February 2009 - Olena-patches

milena r3433: Fix dimensions bug
by Fabien Freling 27 Feb '09

27 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-27 Fabien Freling <fabien.freling(a)lrde.epita.fr> Fix dimensions bug. * mln/io/dicom/load.hh: Fix dimensions bug. --- load.hh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) Index: trunk/milena/mln/io/dicom/load.hh =================================================================== --- trunk/milena/mln/io/dicom/load.hh (revision 3432) +++ trunk/milena/mln/io/dicom/load.hh (revision 3433) @@ -139,14 +139,14 @@ 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) + for (int i = 0; i < ndims; ++i) { vmin[i] = 0; - vmax[i] = dims[ndims - i - 1] - 1; - if (i == ndims - 1) + vmax[i] = dims[i] - 1; + if (i == 0) vdims[i] = 1; else - vdims[i] = dims[ndims - i - 2] * vdims[i + 1]; + vdims[i] = dims[i - 1] * vdims[i - 1]; } mln_site(I) pmin(vmin); @@ -169,9 +169,9 @@ { ima(p) += ((unsigned char) dataBuffer[(index * bytes_allocated + j) * samples_per_pixel]) * 256 * j; } - /*std::cout << "[ x = " << p.to_site().to_vec()[2] + /*std::cout << "[ x = " << p.to_site().to_vec()[0] << " | y = " << p.to_site().to_vec()[1] - << " | z = " << p.to_site().to_vec()[0] + << " | z = " << p.to_site().to_vec()[2] << " ] => " << ima(p) << std::endl;*/ }

