URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-23 Fabien Freling <fabien.freling@lrde.epita.fr> Add DICOM support. * mln/io/dicom/load.hh: DICOM support through GDCM library. --- load.hh | 388 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 388 insertions(+) Index: trunk/milena/mln/io/dicom/load.hh =================================================================== --- trunk/milena/mln/io/dicom/load.hh (revision 0) +++ trunk/milena/mln/io/dicom/load.hh (revision 3418) @@ -0,0 +1,388 @@ +// Copyright (C) 2009 EPITA Research and Development Laboratory +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +/* + * + * Copyright (C) 1994-2005, 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: dcmdata + * + * Author: Gerd Ehlers + * + * Purpose: List the contents of a dicom file + * + * Last Update: $Author: meichel $ + * Update Date: $Date: 2005/12/08 15:40:46 $ + * CVS/RCS Revision: $Revision: 1.55 $ + * Status: $State: Exp $ + * + * CVS/RCS Log at end of file + * + */ + +#ifndef MLN_IO_DICOM_LOAD_HH +# define MLN_IO_DICOM_LOAD_HH + +/*! + * \file mln/io/dicom/load.hh + * + * \brief Define a function which loads an image of kind dicom with + * given path. + * + */ + +# include <mln/io/pnm/load.hh> + +# include <dcmtk/config/osconfig.h> /* make sure OS specific configuration is included first */ +# include <dcmtk/ofstd/ofstream.h> +# include <dcmtk/dcmdata/dctk.h> +# include <dcmtk/dcmdata/dcdebug.h> +# include <dcmtk/dcmdata/cmdlnarg.h> +# include <dcmtk/ofstd/ofconapp.h> +# include <dcmtk/dcmdata/dcuid.h> /* for dcmtk version name */ +# include <dcmtk/dcmdata/dcistrmz.h> /* for dcmZlibExpectRFC1950Encoding */ + +# define INCLUDE_CSTDLIB +# define INCLUDE_CSTRING +# include <dcmtk/ofstd/ofstdinc.h> + +# ifdef WITH_ZLIB +# include <zlib.h> /* for zlibVersion() */ +# endif + +# define SHORTCOL 3 +# define LONGCOL 20 +# define PATH_SEPARATOR '/' + + + +namespace mln +{ + + namespace io + { + + namespace dicom + { + + /*! Load a dicom image in a Milena image. + * + * \param[out] ima A reference to the image which will receive + * data. + * \param[in] filename The source. + */ + template <typename I> + void load(Image<I>& ima, + const std::string& filename); + + /*! Load a dicom image in a Milena image. To use this routine, you + * should specialize the template whith the value type of the + * image loaded. (ex : load<value::int_u8>("...") ) + * + * \param[in] filename The image source. + * + * \return An image2d which contains loaded data. + */ + template <typename V> + image2d<V> load(const std::string& filename); + + /*! Load a dicom image in a Milena image. To use this routine, you + * should specialize the template whith the value type of the + * image loaded. (ex : load<value::int_u8>("...") ) + * + * \param[in] filename The image source. + * + * \return An image2d which contains loaded data. + */ + template <typename V> + image3d<V> load(const std::string& filename); + +# ifndef MLN_INCLUDE_ONLY + + template <typename V> + inline + image2d<V> load(const std::string& filename) + { + trace::entering("mln::io::dicom::load"); + image2d<V> ima;// = io::pnm::load<V>(DICOM, filename); + trace::exiting("mln::io::dicom::load"); + return ima; + } + + template <typename V> + inline + image3d<V> load(const std::string& filename) + { + trace::entering("mln::io::dicom::load"); + image2d<V> ima;// = io::pnm::load<V>(DICOM, filename); + trace::exiting("mln::io::dicom::load"); + return ima; + } + + + + + + + static OFBool printAllInstances = OFTrue; + static OFBool prependSequenceHierarchy = OFFalse; + static int printTagCount = 0; + static const int MAX_PRINT_TAG_NAMES = 1024; + static const char* printTagNames[MAX_PRINT_TAG_NAMES]; + static const DcmTagKey* printTagKeys[MAX_PRINT_TAG_NAMES]; + static OFCmdUnsignedInt maxReadLength = 4096; // default is 4 KB + + static OFBool addPrintTagName(const char* tagName) + { + if (printTagCount >= MAX_PRINT_TAG_NAMES) { + std::cerr << "error: too many print Tag options (max: " << MAX_PRINT_TAG_NAMES << ")" << endl; + return OFFalse; + } + + unsigned int group = 0xffff; + unsigned int elem = 0xffff; + if (sscanf(tagName, "%x,%x", &group, &elem) != 2) + { + /* it is a name */ + const DcmDataDictionary& globalDataDict = dcmDataDict.rdlock(); + const DcmDictEntry *dicent = globalDataDict.findEntry(tagName); + if (dicent == NULL) + { + std::cerr << "error: unrecognised tag name: '" << tagName << "'" << endl; + dcmDataDict.unlock(); + return OFFalse; + } + else + { + /* note for later */ + printTagKeys[printTagCount] = new