
{
return false;
}
//
// sniff for the DICM signature first at 128
// then at zero, and if either place has it then
// ask GDCM to try reading it.
//
// There isn't a definitive way to check for DICOM files;
// This was actually cribbed from DICOMParser in VTK
bool dicomsig(false);
for (long off = 128; off >= 0; off -= 128)
{
file.seekg(off, std::ios_base::beg);
if (file.fail() || file.eof())
{
return false;
}
char buf[5];
file.read(buf, 4);
if (file.fail())
{
return false;
}
buf[4] = '\0';
const std::string sig{ buf };
if (sig == "DICM")
{
dicomsig = true;
}
}
// Do not allow CanRead to return true for non-compliant DICOM files
#define GDCMPARSER_IGNORE_MAGIC_NUMBER
#if defined(GDCMPARSER_IGNORE_MAGIC_NUMBER)
//
// Try it anyways...
//
if (!dicomsig)
{
file.seekg(0, std::ios_base::beg);
dicomsig = readNoPreambleDicom(file);
}
#endif // GDCMPARSER_IGNORE_MAGIC_NUMBER
if (dicomsig)
{
// Check to see if its a valid dicom file gdcm is able to parse:
// We are parsing the header one time here:
gdcm::ImageReader reader;
reader.SetFileName(filename);
if (reader.Read())
{
return true;
}
}
return false;
}
void
GDCMImageIO::Read(void * pointer)
{
// ensure file can be opened for reading, before doing any more work
std::ifstream inputFileStream;
// let any exceptions propagate
this->OpenFileForReading(inputFileStream, m_FileName);
inputFileStream.close();
itkAssertInDebugAndIgnoreInReleaseMacro(gdcm::ImageHelper::GetForceRescaleInterceptSlope());
gdcm::ImageReader reader;
reader.SetFileName(m_FileName.c_str());
if (!reader.Read())
{
itkExceptionMacro(<< "Cannot read requested file");
}
gdcm::Image & image = reader.GetImage();
#ifndef NDEBUG
gdcm::PixelFormat pixeltype_debug = image.GetPixelFormat();
itkAssertInDebugAndIgnoreInReleaseMacro(image.GetNumberOfDimensions() == 2 || image.GetNumberOfDimensions() == 3);
#endif
SizeValueType len = image.GetBufferLength();
// Decompress the Pixel Data buffer.
if (image.GetTransferSyntax().IsEncapsulated())
{
gdcm::ImageChangeTransferSyntax icts;
icts.SetInput(image);
icts.SetTransferSyntax(gdcm::TransferSyntax::ImplicitVRLittleEndian);
if (!icts.Change())
{
itkExceptionMacro(<< "Failed to change to Implicit Transfer Syntax");
}
image = icts.GetOutput();
}
// I think ITK only allow RGB image by pixel (and not by plane)
if (image.GetPlanarConfiguration() == 1)
{
gdcm::ImageChangePlanarConfiguration icpc;
icpc.SetInput(image);
icpc.SetPlanarConfiguration(0);
if (!icpc.Change())
{
itkExceptionMacro(<< "Failed to change to Planar Configuration");
}
image = icpc.GetOutput();
}
gdcm::PhotometricInterpretation pi = image.GetPhotometricInterpretation();
if (m_SingleBit)
{
const size_t x = m_Dimensions[0] * m_Dimensions[1] * m_Dimensions[2];
if (x > len * 8)
{
itkExceptionMacro(<< "Failed to load SINGLEBIT image, buffer size " << len);
}
len = x;
}
else if (pi == gdcm::PhotometricInterpretation::PALETTE_COLOR)
{
gdcm::ImageApplyLookupTable ialut;
ialut.SetInput(image);
ialut.Apply();
image = ialut.GetOutput();
len *= 3;
}