1 0

r3432: Clean sandbox
by Fabien Freling 27 Feb '09

27 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-27 Fabien Freling <fabien.freling(a)lrde.epita.fr> Clean sandbox. * fabien/dcmtk/Makefile: New. * fabien/dcmtk/dicom.cc: New. * fabien/dcmtk: New. * fabien/dicom/load.hh: Remove. * fabien/dicom/save.hh: Remove. * fabien/dicom: Remove. * fabien/gdcm/Makefile: Remove. * fabien/gdcm/dump2pgm.cc: Remove. * fabien/gdcm/gdcm.cc: Remove. * fabien/gdcm/load.hh: Remove. * fabien/gdcm: Remove. * fabien/igr/Makefile: New. * fabien/igr/dump2pbm.cc: New. * fabien/igr/seg_vol_irm.cc: New. --- dcmtk/Makefile | 2 dcmtk/dicom.cc | 14 dcmtk/load.hh | 388 +++++++++++++++++++++ dcmtk/save.hh | 951 +++++++++++++++++++++++++++++++++++++++++++++++++++++ igr/Makefile | 15 igr/dump2pbm.cc | 35 + igr/seg_vol_irm.cc | 267 ++++++++++++++ 7 files changed, 1672 insertions(+) Index: trunk/milena/sandbox/fabien/igr/seg_vol_irm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/seg_vol_irm.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/seg_vol_irm.cc (revision 3432) @@ -0,0 +1,267 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development +// Laboratory (LRDE) +// +// 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. + +#include <mln/core/concept/image.hh> +#include <mln/core/concept/neighborhood.hh> +#include <mln/core/alias/neighb1d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/alias/neighb3d.hh> + +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u12.hh> +#include <mln/value/int_u16.hh> +#include <mln/value/rgb8.hh> + +#include <mln/io/pgm/all.hh> +#include <mln/io/pbm/all.hh> +#include <mln/io/ppm/all.hh> +#include <mln/io/cloud/all.hh> +#include <mln/io/dump/all.hh> +#include <mln/io/dicom/load.hh> + +#include <mln/labeling/flat_zones.hh> +#include <mln/labeling/background.hh> +#include <mln/literal/colors.hh> +#include <mln/norm/l1.hh> + +#include <mln/geom/bbox.hh> + +#include <mln/labeling/blobs.hh> +#include <mln/labeling/compute.hh> +#include <mln/labeling/fill_holes.hh> +#include <mln/labeling/n_max.hh> + +#include <mln/level/compare.hh> +#include <mln/level/compute.hh> +#include <mln/level/transform.hh> + +#include <mln/fun/internal/selector.hh> + +#include <mln/fun/v2b/threshold.hh> +#include <mln/level/transform.hh> + +#include <mln/accu/count.hh> +#include <mln/accu/center.hh> +#include <mln/accu/max.hh> + +#include <mln/histo/compute.hh> + +#include <mln/set/compute.hh> +#include <mln/value/label_16.hh> +#include <mln/data/fill.hh> +#include <mln/pw/all.hh> + +#include <mln/morpho/elementary/gradient_internal.hh> +#include <mln/morpho/opening_area.hh> + +#include <mln/convert/from_to.hh> + +//FIXME: remove +#include <mln/essential/2d.hh> +#include <iostream> +#include <mln/debug/println.hh> + +using namespace mln; +using value::int_u8; +using value::int_u12; +using value::int_u16; +using value::rgb8; +using value::label_16; + + + +template <typename T> +struct L_to_int_u8 +: mln::fun::internal::selector_<int_u8, T, L_to_int_u8<T> >::ret +{ + typedef int_u8 result; + int_u8 operator()(const T& t) const; +}; + + +template <typename T> +inline +int_u8 +L_to_int_u8<T>::operator()(const T& t) const +{ + return static_cast<int_u8>(t == 0 ? 0 : 1 + ((unsigned) t - 1) % 255); +} + + +template <typename I> +unsigned +find_threshold_value(const Image& input_) +{ + const I& input = exact(input_); + + histo::array<mln_value(I)> arr_histo = histo::compute(input); + + image1d<unsigned> ima_histo; + convert::from_to(arr_histo, ima_histo); + + ima_histo(point1d(0)) = 0; + + //ima_histo = morpho::opening_area(ima_histo, c2(), 5); + //mln_fwd_piter(image1d<unsigned>) p(ima_histo.domain()); + for (unsigned int i = 1; i < ima_histo.nelements(); ++i) + { + ima_histo(point1d(i)) += ima_histo(point1d(i - 1)); + } + accu::max<unsigned> max_accu; + unsigned max = level::compute(max_accu, ima_histo); + for (unsigned int i = 0; i < ima_histo.nelements(); ++i) + { + //std::cout << "[" < " << ((ima_histo(point1d(i)) * 100) / max) << std::endl; + if (((ima_histo(point1d(i)) * 100) / max) > 70) + return i; + } +} + + +template <typename I, typename N, typename L> +mln_ch_value(I, bool) +igr(const Image& input_, const mln::Neighborhood<N>& nbh_, L& nlabels) +{ + const I& input = exact(input_); + const N& nbh = exact(nbh_); + + // Threshold. + + unsigned threshold_value = find_threshold_value(input_); + mln_ch_value(I, bool) ima_thres; + initialize(ima_thres, input); + data::fill((ima_thres | pw::value(input) < pw::cst(threshold_value)).rw(), true); + + return ima_thres; + + // Labeling. + + /*mln_ch_value(I, L) labels = labeling::flat_zones(threshold, nbh, nlabels); + accu::count<int_u8> a_; + util::array<unsigned> a = labeling::compute(a_, threshold, labels, nlabels); + + // We keep the third and second biggest object. + + mln_ch_value(I, bool) big_second; + initialize(big_second, input); + data::fill(big_second, false); + + util::array<L> arr_big = labeling::n_max<L>(a, 3); + data::fill((big_second | (pw::value(labels) == arr_big[2])).rw(), true); + mln_VAR(big_third, threshold | pw::value(labels) == arr_big[3]); + + // Fill holes. + + big_second = labeling::fill_holes(big_second, nbh, nlabels); + + // Gradient. + + mln_ch_value(I, bool) gradient = morpho::elementary::gradient_internal(big_second, nbh); + mln_VAR(gradient_map, gradient | pw::value(gradient) == true); + + mln_ch_value(I, rgb8) result = level::convert(rgb8(), input); + data::fill((result | gradient_map.domain()).rw(), literal::red); + + // Center. + + accu::center<mln_site(I)> center_; + mln_site(I) center = set::compute(center_, big_third.domain()); + result(center) = literal::blue; + + // Distance. + + mln_fwd_piter(gradient_map_t) p(gradient_map.domain()); + p_array<mln_site(I)> arr; + for_all(p) + { + if (mln::norm::l1_distance(p.to_site().to_vec(), center.to_vec()) < 200) + { + result(p) = literal::green; + + arr.append(p); + } + } + + // Save the cloud in a file. + + io::cloud::save(arr, "cloud.txt"); + + return result;*/ +} + +int main() +{ + //trace::quiet = false; + + label_16 nlabels; + + std::cout << "Processing IM_0043..." << std::endl; + image3d<int_u12> im43; + io::dicom::load(im43, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0043.dcm"); + io::dump::save(igr(im43, c6(), nlabels), "IM_0043.dump"); + + std::cout << "Processing IM_0046..." << std::endl; + image3d<int_u12> im46; + io::dicom::load(im46, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0046.dcm"); + io::dump::save(igr(im46, c6(), nlabels), "IM_0046.dump"); + + std::cout << "Processing IM_0049..." << std::endl; + image2d<int_u12> im49; + io::dicom::load(im49, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm"); + io::pbm::save(igr(im49, c6(), nlabels), "IM_0049.pbm"); + + std::cout << "Processing IM_0052..." << std::endl; + image3d<int_u12> im52; + io::dicom::load(im52, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm"); + io::dump::save(igr(im52, c6(), nlabels), "IM_0052.dump"); + + std::cout << "Processing IM_0055..." << std::endl; + image2d<int_u12> im55; + io::dicom::load(im55, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm"); + io::pbm::save(igr(im55, c6(), nlabels), "IM_0055.pbm"); + + std::cout << "Processing IM_0058..." << std::endl; + image2d<int_u12> im58; + io::dicom::load(im58, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm"); + io::pbm::save(igr(im58, c6(), nlabels), "IM_0058.pbm"); + + std::cout << "Processing IM_0061..." << std::endl; + image3d<int_u12> im61; + io::dicom::load(im61, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm"); + io::dump::save(igr(im61, c6(), nlabels), "IM_0061.dump"); + + std::cout << "Processing IM_0064..." << std::endl; + image3d<int_u12> im64; + io::dicom::load(im64, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm"); + io::dump::save(igr(im64, c6(), nlabels), "IM_0064.dump"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/dump2pbm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/dump2pbm.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/dump2pbm.cc (revision 3432) @@ -0,0 +1,35 @@ + +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> +#include <mln/debug/slices_2d.hh> + +#include <mln/value/int_u16.hh> +#include <mln/io/dump/load.hh> +#include <mln/io/pbm/save.hh> + +#include <mln/literal/colors.hh> + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.dump output.pbm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u16; + + if (argc != 3) + usage(argv); + + image3d<bool> vol; + io::dump::load(vol, argv[1]); + + int_u16 bg = 0; + image2d<bool> ima = debug::slices_2d(vol, 1.f, bg); + io::pbm::save(ima, argv[2]); +} Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3432) @@ -0,0 +1,15 @@ +all: seg_vol_irm.cc + g++ -I../../../ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/Common/ \ + -I/Users/HiSoKa/Downloads/gdcmbin/Source/Common/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/DataDictionary/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/MediaStorageAndFileFormat/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/DataStructureAndEncodingDefinition/ \ + -L/Users/HiSoKa/Downloads/gdcmbin/bin \ + -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \ + -framework CoreFoundation \ + -g \ + seg_vol_irm.cc -o seg_vol_irm + +clean: + rm -rf *.dump *.p?m Index: trunk/milena/sandbox/fabien/dcmtk/dicom.cc =================================================================== --- trunk/milena/sandbox/fabien/dcmtk/dicom.cc (revision 0) +++ trunk/milena/sandbox/fabien/dcmtk/dicom.cc (revision 3432) @@ -0,0 +1,14 @@ +#include <mln/core/image/image2d.hh> +#include <mln/value/int_u8.hh> + +#include "load.hh" + +int main() +{ + using namespace mln; + using value::int_u8; + + image2d<int_u8> lena; + + io::dicom::load(lena, "/Users/HiSoKa/Work/LRDE/Olena/resources/data/IM_0001"); +} Index: trunk/milena/sandbox/fabien/dcmtk/save.hh =================================================================== --- trunk/milena/sandbox/fabien/dcmtk/save.hh (revision 0) +++ trunk/milena/sandbox/fabien/dcmtk/save.hh (revision 3432) @@ -0,0 +1,951 @@ +/* + * + * 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: Andreas Barth + * + * Purpose: create a Dicom FileFormat or DataSet from an ASCII-dump + * + * Last Update: $Author: onken $ + * Update Date: $Date: 2005/12/16 09:07:03 $ + * CVS/RCS Revision: $Revision: 1.51 $ + * Status: $State: Exp $ + * + * CVS/RCS Log at end of file + * + */ + +/* + * Input File Description: + * The input file be an output of dcmdump. One element (Tag, VR, value) must + * be written into one line separated by arbitrary spaces or tab characters. + * A # begins a comment that ends at the line end. Empty lines are allowed. + * This parts of a line have the following syntax: + * Tag: (gggg,eeee) + * with gggg and eeee are 4 character hexadecimal values representing + * group- and element-tag. Spaces and Tabs can be anywhere in a Tag + * specification + * VR: Value Representation must be written as 2 characters as in Part 6 + * of the DICOM 3.0 standard. No Spaces or Tabs are allowed between the + * two characters. If the VR can determined from the Tag, this part of + * a line is optional. + * Value: There are several rules for writing values: + * 1. US, SS, SL, UL, FD, FL are written as + * decimal strings that can be read by scanf. + * 2. AT is written as (gggg,eeee) with additional spaces stripped off + * automatically and gggg and eeee being decimal strings that + * can be read by scanf. + * 3. OB, OW values are written as byte or word hexadecimal values + * separated by '\' character. Alternatively, OB or OW values can + * be read from a separate file by writing the filename prefixed + * by a '=' character (e.g. =largepixeldata.dat). The contents of + * the file will be read as is. OW data is expected to be little + * endian ordered and will be swapped if necessary. No checks will + * be made to ensure that the amount of data is reasonable in terms + * of other attributes such as Rows or Columns. + * 4. UI is written as =Name in data dictionary or as + * unique identifer string (see 6.) , e.g. [1.2.840.....] + * 5. Strings without () <> [] spaces, tabs and # can be + * written directly + * 6. Other strings with must be surrounded by [ ]. No + * bracket structure is passed. The value ends at the last ] in + * the line. Anything after the ] is interpreted as comment. + * 7. ( < are interpreted special and may not be used when writing + * an input file by hand as beginning characters of a string. + * Multiple Value are separated by \ + * The sequence of lines must not be ordered but they can. + * References in DICOM Directories are not supported. + * Semantic errors are not detected. + * + * Examples: + * (0008,0020) DA [19921012] # 8, 1 StudyDate + * (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID + * (0002,0012) UI [1.2.276.0.7230010.100.1.1] + * (0020,0032) DS [0.0\0.0] # 8, 2 ImagePositionPatient + * (0028,0009) AT (3004,000c) # 4, 1 FrameIncrementPointer + * (0028,0010) US 256 # 4, 1 Rows + * (0002,0001) OB 01\00 + * + */ + +#include "dcmtk/config/osconfig.h" + +#define INCLUDE_CSTDLIB +#define INCLUDE_CSTDIO +#define INCLUDE_CCTYPE +#include "dcmtk/ofstd/ofstdinc.h" + +#ifdef HAVE_SYS_TYPES_H +#include <sys/types.h> +#endif +#ifdef HAVE_SYS_STAT_H +#include <sys/stat.h> +#endif +#ifdef HAVE_STAT_H +#include <stat.h> +#endif +#ifdef HAVE_GUSI_H +#include <GUSI.h> +#endif + +#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/ofstd/ofstd.h" +#include "dcmtk/dcmdata/dcuid.h" /* for dcmtk version name */ + +#ifdef WITH_ZLIB +#include <zlib.h> /* for zlibVersion() */ +#endif + +#define OFFIS_CONSOLE_APPLICATION "dump2dcm" + +static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v" + OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $"; + +#define SHORTCOL 3 +#define LONGCOL 21 + +// Maximum Line Size + +const unsigned int DCM_DumpMaxLineSize = 4096; + + +// Field definition separators + +#define DCM_DumpCommentChar '#' +#define DCM_DumpTagDelim ')' +#define DCM_DumpOpenString '[' +#define DCM_DumpCloseString ']' +#define DCM_DumpOpenDescription '(' +#define DCM_DumpOpenFile '<' +#define DCM_DumpCloseFile '>' + +static void +stripWhitespace(char* s) +{ + char* p; + + if (s == NULL) return; + + p = s; + while (*s != '\0') { + if (isspace(*s) == OFFalse) { + *p++ = *s; + } + s++; + } + *p = '\0'; +} + +static char* +stripTrailingWhitespace(char* s) +{ + int i, n; + if (s == NULL) return s; + + n = strlen(s); + for (i = n - 1; i >= 0 && isspace(s[i]); i--) + s[i] = '\0'; + return s; +} + + +static char * +stripPrecedingWhitespace(char * s) +{ + char * p; + if (s == NULL) return s; + + for(p = s; *p && isspace(*p); p++) + ; + + return p; +} + +static OFBool +onlyWhitespace(const char* s) +{ + int len = strlen(s); + int charsFound = OFFalse; + + for (int i=0; (!charsFound) && (i<len); i++) { + charsFound = !isspace(s[i]); + } + return (!charsFound)?