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/*
*
* Copyright (C) 1998-2005, OFFIS
*
* This software and supporting documentation were developed by
*
* Kuratorium OFFIS e.V.
* Healthcare Information and Communication Systems
* Escherweg 2
* D-26121 Oldenburg, Germany
*
* THIS SOFTWARE IS MADE AVAILABLE, AS IS, AND OFFIS MAKES NO WARRANTY
* REGARDING THE SOFTWARE, ITS PERFORMANCE, ITS MERCHANTABILITY OR
* FITNESS FOR ANY PARTICULAR USE, FREEDOM FROM ANY COMPUTER DISEASES OR
* ITS CONFORMITY TO ANY SPECIFICATION. THE ENTIRE RISK AS TO QUALITY AND
* PERFORMANCE OF THE SOFTWARE IS WITH THE USER.
*
* Module: dcmpstat
*
* Authors: Marco Eichelberg, Joerg Riesmeier
*
* Purpose: This application reads a DICOM image, adds a Modality LUT,
* a VOI LUT or a Presentation LUT to the image and writes it back.
* The LUT has a gamma curve shape or can be imported from an external
* file.
*
* Last Update: $Author: meichel $
* Update Date: $Date: 2005/12/08 15:46:03 $
* Source File: $Source: /share/dicom/cvs-depot/dcmtk/dcmpstat/apps/dcmmklut.cc,v $
* CVS/RCS Revision: $Revision: 1.39 $
* Status: $State: Exp $
*
* CVS/RCS Log at end of file
*
*/
#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
#ifdef HAVE_GUSI_H
#include <GUSI.h>
#endif
#include "dcmtk/ofstd/ofstream.h"
#include "dcmtk/dcmdata/dctk.h"
#include "dcmtk/dcmdata/cmdlnarg.h"
#include "dcmtk/dcmdata/dcuid.h" /* for dcmtk version name */
#include "dcmtk/ofstd/ofconapp.h"
#include "dcmtk/ofstd/ofstring.h"
#include "dcmtk/dcmimgle/dicrvfit.h"
#include "dcmtk/dcmimgle/digsdfn.h"
#include "dcmtk/dcmimgle/diutils.h"
#include "dcmtk/ofstd/ofstream.h"
#include "dcmtk/ofstd/ofstd.h"
#include "dcmtk/dcmdata/dcdebug.h"
#define INCLUDE_CSTDLIB
#define INCLUDE_CSTDIO
#define INCLUDE_CMATH
#define INCLUDE_CCTYPE
#include "dcmtk/ofstd/ofstdinc.h"
#ifdef WITH_ZLIB
#include <zlib.h> /* for zlibVersion() */
#endif
#define OFFIS_CONSOLE_APPLICATION "dcmmklut"
static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v"
OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $";
OFBool opt_verbose = OFFalse;
OFBool opt_debug = OFFalse;
// ********************************************
enum LUT_Type
{
LUT_Modality,
LUT_Presentation,
LUT_VOI
};
OFCondition readMapFile(const char *filename,
double *&inputXData,
double *&inputYData,
unsigned long &inputEntries,
double &inputXMax,
double &inputYMax)
{
OFCondition result = EC_IllegalCall;
if ((filename != NULL) && (strlen(filename) > 0))
{
if (opt_verbose)
CERR << "reading map file ..." << endl;
unsigned char buffer[1000];
FILE *inf = fopen(filename, "rb");
if (inf != NULL)
{
if (fread(buffer, 1, 264, inf) == 264)
{
if (fread(buffer + 264, 1, 1, inf) == 0)
{
if ((buffer[0] == 0x8a) && (buffer[1] == 0x3f) && (buffer[2] == 0x0) && (buffer[3] == 0x0))
{
inputEntries = 256;
inputXMax = 255;
inputYMax = 255;
inputXData = new double[inputEntries];
inputYData = new double[inputEntries];
if ((inputXData != NULL) && (inputYData != NULL))
{
for (unsigned long i = 0; i < inputEntries; i++)
{
inputXData[i] = i;
inputYData[i] = (double)buffer[i + 8];
}
result = EC_Normal;
}
} else
CERR << "Warning: magic word wrong, not a map file ... ignoring !" << endl;
} else
CERR << "Warning: file too large, not a map file ... ignoring !" << endl;
} else
CERR << "Warning: read error in map file ... ignoring !" << endl;
fclose(inf);
} else
CERR << "Warning: cannot open map file ... ignoring !" << endl;
}
return result;
}
OFCondition readTextFile(const char *filename,
double *&inputXData,
double *&inputYData,
unsigned long &inputEntries,
double &inputXMax,
double &inputYMax)
{
if ((filename != NULL) && (strlen(filename) > 0))
{
if (opt_verbose)
CERR << "reading text file ..." << endl;
#ifdef HAVE_IOS_NOCREATE
ifstream file(filename, ios::in|ios::nocreate);
#else
ifstream file(filename, ios::in);
#endif
if (file)
{
inputEntries = 0;
inputXMax = 0;
inputYMax = 0;
unsigned long count = 0;
double xmax = 0;
double ymax = 0;
char c;
while (file.get(c))
{
if (c == '#') // comment character
{
while (file.get(c) && (c != '\n') && (c != '\r')); // skip comments
}
else if (!isspace(c)) // skip whitespaces
{
file.putback(c);
if (inputEntries == 0) // read number of entries
{
char str[6];
file.get(str, sizeof(str));
if (strcmp(str, "count") == 0) // check for key word: count
{
file >> inputEntries;
if (inputEntries > 0)
{
inputXData = new double[inputEntries];
inputYData = new double[inputEntries];
if ((inputXData == NULL) || (inputYData == NULL))
return EC_IllegalCall;
} else {
CERR << "Error: invalid or missing value for number of entries in text file ... ignoring !" << endl;
return EC_IllegalCall; // abort
