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diinpxt.h
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diinpxt.h
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/*
*
* Copyright (C) 1996-2021, OFFIS e.V.
* All rights reserved. See COPYRIGHT file for details.
*
* This software and supporting documentation were developed by
*
* OFFIS e.V.
* R&D Division Health
* Escherweg 2
* D-26121 Oldenburg, Germany
*
*
* Module: dcmimgle
*
* Author: Joerg Riesmeier
*
* Purpose: DicomInputPixelTemplate (Header)
*
*/
#ifndef DIINPXT_H
#define DIINPXT_H
#include "dcmtk/config/osconfig.h"
#include "dcmtk/dcmdata/dcpixel.h"
#include "dcmtk/ofstd/ofbmanip.h"
#include "dcmtk/ofstd/ofcast.h"
#include "dcmtk/ofstd/ofdiag.h" /* for DCMTK_DIAGNOSTIC macros */
#include "dcmtk/dcmimgle/diinpx.h"
#include "dcmtk/dcmimgle/didocu.h"
#include "dcmtk/dcmimgle/dipxrept.h"
/*--------------------*
* helper functions *
*--------------------*/
static inline Uint8 expandSign(const Uint8 Value,
const Uint8,
const Uint8)
{
return Value;
}
static inline Uint16 expandSign(const Uint16 Value,
const Uint16,
const Uint16)
{
return Value;
}
static inline Uint32 expandSign(const Uint32 Value,
const Uint32,
const Uint32)
{
return Value;
}
static inline Sint8 expandSign(const Sint8 Value,
const Sint8 SignBit,
const Sint8 SignMask)
{
return (Value & SignBit) ? (Value | SignMask) : Value;
}
static inline Sint16 expandSign(const Sint16 Value,
const Sint16 SignBit,
const Sint16 SignMask)
{
return (Value & SignBit) ? (Value | SignMask) : Value;
}
static inline Sint32 expandSign(const Sint32 Value,
const Sint32 SignBit,
const Sint32 SignMask)
{
return (Value & SignBit) ? (Value | SignMask) : Value;
}
static Uint32 getPixelData(DcmPixelData *PixelData,
Uint8 *&pixel)
{
PixelData->getUint8Array(pixel);
return PixelData->getLength();
}
static Uint32 getPixelData(DcmPixelData *PixelData,
Uint16 *&pixel)
{
PixelData->getUint16Array(pixel);
return PixelData->getLength();
}
/*---------------------*
* class declaration *
*---------------------*/
/** Template class to convert DICOM pixel stream to intermediate representation
*/
template<class T1, class T2>
class DiInputPixelTemplate
: public DiInputPixel,
public DiPixelRepresentationTemplate<T2>
{
public:
/** constructor
*
** @param document pointer to DICOM image object
* @param alloc number of bits allocated for each pixel
* @param stored number of bits stored for each pixel
* @param high position of high bit within bits allocated
* @param first first frame to be processed
* @param number number of frames to be processed
* @param fsize number of pixels per frame (frame size)
* @param fileCache pointer to file cache object used for partial read
* @param fragment current pixel item fragment (for encapsulated pixel data)
*/
DiInputPixelTemplate(const DiDocument *document,
const Uint16 alloc,
const Uint16 stored,
const Uint16 high,
const unsigned long first,
const unsigned long number,
const unsigned long fsize,
DcmFileCache *fileCache,
Uint32 &fragment)
: DiInputPixel(stored, first, number, fsize),
Data(NULL)
{
MinValue[0] = 0;
MinValue[1] = 0;
MaxValue[0] = 0;
MaxValue[1] = 0;
if (this->isSigned())
{
AbsMinimum = -OFstatic_cast(double, DicomImageClass::maxval(Bits - 1, 0));
AbsMaximum = OFstatic_cast(double, DicomImageClass::maxval(Bits - 1));
} else {
AbsMinimum = 0;
AbsMaximum = OFstatic_cast(double, DicomImageClass::maxval(Bits));
}
if ((document != NULL) && (document->getPixelData() != NULL))
convert(document, alloc, stored, high, fileCache, fragment);