(OFTrue):(OFFalse); +} + +static char* +getLine(char* line, int maxLineLen, FILE* f, const unsigned long lineNumber) +{ + char* s; + + s = fgets(line, maxLineLen, f); + + // if line is too long, throw rest of it away + if (s && strlen(s) == size_t(maxLineLen-1) && s[maxLineLen-2] != '\n') + { + int c = fgetc(f); + while(c != '\n' && c != EOF) + c = fgetc(f); + CERR << "line " << lineNumber << " too long." << endl; + } + + /* strip any trailing white space */ + stripTrailingWhitespace(s); + + return s; +} + +static OFBool +isaCommentLine(const char* s) +{ + OFBool isComment = OFFalse; /* assumption */ + int len = strlen(s); + int i = 0; + for (i=0; i<len && isspace(s[i]); i++) /*loop*/; + isComment = (s[i] == DCM_DumpCommentChar); + return isComment; +} + +static OFBool +parseTag(char* & s, DcmTagKey& key) +{ + OFBool ok = OFTrue; + char * p; + unsigned int g, e; + + // find tag begin + p = strchr(s, DCM_DumpTagDelim); + if (p) + { + // string all white spaces and read tag + int len = p-s+1; + p = new char[len+1]; + OFStandard::strlcpy(p, s, len+1); + stripWhitespace(p); + s += len; + + if (sscanf(p, "(%x,%x)", &g, &e) == 2) { + key.set(g, e); + } else { + ok = OFFalse; + } + delete[] p; + } + else ok = OFFalse; + + return ok; +} + + +static OFBool +parseVR(char * & s, DcmEVR & vr) +{ + OFBool ok = OFTrue; + + s = stripPrecedingWhitespace(s); + + // Are there two upper characters? + if (isupper(*s) && isupper(*(s+1))) + { + char c_vr[3]; + OFStandard::strlcpy(c_vr, s, 3); + // Convert to VR + DcmVR dcmVR(c_vr); + vr = dcmVR.getEVR(); + s+=2; + } + else if ((*s == 'p')&&(*(s+1) == 'i')) + { + vr = EVR_pixelItem; + s+=2; + } + else if (((*s == 'o')&&(*(s+1) == 'x')) || ((*s == 'x')&&(*(s+1) == 's')) || + (*s == 'n')&&(*(s+1) == 'a') || ((*s == 'u')&&(*(s+1) == 'p'))) + { + // swallow internal VRs + vr = EVR_UNKNOWN; + s+=2; + } + else ok = OFFalse; + + return ok; +} + + +static int +searchLastClose(char *s, char closeChar) +{ + // search last close bracket in a line + // no bracket structure will be considered + + char * found = NULL; + char * p = s; + + while(p && *p) + { + p = strchr(p, closeChar); + if (p) + { + found = p; + p++; + } + } + + if (found) + return (found - s) + 1; + else + return 0; +} + + +static int +searchCommentOrEol(char *s) +{ + char * comment = strchr(s, DCM_DumpCommentChar); + if (comment) + return comment - s; + else if (s) + return strlen(s); + else + return 0; +} + + +static char* +convertNewlineCharacters(char* s) +{ + // convert the string "\n" into the \r\n combination required by DICOM + if (s == NULL || s[0] == '\0') return s; + int len = strlen(s); + int i = 0; + for (i=0; i<(len-1); i++) { + if (s[i] == '\\' && s[i+1] == 'n') { + s[i] = '\r'; + s[i+1] = '\n'; + i++; + } + } + + return s; +} + +static OFBool +parseValue(char * & s, char * & value, const DcmEVR & vr) +{ + OFBool ok = OFTrue; + int len; + value = NULL; + + s = stripPrecedingWhitespace(s); + + switch (*s) + { + case DCM_DumpOpenString: + len = searchLastClose(s, DCM_DumpCloseString); + if (len == 0) + ok = OFFalse; + else if (len > 2) + { + value = new char[len-1]; + OFStandard::strlcpy(value, s+1, len-1); + value = convertNewlineCharacters(value); + } + else + value = NULL; + break; + + case DCM_DumpOpenDescription: + /* need to distinguish vr=AT from description field */ + /* NB: if the vr is unknown this workaround will not succeed */ + if (vr == EVR_AT) + { + len = searchLastClose(s, DCM_DumpTagDelim); + if (len >= 11) // (gggg,eeee) allow non-significant spaces + { + char *pv = s; + DcmTagKey tag; + if (parseTag(pv, tag)) // check for valid tag format + { + value = new char[len+1]; + OFStandard::strlcpy(value, s, len+1); + stripWhitespace(value); + } else + ok = OFFalse; // skip description + } + else + ok = OFFalse; // skip description + } + break; + + case DCM_DumpOpenFile: + ok = OFFalse; // currently not supported + break; + + case DCM_DumpCommentChar: + break; + + default: + len = searchCommentOrEol(s); + if (len) + { + value = new char[len+1]; + OFStandard::strlcpy(value, s, len+1); + stripTrailingWhitespace(value); + } + break; + } + return ok; +} + + +static unsigned long +fileSize(const char *fname) +{ + struct stat s; + unsigned long nbytes = 0; + + if (stat(fname, &s) == 0) { + nbytes = s.st_size; + } + return nbytes; +} + +static OFCondition +putFileContentsIntoElement(DcmElement* elem, const char* filename) +{ + FILE* f = NULL; + OFCondition ec = EC_Normal; + + if ((f = fopen(filename, "rb")) == NULL) { + CERR << "ERROR: cannot open binary data file: " << filename << endl; + return EC_InvalidTag; + } + + unsigned long len = fileSize(filename); + unsigned long buflen = len; + if (buflen & 1) buflen++; /* if odd then make even (DICOM required even length values) */ + + Uint8* buf = new Uint8[buflen]; + if (buf == NULL) { + CERR << "ERROR: out of memory reading binary data file: " << filename << endl; + ec = EC_MemoryExhausted; + } else if (fread(buf, 1, OFstatic_cast(size_t, len), f) != len) { + CERR << "ERROR: error reading binary data file: " << filename << ": "; + perror(NULL); + ec = EC_CorruptedData; + } else { + /* assign buffer to attribute */ + DcmEVR evr = elem->getVR(); + if (evr == EVR_OB) { + /* put 8 bit OB data into the attribute */ + ec = elem->putUint8Array(buf, buflen); + } else if (evr == EVR_OW) { + /* put 16 bit OW data into the attribute */ + swapIfNecessary(gLocalByteOrder, EBO_LittleEndian, buf, buflen, sizeof(Uint16)); + ec = elem->putUint16Array(OFreinterpret_cast(Uint16 *, buf), buflen / 2); + } else if (evr == EVR_pixelItem) { + /* pixel item not yet supported */ + } + } + + fclose(f); + delete[] buf; + return ec; +} + +static OFCondition +insertIntoSet(DcmStack & stack, DcmTagKey tagkey, DcmEVR vr, char * value) +{ + // insert new Element into dataset or metaheader + + OFCondition l_error = EC_Normal; + OFCondition newElementError = EC_Normal; + + if (stack.empty()) + l_error = EC_CorruptedData; + + if (l_error == EC_Normal) + { + DcmElement * newElement = NULL; + DcmObject * topOfStack = stack.top(); + + // convert tagkey to tag including VR + DcmTag tag(tagkey); + DcmVR dcmvr(vr); + + const DcmEVR tagvr = tag.getEVR(); + if (tagvr != vr && vr != EVR_UNKNOWN && tagvr != EVR_UNKNOWN && + (tagkey != DCM_LUTData || (vr != EVR_US && vr != EVR_SS && vr != EVR_OW)) && + (tagvr != EVR_xs || (vr != EVR_US && vr != EVR_SS)) && + (tagvr != EVR_ox || (vr != EVR_OB && vr != EVR_OW)) && + (tagvr != EVR_na || vr != EVR_pixelItem)) + { + CERR << "Warning: Tag " << tag << " with wrong VR " + << dcmvr.getVRName() << " found, correct is " + << tag.getVR().getVRName() << endl; + } + + if (vr != EVR_UNKNOWN) + tag.setVR(dcmvr); + + // create new element + newElementError = newDicomElement(newElement, tag); + + if (newElementError == EC_Normal) + { + // tag describes an Element + if (!newElement) + // Tag was ambiguous + l_error = EC_InvalidVR; + else + { + // fill value + if (value) + { + if (value[0] == '=' && (tag.getEVR() == EVR_OB || tag.getEVR() == EVR_OW)) + { + /* + * Special case handling for OB or OW data. + * Allow a value beginning with a '=' character to represent + * a file containing data to be used as the attribute value. + * A '=' character is not a normal value since OB and OW values + * must be written as multivalued hexidecimal (e.g. "00\ff\0d\8f"); + */ + l_error = putFileContentsIntoElement(newElement, value+1); + } + else if (tag.getEVR() == EVR_pixelItem) + { + /* pixel items not yet supported */ + l_error = EC_InvalidTag; + } else { + l_error = newElement->putString(value); + } + } + + // insert element into hierarchy + if (l_error == EC_Normal) + { + switch(topOfStack->ident()) + { + case EVR_item: + case EVR_dirRecord: + case EVR_dataset: + case EVR_metainfo: + { + DcmItem *item = OFstatic_cast(DcmItem *, topOfStack); + item -> insert(newElement); + if (newElement->ident() == EVR_SQ || newElement->ident() == EVR_pixelSQ) + stack.push(newElement); + } + break; + default: + l_error = EC_InvalidTag; + break; + } + } + } + } + else if (newElementError == EC_SequEnd) + { + // pop stack if stack object was a sequence + if (topOfStack->ident() == EVR_SQ || topOfStack->ident() == EVR_pixelSQ) + stack.pop(); + else + l_error = EC_InvalidTag; + } + else if (newElementError == EC_ItemEnd) + { + // pop stack if stack object was an item + switch (topOfStack->ident()) + { + case EVR_item: + case EVR_dirRecord: + case EVR_dataset: + case EVR_metainfo: + stack.pop(); + break; + + default: + l_error = EC_InvalidTag; + break; + } + } + else if (newElementError == EC_InvalidTag) + { + if (tag.getXTag() == DCM_Item) + { + DcmItem * item = NULL; + if (topOfStack->getTag().getXTag() == DCM_DirectoryRecordSequence) + { + // an Item must be pushed to the stack + item = new DcmDirectoryRecord(tag, 0); + OFstatic_cast(DcmSequenceOfItems *, topOfStack) -> insert(item); + stack.push(item); + } + else if (topOfStack->ident() == EVR_SQ) + { + // an item must be pushed to the stack + item = new DcmItem(tag); + OFstatic_cast(DcmSequenceOfItems *, topOfStack) -> insert(item); + stack.push(item); + } + else + l_error = EC_InvalidTag; + } + else + l_error = EC_InvalidTag; + } + else + { + l_error = EC_InvalidTag; + } + } + + return l_error; +} + +static OFBool +readDumpFile(DcmMetaInfo * metaheader, DcmDataset * dataset, + FILE * infile, const char * ifname, const OFBool stopOnErrors, + const unsigned long maxLineLength) +{ + char * lineBuf = new char[maxLineLength]; + int lineNumber = 0; + OFBool errorOnThisLine = OFFalse; + char * parse = NULL; + char * value = NULL; + DcmEVR vr = EVR_UNKNOWN; + int errorsEncountered = 0; + DcmTagKey tagkey; + DcmStack metaheaderStack; + DcmStack datasetStack; + + if (metaheader) + metaheaderStack.push(metaheader); + + datasetStack.push(dataset); + + while(getLine(lineBuf, int(maxLineLength), infile, lineNumber+1)) + { + lineNumber++; + + // ignore empty lines and comment lines + if (onlyWhitespace(lineBuf)) + continue; + if (isaCommentLine(lineBuf)) + continue; + + errorOnThisLine = OFFalse; + + parse = &lineBuf[0]; + + // parse tag an the line + if (!parseTag(parse, tagkey)) + { + CERR << OFFIS_CONSOLE_APPLICATION ": "<< ifname << ": " + << "no Tag found (line " << lineNumber << ")"<< endl; + errorOnThisLine = OFTrue; + } + + // parse optional VR + if (!errorOnThisLine && !parseVR(parse, vr)) + vr = EVR_UNKNOWN; + + // parse optional value + if (!errorOnThisLine && !parseValue(parse, value, vr)) + { + CERR << OFFIS_CONSOLE_APPLICATION ": "<< ifname << ": " + << "incorrect value specification (line " << lineNumber << ")"<< endl; + errorOnThisLine = OFTrue; + } + + + // insert new element that consists of tag, VR, and value + if (!errorOnThisLine) + { + OFCondition l_error = EC_Normal; + if (tagkey.getGroup() == 2) + { + if (metaheader) + l_error = insertIntoSet(metaheaderStack, tagkey, vr, value); + } + else + l_error = insertIntoSet(datasetStack, tagkey, vr, value); + + if (value) + { + delete[] value; + value = NULL; + } + if (l_error != EC_Normal) + { + errorOnThisLine = OFTrue; + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Error in creating Element: " + << l_error.text() << " (line " << lineNumber << ")"<< endl; + } + + } + + if (errorOnThisLine) + errorsEncountered++; + } + + + // test blocking structure + if (metaheader && metaheaderStack.card() != 1) + { + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Block Error in metaheader" << endl; + errorsEncountered++; + } + + if (datasetStack.card() != 1) + { + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Block Error in dataset" << endl; + errorsEncountered++; + } + + delete[] lineBuf; + + if (errorsEncountered) + { + CERR << errorsEncountered << " Errors found in " << ifname << endl; + return !stopOnErrors; + } + else + return OFTrue; +} + +// ******************************************** + +int main(int argc, char *argv[]) +{ +#ifdef HAVE_GUSI_H + GUSISetup(GUSIwithSIOUXSockets); + GUSISetup(GUSIwithInternetSockets); +#endif + + SetDebugLevel(( 0 )); + + OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION , "Convert ASCII dump to DICOM file", rcsid); + OFCommandLine cmd; + + cmd.setOptionColumns(LONGCOL, SHORTCOL); + cmd.setParamColumn(LONGCOL + SHORTCOL + 4); + + cmd.addParam("dumpfile-in", "dump input filename"); + cmd.addParam("dcmfile-out", "DICOM output filename"); + + 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("input options:", LONGCOL, SHORTCOL + 2); + cmd.addOption("--line", "+l", 1, "[m]ax-length: integer", + "maximum line length m (default 4096)"); + + cmd.addGroup("output options:"); + cmd.addSubGroup("output file format:"); + cmd.addOption("--write-file", "+F", "write file format (default)"); + cmd.addOption("--write-dataset", "-F", "write data set without file meta information"); + cmd.addSubGroup("output transfer syntax:"); + cmd.addOption("--write-xfer-little", "+te", "write with explicit VR little endian (default)"); + cmd.addOption("--write-xfer-big", "+tb", "write with explicit VR big endian TS"); + cmd.addOption("--write-xfer-implicit", "+ti", "write with implicit VR little endian TS"); + cmd.addSubGroup("error handling:"); + cmd.addOption("--stop-on-error", "-E", "do not write if dump is damaged (default)"); + cmd.addOption("--ignore-errors", "+E", "attempt to write even if dump is damaged"); + cmd.addSubGroup("post-1993 value representations:"); + cmd.addOption("--enable-new-vr", "+u", "enable support for new VRs (UN/UT) (default)"); + cmd.addOption("--disable-new-vr", "-u", "disable support for new VRs, convert to OB"); + cmd.addSubGroup("group length encoding:"); + cmd.addOption("--group-length-recalc", "+g=", "recalculate group lengths if present (default)"); + cmd.addOption("--group-length-create", "+g", "always write with group length elements"); + cmd.addOption("--group-length-remove", "-g", "always write without group length elements"); + cmd.addSubGroup("length encoding in sequences and items:"); + cmd.addOption("--length-explicit", "+e", "write with explicit lengths (default)"); + cmd.addOption("--length-undefined", "-e", "write with undefined lengths"); + cmd.addSubGroup("data set trailing padding (not with --write-dataset):"); + cmd.addOption("--padding-retain", "-p=", "do not change padding\n(default if not --write-dataset)"); + cmd.addOption("--padding-off", "-p", "no padding (implicit if --write-dataset)"); + cmd.addOption("--padding-create", "+p", 2, "[f]ile-pad [i]tem-pad: integer", + "align file on multiple of f bytes\nand items on multiple of i bytes"); + + int opt_debugMode = 0; + const char* ifname = NULL; + const char* ofname = NULL; + E_TransferSyntax oxfer = EXS_LittleEndianExplicit; + E_EncodingType oenctype = EET_ExplicitLength; + E_GrpLenEncoding oglenc = EGL_recalcGL; + E_PaddingEncoding opadenc = EPD_withoutPadding; + OFCmdUnsignedInt opt_filepad = 0; + OFCmdUnsignedInt opt_itempad = 0; + OFCmdUnsignedInt opt_linelength = DCM_DumpMaxLineSize; + OFBool verbosemode = OFFalse; + OFBool stopOnErrors = OFTrue; + OFBool createFileFormat = OFTrue; + + /* 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, ifname); + cmd.getParam(2, ofname); + + if (cmd.findOption("--verbose")) verbosemode = OFTrue; + if (cmd.findOption("--debug")) opt_debugMode = 5; + + if (cmd.findOption("--line")) + { + app.checkValue(cmd.getValueAndCheckMin(opt_linelength, 80)); + } + + cmd.beginOptionBlock(); + if (cmd.findOption("--write-file")) createFileFormat = OFTrue; + if (cmd.findOption("--write-dataset")) createFileFormat = OFFalse; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--write-xfer-little")) oxfer = EXS_LittleEndianExplicit; + if (cmd.findOption("--write-xfer-big")) oxfer = EXS_BigEndianExplicit; + if (cmd.findOption("--write-xfer-implicit")) oxfer = EXS_LittleEndianImplicit; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--stop-on-error")) stopOnErrors = OFTrue; + if (cmd.findOption("--ignore-errors")) stopOnErrors = OFFalse; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--enable-new-vr")) + { + dcmEnableUnknownVRGeneration.set(OFTrue); + dcmEnableUnlimitedTextVRGeneration.set(OFTrue); + } + if (cmd.findOption("--disable-new-vr")) + { + dcmEnableUnknownVRGeneration.set(OFFalse); + dcmEnableUnlimitedTextVRGeneration.set(OFFalse); + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--group-length-recalc")) oglenc = EGL_recalcGL; + if (cmd.findOption("--group-length-create")) oglenc = EGL_withGL; + if (cmd.findOption("--group-length-remove")) oglenc = EGL_withoutGL; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--length-explicit")) oenctype = EET_ExplicitLength; + if (cmd.findOption("--length-undefined")) oenctype = EET_UndefinedLength; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--padding-retain")) + { + if (!createFileFormat) app.printError("--padding-retain not allowed with --write-dataset"); + opadenc = EPD_noChange; + } + if (cmd.findOption("--padding-off")) opadenc = EPD_withoutPadding; + if (cmd.findOption("--padding-create")) + { + if (!createFileFormat) app.printError("--padding-create not allowed with --write-dataset"); + app.checkValue(cmd.getValueAndCheckMin(opt_filepad, 0)); + app.checkValue(cmd.getValueAndCheckMin(opt_itempad, 0)); + opadenc = EPD_withPadding; + } + cmd.endOptionBlock(); + + } + + DcmFileFormat fileformat; + DcmMetaInfo * metaheader = fileformat.getMetaInfo(); + DcmDataset * dataset = fileformat.getDataset(); + + 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; + } + + if (verbosemode) + COUT << "reading dump file: " << ifname << endl; + + // open input dump file + if ((ifname == NULL) || (strlen(ifname) == 0)) + { + CERR << "invalid input filename: <empty string>" << endl; + return 1; + } + FILE * dumpfile = fopen(ifname, "r"); + if (!dumpfile) + { + CERR << "input file does not exist: " << ifname << endl; + return 1; + } + + // read dump file into metaheader and dataset + if (readDumpFile(metaheader, dataset, dumpfile, ifname, stopOnErrors, + OFstatic_cast(unsigned long, opt_linelength))) + { + // write into file format or dataset + if (verbosemode) + COUT << "writing DICOM file" << endl; + + OFCondition l_error = fileformat.saveFile(ofname, oxfer, oenctype, oglenc, opadenc, + OFstatic_cast(Uint32, opt_filepad), OFstatic_cast(Uint32, opt_itempad), !createFileFormat); + + if (l_error == EC_Normal) + COUT << "dump successfully converted." << endl; + else + { + CERR << "Error: " << l_error.text() + << ": writing file: " << ofname << endl; + return 1; + } + } + + return 0; +} Index: trunk/milena/sandbox/fabien/dcmtk/Makefile =================================================================== --- trunk/milena/sandbox/fabien/dcmtk/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/dcmtk/Makefile (revision 3432) @@ -0,0 +1,2 @@ +all: dicom.cc + g++-4.2 -DHAVE_CONFIG_H -I../../../ -I/opt/local/include/ -L/opt/local/lib/ -ldcmdata -ldcmdsig -ldcmimage -ldcmimgle -ldcmjpeg -ldcmnet -ldcmpstat -ldcmqrdb -ldcmsr -ldcmtls -ldcmwlm dicom.cc -o dicom Index: trunk/milena/sandbox/fabien/dcmtk/load.hh =================================================================== --- trunk/milena/sandbox/fabien/dcmtk/load.hh (revision 0) +++ trunk/milena/sandbox/fabien/dcmtk/load.hh (revision 3432) @@ -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& 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& 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& 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& 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