}
} else {
CERR << "Error: missing keyword 'count' for number of entries in text file ... ignoring !" << endl;
return EC_IllegalCall; // abort
}
}
else if ((inputXMax == 0.0) && (c == 'x')) // read x maxvalue (optional)
{
char str[5];
file.get(str, sizeof(str));
if (strcmp(str, "xMax") == 0) // check for key word: xMax
{
file >> inputXMax;
if (inputXMax <= 0)
{
if (opt_debug)
CERR << "Warning: invalid value for xMax in text file ...ignoring !" << endl;
}
} else {
CERR << "Error: invalid text file ... ignoring !" << endl;
return EC_IllegalCall; // abort
}
}
else if ((inputYMax == 0.0) && (c == 'y')) // read y maxvalue (optional)
{
char str[5];
file.get(str, sizeof(str));
if (strcmp(str, "yMax") == 0) // check for key word: yMax
{
file >> inputYMax;
if (inputYMax <= 0)
{
if (opt_debug)
CERR << "Warning: invalid value for yMax in text file ...ignoring !" << endl;
}
} else {
CERR << "Error: invalid text file ... ignoring !" << endl;
return EC_IllegalCall; // abort
}
} else {
if (count < inputEntries)
{
file >> inputXData[count]; // read x value
file >> inputYData[count]; // read y value
if (file.fail())
{
if (opt_debug)
CERR << "Warning: missing y value in text file ... ignoring last entry !" << endl;
} else {
if ((count > 0) && (inputXData[count] <= xmax))
{
if (opt_debug)
CERR << "Warning: x values in text file not strictly monotonous ... ignoring entry #" << (count + 1) << " !" << endl;
} else {
xmax = inputXData[count];
if (inputYData[count] > ymax)
ymax = inputYData[count];
if ((inputXMax != 0) && (inputXData[count] > inputXMax))
{
if (opt_debug)
{
CERR << "Warning: x value (" << inputXData[count] << ") exceeds maximum value (";
CERR << inputXMax << ") in text file ..." << endl << " ... ignoring value !" << endl;
}
}
else if ((inputYMax != 0) && (inputYData[count] > inputYMax))
{
if (opt_debug)
{
CERR << "Warning: y value (" << inputYData[count] << ") exceeds maximum value (";
CERR << inputYMax << ") in text file ..." << endl << " ... ignoring value !" << endl;
}
} else
count++;
}
}
} else {
if (opt_debug)
CERR << "Warning: too many values in text file ... ignoring last line(s) !" << endl;
break;
}
}
}
}
if (count < inputEntries)
{
inputEntries = count;
if (opt_debug)
CERR << "Warning: automatically setting number of entries in text file to " << inputEntries << " !" << endl;
}
if (inputXMax == 0) // automatic calculation
inputXMax = xmax;
if (inputYMax == 0)
inputYMax = ymax;
if (/*(inputXMax > 0) && (inputYMax > 0) &&*/ (inputEntries > 0) && (inputXData != NULL) && (inputYData != NULL))
return EC_Normal;
else
CERR << "Warning: invalid text file ... ignoring !" << endl;
} else
CERR << "Warning: can't open text file ... ignoring !" << endl;
}
return EC_IllegalCall;
}
OFCondition writeTextOutput(const char *filename,
const unsigned long numberOfEntries,
const signed long firstMapped,
const Uint16 *outputData,
const OFString &header)
{
OFCondition result = EC_IllegalCall;
if ((filename != NULL) && (strlen(filename) > 0))
{
if ((outputData != NULL) && (numberOfEntries > 0))
{
if (opt_verbose)
CERR << "writing text file ..." << endl;
ofstream file(filename);
if (file)
{
file << header << endl;
for (unsigned long i = 0; i < numberOfEntries; i++)
file << (firstMapped + (signed long)i) << "\t" << outputData[i] << endl;
} else
CERR << "Warning: can't create output text file ... ignoring !" << endl;
}
}
return result;
}
OFCondition convertInputLUT(const unsigned int numberOfBits,
const unsigned long numberOfEntries,
const signed long firstMapped,
double *inputXData,
double *inputYData,
const unsigned long inputEntries,
const double inputXMax,
const double inputYMax,
const unsigned int order,
Uint16 *outputData,
OFString &header,
char *explanation)
{
OFCondition result = EC_IllegalCall;
if ((inputXData != NULL) && (inputYData != NULL) && (inputEntries > 0) && (inputYMax > 0) && (outputData != NULL))
{
OFOStringStream oss;
if (explanation !=NULL)
{
if (strlen(explanation) == 0)
{
sprintf(explanation, "LUT created from %u->%u bit data, descriptor %u/%ld/%u",
DicomImageClass::tobits((int)inputXMax), DicomImageClass::tobits((int)inputYMax),
(numberOfEntries < 65536) ? (Uint16)numberOfEntries : 0, firstMapped, numberOfBits);
}
oss << "# " << explanation << endl;
}
const double factor = (double)(DicomImageClass::maxval(numberOfBits)) / inputYMax;
if (factor != 1.0)
{
if (opt_verbose)
{
CERR.setf(ios::fixed, ios::floatfield);
CERR << "multiplying input values by " << factor << " ..." << endl;
}
for (unsigned long i = 0; i < inputEntries; i++)
inputYData[i] *= factor;
}
if (numberOfEntries == inputEntries)
{
if (opt_verbose)
CERR << "importing LUT data directly ..." << endl;
