From: jpr Date: Wed, 4 Feb 2004 17:23:56 +0000 (+0000) Subject: doxygenation X-Git-Tag: Version0.4~18 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=0574f31372f78bf8399e42ee04bd0010e684c440;p=gdcm.git doxygenation --- diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 6aa3cadb..31bf7bc3 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -21,10 +21,7 @@ * to be parsed *inside* the SeQuences, * when they have an actual length * @param ignore_shadow = true if user wants to skip shadow groups - during parsing, to save memory space - *\TODO : may be we need one more bool, - * to allow skipping the private elements while parsing the header - * in order to save space + * during parsing, to save memory space */ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error, @@ -65,7 +62,7 @@ gdcmHeader::gdcmHeader(const char *InFilename, /** * \ingroup gdcmHeader - * \brief + * \brief Constructor * @param exception_on_error */ gdcmHeader::gdcmHeader(bool exception_on_error) : @@ -86,6 +83,7 @@ gdcmHeader::~gdcmHeader (void) { // see gdcmParser.cxx //----------------------------------------------------------------------------- // Public + /** * \ingroup gdcmHeader * \brief This predicate, based on hopefully reasonable heuristics, @@ -109,7 +107,7 @@ bool gdcmHeader::IsReadable(void) { if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) return false; // "High Bit" if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) - return false; // "Pixel Representation" + return false; // "Pixel Representation" i.e. 'Sign' return true; } @@ -117,7 +115,6 @@ bool gdcmHeader::IsReadable(void) { * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGBaseLineProcess1 one. - * * @return True when JPEGBaseLineProcess1found. False in all other cases. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { @@ -136,7 +133,6 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGExtendedProcess2-4 one. - * * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { @@ -151,7 +147,6 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGExtendeProcess3-5 one. - * * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { @@ -170,7 +165,6 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. - * * @return True when JPEGSpectralSelectionProcess6-8 found. False in all * other cases. */ @@ -190,7 +184,6 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a RLE Lossless one. - * * @return True when RLE Lossless found. False in all * other cases. */ @@ -211,7 +204,6 @@ bool gdcmHeader::IsRLELossLessTransferSyntax(void) { * \ingroup gdcmHeader * \brief Determines if Transfer Syntax was already encountered * and if it corresponds to a JPEG Lossless one. - * * @return True when RLE Lossless found. False in all * other cases. */ @@ -233,8 +225,7 @@ bool gdcmHeader::IsJPEGLossless(void) { /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG200 one.0 - * + * and if it corresponds to a JPEG2000 one * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ @@ -258,6 +249,9 @@ bool gdcmHeader::IsJPEG2000(void) { */ bool gdcmHeader::IsDicomV3(void) { // Checking if Transfert Syntax exists is enough + // Anyway, it's to late check if the 'Preamble' was found ... + // And ... would it be a rich idea to check ? + // (some 'no Preamble' DICOM images exist !) return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); } @@ -280,7 +274,7 @@ int gdcmHeader::GetXSize(void) { * \brief Retrieve the number of lines of image. * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() * @return The encountered size when found, 1 by default - * (The file contains a Signal, not an Image). + * (The ACR-MEMA file contains a Signal, not an Image). */ int gdcmHeader::GetYSize(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0010); @@ -300,7 +294,7 @@ int gdcmHeader::GetYSize(void) { * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third * dimension. When absent we consider the third dimension as - * being the "Planes" tag content. + * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ int gdcmHeader::GetZSize(void) { @@ -310,9 +304,7 @@ int gdcmHeader::GetZSize(void) { if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); - // We then consider the "Planes" entry as the third dimension [we - // cannot retrieve by name since "Planes tag is present both in - // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. + // We then consider the "Planes" entry as the third dimension StrSize = GetEntryByNumber(0x0028,0x0012); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); @@ -323,7 +315,6 @@ int gdcmHeader::GetZSize(void) { * \ingroup gdcmHeader * \brief Retrieve the number of Bits Stored (actually used) * (as opposite to number of Bits Allocated) - * * @return The encountered number of Bits Stored, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ @@ -339,11 +330,10 @@ int gdcmHeader::GetBitsStored(void) { * \ingroup gdcmHeader * \brief Retrieve the number of Bits Allocated * (8, 12 -compacted ACR-NEMA files, 16, ...) - * * @return The encountered number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsAllocated(void) { // TODO : move to gdcmFile +int gdcmHeader::GetBitsAllocated(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0100); if (StrSize == GDCM_UNFOUND) return 0; // It's supposed to be mandatory @@ -355,15 +345,14 @@ int gdcmHeader::GetBitsAllocated(void) { // TODO : move to gdcmFile * \ingroup gdcmHeader * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB -1 or 3 Planes-) - * * @return The encountered number of Samples Per Pixel, 1 by default. * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel(void) { // TODO : move to gdcmFile +int gdcmHeader::GetSamplesPerPixel(void) { std::string