1 0

3431: Make test::predicate more robust.
by Guillaume Lazzara 27 Feb '09

27 Feb '09

* mln/test/predicate.hh: add predicate_tests() function and call it in test::impl::* functions. Fix a wrong pixter type. --- milena/ChangeLog | 8 ++++ milena/mln/test/predicate.hh | 96 +++++++++++++++++++++++++++++++---------- 2 files changed, 80 insertions(+), 24 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 6f46274..85e2329 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,13 @@ 2009-02-27 Guillaume Lazzara <z(a)lrde.epita.fr> + Make test::predicate more robust. + + * mln/test/predicate.hh: add predicate_tests() function and call it + in test::impl::* functions. + Fix a wrong pixter type. + +2009-02-27 Guillaume Lazzara <z(a)lrde.epita.fr> + Small fixes for doc generation. * doc/Doxyfile.in: add doc/tutorial/img to IMAGE_PATH. diff --git a/milena/mln/test/predicate.hh b/milena/mln/test/predicate.hh index f2f44e3..2949490 100644 --- a/milena/mln/test/predicate.hh +++ b/milena/mln/test/predicate.hh @@ -1,4 +1,4 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory // (LRDE) // // This file is part of the Olena Library. This library is free @@ -44,38 +44,77 @@ namespace mln namespace test { - /*! Test if all pixel values of \p ima verify the predicate \p - * f. - * - * \param[in] ima The image. - * \param[in] f The predicate. - */ + /// Test if all pixel values of \p ima verify the predicate \p + /// f. + /// + /// \param[in] ima The image. + /// \param[in] f The predicate. template <typename I, typename F> bool predicate(const Image& ima, const Function_v2b<F>& f); - /*! Test if all pixel values of \p lhs and \p rhs verify the - * predicate \p f. - * - * \param[in] lhs The image. - * \param[in] rhs The image. - * \param[in] f The predicate. - */ + /// Test if all pixel values of \p lhs and \p rhs verify the + /// predicate \p f. + /// + /// \param[in] lhs The image. + /// \param[in] rhs The image. + /// \param[in] f The predicate. template <typename I, typename J, typename F> bool predicate(const Image& lhs, const Image<J>& rhs, const Function_vv2b<F>& f); - /*! Test if all points of \p pset verify the predicate \p f. - * - * \param[in] pset The point set. - * \param[in] f The predicate. - */ + /// Test if all points of \p pset verify the predicate \p f. + /// + /// \param[in] pset The point set. + /// \param[in] f The predicate. template <typename S, typename F> bool predicate(const Site_Set<S>& pset, const Function_p2b<F>& f); # ifndef MLN_INCLUDE_ONLY + namespace internal + { + + template <typename I, typename F> + inline + void predicate_tests(const Image& ima, + const Function_v2b<F>& f) + { + mln_precondition(exact(ima).is_valid()); + (void) ima; + (void) f; + } + + template <typename I, typename J, typename F> + inline + void predicate_tests(const Image& lhs_, + const Image<J>& rhs_, + const Function_vv2b<F>& f) + { + const I& lhs = exact(lhs_); + const J& rhs = exact(rhs_); + + mln_precondition(lhs.is_valid()); + mln_precondition(rhs.is_valid()); + mln_precondition(lhs.domain() == rhs.domain()); + (void) lhs; + (void) rhs; + (void) f; + } + + template <typename S, typename F> + inline + void predicate_tests(const Site_Set<S>& pset, + const Function_p2b<F>& f) + { + mln_precondition(exact(pset).is_valid()); + (void) pset; + (void) f; + } + + } // end of namespace mln::test::internal + namespace impl { @@ -83,6 +122,8 @@ namespace mln inline bool predicate_(trait::image::speed::any, const I& ima, const F& f) { + internal::predicate_tests(ima, f); + mln_piter(I) p(ima.domain()); for_all(p) if (! f(ima(p))) @@ -94,6 +135,8 @@ namespace mln inline bool predicate_(trait::image::speed::fastest, const I& ima, const F& f) { + internal::predicate_tests(ima, f); + mln_pixter(const I) pxl(ima); for_all(pxl) if (! f(pxl.val())) @@ -107,6 +150,8 @@ namespace mln trait::image::speed::any, const I& lhs, const J& rhs, const F& f) { + internal::predicate_tests(lhs, rhs, f); + mln_piter(I) p(lhs.domain()); for_all(p) if (! f(lhs(p), rhs(p))) @@ -120,8 +165,10 @@ namespace mln trait::image::speed::fastest, const I& lhs, const J& rhs, const F& f) { + internal::predicate_tests(lhs, rhs, f); + mln_pixter(const I) pxl1(lhs); - mln_pixter(const I) pxl2(rhs); + mln_pixter(const J) pxl2(rhs); for_all_2(pxl1, pxl2) if (! f(pxl1.val(), pxl2.val())) return false; @@ -132,6 +179,8 @@ namespace mln inline bool predicate_(const Site_Set<S>& pset, const F& f) { + internal::predicate_tests(pset, f); + mln_piter(S) p(exact(pset)); for_all(p) if (! f(p)) @@ -148,7 +197,7 @@ namespace mln inline bool predicate(const Image& ima, const Function_v2b<F>& f) { - mln_precondition(exact(ima).is_valid()); + internal::predicate_tests(ima, f); return impl::predicate_(mln_trait_image_speed(I)(), exact(ima), exact(f)); } @@ -161,9 +210,7 @@ namespace mln const I& lhs = exact(lhs_); const J& rhs = exact(rhs_); - mln_precondition(lhs.is_valid()); - mln_precondition(rhs.is_valid()); - mln_precondition(lhs.domain() == rhs.domain()); + internal::predicate_tests(lhs_, rhs_, f); return impl::predicate_(mln_trait_image_speed(I)(), mln_trait_image_speed(J)(), @@ -175,6 +222,7 @@ namespace mln inline bool predicate(const Site_Set<S>& pset, const Function_p2b<F>& f) { + internal::predicate_tests(pset, f); return impl::predicate_(exact(pset), exact(f)); } -- 1.5.6.5