else if (pi == gdcm::PhotometricInterpretation::MONOCHROME1)
{
// ITK does not carry color space associated with an image. It is pretty
// much assumed that scalar image is expressed in MONOCHROME2 (aka min-is-black)
gdcm::ImageChangePhotometricInterpretation icpi;
icpi.SetInput(image);
icpi.SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2);
if (!icpi.Change())
{
itkExceptionMacro(<< "Failed to change to Photometric Interpretation");
}
itkWarningMacro(<< "Converting from MONOCHROME1 to MONOCHROME2 may impact the meaning of DICOM attributes related "
"to pixel values.");
image = icpi.GetOutput();
}
if (!image.GetBuffer((char *)pointer))
{
itkExceptionMacro(<< "Failed to get the buffer!");
}
if (m_SingleBit)
{
const auto copy = make_unique_for_overwrite<unsigned char[]>(len);
unsigned char * t = reinterpret_cast<unsigned char *>(pointer);
size_t j = 0;
for (size_t i = 0; i < len / 8; ++i)
{
const unsigned char c = t[i];
copy[j + 0] = (c & 0x01) ? 255 : 0;
copy[j + 1] = (c & 0x02) ? 255 : 0;
copy[j + 2] = (c & 0x04) ? 255 : 0;
copy[j + 3] = (c & 0x08) ? 255 : 0;
copy[j + 4] = (c & 0x10) ? 255 : 0;
copy[j + 5] = (c & 0x20) ? 255 : 0;
copy[j + 6] = (c & 0x40) ? 255 : 0;
copy[j + 7] = (c & 0x80) ? 255 : 0;
j += 8;
}
memcpy((char *)pointer, copy.get(), len);
}
else
{
const gdcm::PixelFormat & pixeltype = image.GetPixelFormat();
#ifndef NDEBUG
// ImageApplyLookupTable is meant to change the pixel type for PALETTE_COLOR images
// (from single values to triple values per pixel)
if (pi != gdcm::PhotometricInterpretation::PALETTE_COLOR)
{
itkAssertInDebugAndIgnoreInReleaseMacro(pixeltype_debug == pixeltype);
}
#endif
if (m_RescaleSlope != 1.0 || m_RescaleIntercept != 0.0)
{
gdcm::Rescaler r;
r.SetIntercept(m_RescaleIntercept);
r.SetSlope(m_RescaleSlope);
r.SetPixelFormat(pixeltype);
gdcm::PixelFormat outputpt = r.ComputeInterceptSlopePixelType();
const auto copy = make_unique_for_overwrite<char[]>(len);
memcpy(copy.get(), (char *)pointer, len);
r.Rescale((char *)pointer, copy.get(), len);
// WARNING: sizeof(Real World Value) != sizeof(Stored Pixel)
len = len * outputpt.GetPixelSize() / pixeltype.GetPixelSize();
}
// Y'CbCr to RGB
// GDCM 3.0.3
const bool ybr =
m_NumberOfComponents == 3 &&
(pi == gdcm::PhotometricInterpretation::YBR_FULL || pi == gdcm::PhotometricInterpretation::YBR_FULL_422) &&
(pixeltype == gdcm::PixelFormat::UINT8 || pixeltype == gdcm::PixelFormat::INT8);
if (ybr && m_ReadYBRtoRGB)
{
if (len % 3 != 0)
{
itkExceptionMacro(<< "Buffer size " << len << " is not valid");
}
YCbCr_to_RGB(reinterpret_cast<unsigned char *>(pointer), static_cast<size_t>(len));
}
}
#ifndef NDEBUG
// \postcondition
// Now that len was updated (after unpacker 12bits -> 16bits, rescale...) ,
// can now check compat:
const SizeValueType numberOfBytesToBeRead = static_cast<SizeValueType>(this->GetImageSizeInBytes());
itkAssertInDebugAndIgnoreInReleaseMacro(numberOfBytesToBeRead == len); // programmer error
#endif
}
void
GDCMImageIO::InternalReadImageInformation()
{
// Reset, a user can re-use IO.