for (unsigned long i = 0; i < numberOfEntries; i++)
outputData[i] = (Uint16)inputYData[i];
result = EC_Normal;
} else {
if (opt_verbose)
CERR << "using polynomial curve fitting algorithm ..." << endl;
double *coeff = new double[order + 1];
if (DiCurveFitting<double, double>::calculateCoefficients(inputXData, inputYData, (unsigned int)inputEntries, order, coeff))
{
if (DiCurveFitting<double, Uint16>::calculateValues(0, inputXMax, outputData, (unsigned int)numberOfEntries, order, coeff))
{
oss << "# using polynomial curve fitting algorithm (order = " << order << ")" << endl;
oss << "# equation: y = C0 + C1*x + C2*x^2 + C3*x^3 + ... + Cn*x^n" << endl;
oss << "# where: ";
for (unsigned int i = 0; i <= order; i++)
{
oss << "C" << i << " = ";
oss.setf(ios::fixed, ios::floatfield);
//oss.setf(ios::showpos);
oss.precision(5);
oss.width(10);
oss << coeff[i] << endl;
if (i < order)
{
oss << "# ";
if (i < 9)
oss << " ";
}
}
result = EC_Normal;
}
}
delete[] coeff;
}
if (result == EC_Normal)
{
oss << OFStringStream_ends;
OFSTRINGSTREAM_GETSTR(oss, tmpString)
header += tmpString;
OFSTRINGSTREAM_FREESTR(tmpString)
} else
CERR << "Warning: can't create lookup table from text file ... ignoring !" << endl;
}
return result;
}
void gammaLUT(const unsigned int numberOfBits,
const unsigned long numberOfEntries,
const signed long firstMapped,
const OFBool byteAlign,
const double gammaValue,
Uint16 *outputData,
OFString &header,
char *explanation)
{
if (outputData != NULL)
{
if (opt_verbose)
CERR << "computing gamma function ..." << endl;
OFOStringStream oss;
if (explanation != NULL)
{
if (strlen(explanation) == 0)
{
char gammabuf[16];
OFStandard::ftoa(gammabuf, sizeof(gammabuf), gammaValue, OFStandard::ftoa_format_f, 3, 1);
sprintf(explanation, "LUT with gamma %s, descriptor %u/%ld/%u", gammabuf,
(numberOfEntries < 65536) ? (Uint16)numberOfEntries : 0, firstMapped, numberOfBits);
}
oss << "# " << explanation << endl;
}
Uint16 maxValue = 0xFFFF >> (16 - numberOfBits);
double step = (double)maxValue / ((double)numberOfEntries - 1.0);
double gammaExp = 1.0 / gammaValue;
double factor = (double)maxValue / pow((double)maxValue, gammaExp);
double val;
unsigned long i = 0;
if (byteAlign)
{
Uint8 *data8 = (Uint8 *)outputData;
for (i = 0; i < numberOfEntries; i++)
{
val = factor * pow(i * step, gammaExp);
data8[i] = (Uint8)val;
}
data8[numberOfEntries]=0; //create padding value
} else {
for (i = 0; i < numberOfEntries; i++)
{
val = factor * pow(i * step, gammaExp);
outputData[i]= (Uint16)val;
}
}
oss << OFStringStream_ends;
OFSTRINGSTREAM_GETSTR(oss, tmpString)
header += tmpString;
OFSTRINGSTREAM_FREESTR(tmpString)
}
}
void applyInverseGSDF(const unsigned int numberOfBits,
const unsigned long numberOfEntries,
const OFBool byteAlign,
const unsigned int minDensity,
const unsigned int maxDensity,
const unsigned int illumination,
const unsigned int reflection,
Uint16 *outputData,
OFString &header,
char *explanation)
{
if (outputData != NULL)
{
if (opt_verbose)
CERR << "applying inverse GSDF ..." << endl;
OFOStringStream oss;
if ((explanation != NULL) && (strlen(explanation) > 0))
strcat(explanation, ", inverse GSDF");
const double l0 = (double)illumination;
const double la = (double)reflection;
const double dmin = (double)minDensity / 100;
const double dmax = (double)maxDensity / 100;
const double lmin = la + l0 * pow((double)10, -dmax);
const double lmax = la + l0 * pow((double)10, -dmin);
const double jmin = DiGSDFunction::getJNDIndex(lmin);
const double jmax = DiGSDFunction::getJNDIndex(lmax);
const double factor = (double)DicomImageClass::maxval(numberOfBits) / (jmax - jmin);
const double density = (dmax - dmin) / (double)DicomImageClass::maxval(numberOfBits);
unsigned long i;
if (byteAlign)
{
Uint8 *data8 = (Uint8 *)outputData;
for (i = 0; i < numberOfEntries; i++)
data8[i] = (Uint8)((DiGSDFunction::getJNDIndex(la + l0 * pow((double)10, -(dmin + (double)data8[i] * density))) - jmin) * factor);
} else {
for (i = 0; i < numberOfEntries; i++)
outputData[i] = (Uint16)((DiGSDFunction::getJNDIndex(la + l0 * pow((double)10, -(dmin + (double)outputData[i] * density))) - jmin) * factor);
}
oss << "# applied inverse GSDF with Dmin/max = " << minDensity << "/" << maxDensity << ", L0/La = "
<< illumination << "/" << reflection << endl;
oss << OFStringStream_ends;
OFSTRINGSTREAM_GETSTR(oss, tmpString)
header += tmpString;
OFSTRINGSTREAM_FREESTR(tmpString)
}
}
#ifndef RAND_MAX
/* some brain-dead systems such as SunOS 4.1.3 do not define any constant
* for the upper limit of rand() calls. We hope that such systems at least
* keep within the SysV specs and return values up to 2^15-1.