1 0

3430: Small fixes for doc generation.
by Guillaume Lazzara 27 Feb '09

27 Feb '09

* doc/Doxyfile.in: add doc/tutorial/img to IMAGE_PATH. * doc/doc.mk: Set the path to doc/tutorial/img in a variable. * doc/tutorial/Makefile.am: Add IMG_SRCDIR to to TEXINPUTS. * img/small-enlarged.png, * img/small.png: move... * doc/tutorial/img/small-enlarged.png, * doc/tutorial/img/small.png: ... here. * doc/tutorial/samples/accu-wrong-instanciation.cc.raw: use a different accumulator. * doc/tutorial/tools/sample_utils.hh: do not include all io headers. --- milena/ChangeLog | 20 ++++++++++++++++++++ milena/doc/Doxyfile.in | 2 +- milena/doc/doc.mk | 2 ++ milena/doc/tutorial/Makefile.am | 2 +- milena/{ => doc/tutorial}/img/small-enlarged.png | Bin 91556 -> 91556 bytes milena/{ => doc/tutorial}/img/small.png | Bin 22653 -> 22653 bytes .../samples/accu-wrong-instanciation.cc.raw | 2 +- milena/doc/tutorial/tools/sample_utils.hh | 4 +++- 8 files changed, 28 insertions(+), 4 deletions(-) rename milena/{ => doc/tutorial}/img/small-enlarged.png (100%) rename milena/{ => doc/tutorial}/img/small.png (100%) diff --git a/milena/ChangeLog b/milena/ChangeLog index e26f8d4..6f46274 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,23 @@ +2009-02-27 Guillaume Lazzara <z(a)lrde.epita.fr> + + Small fixes for doc generation. + + * doc/Doxyfile.in: add doc/tutorial/img to IMAGE_PATH. + + * doc/doc.mk: Set the path to doc/tutorial/img in a variable. + + * doc/tutorial/Makefile.am: Add IMG_SRCDIR to to TEXINPUTS. + + * img/small-enlarged.png, + * img/small.png: move... + * doc/tutorial/img/small-enlarged.png, + * doc/tutorial/img/small.png: ... here. + + * doc/tutorial/samples/accu-wrong-instanciation.cc.raw: use a + different accumulator. + + * doc/tutorial/tools/sample_utils.hh: do not include all io headers. + 2009-02-26 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add int_u12 type and fix DICOM support. diff --git a/milena/doc/Doxyfile.in b/milena/doc/Doxyfile.in index cda47dc..5d657a4 100644 --- a/milena/doc/Doxyfile.in +++ b/milena/doc/Doxyfile.in @@ -96,7 +96,7 @@ EXAMPLE_PATH = @top_srcdir@/milena/doc/tutorial/samples \ @top_srcdir@/milena/doc/tutorial/outputs EXAMPLE_PATTERNS = EXAMPLE_RECURSIVE = NO -IMAGE_PATH = @top_srcdir@/milena/img \ +IMAGE_PATH = @top_srcdir@/milena/doc/tutorial/img \ @top_srcdir@/milena/doc/tutorial/figures \ @top_builddir@/milena/doc/tutorial/figures INPUT_FILTER = diff --git a/milena/doc/doc.mk b/milena/doc/doc.mk index b41750d..938c4c3 100644 --- a/milena/doc/doc.mk +++ b/milena/doc/doc.mk @@ -4,10 +4,12 @@ include $(top_srcdir)/milena/tests/tests.mk AM_CPPFLAGS += -I$(top_srcdir)/milena/doc/tutorial/tools + TUTORIAL_SRCDIR = $(top_srcdir)/milena/doc/tutorial OUTPUTS_SRCDIR = $(TUTORIAL_SRCDIR)/outputs FIGURES_SRCDIR = $(TUTORIAL_SRCDIR)/figures SAMPLES_SRCDIR = $(TUTORIAL_SRCDIR)/samples +IMG_SRCDIR = $(TUTORIAL_SRCDIR)/img TUTORIAL_BUILDDIR = $(top_builddir)/milena/doc/tutorial OUTPUTS_BUILDDIR = $(TUTORIAL_BUILDDIR)/outputs diff --git a/milena/doc/tutorial/Makefile.am b/milena/doc/tutorial/Makefile.am index ceb4534..53c9521 100644 --- a/milena/doc/tutorial/Makefile.am +++ b/milena/doc/tutorial/Makefile.am @@ -3,7 +3,7 @@ SUBDIRS = samples .PHONY: tutorial tuto_html include $(top_srcdir)/milena/doc/doc.mk -TEXINPUTS = $(TUTORIAL_SRCDIR):$(TUTORIAL_BUILDDIR):$(OUTPUTS_SRCDIR): +TEXINPUTS = $(TUTORIAL_SRCDIR):$(TUTORIAL_BUILDDIR):$(OUTPUTS_SRCDIR):$(IMG_SRCDIR): tutorial: data fig-convert TEXINPUTS=$(TEXINPUTS) pdflatex $(TUTORIAL_SRCDIR)/tutorial.tex diff --git a/milena/img/small-enlarged.png b/milena/doc/tutorial/img/small-enlarged.png similarity index 100% rename from milena/img/small-enlarged.png rename to milena/doc/tutorial/img/small-enlarged.png diff --git a/milena/img/small.png b/milena/doc/tutorial/img/small.png similarity index 100% rename from milena/img/small.png rename to milena/doc/tutorial/img/small.png diff --git a/milena/doc/tutorial/samples/accu-wrong-instanciation.cc.raw b/milena/doc/tutorial/samples/accu-wrong-instanciation.cc.raw index 25e943d..895c9f4 100644 --- a/milena/doc/tutorial/samples/accu-wrong-instanciation.cc.raw +++ b/milena/doc/tutorial/samples/accu-wrong-instanciation.cc.raw @@ -1 +1 @@ -level::compute(accu::meta::bbox, ima); +level::compute(accu::meta::max, ima); diff --git a/milena/doc/tutorial/tools/sample_utils.hh b/milena/doc/tutorial/tools/sample_utils.hh index 36536ba..d819cff 100644 --- a/milena/doc/tutorial/tools/sample_utils.hh +++ b/milena/doc/tutorial/tools/sample_utils.hh @@ -29,7 +29,9 @@ # define DOC_TUTORIAL_TOOLS_SAMPLE_UTILS_HH # include <mln/core/image/image2d.hh> -# include <mln/io/all.hh> +# include <mln/io/pbm/all.hh> +# include <mln/io/pgm/all.hh> +# include <mln/io/ppm/all.hh> namespace doc { -- 1.5.6.5

1 0

milena r3429: Add int_u12 type and fix DICOM support
by Fabien Freling 26 Feb '09

26 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-26 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add int_u12 type and fix DICOM support. * mln/convert/from_to.hxx: Convert histo::array into image1d. * mln/core/image/image1d.hh: Convert histo::array into image1d. * mln/io/all.hh: Add dicom include file. * mln/io/dicom/load.hh: Fix load support. * mln/value/int_u12.hh: New, implement int_u12 type. --- image1d.hh | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) Index: trunk/milena/mln/core/image/image1d.hh =================================================================== --- trunk/milena/mln/core/image/image1d.hh (revision 3428) +++ trunk/milena/mln/core/image/image1d.hh (revision 3429) @@ -118,6 +118,27 @@ + // Forward declaration. + template <typename T> struct image1d; + + + + namespace convert + { + + namespace over_load + { + + // histo::array -> image1d. + template <typename V, typename T> + void from_to_(const histo::array<V>& from, image1d<T>& to); + + } // end of namespace mln::convert::over_load + + } // end of namespace mln::convert + + + /*! \brief Basic 1D image class. * * The parameter \c T is the type of pixel values. This image class @@ -520,9 +541,33 @@ # include <mln/core/w_window.hh> + namespace mln { + + namespace convert + { + + namespace over_load + { + + // histo::array -> image1d. + template <typename V, typename T> + inline + void + from_to_(const histo::array<V>& from, image1d<T>& to) + { + to.init_(make::box1d(from.nvalues()), 0); + for (unsigned i = 0; i < from.nvalues(); ++i) + from_to(from[i], to(point1d(i))); + } + + } // end of namespace mln::convert::over_load + + } // end of namespace mln::convert + + namespace trait { Index: trunk/milena/mln/value/int_u12.hh =================================================================== --- trunk/milena/mln/value/int_u12.hh (revision 0) +++ trunk/milena/mln/value/int_u12.hh (revision 3429) @@ -0,0 +1,55 @@ +// 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. + +#ifndef MLN_VALUE_INT_U12_HH +# define MLN_VALUE_INT_U12_HH + +/*! \file mln/value/int_u12.hh + * + * \brief Define the alias value::int_u12. + */ + +# include <mln/value/int_u.hh> + + +namespace mln +{ + + namespace value + { + + + /// Alias for unsigned 12-bit integers. + typedef int_u<12> int_u12; + + + } // end of namespace mln::value + +} // end of namespace mln + + +#endif // ! MLN_VALUE_INT_U12_HH Index: trunk/milena/mln/convert/from_to.hxx =================================================================== --- trunk/milena/mln/convert/from_to.hxx (revision 3428) +++ trunk/milena/mln/convert/from_to.hxx (revision 3429) @@ -65,6 +65,8 @@ template <typename D> class window; template <typename D, typename W> class w_window; + template <typename T> struct image1d; + namespace algebra { template <unsigned n, typename T> class vec; template <unsigned d, typename C> class h_vec; @@ -76,6 +78,10 @@ } } + namespace histo { + template <typename T> struct array; + } + namespace util { template <typename T> class array; } @@ -360,6 +366,11 @@ void from_to_(const std::set<P,_C>& from, Site_Set<S>& to); + // histo::array -> image1d + template <typename V, typename T> + void + from_to_(const histo::array<V>& from, image1d<T>& to); + } // end of namespace mln::convert::over_load } // end of namespace mln::convert Index: trunk/milena/mln/io/dicom/load.hh =================================================================== --- trunk/milena/mln/io/dicom/load.hh (revision 3428) +++ trunk/milena/mln/io/dicom/load.hh (revision 3429) @@ -95,9 +95,8 @@ void load(Image& ima_, const std::string& filename) { - trace::entering("mln::io::gdcm::load"); + trace::entering("mln::io::dicom::load"); - using value::int_u16; I& ima = exact(ima_); gdcm::ImageReader r; @@ -119,9 +118,18 @@ int ndims = image.GetNumberOfDimensions(); const unsigned int* dims = image.GetDimensions(); - unsigned short bytes_allocated = image.GetPixelFormat().GetBitsAllocated() / 8; + unsigned short bits_allocated = image.GetPixelFormat().GetBitsAllocated(); + unsigned short bytes_allocated = bits_allocated / 8; + unsigned short bits_stored = image.GetPixelFormat().GetBitsStored(); unsigned short samples_per_pixel = image.GetPixelFormat().GetSamplesPerPixel(); + unsigned int offset = 8 - (bits_allocated - bits_stored); + unsigned int off_pow = 1; + for (int i = 0; i < offset; ++i) + { + off_pow *= 2; + } + if (mln_site_(I)::dim != ndims) { std::cerr << "error: dimension mismatch" << std::endl; @@ -154,13 +162,18 @@ { index += p.to_site().to_vec()[i] * vdims[i]; } - ima(p) = dataBuffer[index * bytes_allocated * samples_per_pixel]; - // FIXME: RGB support, HighBit - for (int j = 1; j < bytes_allocated; ++j) - { - ima(p) *= 256; - ima(p) += dataBuffer[(index * bytes_allocated + j) * samples_per_pixel]; - } + + ima(p) = (unsigned char) dataBuffer[(index * bytes_allocated) * samples_per_pixel]; + // FIXME: RGB support, HighBit if HB == 1 + for (int j = 0; j < bytes_allocated; ++j) + { + ima(p) += ((unsigned char) dataBuffer[(index * bytes_allocated + j) * samples_per_pixel]) * 256 * j; + } + /*std::cout << "[ x = " << p.to_site().to_vec()[2] + << " | y = " << p.to_site().to_vec()[1] + << " | z = " << p.to_site().to_vec()[0] + << " ] => " << ima(p) + << std::endl;*/ } delete(dataBuffer); Index: trunk/milena/mln/io/all.hh =================================================================== --- trunk/milena/mln/io/all.hh (revision 3428) +++ trunk/milena/mln/io/all.hh (revision 3429) @@ -48,6 +48,7 @@ # include <mln/io/cloud/all.hh> # include <mln/io/dump/all.hh> +# include <mln/io/dicom/load.hh> # include <mln/io/pbm/all.hh> # include <mln/io/pfm/all.hh> # include <mln/io/pgm/all.hh>

1 0

r3428: Continue experiments about attribute and morpho math
by Edwin Carlinet 26 Feb '09