m_RescaleIntercept = 0.0;
m_RescaleSlope = 1.0;
m_SingleBit = false;
// ensure file can be opened for reading, before doing any more work
std::ifstream inputFileStream;
// let any exceptions propagate
this->OpenFileForReading(inputFileStream, m_FileName);
inputFileStream.close();
// In general this should be relatively safe to assume
gdcm::ImageHelper::SetForceRescaleInterceptSlope(true);
gdcm::ImageReader reader;
reader.SetFileName(m_FileName.c_str());
if (!reader.Read())
{
itkExceptionMacro(<< "Cannot read requested file");
}
const gdcm::Image & image = reader.GetImage();
const gdcm::File & f = reader.GetFile();
const gdcm::DataSet & ds = f.GetDataSet();
const unsigned int * dims = image.GetDimensions();
const gdcm::PixelFormat & pixeltype = image.GetPixelFormat();
switch (pixeltype)
{
case gdcm::PixelFormat::INT8:
m_InternalComponentType = IOComponentEnum::CHAR; // Is it signed char ?
break;
case gdcm::PixelFormat::UINT8:
m_InternalComponentType = IOComponentEnum::UCHAR;
break;
/* INT12 / UINT12 should not happen anymore in any modern DICOM */
case gdcm::PixelFormat::INT12:
m_InternalComponentType = IOComponentEnum::SHORT;
break;
case gdcm::PixelFormat::UINT12:
m_InternalComponentType = IOComponentEnum::USHORT;
break;
case gdcm::PixelFormat::INT16:
m_InternalComponentType = IOComponentEnum::SHORT;
break;
case gdcm::PixelFormat::UINT16:
m_InternalComponentType = IOComponentEnum::USHORT;
break;
// RT / SC have 32bits
case gdcm::PixelFormat::INT32:
m_InternalComponentType = IOComponentEnum::INT;
break;
case gdcm::PixelFormat::UINT32:
m_InternalComponentType = IOComponentEnum::UINT;
break;
// case gdcm::PixelFormat::FLOAT16: // TODO
case gdcm::PixelFormat::FLOAT32:
m_InternalComponentType = IOComponentEnum::FLOAT;
break;
case gdcm::PixelFormat::FLOAT64:
m_InternalComponentType = IOComponentEnum::DOUBLE;
break;
case gdcm::PixelFormat::SINGLEBIT:
m_SingleBit = true;
m_InternalComponentType = IOComponentEnum::UCHAR;
break;
default:
itkExceptionMacro("Unhandled PixelFormat: " << pixeltype);
}
gdcm::PixelFormat::ScalarType outputpt = pixeltype.GetScalarType();
if (!m_SingleBit)
{
m_RescaleIntercept = image.GetIntercept();
m_RescaleSlope = image.GetSlope();
if (m_RescaleSlope != 1.0 || m_RescaleIntercept != 0.0)
{
gdcm::Rescaler r;
r.SetIntercept(m_RescaleIntercept);
r.SetSlope(m_RescaleSlope);
r.SetPixelFormat(pixeltype);
outputpt = r.ComputeInterceptSlopePixelType();
}
if (pixeltype > outputpt)
{
itkAssertInDebugOrThrowInReleaseMacro("Pixel type larger than output type")
}
}
else
{
outputpt = gdcm::PixelFormat::UINT8;
}
m_ComponentType = IOComponentEnum::UNKNOWNCOMPONENTTYPE;
switch (outputpt)
{
case gdcm::PixelFormat::INT8:
m_ComponentType = IOComponentEnum::CHAR; // Is it signed char ?