if ((PixelCount == 0) || (PixelStart + PixelCount > Count)) // check for corrupt pixel length
{
PixelCount = Count - PixelStart;
DCMIMGLE_DEBUG("setting number of pixels to be processed (PixelCount) to " << PixelCount);
}
}
/** destructor
*/
virtual ~DiInputPixelTemplate()
{
#if defined(HAVE_STD__NOTHROW) && defined(HAVE_NOTHROW_DELETE)
/* use a non-throwing delete (if available) */
operator delete[] (Data, std::nothrow);
#else
delete[] Data;
#endif
}
#include DCMTK_DIAGNOSTIC_PUSH
#include DCMTK_DIAGNOSTIC_IGNORE_CONST_EXPRESSION_WARNING
/** determine minimum and maximum pixel value
*
** @return status, true if successful, false otherwise
*/
int determineMinMax()
{
if (Data != NULL)
{
DCMIMGLE_DEBUG("determining minimum and maximum pixel values for input data");
T2 *p = Data;
unsigned long i;
const double absrange = getAbsMaxRange();
const unsigned long ocnt = (absrange <= 10000000.0) ? OFstatic_cast(unsigned long, absrange) : 0 /* no LUT */;
Uint8 *lut = NULL;
if ((sizeof(T2) <= 2) && (ocnt > 0) && (Count > 3 * ocnt)) // optimization criteria
{
lut = new Uint8[ocnt];
if (lut != NULL)
{
DCMIMGLE_DEBUG("using optimized routine with additional LUT");
OFBitmanipTemplate<Uint8>::zeroMem(lut, ocnt);
Uint8 *q = lut - OFstatic_cast(T2, getAbsMinimum());
for (i = Count; i != 0; --i) // fill lookup table
*(q + *(p++)) = 1;
q = lut;
for (i = 0; i < ocnt; ++i) // search for minimum
{
if (*(q++) != 0)
{
MinValue[0] = OFstatic_cast(T2, OFstatic_cast(double, i) + getAbsMinimum());
break;
}
}
q = lut + ocnt;
for (i = ocnt; i != 0; --i) // search for maximum
{
if (*(--q) != 0)
{
MaxValue[0] = OFstatic_cast(T2, OFstatic_cast(double, i - 1) + getAbsMinimum());
break;
}
}
if (Count >= PixelCount) // use global min/max value
{
MinValue[1] = MinValue[0];
MaxValue[1] = MaxValue[0];
} else { // calculate min/max for selected range
OFBitmanipTemplate<Uint8>::zeroMem(lut, ocnt);
p = Data + PixelStart;
q = lut - OFstatic_cast(T2, getAbsMinimum());
for (i = PixelCount; i != 0; --i) // fill lookup table
*(q + *(p++)) = 1;
q = lut;
for (i = 0; i < ocnt; ++i) // search for minimum
{
if (*(q++) != 0)
{
MinValue[1] = OFstatic_cast(T2, OFstatic_cast(double, i) + getAbsMinimum());
break;
}
}
q = lut + ocnt;
for (i = ocnt; i != 0; --i) // search for maximum
{
if (*(--q) != 0)
{
MaxValue[1] = OFstatic_cast(T2, OFstatic_cast(double, i - 1) + getAbsMinimum());
break;
}
}
}
}
}
if (lut == NULL) // use conventional method
{
T2 value = *p;
MinValue[0] = value;
MaxValue[0] = value;
for (i = Count; i > 1; --i)
{
value = *(++p);
if (value < MinValue[0])
MinValue[0] = value;
else if (value > MaxValue[0])
MaxValue[0] = value;
}
if (Count <= PixelCount) // use global min/max value
{
MinValue[1] = MinValue[0];
MaxValue[1] = MaxValue[0];
} else { // calculate min/max for selected range
p = Data + PixelStart;
value = *p;
MinValue[1] = value;
MaxValue[1] = value;
for (i = PixelCount; i > 1; --i)
{
value = *(++p);
if (value < MinValue[1])
MinValue[1] = value;
else if (value > MaxValue[1])
MaxValue[1] = value;
}
}
}
delete[] lut;
return 1;
}
return 0;
}
#include DCMTK_DIAGNOSTIC_POP
/** get pixel representation
*
** @return pixel representation
*/
inline EP_Representation getRepresentation() const
{
return DiPixelRepresentationTemplate<T2>::getRepresentation();
}
/** get pointer to input pixel data
*
** @return pointer to input pixel data
*/
inline const void *getData() const
{
return OFstatic_cast(const void *, Data);
}
/** get reference to pointer to input pixel data
*
** @return reference to pointer to input pixel data
*/
virtual void *getDataPtr()
{
