Index: src/dicomdict.cpp =================================================================== --- src/dicomdict.cpp (revision 8784) +++ src/dicomdict.cpp (working copy) @@ -5,6 +5,9 @@ * * Many thanks to Judd Storrs, who wrote most of the code in this * file. Anything ugly or wrong, I added later. Andy + * + * Minor changes Copyright Kris Thielemans 2011: + * make dicomdict('get') and dicomdict('set',filename) work properly and add doc-string * * The GNU Octave dicom package is free software: you can redistribute * it and/or modify it under the terms of the GNU General Public @@ -24,9 +27,9 @@ #include "octave/oct.h" #include "load-path.h" -#include "gdcmDict.h" -#include "gdcmVR.h" -#include "gdcmVM.h" +#include "gdcm-2.0/gdcmDict.h" +#include "gdcm-2.0/gdcmVR.h" +#include "gdcm-2.0/gdcmVM.h" #include "dicomdict.h" @@ -35,6 +38,7 @@ #define QUOTED(x) QUOTED_(x) const char * factory_dicom_dict_filename="octavedicom.dic"; +static std::string dic_filename(factory_dicom_dict_filename); std::map tagmap ; std::map keymap ; @@ -46,13 +50,20 @@ dict[k] = e ; } -void load_dict(const char *filename); DEFUN_DLD (OCT_FN_NAME, args, nargout, -"TODO: write help\n\ -Finds dictionary files anywhere in the path.\n") { + "-*- texinfo -*- \n\ +@deftypefn {Loadable Function} {@var{dictionary_name} =} "QUOTED(OCT_FN_NAME)" (@code{get}) \n\ +@deftypefnx {Loadable Function} {} "QUOTED(OCT_FN_NAME)" (@code{factory}) \n\ +@deftypefnx {Loadable Function} {} "QUOTED(OCT_FN_NAME)" (@code{set}, @var{dictionary_name}) \n\ +The first usage returns the filename of the dictionary that is currently being used.\n\ +Using @code{factory} resets the dictionary to the default.\n\ +Using @code{set} allows setting the dictionary for future operations.\n\ +In this case, the dictionary file @var{dictionary_name} can be anywhere in the path.\n\ +\n\ +@seealso{dicomread, dicomwrite}\n\ +@end deftypefn \n") { octave_value_list retval; // create object to store return values - static std::string dic_filename(factory_dicom_dict_filename); if (args.length()>2 || args.length()<1) { error(QUOTED(OCT_FN_NAME)": takes 1 or 2 arguments, got %i.",args.length ()); return retval; @@ -77,7 +88,7 @@ return retval; } else { - error(QUOTED(OCT_FN_NAME)": single arg must either be 'set' or 'factory'.",args.length ()); + error(QUOTED(OCT_FN_NAME)": single arg must either be 'get' or 'factory'.",args.length ()); return retval; } } @@ -92,6 +103,7 @@ error(QUOTED(OCT_FN_NAME)": when 2 args are given, the first must be 'set'.",args.length ()); return retval; } + load_dict(arg1str.c_str()); //if (octave_dicom_dict == NULL) octave_dicom_dict = new OctaveDicomDict(); //TODO where should this be freed? //octave_dicom_dict.load_file(arg1str.c_str()); // second arg is filename return retval; @@ -231,6 +243,9 @@ } }; +const char * const get_current_dict() { + return dic_filename.c_str(); +} void load_dict(const char * filename) { // reset, if required @@ -239,7 +254,7 @@ keymap.clear() ; dict.clear() ; } - + // find dic if it is anywhere in the search path (same path as for m-files etc) std::string resolved_filename=load_path::find_file(std::string(filename)) ; @@ -305,6 +320,8 @@ } while ( ++elem ) ; } while ( ++group ) ; } + // save filename + dic_filename = resolved_filename; } void lookup_keyword(std::string & keyword, const gdcm::Tag & tag) { Index: src/dicomdict.h =================================================================== --- src/dicomdict.h (revision 8784) +++ src/dicomdict.h (working copy) @@ -17,6 +17,8 @@ * Public License version 3. * */ +void load_dict(const char *filename); +const char * const get_current_dict(); void lookup_keyword(std::string & keyword, const gdcm::Tag & tag); void lookup_tag(gdcm::Tag & tag, const std::string & keyword); Index: src/dicomlookup.cpp =================================================================== --- src/dicomlookup.cpp (revision 8784) +++ src/dicomlookup.cpp (working copy) @@ -20,9 +20,9 @@ #include "octave/oct.h" -#include "gdcmDict.h" -#include "gdcmVR.h" -#include "gdcmVM.h" +#include "gdcm-2.0/gdcmDict.h" +#include "gdcm-2.0/gdcmVR.h" +#include "gdcm-2.0/gdcmVM.h" #include "dicomdict.h" @@ -71,4 +71,4 @@ } error(QUOTED(OCT_FN_NAME_LU)": takes 1 or 2 arguments, got %i. see help",args.length ()); return retval; -} \ No newline at end of file +} Index: src/dicomwrite.cpp =================================================================== --- src/dicomwrite.cpp (revision 8784) +++ src/dicomwrite.cpp (working copy) @@ -21,11 +21,11 @@ #include "octave/oct.h" #include "octave/ov-struct.h" -#include "gdcmDictEntry.h" -#include "gdcmImage.h" -#include "gdcmImageWriter.h" -#include "gdcmFileDerivation.h" -#include "gdcmUIDGenerator.h" +#include "gdcm-2.0/gdcmDictEntry.h" +#include "gdcm-2.0/gdcmImage.h" +#include "gdcm-2.0/gdcmImageWriter.h" +#include "gdcm-2.0/gdcmFileDerivation.h" +#include "gdcm-2.0/gdcmUIDGenerator.h" #include "dicomdict.h" @@ -388,4 +388,4 @@ w->SetFile( fd.GetFile() ); return ; -} \ No newline at end of file +} Index: src/dicominfo.cpp =================================================================== --- src/dicominfo.cpp (revision 8784) +++ src/dicominfo.cpp (working copy) @@ -3,12 +3,22 @@ * Contact: blondandy using the sf.net system, * * + * Changes Copyright Kris Thielemans 2011: + * - support usage dicominfo(filename, 'dictionary', dictname) + * - support FL, FD and SL VRs, which means that many more fields are now read correctly from the dicom file. + * - check if the VR in the file is the same as the one in the dictionary. If not, issue a warning but use the VR from the file. + * - assign values to private dicom fields, just like with others + * - changed convention for private fields to use lower-case for the hexadecimal numbers to be compatible with Matlab + * - if an entry is not in the dictionary, determine its VR from the file (if possible) and assign anyway. + * - updated doc-string + * + * * The GNU Octave dicom package is free software: you can redistribute * it and/or modify it under the terms of the GNU General Public * License as published by the Free Software Foundation, either * version 3 of the License, or (at your option) any later version. * - * The GNU Octave dicom packag is distributed in the hope that it + * The GNU Octave dicom package 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. @@ -32,18 +42,18 @@ #include "octave/oct.h" #include "octave/ov-struct.h" -#include "gdcmSystem.h" -#include "gdcmReader.h" -#include "gdcmWriter.h" -#include "gdcmAttribute.h" -#include "gdcmDataSet.h" -#include "gdcmGlobal.h" -#include "gdcmDicts.h" -#include "gdcmDict.h" -#include "gdcmCSAHeader.h" -#include "gdcmPrivateTag.h" -#include "gdcmVR.h" -#include "gdcmSequenceOfItems.h" +#include "gdcm-2.0/gdcmSystem.h" +#include "gdcm-2.0/gdcmReader.h" +#include "gdcm-2.0/gdcmWriter.h" +#include "gdcm-2.0/gdcmAttribute.h" +#include "gdcm-2.0/gdcmDataSet.h" +#include "gdcm-2.0/gdcmGlobal.h" +#include "gdcm-2.0/gdcmDicts.h" +#include "gdcm-2.0/gdcmDict.h" +#include "gdcm-2.0/gdcmCSAHeader.h" +#include "gdcm-2.0/gdcmPrivateTag.h" +#include "gdcm-2.0/gdcmVR.h" +#include "gdcm-2.0/gdcmSequenceOfItems.h" #include "dicomdict.h" @@ -82,22 +92,26 @@ #else DEFUN_DLD (OCT_FN_NAME, args, nargout, "-*- texinfo -*- \n\ - @deftypefn {Loadable Function} {} "QUOTED(OCT_FN_NAME)" (@var{filename}) \n\ - @deftypefnx {Loadable Function} {} @var{info} = "QUOTED(OCT_FN_NAME)" (@var{filename}) \n\ + @deftypefn {Loadable Function} {@var{info}} = "QUOTED(OCT_FN_NAME)" (@var{filename}) \n\ + @deftypefnx {Loadable