break;
case gdcm::PixelFormat::UINT8:
m_ComponentType = IOComponentEnum::UCHAR;
break;
/* INT12 / UINT12 should not happen anymore in any modern DICOM */
case gdcm::PixelFormat::INT12:
m_ComponentType = IOComponentEnum::SHORT;
break;
case gdcm::PixelFormat::UINT12:
m_ComponentType = IOComponentEnum::USHORT;
break;
case gdcm::PixelFormat::INT16:
m_ComponentType = IOComponentEnum::SHORT;
break;
case gdcm::PixelFormat::UINT16:
m_ComponentType = IOComponentEnum::USHORT;
break;
// RT / SC have 32bits
case gdcm::PixelFormat::INT32:
m_ComponentType = IOComponentEnum::INT;
break;
case gdcm::PixelFormat::UINT32:
m_ComponentType = IOComponentEnum::UINT;
break;
// case gdcm::PixelFormat::FLOAT16: // TODO
case gdcm::PixelFormat::FLOAT32:
m_ComponentType = IOComponentEnum::FLOAT;
break;
case gdcm::PixelFormat::FLOAT64:
m_ComponentType = IOComponentEnum::DOUBLE;
break;
default:
itkExceptionMacro("Unhandled PixelFormat: " << outputpt);
}
m_NumberOfComponents = pixeltype.GetSamplesPerPixel();
const gdcm::PhotometricInterpretation & pi = image.GetPhotometricInterpretation();
if (pi == gdcm::PhotometricInterpretation::PALETTE_COLOR)
{
// PALETTE_COLOR is always expanded in RGB image
itkAssertInDebugAndIgnoreInReleaseMacro(m_NumberOfComponents == 1);
m_NumberOfComponents = 3;
}
if (m_NumberOfComponents == 1)
{
this->SetPixelType(IOPixelEnum::SCALAR);
}
else if (m_NumberOfComponents == 3)
{
// GDCM 3.0.3
const bool rgb_from_ybr =
m_ReadYBRtoRGB &&
(pi == gdcm::PhotometricInterpretation::YBR_FULL || pi == gdcm::PhotometricInterpretation::YBR_FULL_422) &&
(outputpt == gdcm::PixelFormat::UINT8 || outputpt == gdcm::PixelFormat::INT8);
const bool ybr_jp2 =
pi == gdcm::PhotometricInterpretation::YBR_ICT || pi == gdcm::PhotometricInterpretation::YBR_RCT;
const bool rgb = pi == gdcm::PhotometricInterpretation::RGB ||
pi == gdcm::PhotometricInterpretation::PALETTE_COLOR || rgb_from_ybr || ybr_jp2;
if (rgb)
{
this->SetPixelType(IOPixelEnum::RGB);
}
else
{
this->SetPixelType(IOPixelEnum::VECTOR);
}
}
else
{
this->SetPixelType(IOPixelEnum::VECTOR);
}
m_Dimensions[0] = dims[0];
m_Dimensions[1] = dims[1];
double spacing[3];
// FIXME
//
// This is a WORKAROUND for a bug in GDCM -- in
// ImageHeplper::GetSpacingTagFromMediaStorage it was not
// handling some MediaStorage types
// so we have to punt here.
gdcm::MediaStorage ms;
ms.SetFromFile(f);
switch (ms)
{
case gdcm::MediaStorage::HardcopyGrayscaleImageStorage:
case gdcm::MediaStorage::GEPrivate3DModelStorage:
case gdcm::MediaStorage::Philips3D:
case gdcm::MediaStorage::VideoEndoscopicImageStorage:
case gdcm::MediaStorage::UltrasoundMultiFrameImageStorage:
case gdcm::MediaStorage::UltrasoundImageStorage: // ??
case gdcm::MediaStorage::UltrasoundImageStorageRetired:
case gdcm::MediaStorage::UltrasoundMultiFrameImageStorageRetired:
{
std::vector<double> sp;
gdcm::Tag spacingTag(0x0028, 0x0030);
if (ds.FindDataElement(spacingTag) && !ds.GetDataElement(spacingTag).IsEmpty())
{
gdcm::DataElement de = ds.GetDataElement(spacingTag);
std::stringstream m_Ss;
gdcm::Element<gdcm::VR::DS, gdcm::VM::VM1_n> m_El;
const gdcm::ByteValue * bv = de.GetByteValue();
assert(bv);
std::string s = std::string(bv->GetPointer(), bv->GetLength());
m_Ss.str(s);
// Erroneous file CT-MONO2-8-abdo.dcm,
// The spacing is something like that [0.2\0\0.200000],
// TODO throw an exception that VM is not compatible.
m_El.SetLength(16);
m_El.Read(m_Ss);
assert(m_El.GetLength() == 2);
for (unsigned long i = 0; i < m_El.GetLength(); ++i)
{
sp.push_back(m_El.GetValue(i));
}
std::swap(sp[0], sp[1]);
assert(sp.size() == 2);
spacing[0] = sp[0];
spacing[1] = sp[1];
}
else
{
spacing[0] = 1.0;
spacing[1] = 1.0;
}
spacing[2] = 1.0; // punt?