*/
#define RAND_MAX 32767
#endif
void mixingUpLUT(const unsigned long numberOfEntries,
const OFBool byteAlign,
const unsigned long randomCount,
const unsigned int randomSeed,
Uint16 *outputData,
char *explanation)
{
if (outputData != NULL)
{
if (opt_verbose)
CERR << "mixing up LUT entries ..." << endl;
if ((explanation != NULL) && (strlen(explanation) > 0))
strcat(explanation, ", mixed-up entries");
srand(randomSeed);
unsigned long i, i1, i2;
const double factor = (double)(numberOfEntries - 1) / RAND_MAX;
if (byteAlign)
{
Uint8 temp;
Uint8 *data8 = (Uint8 *)outputData;
for (i = 0; i < randomCount; i++)
{
i1 = (unsigned long)(rand() * factor);
i2 = (unsigned long)(rand() * factor);
if (i1 != i2)
{
temp = data8[i1];
data8[i1] = data8[i2];
data8[i2] = temp;
}
}
} else {
Uint16 temp;
for (i = 0; i < randomCount; i++)
{
i1 = (unsigned long)(rand() * factor);
i2 = (unsigned long)(rand() * factor);
if (i1 != i2)
{
temp = outputData[i1];
outputData[i1] = outputData[i2];
outputData[i2] = temp;
}
}
}
}
}
OFCondition createLUT(const unsigned int numberOfBits,
const unsigned long numberOfEntries,
const signed long firstMapped,
const OFBool byteAlign,
DcmEVR lutVR,
DcmItem &item,
Uint16 *data,
const char *explanation = NULL)
{
OFCondition result = EC_Normal;
Uint16 numEntries16 = 0;
if (numberOfEntries == 0)
CERR << "Warning: creating LUT without LUT data" << endl;
if (numberOfEntries > 65536)
{
CERR << "Error: cannot create LUT with more than 65536 entries" << endl;
return EC_IllegalCall;
}
if (numberOfEntries < 65536)
numEntries16 = (Uint16)numberOfEntries;
if ((numberOfBits < 8) || (numberOfBits > 16))
{
CERR << "Error: cannot create LUT with " << numberOfBits << " bit entries, only 8..16" << endl;
return EC_IllegalCall;
}
DcmElement *descriptor = NULL;
if (firstMapped < 0)
{
// LUT Descriptor is SS
if (firstMapped < -32768)
{
CERR << "Error: cannot create LUT - first value mapped < -32768" << endl;
return EC_IllegalCall;
}
descriptor = new DcmSignedShort(DcmTag(DCM_LUTDescriptor, EVR_SS));
if (descriptor)
{
if (EC_Normal==result) result = descriptor->putSint16((Sint16)numEntries16, 0);
if (EC_Normal==result) result = descriptor->putSint16((Sint16)firstMapped, 1);
if (EC_Normal==result) result = descriptor->putSint16((Sint16)numberOfBits, 2);
if (EC_Normal==result) result = item.insert(descriptor, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
} else {
// LUT Descriptor is US
if (firstMapped > 0xFFFF)
{
CERR << "Error: cannot create LUT - first value mapped > 65535" << endl;
return EC_IllegalCall;
}
descriptor = new DcmUnsignedShort(DcmTag(DCM_LUTDescriptor, EVR_US));
if (descriptor)
{
if (EC_Normal==result) result = descriptor->putUint16(numEntries16, 0);
if (EC_Normal==result) result = descriptor->putUint16((Uint16)firstMapped, 1);
if (EC_Normal==result) result = descriptor->putUint16(numberOfBits, 2);
if (EC_Normal==result) result = item.insert(descriptor, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
}
unsigned long wordsToWrite = 0;
if (byteAlign)
{
// the array is now in little endian byte order. Swap to local byte order if neccessary.