return OFstatic_cast(void *, Data);
}
/** remove reference to (internally handled) pixel data
*/
inline void removeDataReference()
{
Data = NULL;
}
/** get minimum pixel value
*
** @param idx specifies whether to return the global minimum (0) or
* the minimum of the selected pixel range (1, see PixelStart/Range)
*
** @return minimum pixel value
*/
inline double getMinValue(const int idx) const
{
return (idx == 0) ? OFstatic_cast(double, MinValue[0]) : OFstatic_cast(double, MinValue[1]);
}
/** get maximum pixel value
*
** @param idx specifies whether to return the global maximum (0) or
* the maximum of the selected pixel range (1, see PixelStart/Range)
*
** @return maximum pixel value
*/
inline double getMaxValue(const int idx) const
{
return (idx == 0) ? OFstatic_cast(double, MaxValue[0]) : OFstatic_cast(double, MaxValue[1]);
}
private:
/** convert pixel data from DICOM dataset to input representation
*
** @param document pointer to DICOM image object
* @param bitsAllocated number of bits allocated for each pixel
* @param bitsStored number of bits stored for each pixel
* @param highBit position of high bit within bits allocated
* @param fileCache pointer to file cache object used for partial read
* @param fragment current pixel item fragment (for encapsulated pixel data)
*/
void convert(const DiDocument *document,
const Uint16 bitsAllocated,
const Uint16 bitsStored,
const Uint16 highBit,
DcmFileCache *fileCache,
Uint32 &fragment)
{
T1 *pixel = NULL;
OFBool deletePixel = OFFalse;
Uint32 lengthBytes = 0;
DcmPixelData *pixelData = document->getPixelData();
const Uint16 bitsof_T1 = bitsof(T1);
const Uint16 bitsof_T2 = bitsof(T2);
const OFBool uncompressed = pixelData->canWriteXfer(EXS_LittleEndianExplicit, EXS_Unknown);
/* check whether to use partial read */
if ((document->getFlags() & CIF_UsePartialAccessToPixelData) && (PixelCount > 0) && (bitsAllocated % 8 == 0))
{
/* Bits Allocated is always a multiple of 8 (see above), same for bits of T1 */
const Uint32 byteFactor = bitsAllocated / 8;
const Uint32 bytes_T1 = bitsof_T1 / 8;
const Uint32 count_T1 = (byteFactor == bytes_T1) ? PixelCount : (PixelCount * byteFactor + bytes_T1 - 1) / bytes_T1;
#ifdef DEBUG
DCMIMGLE_TRACE("PixelCount: " << PixelCount << ", byteFactor: " << byteFactor << ", bytes_T1: " << bytes_T1 << ", count_T1: " << count_T1);
#endif
/* allocate temporary buffer, even number of bytes required for getUncompressedFrame() */
const Uint32 extraByte = ((sizeof(T1) == 1) && (count_T1 & 1)) ? 1 : 0;
#ifdef HAVE_STD__NOTHROW
/* use a non-throwing new here (if available) because the allocated buffer can be huge */
pixel = new (std::nothrow) T1[count_T1 + extraByte];
#else
/* make sure that the pointer is set to NULL in case of error */
try
{
pixel = new T1[count_T1 + extraByte];
}
catch (STD_NAMESPACE bad_alloc const &)
{
pixel = NULL;
}
#endif
if (pixel != NULL)
{
if (uncompressed)
{
DCMIMGLE_DEBUG("using partial read access to uncompressed pixel data");
const Uint32 offset = PixelStart * byteFactor;
const Uint32 bufSize = PixelCount * byteFactor;
const OFCondition status = pixelData->getPartialValue(pixel, offset, bufSize, fileCache);
if (status.good())
{
PixelStart = 0;
lengthBytes = bufSize;
} else {
DCMIMGLE_ERROR("can't access partial value from byte offset " << offset << " to "
<< (offset + bufSize - 1) << ": " << status.text());
}
} else {
DCMIMGLE_DEBUG("using partial read access to compressed pixel data");
OFCondition status = EC_IllegalCall;
OFString decompressedColorModel;
const Uint32 fsize = FrameSize * byteFactor;