}
break;
default:
{
const double * sp;
sp = image.GetSpacing();
spacing[0] = sp[0];
spacing[1] = sp[1];
spacing[2] = sp[2];
}
break;
}
const double * origin = image.GetOrigin();
for (unsigned int i = 0; i < 3; ++i)
{
m_Spacing[i] = spacing[i];
m_Origin[i] = origin[i];
}
if (image.GetNumberOfDimensions() == 3)
{
m_Dimensions[2] = dims[2];
}
else
{
m_Dimensions[2] = 1;
}
const double * dircos = image.GetDirectionCosines();
vnl_vector<double> rowDirection(3), columnDirection(3);
rowDirection[0] = dircos[0];
rowDirection[1] = dircos[1];
rowDirection[2] = dircos[2];
columnDirection[0] = dircos[3];
columnDirection[1] = dircos[4];
columnDirection[2] = dircos[5];
vnl_vector<double> sliceDirection = vnl_cross_3d(rowDirection, columnDirection);
// orthogonalize
sliceDirection.normalize();
rowDirection = vnl_cross_3d(columnDirection, sliceDirection).normalize();
columnDirection = vnl_cross_3d(sliceDirection, rowDirection);
this->SetDirection(0, rowDirection);
this->SetDirection(1, columnDirection);
this->SetDirection(2, sliceDirection);
// Now copying the gdcm dictionary to the itk dictionary:
MetaDataDictionary & dico = this->GetMetaDataDictionary();
// in the case of re-use by ImageSeriesReader, clear the dictionary
// before populating it.
dico.Clear();
gdcm::StringFilter sf;
sf.SetFile(f);
auto it = ds.Begin();
// Copy of the header->content
for (; it != ds.End(); ++it)
{
const gdcm::DataElement & ref = *it;
const gdcm::Tag & tag = ref.GetTag();
// Compute VR from the toplevel file, and the currently processed dataset:
gdcm::VR vr = gdcm::DataSetHelper::ComputeVR(f, ds, tag);
// Process binary field and encode them as mime64: only when we do not know
// of any better
// representation. VR::US is binary, but user want ASCII representation.
if (vr & (gdcm::VR::OB | gdcm::VR::OF | gdcm::VR::OW | gdcm::VR::SQ | gdcm::VR::UN))
{
// itkAssertInDebugAndIgnoreInReleaseMacro( vr & gdcm::VR::VRBINARY );
/*
* Old behavior was to skip SQ, Pixel Data element. I decided that it is not safe to mime64
* VR::UN element. There used to be a bug in gdcm 1.2.0 and VR:UN element.