swapIfNecessary(gLocalByteOrder, EBO_LittleEndian, (Uint8 *)data, numberOfEntries + 1, sizeof(Uint16));
wordsToWrite = (numberOfEntries + 1) / 2;
} else
wordsToWrite = numberOfEntries;
if ((wordsToWrite > 32767) && (lutVR != EVR_OW))
{
CERR << "Warning: LUT data >= 64K, writing as OW" << endl;
lutVR = EVR_OW;
}
// write LUT Data as OW, US, or SS
DcmElement *lutdata = NULL;
switch (lutVR)
{
case EVR_US:
lutdata = new DcmUnsignedShort(DcmTag(DCM_LUTData, EVR_US));
if (lutdata)
{
if (EC_Normal==result) result = lutdata->putUint16Array(data, wordsToWrite);
if (EC_Normal==result) result = item.insert(lutdata, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
break;
case EVR_OW:
lutdata = new DcmOtherByteOtherWord(DcmTag(DCM_LUTData, EVR_OW));
if (lutdata)
{
if (EC_Normal==result) result = lutdata->putUint16Array(data, wordsToWrite);
if (EC_Normal==result) result = item.insert(lutdata, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
break;
case EVR_SS:
lutdata = new DcmSignedShort(DcmTag(DCM_LUTData, EVR_SS));
if (lutdata)
{
if (EC_Normal==result) result = lutdata->putSint16Array((Sint16 *)data, wordsToWrite);
if (EC_Normal==result) result = item.insert(lutdata, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
break;
default:
CERR << "Error: unsupported VR for LUT Data" << endl;
return EC_IllegalCall;
/* break; */
}
// create LUT explanation
if (explanation != NULL)
{
DcmElement *explItem = new DcmLongString(DCM_LUTExplanation);
if (explItem)
{
if (result == EC_Normal) result = explItem->putString(explanation);
if (EC_Normal == result) result = item.insert(explItem, OFTrue /*replaceOld*/);
} else
return EC_MemoryExhausted;
}
return result;
}
// ********************************************
#define SHORTCOL 3
#define LONGCOL 14
int main(int argc, char *argv[])
{
int opt_debugMode = 0;
const char *opt_inName = NULL; /* in file name */
const char *opt_outName = NULL; /* out file name */
const char *opt_outText = NULL;
const char *opt_mapName = NULL;
const char *opt_textName = NULL;
const char *opt_explanation = NULL;
OFCmdFloat opt_gammaValue = 1.0;
OFCmdUnsignedInt opt_bits = 16;
OFCmdUnsignedInt opt_entries = 256;
OFCmdSignedInt opt_firstMapped = 0;
OFCmdUnsignedInt opt_randomCount = 0;
OFCmdUnsignedInt opt_randomSeed = 0; /* default: for reproduceable results */
OFCmdUnsignedInt opt_order = 5;
OFCmdUnsignedInt opt_minDensity = 20;
OFCmdUnsignedInt opt_maxDensity = 300;
OFCmdUnsignedInt opt_illumination = 2000;
OFCmdUnsignedInt opt_reflection = 10;
LUT_Type opt_lutType = LUT_VOI;
OFBool opt_inverseGSDF = OFFalse;
OFBool opt_byteAlign = OFFalse;
OFBool opt_replaceMode = OFTrue;
DcmEVR opt_lutVR = EVR_OW;
SetDebugLevel(( 0 ));
OFCommandLine cmd;
OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION , "Create DICOM look-up tables", rcsid);
cmd.setOptionColumns(LONGCOL, SHORTCOL);
cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
cmd.addParam("dcmimg-out", "DICOM output filename" /* , OFCmdParam::PM_Optional */);
cmd.addGroup("general options:", LONGCOL, SHORTCOL + 2);
cmd.addOption("--help", "-h", "print this help text and exit");
cmd.addOption("--version", "print version information and exit", OFTrue /* exclusive */);
cmd.addOption("--verbose", "-v", "verbose mode, print processing details");
cmd.addOption("--debug", "-d", "debug mode, print debug information");
cmd.addGroup("LUT creation options:");
cmd.addSubGroup("LUT type:");
cmd.addOption("--modality", "+Tm", "create as Modality LUT");
cmd.addOption("--presentation", "+Tp", "create as Presentation LUT");
cmd.addOption("--voi", "+Tv", "create as VOI LUT (default)");
cmd.addSubGroup("LUT placement:");
cmd.addOption("--add", "+Pa", "add to existing transform (def. for and only with +Tv)");
cmd.addOption("--replace", "+Pr", "replace existing transform (default for +Tm and +Tp)");
cmd.addSubGroup("LUT content:");
cmd.addOption("--gamma", "+Cg", 1, "[g]amma : float",
"use gamma value (default: 1.0)");
cmd.addOption("--map-file", "+Cm", 1, "[f]ilename : string",
"read input data from MAP file");
cmd.addOption("--text-file", "+Ct", 1, "[f]ilename : string",
"read input data from text file");
cmd.addSubGroup("LUT options:");
cmd.addOption("--inverse-gsdf", "+Og", "apply inverse GSDF (print presentation LUT in OD)");
cmd.addOption("--min-density", 1, "[v]alue : integer (0..65535, default: 20)",
"set min density to v (in hundreds of OD)");
cmd.addOption("--max-density", 1, "[v]alue : integer (0..65535, default: 300)",
"set max density to v (in hundreds of OD)");
cmd.addOption("--illumination", "+Oi", 1, "[v]alue : integer (0..65535, default: 2000)",
"set illumination to v (in cd/m^2)");
cmd.addOption("--reflection", "+Or", 1, "[v]alue : integer (0..65535, default: 10)",
"set reflected ambient light to v (in cd/m^2)");
cmd.addSubGroup("LUT structure:");
cmd.addOption("--bits", "-b", 1, "[n]umber : integer",
"create LUT with n bit values (8..16, default: 16)");