for (Uint32 frame = 0; frame < NumberOfFrames; ++frame)
{
/* make sure that the buffer always has an even number of bytes as required for getUncompressedFrame() */
const Uint32 bufSize = (fsize & 1) ? fsize + 1 : fsize;
status = pixelData->getUncompressedFrame(document->getDataset(), FirstFrame + frame, fragment,
OFreinterpret_cast(Uint8 *, pixel) + lengthBytes, bufSize, decompressedColorModel, fileCache);
if (status.good())
{
DCMIMGLE_TRACE("successfully decompressed frame " << FirstFrame + frame);
lengthBytes += fsize;
} else {
DCMIMGLE_ERROR("can't decompress frame " << FirstFrame + frame << ": " << status.text());
break;
}
}
if (status.good())
PixelStart = 0;
/* check whether color model changed during decompression */
if (!decompressedColorModel.empty() && (decompressedColorModel != document->getPhotometricInterpretation()))
{
DCMIMGLE_WARN("Photometric Interpretation of decompressed pixel data deviates from original image: "
<< decompressedColorModel);
}
}
deletePixel = OFTrue;
} else
DCMIMGLE_DEBUG("cannot allocate memory buffer for 'pixel' in DiInputPixelTemplate::convert()");
} else {
DCMIMGLE_DEBUG("reading uncompressed pixel data completely into memory");
/* always access complete pixel data */
lengthBytes = getPixelData(pixelData, pixel);
}
if ((pixel != NULL) && (lengthBytes > 0))
{
const Uint32 length_T1 = lengthBytes / sizeof(T1);
/* need to split 'length' in order to avoid integer overflow for large pixel data */
const Uint32 length_B1 = lengthBytes / bitsAllocated;
const Uint32 length_B2 = lengthBytes % bitsAllocated;
// # old code: Count = ((lengthBytes * 8) + bitsAllocated - 1) / bitsAllocated;
Count = 8 * length_B1 + (8 * length_B2 + bitsAllocated - 1) / bitsAllocated;
unsigned long i;
#ifdef HAVE_STD__NOTHROW
/* use a non-throwing new here (if available) because the allocated buffer can be huge */
Data = new (std::nothrow) T2[Count];
#else
/* make sure that the pointer is set to NULL in case of error */
try
{
Data = new T2[Count];
}
catch (STD_NAMESPACE bad_alloc const &)
{
Data = NULL;
}
#endif
if (Data != NULL)
{
DCMIMGLE_TRACE("Input length: " << lengthBytes << " bytes, Pixel count: " << Count
<< " (" << PixelCount << "), In: " << bitsof_T1 << " bits, Out: " << bitsof_T2
<< " bits (" << (this->isSigned() ? "signed" : "unsigned") << ")");
const T1 *p = pixel;
T2 *q = Data;
if (bitsof_T1 == bitsAllocated) // case 1: equal 8/16 bit
{
if (bitsStored == bitsAllocated)
{
DCMIMGLE_DEBUG("convert input pixel data: case 1a (single copy)");
for (i = Count; i != 0; --i)
*(q++) = OFstatic_cast(T2, *(p++));
}
else /* bitsStored < bitsAllocated */
{
T1 mask = 0;
for (i = 0; i < bitsStored; ++i)
mask |= OFstatic_cast(T1, 1 << i);
const T2 sign = 1 << (bitsStored - 1);
T2 smask = 0;
for (i = bitsStored; i < bitsof_T2; ++i)
smask |= OFstatic_cast(T2, 1 << i);
const Uint16 shift = highBit + 1 - bitsStored;
if (shift == 0)
{
DCMIMGLE_DEBUG("convert input pixel data: case 1b (mask & sign)");
for (i = length_T1; i != 0; --i)
*(q++) = expandSign(OFstatic_cast(T2, *(p++) & mask), sign, smask);
}
else /* shift > 0 */
{
DCMIMGLE_DEBUG("convert input pixel data: case 1c (shift & mask & sign)");
for (i = length_T1; i != 0; --i)
*(q++) = expandSign(OFstatic_cast(T2, (*(p++) >> shift) & mask), sign, smask);
}
}
}
else if ((bitsof_T1 > bitsAllocated) && (bitsof_T1 % bitsAllocated == 0)) // case 2: divisor of 8/16 bit
{
const Uint16 times = bitsof_T1 / bitsAllocated;
T1 mask = 0;
for (i = 0; i < bitsStored; ++i)
mask |= OFstatic_cast(T1, 1 << i);
Uint16 j;
T1 value;
if ((bitsStored == bitsAllocated) && (bitsStored == bitsof_T2))