26 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-26 Edwin Carlinet <carlinet(a)lrde.epita.fr> Continue experiments about attribute and morpho math. * edwin/attributes/occupation.hh: Correct bugs. * edwin/tree/tree.cc: Test file. --- attributes/occupation.hh | 6 +- tree/Makefile | 2 tree/tree.cc | 117 +++++++++++++++++++++++------------------------ 3 files changed, 62 insertions(+), 63 deletions(-) Index: trunk/milena/sandbox/edwin/tree/tree.cc =================================================================== --- trunk/milena/sandbox/edwin/tree/tree.cc (revision 3427) +++ trunk/milena/sandbox/edwin/tree/tree.cc (revision 3428) @@ -18,42 +18,13 @@ #include <mln/morpho/tree/compute_attribute_image.hh> #include <mln/morpho/attribute/card.hh> #include "../attributes/occupation.hh" +#include "propagate.hh" #include <mln/debug/println.hh> namespace mln { - - template <typename T, typename A> - void - back_propagate(const T& t, A& a) - // a value propagates from the representative point to every point - // of the component at the same level (NOT to the branch points!) - { - mln_fwd_piter(T) p(t.domain()); - for_all(p) - if (! t.is_a_node(p)) - { - mln_assertion(t.is_a_node(t.parent(p))); - a(p) = a(t.parent(p)); // ...here! - } - } - - - template <typename T, typename A> - void - back_propagate_II(const T& t, A& a) - // a value propagates from a representative point to every point - // of the component and the children components (branch). - { - mln_bkd_piter(T) p(t.domain()); - for_all(p) - if (t.is_a_node(p) && a(t.parent(p)) == true) - a(p) = a(t.parent(p)); - } - - template <typename T, typename A> inline void @@ -67,33 +38,65 @@ mln_fwd_piter(N) n(t.nodes()); for_all(n) // We only keep "highest" nodes at 'true' => largest component. - aa(n) = (a(n) == true && a(t.parent(n)) == false); + //aa(n) = (a(n) == true && a(t.parent(n)) == false); + aa(n) = a(n); if (echo) io::pbm::save(aa, "before.pbm"); if (echo > 1) debug::println("aa (before)", aa); - back_propagate_II(t, aa); - back_propagate(t, aa); + //back_propagate_subbranch(t, aa, true); + //if (echo > 1) debug::println("aa (After subbranch propagation)", aa); + back_propagate_level(t, aa); - if (echo > 1) debug::println("aa (after)", aa); + if (echo > 1) debug::println("aa (Final)", aa); io::pbm::save(aa, "out.pbm"); } + + } // mln +int echo = 0; + +template <typename I, typename A> +inline +void +create_tree_and_compute(I& f_, A a_, float lambda = mln_min(float), float lambda2 = mln_max(float)) +{ + using namespace mln; + using value::int_u8; + + I f = exact(f_); + typedef p_array< mln_site(I) > S; + S s = level::sort_psites_decreasing(f); + typedef morpho::tree::data<I,S> tree_t; + tree_t t(f, s, c4()); + + mln_VAR(a, morpho::tree::compute_attribute_image(a_, t)); + + if (echo > 1) + { + debug::println("parent imagee", t.parent_image()); + debug::println("a", a); + debug::println("a | nodes", a | t.nodes()); + } + + image2d<bool> b = duplicate((pw::value(a) < pw::cst(lambda1) && pw::value(a) < pw::cst(lambda2)) | a.domain()); + sample(t, b, echo); +} void usage(char* argv[]) { std::cerr << "usage: " << argv[0] << " input.pgm echo lambda" << std::endl; - std::cerr << " echo: 0 (none) or 1 (verbose)" << std::endl; + std::cerr << "\techo:\t0 (none)" << std::endl + << "\t\t1 (img output)" << std::endl + << "\t\t2 (debug)" << std::endl; abort(); } - - int main(int argc, char* argv[]) { using namespace mln; @@ -104,12 +107,7 @@ if (argc != 4) usage(argv); - int echo = std::atoi(argv[2]); - if (echo != 0 && echo != 1) - { - std::cerr << "bad 'echo' value!" << std::endl; - usage(argv); - } + echo = std::atoi(argv[2]); typedef image2d<int_u8> I; @@ -121,25 +119,26 @@ // I f = morpho::elementary::gradient(input, nbh); if (echo > 1) debug::println("f", f); + // test de volume + typedef image1d<int> IM; + IM img(6); + morpho::attribute::volume<IM> accu; + img.element(0) = 50; + img.element(1) = 40; + img.element(2) = 20; + img.element(3) = 20; + img.element(4) = 40; + img.element(5) = 50; - typedef p_array<point2d> S; - S s = level::sort_psites_decreasing(f); + mln_piter_(image1d<int>) p(img.domain()); - typedef morpho::tree::data<I,S> tree_t; - tree_t t(f, s, nbh); - - morpho::attribute::occupation a_; - mln_VAR(a, morpho::tree::compute_attribute_image(a_, t)); + for_all(p) + accu.take(img(p)); - if (echo > 1) - { - debug::println("parent imagee", t.parent_image()); - debug::println("a", a); - debug::println("a | nodes", a | t.nodes()); - } + std::cout << "Volume:" << accu.to_result() << std::endl; + //create_tree_and_compute(img, morpho::attribute::volume<I2>()); + // - image2d<bool> b = duplicate((pw::value(a) < pw::cst(atoi(argv[3]))) | a.domain()); - if (echo > 1) debug::println("b", b | t.nodes()); + create_tree_and_compute(f, morpho::attribute::card(), std::atof(argv[3])); - sample(t, b, echo); } Index: trunk/milena/sandbox/edwin/tree/Makefile =================================================================== --- trunk/milena/sandbox/edwin/tree/Makefile (revision 3427) +++ trunk/milena/sandbox/edwin/tree/Makefile (revision 3428) @@ -14,7 +14,7 @@ LD=g++ LDFLAGS= -all: $(TARGET) +all: clean $(TARGET) $(TARGET): $(OBJS) $(SRC) $(LD) $(LDFLAGS) -o $@ $(OBJS) Index: trunk/milena/sandbox/edwin/attributes/occupation.hh =================================================================== --- trunk/milena/sandbox/edwin/attributes/occupation.hh (revision 3427) +++ trunk/milena/sandbox/edwin/attributes/occupation.hh (revision 3428) @@ -157,7 +157,7 @@ volume_.take(v); if (v < min_) min_ = v; - else if (v > max_) + if (v > max_) max_ = v; } @@ -178,7 +178,7 @@ volume_.take(other.volume_); if (other.min_ < min_) min_ = other.min_; - else if (other.max_ > max_) + if (other.max_ > max_) max_ = other.max_; } @@ -205,7 +205,7 @@ double occupation::to_result() const { - return (double)volume_.to_result() / (double)(volume_.area() * (max_ - min_)); + return (double)volume_.to_result() / (double)(volume_.area() * height()); } template <typename I>

1 0

r3426: Separate propagation method and some tries about attributes
by Edwin Carlinet 25 Feb '09