cmd.addOption("--entries", "-e", 1, "[n]umber : integer",
"create LUT with n entries (1..65536, default: 256)");
cmd.addOption("--first-mapped", "-f", 1, "[n]umber : integer",
"first input value mapped (-31768..65535, default: 0)");
cmd.addOption("--random", "-r", 1, "[n]umber : unsigned integer",
"perform n randomly selected permutations on the LUT");
cmd.addOption("--random-seed", "-rs", 1, "[n]umber : unsigned integer",
"initialise the random-number generator with n\n(default: 0, for reproduceable results)");
cmd.addOption("--order", "-o", 1, "[n]umber : integer",
"use polynomial curve fitting algorithm with order n\n(0..99, default: 5)");
cmd.addOption("--explanation", "-E", 1, "[n]ame : string",
"LUT explanation (default: automatically created)");
cmd.addOption("--byte-align", "-a", "create byte-aligned LUT (implies -b 8)");
cmd.addSubGroup("LUT data VR:");
cmd.addOption("--data-ow", "+Dw", "write LUT Data as OW (default)");
cmd.addOption("--data-us", "+Du", "write LUT Data as US");
cmd.addOption("--data-ss", "+Ds", "write LUT Data as SS (minimal support)");
cmd.addGroup("file options:", LONGCOL, SHORTCOL + 2);
cmd.addOption("--dicom-input", "+Fi", 1, "[f]ilename : string",
"read dataset from DICOM file f");
cmd.addOption("--text-output", "+Fo", 1, "[f]ilename : string",
"write LUT data to tabbed text file f");
/* evaluate command line */
prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION);
if (app.parseCommandLine(cmd, argc, argv, OFCommandLine::ExpandWildcards))
{
/* check exclusive options first */
if (cmd.getParamCount() == 0)
{
if (cmd.findOption("--version"))
{
app.printHeader(OFTrue /*print host identifier*/); // uses ofConsole.lockCerr()
CERR << endl << "External libraries used:";
#ifdef WITH_ZLIB
CERR << endl << "- ZLIB, Version " << zlibVersion() << endl;
#else
CERR << " none" << endl;
#endif
return 0;
}
}
/* command line parameters */
cmd.getParam(1, opt_outName);
if (cmd.findOption("--verbose"))
opt_verbose = OFTrue;
if (cmd.findOption("--debug"))
opt_debugMode = 3;
cmd.beginOptionBlock();
if (cmd.findOption("--modality"))
opt_lutType = LUT_Modality;
if (cmd.findOption("--presentation"))
opt_lutType = LUT_Presentation;
if (cmd.findOption("--voi"))
opt_lutType = LUT_VOI;
cmd.endOptionBlock();
if ((opt_lutType == LUT_Modality) || (opt_lutType == LUT_Presentation))
opt_replaceMode = OFTrue;
else
opt_replaceMode = OFFalse;
cmd.beginOptionBlock();
if (cmd.findOption("--add"))
{
app.checkConflict("--add","--modality", (opt_lutType == LUT_Modality));
app.checkConflict("--add","--presentation", (opt_lutType == LUT_Presentation));
opt_replaceMode = OFFalse;
}
if (cmd.findOption("--replace"))
opt_replaceMode = OFTrue;
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--gamma"))
app.checkValue(cmd.getValue(opt_gammaValue));
if (cmd.findOption("--map-file"))
app.checkValue(cmd.getValue(opt_mapName));
if (cmd.findOption("--text-file"))
app.checkValue(cmd.getValue(opt_textName));
cmd.endOptionBlock();
if (cmd.findOption("--inverse-gsdf"))
opt_inverseGSDF = OFTrue;
if (cmd.findOption("--min-density"))
app.checkValue(cmd.getValue(opt_minDensity));
if (cmd.findOption("--max-density"))
app.checkValue(cmd.getValue(opt_maxDensity));
if (cmd.findOption("--illumination"))
app.checkValue(cmd.getValue(opt_illumination));
if (cmd.findOption("--reflection"))
app.checkValue(cmd.getValue(opt_reflection));
if (cmd.findOption("--bits"))
app.checkValue(cmd.getValueAndCheckMinMax(opt_bits, 8, 16));
if (cmd.findOption("--entries"))
app.checkValue(cmd.getValueAndCheckMinMax(opt_entries, 1, 65536));
if (cmd.findOption("--first-mapped"))
app.checkValue(cmd.getValueAndCheckMinMax(opt_firstMapped, -32768, 65535));
if (cmd.findOption("--explanation"))
app.checkValue(cmd.getValue(opt_explanation));
if (cmd.findOption("--random"))
app.checkValue(cmd.getValueAndCheckMinMax(opt_randomCount, 1, 99999));
if (cmd.findOption("--random-seed"))
app.checkValue(cmd.getValue(opt_randomSeed));
if (cmd.findOption("--order"))
app.checkValue(cmd.getValueAndCheckMinMax(opt_order, 0, 99));
if (cmd.findOption("--byte-align"))
{
opt_byteAlign = OFTrue;
opt_bits = 8;
}
cmd.beginOptionBlock();
if (cmd.findOption("--data-ow"))
opt_lutVR = EVR_OW;
if (cmd.findOption("--data-us"))
opt_lutVR = EVR_US;
if (cmd.findOption("--data-ss"))
opt_lutVR = EVR_SS;
cmd.endOptionBlock();
if (cmd.findOption("--dicom-input"))
app.checkValue(cmd.getValue(opt_inName));
if (cmd.findOption("--text-output"))
app.checkValue(cmd.getValue(opt_outText));
}
if ((opt_lutType == LUT_Modality) && (opt_bits != 8) && (opt_bits != 16))
{
CERR << "Error: --modality cannot be used with --bits other than 8 or 16" << endl;
return 1;
}
if ((opt_bits != 8) && opt_byteAlign)
{
CERR << "Error: --byte-align cannot be used with --bits other than 8" << endl;
return 1;
}
SetDebugLevel(( opt_debugMode ));
/* make sure data dictionary is loaded */
if (!dcmDataDict.isDictionaryLoaded())
CERR << "Warning: no data dictionary loaded, check environment variable: " << DCM_DICT_ENVIRONMENT_VARIABLE << endl;