{
if (times == 2)
{
DCMIMGLE_DEBUG("convert input pixel data: case 2a (simple mask)");
for (i = length_T1; i != 0; --i, ++p)
{
*(q++) = OFstatic_cast(T2, *p & mask);
*(q++) = OFstatic_cast(T2, *p >> bitsAllocated);
}
/* check for additional input pixel (in case of odd length when using partial access) */
if (length_T1 * 2 /* times */ < lengthBytes)
{
DCMIMGLE_TRACE("found trailing pixel at the end of odd-length input data ... copying value");
*(q++) = OFstatic_cast(T2, *p & mask);
}
}
else
{
DCMIMGLE_DEBUG("convert input pixel data: case 2b (mask)");
for (i = length_T1; i != 0; --i)
{
value = *(p++);
for (j = times; j != 0; --j)
{
*(q++) = OFstatic_cast(T2, value & mask);
value >>= bitsAllocated;
}
}
}
}
else
{
DCMIMGLE_DEBUG("convert input pixel data: case 2c (shift & mask & sign)");
const T2 sign = 1 << (bitsStored - 1);
T2 smask = 0;
for (i = bitsStored; i < bitsof_T2; ++i)
smask |= OFstatic_cast(T2, 1 << i);
const Uint16 shift = highBit + 1 - bitsStored;
for (i = length_T1; i != 0; --i)
{
value = *(p++) >> shift;
for (j = times; j != 0; --j)
{
*(q++) = expandSign(OFstatic_cast(T2, value & mask), sign, smask);
value >>= bitsAllocated;
}
}
}
}
else if ((bitsof_T1 < bitsAllocated) && (bitsAllocated % bitsof_T1 == 0) // case 3: multiplicand of 8/16
&& (bitsStored == bitsAllocated))
{
DCMIMGLE_DEBUG("convert input pixel data: case 3 (multi copy)");
const Uint16 times = bitsAllocated / bitsof_T1;
Uint16 j;
Uint16 shift;
T2 value;
for (i = length_T1; i != 0; --i)
{
shift = 0;
value = OFstatic_cast(T2, *(p++));
for (j = times; j > 1; --j, --i)
{
shift += bitsof_T1;
value |= OFstatic_cast(T2, *(p++)) << shift;
}
*(q++) = value;
}
}
else // case 4: anything else
{
DCMIMGLE_DEBUG("convert input pixel data: case 4 (general)");
T2 value = 0;
Uint16 bits = 0;
Uint32 skip = highBit + 1 - bitsStored;
Uint32 times;
T1 mask[bitsof_T1];
mask[0] = 1;
for (i = 1; i < bitsof_T1; ++i)
mask[i] = (mask[i - 1] << 1) | 1;
T2 smask = 0;
for (i = bitsStored; i < bitsof_T2; ++i)
smask |= OFstatic_cast(T2, 1 << i);
const T2 sign = 1 << (bitsStored - 1);
const Uint32 gap = bitsAllocated - bitsStored;
i = 0;
while (i < length_T1)
{
if (skip < bitsof_T1)
{
if (skip + bitsStored - bits < bitsof_T1) // -++- --++
{
value |= (OFstatic_cast(T2, (*p >> skip) & mask[bitsStored - bits - 1]) << bits);
skip += bitsStored - bits + gap;
bits = bitsStored;
}
else // ++-- ++++
{
value |= (OFstatic_cast(T2, (*p >> skip) & mask[bitsof_T1 - skip - 1]) << bits);
bits += bitsof_T1 - OFstatic_cast(Uint16, skip);
skip = (bits == bitsStored) ? gap : 0;
++i;
++p;
}
if (bits == bitsStored)
{
*(q++) = expandSign(value, sign, smask);
value = 0;
bits = 0;
}
}
else
{
times = skip / bitsof_T1;
i += times;
p += times;
skip -= times * bitsof_T1;
}
}
}
} else
DCMIMGLE_DEBUG("cannot allocate memory buffer for 'Data' in DiInputPixelTemplate::convert()");
} else {
/* in case of error, reset pixel count variable */
Count = 0;
}
if (deletePixel)
{
/* delete temporary buffer */
#if defined(HAVE_STD__NOTHROW) && defined(HAVE_NOTHROW_DELETE)
/* use a non-throwing delete (if available) */
operator delete[] (pixel, std::nothrow);
#else
delete[] pixel;
#endif
}
}
/// pointer to pixel data
T2 *Data;
/// minimum pixel value ([0] = global, [1] = selected pixel range)
T2 MinValue[2];
/// maximum pixel value ([0] = global, [1] = selected pixel range)
T2 MaxValue[2];
// --- declarations to avoid compiler warnings
DiInputPixelTemplate(const DiInputPixelTemplate<T1,T2> &);
DiInputPixelTemplate<T1,T2> &operator=(const DiInputPixelTemplate<T1,T2> &);
};
#endif