25 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-25 Edwin Carlinet <carlinet(a)lrde.epita.fr> Separate propagation method and some tries about attributes. * edwin/filtres/connectes/Makefile * edwin/filtres/connectes/connected_filter.hh: Fix some bugs. * edwin/tree/Makefile: New. * edwin/tree/propagate.hh: Propagation methods. * edwin/tree/tree.cc: New. * edwin/tree: New. --- filtres/connectes/Makefile | 4 filtres/connectes/connected_filter.hh | 67 +-------------- tree/Makefile | 33 +++++++ tree/propagate.hh | 77 ++++++++++++++++++ tree/tree.cc | 144 ++++++++++++++++++++++++++++++++++ 5 files changed, 259 insertions(+), 66 deletions(-) Index: trunk/milena/sandbox/edwin/tree/propagate.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/propagate.hh (revision 0) +++ trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3426) @@ -0,0 +1,77 @@ +// Copyright (C) 2008 EPITA Research and Development Laboratory (LRDE) +// +// 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. + +#ifndef MLN_MORPHO_TREE_PROPAGATE_HH_ +# define MLN_MORPHO_TREE_PROPAGATE_HH_ + +/// \file mln/morpho/tree/propagate.hh +/// +/// Functions to propagate a node value in the tree. + +#include <mln/morpho/tree/data.hh> + +namespace mln { + namespace morpho { + namespace tree { + + + /// The representative point propagates its value to + /// its non-representative children nodes. + template <typename T, typename A> + void + back_propagate_level(const T& t, A& a) + { + mln_fwd_piter(T) p(t.domain()); + for_all(p) + if (! t.is_a_node(p)) + { + mln_assertion(t.is_a_node(t.parent(p))); + a(p) = a(t.parent(p)); + } + } + + /// The representative point having the right + /// value propagates to the nodes of its sub-branch. + template <typename T, typename A> + void + back_propagate_subbranch(const T& t, A& a, mln_value(A) v) + { + mln_fwd_piter(T) p(t.domain()); + for_all(p) + if (t.is_a_node(p) && a(t.parent(p)) == v) + { + mln_assertion(t.is_a_node(t.parent(p))); + a(p) = a(t.parent(p)); + } + } + } // end of namespace mln::morpho::tree + } // end of namespace mln::morpho +} // end of namespace mln + +#endif /* !MLN_MORPHO_TREE_PROPAGATE_HH_ */ + + Index: trunk/milena/sandbox/edwin/tree/tree.cc =================================================================== --- trunk/milena/sandbox/edwin/tree/tree.cc (revision 0) +++ trunk/milena/sandbox/edwin/tree/tree.cc (revision 3426) @@ -0,0 +1,144 @@ + +#include <mln/core/var.hh> +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/routine/duplicate.hh> +#include <mln/pw/all.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/label_8.hh> + +#include <mln/io/pgm/load.hh> +#include <mln/io/pbm/save.hh> + +#include <mln/level/sort_psites.hh> +#include <mln/morpho/elementary/gradient.hh> + +#include <mln/morpho/tree/data.hh> +#include <mln/morpho/tree/compute_attribute_image.hh> +#include <mln/morpho/attribute/card.hh> + +#include <mln/debug/println.hh> + + +namespace mln +{ + + template <typename T, typename A> + void + back_propagate(const T& t, A& a) + // a value propagates from the representative point to every point + // of the component at the same level (NOT to the branch points!) + { + mln_fwd_piter(T) p(t.domain()); + for_all(p) + if (! t.is_a_node(p)) + { + mln_assertion(t.is_a_node(t.parent(p))); + a(p) = a(t.parent(p)); // ...here! + } + } + + + template <typename T, typename A> + void + back_propagate_II(const T& t, A& a) + // a value propagates from a representative point to every point + // of the component and the children components (branch). + { + mln_bkd_piter(T) p(t.domain()); + for_all(p) + if (t.is_a_node(p) && a(t.parent(p)) == true) + a(p) = a(t.parent(p)); + } + + + template <typename T, typename A> + inline + void + sample(const T& t, const A& a, int echo) + { + A aa; + initialize(aa, a); + data::fill(aa, false); // 'aa' is false /a priori/. + + typedef typename T::nodes_t N; + mln_fwd_piter(N) n(t.nodes()); + for_all(n) + // We only keep "highest" nodes at 'true' => largest component. + aa(n) = (a(n) == true && a(t.parent(n)) == false); + + if (echo) io::pbm::save(aa, "before.pbm"); + if (echo > 1) debug::println("aa (before)", aa); + + back_propagate_II(t, aa); + back_propagate(t, aa); + + if (echo > 1) debug::println("aa (after)", aa); + io::pbm::save(aa, "out.pbm"); + + } + +} // mln + + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pgm echo lambda" << std::endl; + std::cerr << " echo: 0 (none) or 1 (verbose)" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + mln_VAR(nbh, c4()); + + if (argc != 4) + usage(argv); + + int echo = std::atoi(argv[2]); + if (echo != 0 && echo != 1) + { + std::cerr << "bad 'echo' value!" << std::endl; + usage(argv); + } + + typedef image2d<int_u8> I; + + I input; + io::pgm::load(input, argv[1]); + if (echo > 1) debug::println("input", input); + + I f = input; + // I f = morpho::elementary::gradient(input, nbh); + if (echo > 1) debug::println("f", f); + + + typedef p_array<point2d> S; + S s = level::sort_psites_decreasing(f); + + typedef morpho::tree::data<I,S> tree_t; + tree_t t(f, s, nbh); + + morpho::attribute::card a_; + mln_VAR(a, morpho::tree::compute_attribute_image(a_, t)); + + if (echo > 1) + { + debug::println("parent imagee", t.parent_image()); + debug::println("a", a); + debug::println("a | nodes", a | t.nodes()); + } + + image2d<bool> b = duplicate((pw::value(a) < pw::cst(atoi(argv[3]))) | a.domain()); + if (echo > 1) debug::println("b", b | t.nodes()); + + sample(t, b, echo); +} Index: trunk/milena/sandbox/edwin/tree/Makefile =================================================================== --- trunk/milena/sandbox/edwin/tree/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/tree/Makefile (revision 3426) @@ -0,0 +1,33 @@ +TARGET=a.out +SRC=edwin.cc +OBJS=${SRC:.cc=.o} + +OLENADIR=../../.. +MILENADIR=$(OLENADIR)/milena + +CXXFLAGS=-I$(MILENADIR) -I./ + +CXXFLAGS += "-DNDEBUG -O1" + + +CXX=g++ +LD=g++ +LDFLAGS= + +all: $(TARGET) + +$(TARGET): $(OBJS) $(SRC) + $(LD) $(LDFLAGS) -o $@ $(OBJS) + + +$(REF): $(OBJS_REF) $(SRC_REF) + $(LD) $(LDFLAGS) -o $@ $(OBJS_REF) + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< + +%.o: %.hh + $(CXX) $(CXXFLAGS) -c $< + +clean: + rm -f *.o $(REF) $(TARGET) \ No newline at end of file Index: trunk/milena/sandbox/edwin/filtres/connectes/connected_filter.hh =================================================================== --- trunk/milena/sandbox/edwin/filtres/connectes/connected_filter.hh (revision 3425) +++ trunk/milena/sandbox/edwin/filtres/connectes/connected_filter.hh (revision 3426) @@ -74,6 +74,8 @@ void take_as_init_fastest (trait::accumulator::when_pix::use_none, A& accu, const I& input, const unsigned p) { + (void)input; + (void)p; accu.take_as_init (); } @@ -81,6 +83,7 @@ void take_as_init (trait::accumulator::when_pix::use_p, A& accu, const I& input, const P& p) { + (void)input; accu.take_as_init (p); } @@ -88,6 +91,7 @@ void take_as_init (trait::accumulator::when_pix::use_none, A& accu, const I& input, const P& p) { + (void)input; accu.take_as_init (p); } @@ -279,11 +283,11 @@ const typename A::result& lambda) { trace::entering("canvas::morpho::impl::connected_filter_fastest"); - // FIXME: Tests? const I& input = exact(input_); const N& nbh = exact(nbh_); + (void)a_; mln_concrete(I) output; initialize(output, input); @@ -372,71 +376,10 @@ } // end of namespace mln::canvas::morpho::impl - - // Dispatch. - namespace internal { - // Leveling - template <typename I, typename N, typename A> - mln_concrete(I) - leveling_filter_dispatch(metal::false_, - const Image& input, - const Neighborhood<N>& nbh, - const Accumulator<A>& a, - const typename A::result& lambda, - bool increasing) - { - p_array < mln_psite(I) > s = - increasing ? - level::sort_psites_increasing(input) : - level::sort_psites_decreasing(input); - return impl::generic::connected_filter(input, nbh, s, a, lambda); - } - - template <typename I, typename N, typename A> - mln_concrete(I) - leveling_filter_dispatch(metal::true_, - const Image& input, - const Neighborhood<N>& nbh, - const Accumulator<A>& a, - const typename A::result& lambda, - bool increasing) - { - util::array<unsigned> s = - increasing ? - level::sort_offsets_increasing(input) : - level::sort_offsets_decreasing(input); - return impl::connected_filter_fastest(input, nbh, s, a, lambda); - } - - template <typename I, typename N, typename A> - inline - mln_concrete(I) - leveling_filter_dispatch(const Image& input, - const Neighborhood<N>& nbh, - const Accumulator<A>& a, - const typename A::result& lambda, - bool increasing) - { - mlc_or(mlc_equal(mln_trait_accumulator_when_pix(A), - trait::accumulator::when_pix::use_pix), - mlc_equal(mln_trait_accumulator_when_pix(A), - trait::accumulator::when_pix::use_v))::check(); - - enum - { - test = mlc_equal(mln_trait_image_speed(I), - trait::image::speed::fastest)::value - && mlc_equal(mln_trait_accumulator_when_pix(A), - trait::accumulator::when_pix::use_v)::value - && mln_is_simple_neighborhood(N)::value - }; - return leveling_filter_dispatch(metal::bool_<test>(), - input, nbh, a, lambda, increasing); - } // Alegebraic template <typename I, typename N, typename A> Index: trunk/milena/sandbox/edwin/filtres/connectes/Makefile =================================================================== --- trunk/milena/sandbox/edwin/filtres/connectes/Makefile (revision 3425) +++ trunk/milena/sandbox/edwin/filtres/connectes/Makefile (revision 3426) @@ -1,9 +1,6 @@ TARGET=filter -REF=leveling SRC=filter.cc -SRC_REF=leveling.cc OBJS=${SRC:.cc=.o} -OBJS_REF=${SRC_REF:.cc=.o} OLENADIR=../../../../.. MILENADIR=$(OLENADIR)/milena @@ -29,4 +26,4 @@ $(CXX) $(CXXFLAGS) -c $< clean: - rm -f *.o $(REF) $(TARGET) \ No newline at end of file + rm -f *.o *.pgm $(TARGET) \ No newline at end of file

1 0

3425: Update Fred's overload code.
by Thierry Geraud 25 Feb '09

25 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Update Fred's overload code. * fred/overload.cc: Update. overload.cc | 33 +++++++++++++++++++++++---------- 1 file changed, 23 insertions(+), 10 deletions(-) Index: fred/overload.cc --- fred/overload.cc (revision 3424) +++ fred/overload.cc (working copy) @@ -3,6 +3,11 @@ #include <mln/fun/internal/resolve.hh> #include <mln/trait/op/plus.hh> + +#define mln_result__1comma(Tleft, Tright) \ + typename Tleft, Tright ::result + + // Avantage de cette methode: // - la surcharge est rendue effectivement possible pour des familles de types // et permet de passer en argument une fonction meme s'il existe de multiple definitions @@ -163,13 +168,18 @@ { // Default (whatever the category): - // "inf" performs a "min"! - template <template <class> class Category_L, typename L, template <class> class Category_R, typename R> - struct set_binary_< fun::vv2v::plus, Category_L, L, Category_R, R> + // "plus(l, r)" performs "l + r"! + template <template <class> class Category_L, typename L, + template <class> class Category_R, typename R> + struct set_binary_< fun::vv2v::plus, + Category_L, L, + Category_R, R> { typedef set_binary_< fun::vv2v::plus, Category_L, L, Category_R, R> ret; - static mln_trait_op_plus(L,R) exec(const L& t1, const R& t2) + typedef mln_trait_op_plus(L,R) result; + + static result exec(const L& t1, const R& t2) { return t1 + t2; } @@ -194,9 +204,8 @@ template <typename L, typename R> struct plus : Function_vv2v< plus<L,R> > { - typedef mln_trait_op_plus(L,R) result; - typedef mln_fun_internal_resolve(plus) impl; + typedef mln_result(impl) result; result operator()(const L& t1, const R& t2) const { @@ -216,9 +225,10 @@ // A meta-fun can act as a function :-) template <typename L, typename R> - typename fun::vv2v::plus<L,R>::result operator()(const L& t1, const R& t2) const - // Here, we know the result type of vv2v::plus<L,R> so - // we explictly write it. + mln_result__1comma(fun::vv2v::plus<L,R>) + operator()(const L& t1, const R& t2) const + // Here, we do NOT know the result type of vv2v::plus<L,R> so + // we cannot explictly write it. { fun::vv2v::plus<L,R> f; return f(t1, t2); @@ -239,6 +249,7 @@ } // mln::fun + namespace trait { @@ -246,10 +257,11 @@ struct set_precise_binary_< fun::vv2v::plus, rgb, rgb > { typedef set_precise_binary_< fun::vv2v::plus, rgb, rgb > ret; + typedef rgb result; static rgb exec(const rgb& c1, const rgb& c2) { - // "Inf" is component-wise "min". + // "plus" is component-wise "plus". return rgb(c1.r + c2.r, c1.g + c2.g, c1.b + c2.b); @@ -266,6 +278,7 @@ } // mln + using namespace mln; int main()