E_TransferSyntax Xfer= EXS_LittleEndianExplicit;
OFCondition result = EC_Normal;
DcmFileFormat *fileformat = new DcmFileFormat();
if (!fileformat)
{
CERR << "Error: memory exhausted" << endl;
return 1;
}
DcmDataset *dataset = fileformat->getDataset();
if (opt_inName != NULL)
{
OFCondition cond = fileformat->loadFile(opt_inName);
if (! cond.good())
{
CERR << "Error: cannot open file: " << opt_inName << endl;
return 1;
}
Xfer = dataset->getOriginalXfer();
}
/* create Item with LUT */
DcmItem *ditem = new DcmItem();
if (ditem)
{
Uint16 *outputData = new Uint16[opt_entries];
if (outputData == NULL)
result = EC_MemoryExhausted;
else
{
char explStr[1024];
if (opt_explanation != NULL)
strcpy(explStr, opt_explanation);
else
explStr[0] = 0;
OFString headerStr;
double *inputXData = NULL;
double *inputYData = NULL;
unsigned long inputEntries = 0;
double inputXMax = 0;
double inputYMax = 0;
if (readMapFile(opt_mapName, inputXData, inputYData, inputEntries, inputXMax, inputYMax) == EC_Normal)
{
result = convertInputLUT((unsigned int)opt_bits, opt_entries, opt_firstMapped, inputXData, inputYData, inputEntries,
inputXMax, inputYMax, (unsigned int)opt_order, outputData, headerStr, explStr);
}
else if (readTextFile(opt_textName, inputXData, inputYData, inputEntries, inputXMax, inputYMax) == EC_Normal)
{
result = convertInputLUT((unsigned int)opt_bits, opt_entries, opt_firstMapped, inputXData, inputYData, inputEntries,
inputXMax, inputYMax, (unsigned int)opt_order, outputData, headerStr, explStr);
} else {
gammaLUT((unsigned int)opt_bits, opt_entries, opt_firstMapped, opt_byteAlign, opt_gammaValue, outputData, headerStr, explStr);
}
if (result == EC_Normal)
{
if (opt_inverseGSDF)
applyInverseGSDF((unsigned int)opt_bits, opt_entries, opt_byteAlign, (unsigned int)opt_minDensity, (unsigned int)opt_maxDensity,
(unsigned int)opt_illumination, (unsigned int)opt_reflection, outputData, headerStr, explStr);
if (opt_randomCount > 0)
mixingUpLUT(opt_entries, opt_byteAlign, opt_randomCount, (unsigned int)opt_randomSeed, outputData, explStr);
result = createLUT((unsigned int)opt_bits, opt_entries, opt_firstMapped, opt_byteAlign, opt_lutVR, *ditem,
outputData, explStr);
}
delete[] inputXData;
delete[] inputYData;
writeTextOutput(opt_outText, opt_entries, opt_firstMapped, outputData, headerStr);
}
delete[] outputData;
if (EC_Normal != result)
{
CERR << "Error: could not create LUT, bailing out." << endl;
return 1;
}
} else
result = EC_MemoryExhausted;
if (opt_outName != NULL)
{
DcmSequenceOfItems *dseq = NULL;
if (EC_Normal==result)
{
switch (opt_lutType)
{
case LUT_Modality:
{
DcmLongString modalityLUTType(DCM_ModalityLUTType);
modalityLUTType.putString("US"); // unspecified Modality LUT
DcmElement *delem = new DcmLongString(modalityLUTType);
if (delem)
{
ditem->insert(delem, OFTrue /*replaceOld*/);
dseq = new DcmSequenceOfItems(DCM_ModalityLUTSequence);
if (dseq)
{
dataset->insert(dseq, OFTrue);
dseq->insert(ditem);
} else
result = EC_MemoryExhausted;
delete dataset->remove(DCM_RescaleIntercept);
delete dataset->remove(DCM_RescaleSlope);
delete dataset->remove(DCM_RescaleType);
} else
result = EC_MemoryExhausted;
}
break;
case LUT_Presentation:
if (!opt_replaceMode)
{
// search existing sequence
DcmStack stack;
if (EC_Normal == dataset->search(DCM_PresentationLUTSequence, stack, ESM_fromHere, OFFalse))
dseq=(DcmSequenceOfItems *)stack.top();
}
if (dseq==NULL)
{
dseq = new DcmSequenceOfItems(DCM_PresentationLUTSequence);
if (dseq)
dataset->insert(dseq, OFTrue);
else
result = EC_MemoryExhausted;
}
if (dseq)
dseq->insert(ditem);
if (opt_replaceMode)
delete dataset->remove(DCM_PresentationLUTShape);
break;
case LUT_VOI:
if (!opt_replaceMode)
{
// search existing sequence
DcmStack stack;
if (EC_Normal == dataset->search(DCM_VOILUTSequence, stack, ESM_fromHere, OFFalse))
dseq=(DcmSequenceOfItems *)stack.top();
}
if (dseq==NULL)
{
dseq = new DcmSequenceOfItems(DCM_VOILUTSequence);
if (dseq)
dataset->insert(dseq, OFTrue);
else
result = EC_MemoryExhausted;
}
if (dseq)
dseq->insert(ditem);
if (opt_replaceMode)
{
delete dataset->remove(DCM_WindowCenter);
delete dataset->remove(DCM_WindowWidth);
delete dataset->remove(DCM_WindowCenterWidthExplanation);
}
break;
}
}
if (result != EC_Normal)
{
CERR << "error while adding LUT to image dataset. Bailing out."<< endl;
return 1;
}
if (opt_verbose)
CERR << "writing DICOM file ..." << endl;
result = fileformat->saveFile(opt_outName, Xfer);
if (result.bad())
{
CERR << "Error: " << result.text() << ": writing file: " << opt_outName << endl;
return 1;
}
}
return 0;
}
/*
* CVS/RCS Log:
* $Log: dcmmklut.cc,v $
* Revision 1.39 2005/12/08 15:46:03 meichel
* Changed include path schema for all DCMTK header files
*
* Revision 1.38 2005/11/28 15:29:05 meichel
* File dcdebug.h is not included by any other header file in the toolkit
* anymore, to minimize the risk of name clashes of macro debug().
