[Olena-patches] milena r3423: Fix DICOM implementation: was DCMTK, now is GDCM

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-25 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Fix DICOM implementation: was DCMTK, now is GDCM. * mln/io/dicom/load.hh: GDCM version. --- load.hh | 338 ++++++++++++---------------------------------------------------- 1 file changed, 65 insertions(+), 273 deletions(-) Index: trunk/milena/mln/io/dicom/load.hh =================================================================== --- trunk/milena/mln/io/dicom/load.hh (revision 3422) +++ trunk/milena/mln/io/dicom/load.hh (revision 3423) @@ -25,72 +25,27 @@ // 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 + * \file mln/io/magick/load.hh * - * \brief Define a function which loads an image of kind dicom with + * \brief Define a function which loads an image of kind magick with * given path. * */ -# include <mln/io/pnm/load.hh> +# include <mln/core/image/image2d.hh> +# include <mln/core/image/image3d.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 '/' +# include <mln/algebra/vec.hh> +# include <gdcmReader.h> +# include <gdcmImageReader.h> +# include <gdcmWriter.h> +# include <gdcmDataSet.h> +# include <gdcmAttribute.h> namespace mln @@ -112,37 +67,15 @@ 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"); + trace::entering("mln::io::gdcm::load"); + image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); + trace::exiting("mln::io::gdcm::load"); return ima; } @@ -150,228 +83,87 @@ 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"); + trace::entering("mln::io::gdcm::load"); + image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); + trace::exiting("mln::io::gdcm::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) + inline + void load(Image<I>& ima_, + const std::string& filename) { - 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; - } - } - } + trace::entering("mln::io::gdcm::load"); - /* print the tag and its value */ - DcmObject *dobj = stack.top(); - dobj->print(std::cout, printFlags); - } + using value::int_u16; + I& ima = exact(ima_); - 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) + gdcm::ImageReader r; + r.SetFileName(filename.c_str()); + if (!r.Read()) { - int result = 0; + std::cerr << "error: cannot open file '" << filename << "'!"; + abort(); + } - DcmFileFormat dfile; - DcmObject *dset = &dfile; + gdcm::File &file = r.GetFile(); + gdcm::DataSet& ds = file.GetDataSet(); - if (readMode == ERM_dataset) - dset = dfile.getDataset(); + gdcm::Image& image = r.GetImage(); - // Load file + char* dataBuffer = new char[image.GetBufferLength()]; + image.GetBuffer(dataBuffer); - OFCondition cond = dfile.loadFile(ifname, xfer, EGL_noChange, maxReadLength, readMode); + int ndims = image.GetNumberOfDimensions(); + const unsigned int* dims = image.GetDimensions(); - // Read error + unsigned short bytes_allocated = image.GetPixelFormat().GetBitsAllocated() / 8; + unsigned short samples_per_pixel = image.GetPixelFormat().GetSamplesPerPixel(); - if (!cond.good()) + if (mln_site_(I)::dim != ndims) { - std::cerr << "error: " << dfile.error().text() - << ": reading file: "<< ifname << endl; - result = 1; - if (stopOnErrors) - return result; + std::cerr << "error: dimension mismatch" << std::endl; + abort(); } - 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++) + algebra::vec<mln_site_(I)::dim, unsigned int> vmin; + algebra::vec<mln_site_(I)::dim, unsigned int> vmax; + algebra::vec<mln_site_(I)::dim, unsigned int> vdims; + for (int i = ndims - 1; i >= 0; --i) { - unsigned int group = 0xffff; - unsigned int elem = 0xffff; - DcmTagKey searchKey; - const char* tagName = printTagNames[i]; - if (printTagKeys[i]) - searchKey = *printTagKeys[i]; + vmin[i] = 0; + vmax[i] = dims[ndims - i - 1] - 1; + if (i == ndims - 1) + vdims[i] = 1; 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(); - } + vdims[i] = dims[ndims - i - 2] * vdims[i + 1]; } - DcmStack stack; - if (dset->search(searchKey, stack, ESM_fromHere, OFTrue) == EC_Normal) + mln_site(I) pmin(vmin); + mln_site(I) pmax(vmax); + mln_concrete(I) result(box<mln_site(I)>(pmin, pmax)); + initialize(ima, result); + mln_piter(I) p(ima.domain()); + unsigned int index = 0; + for_all(p) { - printResult(ima, stack, printFlags); - if (printAllInstances) + index = 0; + for (int i = 0; i < ndims; ++i) { - while (dset->search(searchKey, stack, ESM_afterStackTop, OFTrue) == EC_Normal) - printResult(ima, stack, printFlags); - } + index += p.to_site().to_vec()[i] * vdims[i]; } - } - } - - return result; - } - - - template <typename I> - inline - void load(Image<I>& ima, - const std::string& filename) + ima(p) = dataBuffer[index * bytes_allocated * samples_per_pixel]; + // FIXME: RGB support, HighBit + for (int j = 1; j < bytes_allocated; ++j) { - trace::entering("mln::io::dicom::load"); - - std::ifstream file(filename.c_str()); - if (! file) - { - std::cerr << "error: cannot open file '" << filename << "'!"; - abort(); + ima(p) *= 256; + ima(p) += dataBuffer[(index * bytes_allocated + j) * samples_per_pixel]; } - - 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); + delete(dataBuffer); trace::exiting("mln::io::dicom::load"); }