*/
if ((m_LoadPrivateTags || tag.IsPublic()) && vr != gdcm::VR::SQ &&
tag != gdcm::Tag(0x7fe0, 0x0010) /* && vr != gdcm::VR::UN*/)
{
const gdcm::ByteValue * bv = ref.GetByteValue();
if (bv)
{
// base64 streams have to be a multiple of 4 bytes in length
int encodedLengthEstimate = 2 * bv->GetLength();
encodedLengthEstimate = ((encodedLengthEstimate / 4) + 1) * 4;
const auto bin = make_unique_for_overwrite<char[]>(encodedLengthEstimate);
auto encodedLengthActual =
static_cast<unsigned int>(itksysBase64_Encode((const unsigned char *)bv->GetPointer(),
static_cast<SizeValueType>(bv->GetLength()),
(unsigned char *)bin.get(),
0));
std::string encodedValue(bin.get(), encodedLengthActual);
EncapsulateMetaData<std::string>(dico, tag.PrintAsPipeSeparatedString(), encodedValue);
}
}
}
else /* if ( vr & gdcm::VR::VRASCII ) */
{
// Only copying field from the public DICOM dictionary
if (m_LoadPrivateTags || tag.IsPublic())
{
EncapsulateMetaData<std::string>(dico, tag.PrintAsPipeSeparatedString(), sf.ToString(tag));
}
}
}
#if defined(ITKIO_DEPRECATED_GDCM1_API)
// Now is a good time to fill in the class member:
char name[512];
this->GetPatientName(name, 512);
this->GetPatientID(name, 512);
this->GetPatientSex(name, 512);
this->GetPatientAge(name, 512);
this->GetStudyID(name, 512);
this->GetPatientDOB(name, 512);
this->GetStudyDescription(name, 512);
this->GetBodyPart(name, 512);
this->GetNumberOfSeriesInStudy(name, 512);
this->GetNumberOfStudyRelatedSeries(name, 512);
this->GetStudyDate(name, 512);
this->GetModality(name, 512);
this->GetManufacturer(name, 512);
this->GetInstitution(name, 512);
this->GetModel(name, 512);
this->GetScanOptions(name, 512);
#endif
}
void
GDCMImageIO::ReadImageInformation()
{
this->InternalReadImageInformation();
}
bool
GDCMImageIO::CanWriteFile(const char * name)
{
std::string filename = name;
if (filename.empty())
{
itkDebugMacro(<< "No filename specified.");
return false;
}
return this->HasSupportedWriteExtension(name, false);
}
void
GDCMImageIO::WriteImageInformation()
{}
void
GDCMImageIO::Write(const void * buffer)
{
// ensure file can be opened for writing, before doing any more work
std::ofstream outputFileStream;
// let any exceptions propagate
this->OpenFileForWriting(outputFileStream, m_FileName);
outputFileStream.close();
// global static:
gdcm::UIDGenerator::SetRoot(m_UIDPrefix.c_str());
// echo "ITK" | od -b
gdcm::FileMetaInformation::AppendImplementationClassUID("111.124.113");
const std::string project_name = std::string("GDCM/ITK ") + itk::Version::GetITKVersion();
gdcm::FileMetaInformation::SetSourceApplicationEntityTitle(project_name.c_str());
gdcm::ImageWriter writer;
gdcm::FileMetaInformation & fmi = writer.GetFile().GetHeader();
gdcm::DataSet & header = writer.GetFile().GetDataSet();
gdcm::Global & g = gdcm::Global::GetInstance();
const gdcm::Dicts & dicts = g.GetDicts();
const gdcm::Dict & pubdict = dicts.GetPublicDict();
MetaDataDictionary & dict = this->GetMetaDataDictionary();
gdcm::Tag tag;
itk::MetaDataDictionary::ConstIterator itr = dict.Begin();
const itk::MetaDataDictionary::ConstIterator end = dict.End();
gdcm::StringFilter sf;
sf.SetFile(writer.GetFile());
while (itr != end)
{
std::string value;
const std::string & key = itr->first; // Needed for bcc32
ExposeMetaData<std::string>(dict, key, value);
// Convert DICOM name to DICOM (group,element)
bool b = tag.ReadFromPipeSeparatedString(key.c_str());
// Anything that has been changed in the MetaData Dict will be pushed
// into the DICOM header:
if (b /*tag != gdcm::Tag(0xffff,0xffff)*/ /*dictEntry*/)
{
const gdcm::DictEntry & dictEntry = pubdict.GetDictEntry(tag);
gdcm::VR::VRType vrtype = dictEntry.GetVR();
if (dictEntry.GetVR() == gdcm::VR::SQ)
{
// How did we reach here ?