DcmTagKey(dicent->getKey()); + } + dcmDataDict.unlock(); + } + else + { + /* tag name has format xxxx,xxxx */ + /* do not lookup in dictionary, tag could be private */ + printTagKeys[printTagCount] = NULL; + } + + printTagNames[printTagCount] = strcpy(OFstatic_cast(char*, malloc(strlen(tagName)+1)), tagName); + printTagCount++; + return OFTrue; + } + + + template <typename I> + static void printResult(Image<I>& ima, DcmStack& stack, size_t printFlags) + { + unsigned long n = stack.card(); + if (n == 0) + return; + + if (prependSequenceHierarchy) { + /* print the path leading up to the top stack elem */ + for (unsigned long i = n - 1; i >= 1; i--) { + DcmObject *dobj = stack.elem(i); + /* do not print if a DCM_Item as this is not + * very helpful to distinguish instances. + */ + if (dobj != NULL && dobj->getTag().getXTag() != DCM_Item) { + char buf[512]; + sprintf(buf, "(%x,%x).", + OFstatic_cast(unsigned, dobj->getGTag()), + OFstatic_cast(unsigned, dobj->getETag())); + std::cout << buf; + } + } + } + + /* print the tag and its value */ + DcmObject *dobj = stack.top(); + dobj->print(std::cout, printFlags); + } + + template <typename I> + static int dumpFile(Image<I>& ima, + const char *ifname, + const E_FileReadMode readMode, + const E_TransferSyntax xfer, + const size_t printFlags, + const OFBool loadIntoMemory, + const OFBool stopOnErrors, + const OFBool writePixelData, + const char *pixelDirectory) + { + int result = 0; + + DcmFileFormat dfile; + DcmObject *dset = &dfile; + + if (readMode == ERM_dataset) + dset = dfile.getDataset(); + + // Load file + + OFCondition cond = dfile.loadFile(ifname, xfer, EGL_noChange, maxReadLength, readMode); + + // Read error + + if (!cond.good()) + { + std::cerr << "error: " << dfile.error().text() + << ": reading file: "<< ifname << endl; + result = 1; + if (stopOnErrors) + return result; + } + + if (loadIntoMemory) + dfile.loadAllDataIntoMemory(); + + if (printTagCount == 0) + { + if (writePixelData) + { + OFString str = ifname; + OFString rname = pixelDirectory; + if ((rname.length() > 0) && (rname[rname.length() - 1] != PATH_SEPARATOR)) + rname += PATH_SEPARATOR; + size_t pos = str.find_last_of(PATH_SEPARATOR); + if (pos == OFString_npos) + rname += str; + else + rname += str.substr(pos + 1); + size_t counter = 0; + dset->print(std::cout, printFlags, 0 /*level*/, rname.c_str(), &counter); + } + else + dset->print(std::cout, printFlags); + } + else + { + /* only print specified tags */ + for (int i = 0; i < printTagCount; i++) + { + unsigned int group = 0xffff; + unsigned int elem = 0xffff; + DcmTagKey searchKey; + const char* tagName = printTagNames[i]; + if (printTagKeys[i]) + searchKey = *printTagKeys[i]; + else + { + if (sscanf(tagName, "%x,%x", &group, &elem) == 2) + searchKey.set(group, elem); + else + { + std::cerr << "Internal ERROR in File " << __FILE__ << ", Line " + << __LINE__ << std::endl + << "-- Named tag inconsistency" << std::endl; + abort(); + } + } + + DcmStack stack; + if (dset->search(searchKey, stack, ESM_fromHere, OFTrue) == EC_Normal) + { + printResult(ima, stack, printFlags); + if (printAllInstances) + { + while (dset->search(searchKey, stack, ESM_afterStackTop, OFTrue) == EC_Normal) + printResult(ima, stack, printFlags); + } + } + } + } + + return result; + } + + + template <typename I> + inline + void load(Image<I>& ima, + const std::string& filename) + { + trace::entering("mln::io::dicom::load"); + + std::ifstream file(filename.c_str()); + if (! file) + { + std::cerr << "error: cannot open file '" << filename << "'!"; + abort(); + } + + int opt_debugMode = 0; + OFBool loadIntoMemory = OFTrue; + size_t printFlags = DCMTypes::PF_shortenLongTagValues /*| DCMTypes::PF_showTreeStructure*/; + OFBool printFilename = OFFalse; + OFBool writePixelData = OFFalse; + E_FileReadMode readMode = ERM_autoDetect; + E_TransferSyntax xfer = EXS_Unknown; + OFBool stopOnErrors = OFTrue; + const char *current = NULL; + const char *pixelDirectory = NULL; + + + /* make sure data dictionary is loaded */ + if (!dcmDataDict.isDictionaryLoaded()) + { + std::cerr << "Warning: no data dictionary loaded, " + << "check environment variable: " + << DCM_DICT_ENVIRONMENT_VARIABLE; + } + + int errorCount = 0; + dumpFile(ima, current, readMode, xfer, printFlags, loadIntoMemory, stopOnErrors, + writePixelData, pixelDirectory); + + trace::exiting("mln::io::dicom::load"); + } + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::io::dicom + + } // end of namespace mln::io + +} // end of namespace mln + + +#endif // ! MLN_IO_DICOM_LOAD_HH