*
* Revision 1.37 2004/02/04 15:44:38 joergr
* Removed acknowledgements with e-mail addresses from CVS log.
*
* Revision 1.36 2003/09/03 16:01:01 meichel
* Fixed bug in command line evaluation
*
* Revision 1.35 2003/04/14 14:28:02 meichel
* Added explicit typecasts in calls to pow(). Needed by Visual C++ .NET 2003.
*
* Revision 1.34 2002/12/04 10:41:33 meichel
* Changed toolkit to use OFStandard::ftoa instead of sprintf for all
* double to string conversions that are supposed to be locale independent
*
* Revision 1.33 2002/11/27 15:47:48 meichel
* Adapted module dcmpstat to use of new header file ofstdinc.h
*
* Revision 1.32 2002/11/26 08:44:25 meichel
* Replaced all includes for "zlib.h" with <zlib.h>
* to avoid inclusion of zlib.h in the makefile dependencies.
*
* Revision 1.31 2002/09/23 18:26:05 joergr
* Added new command line option "--version" which prints the name and version
* number of external libraries used (incl. preparation for future support of
* 'config.guess' host identifiers).
*
* Revision 1.30 2002/08/20 12:21:52 meichel
* Adapted code to new loadFile and saveFile methods, thus removing direct
* use of the DICOM stream classes.
*
* Revision 1.29 2002/05/02 14:10:03 joergr
* Added support for standard and non-standard string streams (which one is
* supported is detected automatically via the configure mechanism).
*
* Revision 1.28 2002/04/16 14:01:25 joergr
* Added configurable support for C++ ANSI standard includes (e.g. streams).
*
* Revision 1.27 2001/11/28 13:58:42 joergr
* Check return value of DcmItem::insert() statements where appropriate to
* avoid memory leaks when insert procedure fails.
*
* Revision 1.26 2001/11/09 16:06:03 joergr
* Renamed some of the getValue/getParam methods to avoid ambiguities reported
* by certain compilers.
*
* Revision 1.25 2001/09/28 13:47:36 joergr
* Added check whether ios::nocreate exists.
*
* Revision 1.24 2001/09/26 15:36:00 meichel
* Adapted dcmpstat to class OFCondition
*
* Revision 1.23 2001/06/07 14:34:08 joergr
* Removed comment.
*
* Revision 1.21 2001/06/01 15:50:06 meichel
* Updated copyright header
*
* Revision 1.20 2000/12/12 16:45:35 meichel
* Minor changes to keep gcc 2.7.x on SunOS 4.1.3 happy
*
* Revision 1.19 2000/12/11 18:18:09 joergr
* Added explicit typecast to keep SunCC 2.0.1 quiet.
*
* Revision 1.18 2000/10/16 12:26:05 joergr
* Added new feature: create inverse GSDF (useful for printer output).
*
* Revision 1.17 2000/07/04 16:09:22 joergr
* Added new option to command line tool allowing to specify the 'seed' value
* for the random-number generator.
*
* Revision 1.16 2000/06/09 10:22:25 joergr
* Added new commandline option allowing to mix-up the LUT entries based on
* a random-number generator (useful to test correct implementation of LUTs).
*
* Revision 1.15 2000/05/30 14:02:43 joergr
* Corrected typo/formatting.
*
* Revision 1.14 2000/03/08 16:28:41 meichel
* Updated copyright header.
*
* Revision 1.13 2000/03/07 16:17:11 joergr
* Added explicit type casts to make Sun CC 2.0.1 happy.
*
* Revision 1.12 2000/03/06 18:21:44 joergr
* Avoid empty statement in the body of if-statements (MSVC6 reports warnings).
*
* Revision 1.11 2000/03/03 14:13:24 meichel
* Implemented library support for redirecting error messages into memory
* instead of printing them to stdout/stderr for GUI applications.
*
* Revision 1.10 2000/02/02 14:38:24 joergr
* Removed space characters before preprocessor directives.
*
* Revision 1.9 1999/10/18 10:21:31 joergr
* Enlarged string buffer for output text file header.
*
* Revision 1.8 1999/10/15 09:35:05 joergr
* Enhanced checking mechanism for input text files.
*
* Revision 1.7 1999/10/14 20:21:29 joergr
* Fixed problems with MSVC.
*
* Revision 1.6 1999/10/14 19:08:48 joergr
* Merged command line tool 'dconvmap' into 'dcmmklut' and enhanced its
* facilities (e.g. integrated new polynomial curve fitting algorithm).
*
* Revision 1.5 1999/07/28 11:21:07 meichel
* New options in dcmmklut:
* - creation of LUTs with 65536 entries
* - creation of LUT data with VR=OW, US or SS
* - creation of LUT descriptor with VR=US or SS
*
* Revision 1.4 1999/05/04 15:27:22 meichel
* Minor code purifications to keep gcc on OSF1 quiet.
*
* Revision 1.3 1999/05/03 14:16:37 joergr
* Minor code purifications to keep Sun CC 2.0.1 quiet.
*
* Revision 1.2 1999/04/28 15:45:05 meichel
* Cleaned up module dcmpstat apps, adapted to new command line class
* and added short documentation.
*
* Revision 1.1 1998/12/14 16:05:48 meichel
* Added sample application that creates Modality and VOI LUTs
* with gamma curve characteristics.
*
* Revision 1.1 1998/11/27 14:50:19 meichel
* Initial Release.
*
*/
|