Function} {@var{info}} = "QUOTED(OCT_FN_NAME)" (@var{filename}, @code{dictionary}, @var{dictionary-name}) \n\ + @deftypefnx {Loadable Function} {} "QUOTED(OCT_FN_NAME)" (@var{filename}, @var{options}) \n\ @deftypefnx {Command} {} "QUOTED(OCT_FN_NAME)" @var{filename} \n\ - @deftypefnx {Command} {} "QUOTED(OCT_FN_NAME)" @var{filename} @var{option} \n\ + @deftypefnx {Command} {} "QUOTED(OCT_FN_NAME)" @var{filename} @var{options} \n\ Get all data from a DICOM file, excluding any actual image. \n\ @var{info} is a nested struct containing the data. \n\ \n\ If no return argument is given, then there will be output similar to \n\ a DICOM dump. \n\ \n\ - @var{option}:\n\ - truncate=n\n\ - where n is the number of characters to limit the dump output display to \ + If the @code{dictionary} argument is used, the given @var{dictionary-name} is used for this operation, \n\ + otherwise, the dictionary set by @code{dicomdict} is used.\n\ + \n\ + @var{options}:\n\ + @code{truncate=n}\n\ + where n is the number of characters to limit the dump output display to @code{n}\ for each value. \n\ \n\ - @seealso{dicomread} \n\ + @seealso{dicomread, dicomdict} \n\ @end deftypefn \n\ ") { octave_value_list retval; // create object to store return values @@ -112,7 +126,13 @@ return retval; } std::string filename = ch.row_as_string (0); - + + std::string current_dict = get_current_dict(); + // TODO the dictionary can be set by the code below + // we really need to catch any errors in this function + // and reset the dictionary to current_dict. + // Currently that's only done when no error occured. + int i; // parse any additional args for (i=1; iGetByteValue() == NULL) return DICOM_NOTHING_ASSIGNED; //const gdcm::DictEntry dictEntry = dicts.GetDictEntry(tag,(const char*)0); + + gdcm::VR vr = elem->GetVR(); // value representation. ie DICOM + gdcm::DictEntry dictEntry ; if (!is_present(tag)) { char fallbackVarname[64]; - snprintf(fallbackVarname,63,"Private_%04X_%04X",tag.GetGroup(),tag.GetElement()); + snprintf(fallbackVarname,63,"Private_%04x_%04x",tag.GetGroup(),tag.GetElement()); varname=std::string(fallbackVarname); +#if 0 *ov=std::string(""); warning(QUOTED(OCT_FN_NAME)": %s", fallbackVarname); return DICOM_NOTHING_ASSIGNED; //TODO maybe could carry on, if we know the VR +#endif } - lookup_entry(dictEntry, tag); - const gdcm::VR vr= dictEntry.GetVR(); // value representation. ie DICOM type. - varname=dictEntry.GetName(); + else { + lookup_entry(dictEntry, tag); + varname=dictEntry.GetName(); + const gdcm::VR dictvr= dictEntry.GetVR(); // value representation. ie DICOM + if (dictvr != vr) { + warning(QUOTED(OCT_FN_NAME)": %s has different VR from dictionary. Using VR from file", varname.c_str()); + } + } + //int tagVarNameBufLen=127; //char *keyword=(char *)malloc((tagVarNameBufLen+1)*sizeof(char)); @@ -271,6 +318,21 @@ memcpy(&usval, elem->GetByteValue()->GetPointer(), 2); *ov=usval; if(chatty) octave_stdout << '[' << usval << "]\n"; + } else if (vr & gdcm::VR::FL) {// float + float val ; + memcpy(&val, elem->GetByteValue()->GetPointer(), 4); + *ov=val; + if(chatty) octave_stdout << '[' << val << "]\n"; + } else if (vr & gdcm::VR::FD) {// double + double val ; + memcpy(&val, elem->GetByteValue()->GetPointer(), sizeof(val)); + *ov=val; + if(chatty) octave_stdout << '[' << val << "]\n"; + } else if (vr & gdcm::VR::SL) {// signed long + int32_t val ; + memcpy(&val, elem->GetByteValue()->GetPointer(), 4); + *ov=val; + if(chatty) octave_stdout << '[' << val << "]\n"; } else if (vr & gdcm::VR::OB) {// other byte if (tag==gdcm::Tag(0x7FE0,0x0010)) { // PixelData if(chatty) octave_stdout << "skipping, leave for dicomread\n"; Index: src/dicomread.cpp =================================================================== --- src/dicomread.cpp (revision 