1 0

3424: Small fixes.
by Guillaume Lazzara 25 Feb '09

25 Feb '09

* tests/unit_test/unit-tests.mk, * doc/tutorial/figures/figures.mk, * doc/tutorial/outputs/outputs.mk, * doc/tutorial/samples/samples.mk, * headers.mk: include new files in distribution. * mln/canvas/morpho/algebraic_filter.hh * mln/canvas/morpho/algebraic_union_find.hh: fix wrong call to find_root. * mln/canvas/morpho/internal/find_root.hh: add missing include. --- milena/ChangeLog | 16 ++++++++++++++++ milena/doc/tutorial/figures/figures.mk | 5 +++++ milena/doc/tutorial/outputs/outputs.mk | 1 + milena/doc/tutorial/samples/samples.mk | 1 + milena/headers.mk | 7 ++++++- milena/mln/canvas/morpho/algebraic_filter.hh | 4 ++-- milena/mln/canvas/morpho/algebraic_union_find.hh | 4 ++-- milena/mln/canvas/morpho/internal/find_root.hh | 2 ++ milena/tests/unit_test/unit-tests.mk | 12 ++++++++++++ 9 files changed, 47 insertions(+), 5 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 62bbc11..131f040 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,19 @@ +2009-02-25 Guillaume Lazzara <z(a)lrde.epita.fr> + + Small fixes. + + * tests/unit_test/unit-tests.mk, + * doc/tutorial/figures/figures.mk, + * doc/tutorial/outputs/outputs.mk, + * doc/tutorial/samples/samples.mk, + * headers.mk: include new files in distribution. + + * mln/canvas/morpho/algebraic_filter.hh + * mln/canvas/morpho/algebraic_union_find.hh: fix wrong call to + find_root. + + * mln/canvas/morpho/internal/find_root.hh: add missing include. + 2009-02-25 Fabien Freling <fabien.freling(a)lrde.epita.fr> Fix DICOM implementation: was DCMTK, now is GDCM. diff --git a/milena/doc/tutorial/figures/figures.mk b/milena/doc/tutorial/figures/figures.mk index 400b2ff..41dba2b 100644 --- a/milena/doc/tutorial/figures/figures.mk +++ b/milena/doc/tutorial/figures/figures.mk @@ -1,6 +1,7 @@ ## Generated by ../generate_dist_files, do not modify. EXTRA_DIST += \ +figures/extend-1.ppm \ figures/ima2d-rot-2.ppm \ figures/tuto3_rw_image-1.ppm \ figures/logical-not-2.pbm \ @@ -17,17 +18,21 @@ figures/ima_save.pbm \ figures/tuto2_first_image-1.pbm \ figures/figures.mk \ figures/fill-subimage-cfun-1.ppm \ +figures/extend-3.ppm \ figures/fill-subdomain-4.ppm \ figures/tuto4_genericity_and_algorithms-7.ppm \ figures/tuto4_genericity_and_algorithms-6.ppm \ +figures/extend-5.ppm \ figures/logical-not-3.pbm \ figures/tuto4_genericity_and_algorithms-3.pbm \ figures/tuto4_genericity_and_algorithms-1.ppm \ +figures/extend-4.ppm \ figures/tuto4_genericity_and_algorithms-8.ppm \ figures/labeling-compute-1.pbm \ figures/tuto3_rw_image-3.ppm \ figures/tuto4_genericity_and_algorithms-4.ppm \ figures/tuto4_genericity_and_algorithms-8.pgm \ +figures/extend-2.ppm \ figures/tuto4_genericity_and_algorithms-2.ppm \ figures/fill-subdomain-1.pbm \ figures/tuto3_rw_image-2.ppm diff --git a/milena/doc/tutorial/outputs/outputs.mk b/milena/doc/tutorial/outputs/outputs.mk index dfba0d6..1e4c9cf 100644 --- a/milena/doc/tutorial/outputs/outputs.mk +++ b/milena/doc/tutorial/outputs/outputs.mk @@ -4,6 +4,7 @@ EXTRA_DIST += \ outputs/win-create-1-display.txt \ outputs/win-create-2.txt \ outputs/accu-right-instanciation.txt \ +outputs/extend.txt \ outputs/ima2d-1.txt \ outputs/borderthickness.txt \ outputs/ima-save.txt \ diff --git a/milena/doc/tutorial/samples/samples.mk b/milena/doc/tutorial/samples/samples.mk index 442eec6..e0e3f5d 100644 --- a/milena/doc/tutorial/samples/samples.mk +++ b/milena/doc/tutorial/samples/samples.mk @@ -30,6 +30,7 @@ samples/fill-subdomain-shorter.cc \ samples/tuto3_rw_image.cc \ samples/ima2d-2.cc \ samples/extension-ignore.cc \ +samples/extend.cc \ samples/Makefile.am \ samples/parray-bbox.cc \ samples/graph-data.cc \ diff --git a/milena/headers.mk b/milena/headers.mk index d3c584f..6460d8f 100644 --- a/milena/headers.mk +++ b/milena/headers.mk @@ -59,7 +59,6 @@ mln/registration/get_rtransf.hh \ mln/registration/internal/rms.hh \ mln/registration/get_rot.hh \ mln/registration/all.hh \ -mln/registration/multiscale.hh \ mln/registration/registration.hh \ mln/registration/essential.hh \ mln/registration/icp.hh \ @@ -116,6 +115,7 @@ mln/data/all.hh \ mln/data/paste.hh \ mln/data/fill_with_image.hh \ mln/data/fill_with_image.spe.hh \ +mln/data/swap.hh \ mln/data/fill_with_value.hh \ mln/data/fill_with_value.spe.hh \ mln/data/fill.hh \ @@ -207,6 +207,7 @@ mln/fun/vv2v/essential.hh \ mln/fun/internal/array_base.hh \ mln/fun/internal/x2x_linear_impl.hh \ mln/fun/internal/ch_function_value_impl.hh \ +mln/fun/internal/resolve.hh \ mln/fun/internal/selector.hh \ mln/fun/v2w_w2v/norm.hh \ mln/fun/p2v/ternary.hh \ @@ -448,8 +449,10 @@ mln/math/essential.hh \ mln/math/acos.hh \ mln/math/round_sat.hh \ mln/opt/at.hh \ +mln/opt/all.hh \ mln/opt/element.hh \ mln/opt/value.hh \ +mln/opt/essential.hh \ mln/binarization/includes.hh \ mln/binarization/all.hh \ mln/binarization/binarization.hh \ @@ -529,6 +532,7 @@ mln/canvas/chamfer.hh \ mln/canvas/distance_geodesic.hh \ mln/canvas/all.hh \ mln/canvas/distance_front.hh \ +mln/canvas/morpho/internal/find_root.hh \ mln/canvas/morpho/all.hh \ mln/canvas/morpho/connected_filter.hh \ mln/canvas/morpho/algebraic_filter.hh \ @@ -1036,6 +1040,7 @@ mln/io/pnm/save.hh \ mln/io/pnm/save_header.hh \ mln/io/txt/all.hh \ mln/io/txt/save.hh \ +mln/io/dicom/load.hh \ mln/io/abort.hh \ mln/io/fits/load.hh \ mln/io/fits/all.hh \ diff --git a/milena/mln/canvas/morpho/algebraic_filter.hh b/milena/mln/canvas/morpho/algebraic_filter.hh index bfcf55e..883b959 100644 --- a/milena/mln/canvas/morpho/algebraic_filter.hh +++ b/milena/mln/canvas/morpho/algebraic_filter.hh @@ -136,7 +136,7 @@ namespace mln if (input.domain().has(n) && deja_vu(n)) { // Do-Union. - P r = find_root(parent, n); + P r = internal::find_root(parent, n); if (r != p) { if (input(r) == input(p) || (activity(r) && data(r) < lambda)) // Equiv(r, p) @@ -258,7 +258,7 @@ namespace mln if (! deja_vu.element(n)) continue; - unsigned r = find_root_fastest(parent, n); + unsigned r = internal::find_root_fastest(parent, n); if (r != p) { if (input.element(r) == input.element(p) diff --git a/milena/mln/canvas/morpho/algebraic_union_find.hh b/milena/mln/canvas/morpho/algebraic_union_find.hh index 75ac3f6..f99ac3d 100644 --- a/milena/mln/canvas/morpho/algebraic_union_find.hh +++ b/milena/mln/canvas/morpho/algebraic_union_find.hh @@ -148,7 +148,7 @@ namespace mln if (input.domain().has(n) && deja_vu(n)) { //do_union(n, p); - P r = find_root(parent, n); + P r = internal::find_root(parent, n); if (r != p) { if (input(r) == input(p) || (activity(r) && f.is_active(data(r)))) // Equiv(r, p) @@ -274,7 +274,7 @@ namespace mln if (! deja_vu.element(n)) continue; - unsigned r = find_root_fastest(parent, n); + unsigned r = internal::find_root_fastest(parent, n); if (r != p) { if (input.element(r) == input.element(p) diff --git a/milena/mln/canvas/morpho/internal/find_root.hh b/milena/mln/canvas/morpho/internal/find_root.hh index 8011122..3ca0717 100644 --- a/milena/mln/canvas/morpho/internal/find_root.hh +++ b/milena/mln/canvas/morpho/internal/find_root.hh @@ -34,6 +34,8 @@ /// /// \todo write a 'parent' image instead? +# include <mln/core/concept/image.hh> + namespace mln { diff --git a/milena/tests/unit_test/unit-tests.mk b/milena/tests/unit_test/unit-tests.mk index 9bb3a70..055ede1 100644 --- a/milena/tests/unit_test/unit-tests.mk +++ b/milena/tests/unit_test/unit-tests.mk @@ -111,6 +111,7 @@ mln_data_memcpy_ \ mln_data_all \ mln_data_paste \ mln_data_fill_with_image \ +mln_data_swap \ mln_data_fill_with_value \ mln_data_fill \ mln_data_essential \ @@ -201,6 +202,7 @@ mln_fun_vv2v_essential \ mln_fun_internal_array_base \ mln_fun_internal_x2x_linear_impl \ mln_fun_internal_ch_function_value_impl \ +mln_fun_internal_resolve \ mln_fun_internal_selector \ mln_fun_v2w_w2v_norm \ mln_fun_p2v_ternary \ @@ -440,8 +442,10 @@ mln_math_essential \ mln_math_acos \ mln_math_round_sat \ mln_opt_at \ +mln_opt_all \ mln_opt_element \ mln_opt_value \ +mln_opt_essential \ mln_binarization_includes \ mln_binarization_all \ mln_binarization_binarization \ @@ -521,6 +525,7 @@ mln_canvas_chamfer \ mln_canvas_distance_geodesic \ mln_canvas_all \ mln_canvas_distance_front \ +mln_canvas_morpho_internal_find_root \ mln_canvas_morpho_all \ mln_canvas_morpho_connected_filter \ mln_canvas_morpho_algebraic_filter \ @@ -1006,6 +1011,7 @@ mln_io_pnm_save \ mln_io_pnm_save_header \ mln_io_txt_all \ mln_io_txt_save \ +mln_io_dicom_load \ mln_io_abort \ mln_io_fits_load \ mln_io_fits_all \ @@ -1180,6 +1186,7 @@ mln_data_memcpy__SOURCES = mln_data_memcpy_.cc mln_data_all_SOURCES = mln_data_all.cc mln_data_paste_SOURCES = mln_data_paste.cc mln_data_fill_with_image_SOURCES = mln_data_fill_with_image.cc +mln_data_swap_SOURCES = mln_data_swap.cc mln_data_fill_with_value_SOURCES = mln_data_fill_with_value.cc mln_data_fill_SOURCES = mln_data_fill.cc mln_data_essential_SOURCES = mln_data_essential.cc @@ -1270,6 +1277,7 @@ mln_fun_vv2v_essential_SOURCES = mln_fun_vv2v_essential.cc mln_fun_internal_array_base_SOURCES = mln_fun_internal_array_base.cc mln_fun_internal_x2x_linear_impl_SOURCES = mln_fun_internal_x2x_linear_impl.cc mln_fun_internal_ch_function_value_impl_SOURCES = mln_fun_internal_ch_function_value_impl.cc +mln_fun_internal_resolve_SOURCES = mln_fun_internal_resolve.cc mln_fun_internal_selector_SOURCES = mln_fun_internal_selector.cc mln_fun_v2w_w2v_norm_SOURCES = mln_fun_v2w_w2v_norm.cc mln_fun_p2v_ternary_SOURCES = mln_fun_p2v_ternary.cc @@ -1509,8 +1517,10 @@ mln_math_essential_SOURCES = mln_math_essential.cc mln_math_acos_SOURCES = mln_math_acos.cc mln_math_round_sat_SOURCES = mln_math_round_sat.cc mln_opt_at_SOURCES = mln_opt_at.cc +mln_opt_all_SOURCES = mln_opt_all.cc mln_opt_element_SOURCES = mln_opt_element.cc mln_opt_value_SOURCES = mln_opt_value.cc +mln_opt_essential_SOURCES = mln_opt_essential.cc mln_binarization_includes_SOURCES = mln_binarization_includes.cc mln_binarization_all_SOURCES = mln_binarization_all.cc mln_binarization_binarization_SOURCES = mln_binarization_binarization.cc @@ -1590,6 +1600,7 @@ mln_canvas_chamfer_SOURCES = mln_canvas_chamfer.cc mln_canvas_distance_geodesic_SOURCES = mln_canvas_distance_geodesic.cc mln_canvas_all_SOURCES = mln_canvas_all.cc mln_canvas_distance_front_SOURCES = mln_canvas_distance_front.cc +mln_canvas_morpho_internal_find_root_SOURCES = mln_canvas_morpho_internal_find_root.cc mln_canvas_morpho_all_SOURCES = mln_canvas_morpho_all.cc mln_canvas_morpho_connected_filter_SOURCES = mln_canvas_morpho_connected_filter.cc mln_canvas_morpho_algebraic_filter_SOURCES = mln_canvas_morpho_algebraic_filter.cc @@ -2075,6 +2086,7 @@ mln_io_pnm_save_SOURCES = mln_io_pnm_save.cc mln_io_pnm_save_header_SOURCES = mln_io_pnm_save_header.cc mln_io_txt_all_SOURCES = mln_io_txt_all.cc mln_io_txt_save_SOURCES = mln_io_txt_save.cc +mln_io_dicom_load_SOURCES = mln_io_dicom_load.cc mln_io_abort_SOURCES = mln_io_abort.cc mln_io_fits_load_SOURCES = mln_io_fits_load.cc mln_io_fits_all_SOURCES = mln_io_fits_all.cc -- 1.5.6.5

1 0

milena r3423: Fix DICOM implementation: was DCMTK, now is GDCM
by Fabien Freling 25 Feb '09

25 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-25 Fabien Freling <fabien.freling(a)lrde.epita.fr> 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& 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& ima, DcmStack& stack, size_t printFlags) + inline + void load(Image& 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& 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& 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"); }

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