}
else if (vrtype & (gdcm::VR::OB | gdcm::VR::OF | gdcm::VR::OW /*|
gdcm::VR::SQ*/
| gdcm::VR::UN))
{
// Custom VR::VRBINARY
// convert value from Base64
const auto bin = make_unique_for_overwrite<uint8_t[]>(value.size());
auto decodedLengthActual =
static_cast<unsigned int>(itksysBase64_Decode((const unsigned char *)value.c_str(),
static_cast<SizeValueType>(0),
(unsigned char *)bin.get(),
static_cast<SizeValueType>(value.size())));
if (/*tag.GetGroup() != 0 ||*/ tag.GetElement() != 0) // ?
{
gdcm::DataElement de(tag);
de.SetByteValue((char *)bin.get(), decodedLengthActual);
de.SetVR(dictEntry.GetVR());
if (tag.GetGroup() == 0x2)
{
fmi.Insert(de);
}
else
{
header.Insert(de);
}
}
}
else // VRASCII
{
// TODO, should we keep:
// (0028,0106) US/SS 0 #2, 1
// SmallestImagePixelValue
// (0028,0107) US/SS 4095 #2, 1
// LargestImagePixelValue
if (!tag.IsGroupLength()) // Get rid of group length, they are not
// useful
{
gdcm::DataElement de(tag);
if (dictEntry.GetVR().IsVRFile())
{
de.SetVR(dictEntry.GetVR());
}
#if GDCM_MAJOR_VERSION == 2 && GDCM_MINOR_VERSION == 0 && GDCM_BUILD_VERSION <= 12
// This will not work in the vast majority of cases but to get at
// least something working in GDCM 2.0.12
de.SetByteValue(value.c_str(), static_cast<uint32_t>(value.size()));
#else
// Even padding string with space. If string is not even, SetByteValue() will
// pad it with '\0' which is not what is expected except for VR::UI
// (see standard section 6.2).
if (vrtype & (gdcm::VR::UI))
{
const std::string si = sf.FromString(tag, value.c_str(), value.size());
de.SetByteValue(si.c_str(), static_cast<uint32_t>(si.size()));
}
else
{
const gdcm::String<> si = sf.FromString(tag, value.c_str(), value.size());
de.SetByteValue(si.c_str(), static_cast<uint32_t>(si.size()));
}
#endif
if (tag.GetGroup() == 0x2)
{
fmi.Insert(de);
}
else
{
header.Insert(de); // value, tag.GetGroup(), tag.GetElement());
}
}
}
}
else
{
// This is not a DICOM entry, then check if it is one of the
// ITK standard ones
if (key == ITK_NumberOfDimensions)
{
unsigned int numberOfDimensions = 0;
ExposeMetaData<unsigned int>(dict, key, numberOfDimensions);
m_GlobalNumberOfDimensions = numberOfDimensions;
m_Origin.resize(m_GlobalNumberOfDimensions);
m_Spacing.resize(m_GlobalNumberOfDimensions);
m_Direction.resize(m_GlobalNumberOfDimensions);
for (unsigned int i = 0; i < m_GlobalNumberOfDimensions; ++i)
{
m_Direction[i].resize(m_GlobalNumberOfDimensions);
}
}
else if (key == ITK_Origin)
{
using DoubleArrayType = Array<double>;
DoubleArrayType originArray(3);
ExposeMetaData<DoubleArrayType>(dict, key, originArray);
m_Origin.resize(3);
m_Origin[0] = originArray[0];
m_Origin[1] = originArray[1];
m_Origin[2] = originArray[2];
}
else if (key == ITK_Spacing)
{
using DoubleArrayType = Array<double>;
DoubleArrayType spacingArray(3);
ExposeMetaData<DoubleArrayType>(dict, key, spacingArray);
m_Spacing.resize(3);
m_Spacing[0] = spacingArray[0];
m_Spacing[1] = spacingArray[1];
m_Spacing[2] = spacingArray[2];
}
else if (key == ITK_ZDirection)
{
using DoubleMatrixType = Matrix<double>;
DoubleMatrixType directionMatrix;
ExposeMetaData<DoubleMatrixType>(dict, key, directionMatrix);
for (int i = 0; i < 3; ++i)
{
for (int j = 0; j < 3; ++j)
{
m_Direction[i][j] = directionMatrix[i][j];
}
}