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STYLE: Simplify itkDCMTKImageIO
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Do not test for no-preamble DICOM file format if standard preamble format is found.
Use DCMTK constants (instead of hardcoding the preamble size, magic word, etc.).
Remove unnecessary "static" keyword from function in anonymous namespace.
Simplified debug message of a DICOM file without preamble.
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@lassoan @thewtex
lassoan authored and thewtex committed Mar 26, 2024
1 parent ac1ebe6 commit decc3e5
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Showing 2 changed files with 90 additions and 92 deletions.
174 changes: 88 additions & 86 deletions Modules/IO/DCMTK/src/itkDCMTKImageIO.cxx
View file
Expand Up @@ -28,25 +28,103 @@
#include "dcmtk/dcmimgle/dcmimage.h"
#include "dcmtk/dcmjpeg/djdecode.h"
#include "dcmtk/dcmjpls/djdecode.h"
#include "dcmtk/dcmdata/dcmetinf.h"
#include "dcmtk/dcmdata/dcrledrg.h"
#include "dcmtk/oflog/oflog.h"

namespace
{

/**
* Helper function to test for 128 byte dicom preamble
* Helper function to test if the file is in standard DICOM file format
* (128-byte dicom preamble followed by "DICM" magic word).
* @param file A stream to test if the file is dicom like
* @return true if the stream has a dicom preamble
*/
static bool
readPreambleDicom(std::ifstream & file)
bool
isPreambleDicom(std::ifstream & file)
{
file.seekg(0, std::ios::beg);
std::vector<char> buffer(DCM_PreambleLen + DCM_MagicLen);
file.read(&buffer[0], buffer.size());
if (!file)
{
return false;
}
const char * magicReadFromFile = &buffer[DCM_PreambleLen];
return strncmp(magicReadFromFile, DCM_Magic, DCM_MagicLen) == 0;
}

/**
* Helper function to test for old non-standard DICOM file format
* (that does not have preamble).
* @param file A stream to test if the file is dicom like
* @return true if the structure of the file is dicom like
*/
bool
isNoPreambleDicom(std::ifstream & file) // NOTE: Similar function is in itkGDCMImageIO.cxx
{
char preamble[132] = "";
file.seekg(0, std::ios::beg);

// 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));
itk::ByteSwapper<unsigned short>::SwapFromSystemToLittleEndian(&groupNo);
file.read(reinterpret_cast<char *>(&tagElementNo), sizeof(unsigned short));
itk::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);

file.read(preamble, sizeof(preamble));
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));
itk::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);

return (preamble[128] == 'D' && preamble[129] == 'I' && preamble[130] == 'C' && preamble[131] == 'M');
auto * uilength = reinterpret_cast<unsigned int *>(lengthChars);
itk::ByteSwapper<unsigned int>::SwapFromSystemToLittleEndian(uilength);

length = (*uilength);
}
if (length <= 0)
{
return false;
}
file.ignore(length);
if (file.eof())
{
return false;
}
} while (groupNo == 2);

itkDebugMacro(<< "No DICOM magic number found, but the file appears to be DICOM without a preamble.");
return true;
}

} // end anonymous namespace
Expand Down Expand Up @@ -151,81 +229,6 @@ DCMTKImageIO::~DCMTKImageIO()
DcmRLEDecoderRegistration::cleanup();
}

/**
* 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 itkGDCMImageIO.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;
}


bool
DCMTKImageIO::CanReadFile(const char * filename)
{
Expand All @@ -241,7 +244,6 @@ DCMTKImageIO::CanReadFile(const char * filename)
{
std::ifstream file;

// look for a preamble
try
{
this->OpenFileForReading(file, filename);
Expand All @@ -250,11 +252,11 @@ DCMTKImageIO::CanReadFile(const char * filename)
{
return false;
}
const bool hasdicompreamble = readPreambleDicom(file);
file.seekg(0, std::ios::beg);
const bool hasdicomsig = readNoPreambleDicom(file);
// check if standard DICOM file (with preamble)
// or non-standard DICOM file (without preamble)
const bool isDICOM = isPreambleDicom(file) || isNoPreambleDicom(file);
file.close();
if (!hasdicomsig && !hasdicompreamble)
if (!isDICOM)
{
return false;
}
Expand Down
8 changes: 2 additions & 6 deletions Modules/IO/GDCM/src/itkGDCMImageIO.cxx
View file
Expand Up @@ -188,12 +188,8 @@ readNoPreambleDicom(std::ifstream & file) // NOTE: This file is duplicated in it
}
} 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
itkDebugMacro(<< "No DICOM magic number found, but the file appears to be DICOM without a preamble.");

return true;
}

Expand Down

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