8784) +++ src/dicomread.cpp (working copy) @@ -19,8 +19,8 @@ */ #include "octave/oct.h" - -#include "gdcmImageReader.h" +#include +#include "gdcm-2.0/gdcmImageReader.h" #define DICOM_ERR -1 #define DICOM_OK 0 @@ -32,9 +32,13 @@ DEFUN_DLD (OCT_FN_NAME, args, nargout, "-*- texinfo -*- \n\ @deftypefn {Loadable Function} {} @var{image} = "QUOTED(OCT_FN_NAME)" (@var{filename}) \n\ + @deftypefnx {Loadable Function} {} @var{image} = "QUOTED(OCT_FN_NAME)" (@var{structure}) \n\ + \n\ Load the image from a DICOM file. \n\ + @var{filename} is a string (giving the filename).\n\ + @var{structure} is a structure with a field @code{Filename} (such as returned by @code{dicominfo}).\n\ @var{image} may be two or three dimensional, depending on the content of the file. \n\ - An integer matrix will be returned, the number of bits will depend on the file. \n\ + An integer or float matrix will be returned, the number of bits will depend on the file. \n\ \n\ @seealso{dicominfo} \n\ @end deftypefn \n\ @@ -44,13 +48,28 @@ error(QUOTED(OCT_FN_NAME)": one arg required: dicom filename"); return retval; } - charMatrix ch = args(0).char_matrix_value (); - if (ch.rows()!=1) { - error(QUOTED(OCT_FN_NAME)": arg should be a filename, 1 row of chars"); + + std::string filename; + // argument processing + // check if 1st argument is a string or a struct with field Filename + // If so, assign to filename variable, otherwise exit. + if (args(0).is_string()) { + filename = args(0).string_value(); + } + else { + octave_scalar_map arg0 = args(0).scalar_map_value (); + if (error_state) { + error(QUOTED(OCT_FN_NAME)": arg should be a filename, 1 row of chars, or a struct returned by dicominfo"); return retval; + } + if (!arg0.contains("Filename")) { + error(QUOTED(OCT_FN_NAME)": if arg is a struct, it should have the Filename field"); + return retval; + } + octave_value tmp = arg0.getfield ("Filename"); + filename = tmp.string_value(); } - std::string filename = ch.row_as_string(0); #if 0 /* TODO support 'frames' stuff, see Matlab docs for dicomread */ int i; // parse any additional args Index: src/_gendicomdict.cpp =================================================================== --- src/_gendicomdict.cpp (revision 8784) +++ src/_gendicomdict.cpp (working copy) @@ -28,17 +28,17 @@ #include "octave/oct.h" -#include "gdcmSystem.h" -#include "gdcmReader.h" -#include "gdcmWriter.h" -#include "gdcmAttribute.h" -#include "gdcmDataSet.h" -#include "gdcmGlobal.h" -#include "gdcmDicts.h" -#include "gdcmDict.h" -#include "gdcmCSAHeader.h" -#include "gdcmPrivateTag.h" -#include "gdcmVR.h" +#include "gdcm-2.0/gdcmSystem.h" +#include "gdcm-2.0/gdcmReader.h" +#include "gdcm-2.0/gdcmWriter.h" +#include "gdcm-2.0/gdcmAttribute.h" +#include "gdcm-2.0/gdcmDataSet.h" +#include "gdcm-2.0/gdcmGlobal.h" +#include "gdcm-2.0/gdcmDicts.h" +#include "gdcm-2.0/gdcmDict.h" +#include "gdcm-2.0/gdcmCSAHeader.h" +#include "gdcm-2.0/gdcmPrivateTag.h" +#include "gdcm-2.0/gdcmVR.h" #define OCT_FN_NAME _gendicomdict #define QUOTED_(x) #x @@ -134,4 +134,4 @@ } *tl = '\0'; return d; -} \ No newline at end of file +} Index: src/Makefile =================================================================== --- src/Makefile (revision 8784) +++ src/Makefile (working copy) @@ -17,10 +17,10 @@ -INCDIRFLAGS = -I/usr/local/include/gdcm-2.0/ +INCDIRFLAGS = LIBDIRFLAGS = -L/usr/local/lib -GDCMLIBFLAGS = -lgdcmcharls -lgdcmzlib -lgdcmjpeg8 -lgdcmjpeg12 \ --lgdcmjpeg16 -lgdcmexpat -lgdcmopenjpeg -lgdcmCommon \ +GDCMLIBFLAGS = -lgdcmcharls -lgdcmjpeg8 -lgdcmjpeg12 \ +-lgdcmjpeg16 -lgdcmCommon \ -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF DEBUGFLAG = -g @@ -60,4 +60,4 @@ mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomlookup.cpp clean: - rm *.o *.oct *~ + rm -f *.o *.oct *~