StrSize = GetEntryByNumber(0x0028,0x0002); if (StrSize == GDCM_UNFOUND) return 1; // Well, it's supposed to be mandatory ... - // but sometimes it's missing : we assume Gray pixels + // but sometimes it's missing : *we* assume Gray pixels return atoi(StrSize.c_str()); } @@ -371,7 +360,6 @@ int gdcmHeader::GetSamplesPerPixel(void) { // TODO : move to gdcmFile * \ingroup gdcmHeader * \brief Retrieve the Planar Configuration for RGB images * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) - * * @return The encountered Planar Configuration, 0 by default. */ int gdcmHeader::GetPlanarConfiguration(void) { @@ -395,6 +383,8 @@ int gdcmHeader::GetPixelSize(void) { return 2; if (PixelType == "32U" || PixelType == "32S") return 4; + if (PixelType == "FD") + return 8; dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } @@ -409,6 +399,7 @@ int gdcmHeader::GetPixelSize(void) { * - 16S signed 16 bit, * - 32U unsigned 32 bit, * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. * \ 24 bit images appear as 8 bit * @return 0S if nothing found. NOT USABLE file. The caller has to check @@ -419,6 +410,8 @@ std::string gdcmHeader::GetPixelType(void) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); BitsAlloc = std::string("16"); } + if (BitsAlloc == "64") // ) + return ("FD"); if (BitsAlloc == "12") // It will be unpacked BitsAlloc = std::string("16"); else if (BitsAlloc == "24") // (in order no to be messed up @@ -442,6 +435,7 @@ std::string gdcmHeader::GetPixelType(void) { * \ingroup gdcmHeader * \brief Recover the offset (from the beginning of the file) * \ of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset */ size_t gdcmHeader::GetPixelOffset(void) { // @@ -506,12 +500,12 @@ size_t gdcmHeader::GetPixelAreaLength(void) { * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' * \ are NOT considered as LUT, since nobody knows * \ how to deal with them - * @return a Boolean + * \ Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found */ bool gdcmHeader::HasLUT(void) { - // Check the presence of the LUT Descriptors - + // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) return false; @@ -520,11 +514,7 @@ bool gdcmHeader::HasLUT(void) { return false; // LutDescriptorBlue if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) - return false; - - // It is not enough : - // we check also - + return false; // Red Palette Color Lookup Table Data if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) return false; @@ -542,7 +532,8 @@ bool gdcmHeader::HasLUT(void) { * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * \ else 0 * @return Lookup Table number of Bits , 0 by default - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item */ int gdcmHeader::GetLUTNbits(void) { std::vector tokens; @@ -716,20 +707,16 @@ std::string gdcmHeader::GetTransfertSyntaxName(void) { } /** - * \ingroup gdcmFile + * \ingroup gdcmHeader * \brief Sets the Pixel Area size in the Header * --> not-for-rats function - * - * \warning WARNING doit-etre etre publique ? - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions - * * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { std::string content1; char car[20]; - + // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... // TODO deal with multiplicity (see gdcmData/icone.dcm) sprintf(car,"%d",ImageDataSize); @@ -743,8 +730,17 @@ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { SetEntryByNumber(content1, GrPixel, NumPixel); } -bool gdcmHeader::operator<(gdcmHeader &header) -{ + +/** + * \ingroup gdcmHeader + * \brief compares 2 Headers, according to DICOMDIR rules + * --> not-for-rats function + * \warning does NOT work with ACR-NEMA files + * \todo find a trick to solve the pb (use RET fields ?) + * @param header + * @return true if 'smaller' + */ + bool gdcmHeader::operator<(gdcmHeader &header){ std::string s1,s2; // Patient Name diff --git a/src/gdcmHeaderHelper.cxx b/src/gdcmHeaderHelper.cxx index 31fd9ab7..16d11576 100644 --- a/src/gdcmHeaderHelper.cxx +++ b/src/gdcmHeaderHelper.cxx @@ -61,7 +61,7 @@ // Constructor / Destructor /** * \ingroup gdcmHeaderHelper - * \brief cstor + * \brief constructor */ gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( ) { @@ -69,7 +69,14 @@ gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( ) { /** * \ingroup gdcmHeaderHelper - * \brief cstor + * \brief constructor + * @param InFilename Name of the file to deal with + * @param exception_on_error + * @param enable_sequences = true to allow the header + * to be parsed *inside* the SeQuences, + * when they have an actual length + * @param ignore_shadow = true if user wants to skip shadow groups + * during parsing, to save memory space */ gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename, bool exception_on_error, @@ -89,7 +96,7 @@ gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename, // Public /** * \ingroup gdcmHeaderHelper - * \brief Return the size (in bytes) of a single pixel of data. + * \brief Returns the size (in bytes) of a single pixel of data. * @return The size in bytes of a single pixel of data. * */ @@ -125,10 +132,10 @@ int gdcmHeaderHelper::GetPixelSize() { * - 32S signed 32 bit, * - FD Double, * \warning 12 bit images appear as 16 bit. - * \ 24 bit images appear as 8 bit - * \ 64 bit means 'DOUBLE' images - * \ (no DOUBLE images in kosher DICOM, - * \ but so usefull for people that miss them ;-) + * 24 bit images appear as 8 bit + * 64 bit means 'DOUBLE' images + * (no DOUBLE images in kosher DICOM, + * but so usefull for people that miss them ;-) * @return */ std::string gdcmHeaderHelper::GetPixelType() { @@ -244,6 +251,11 @@ float gdcmHeaderHelper::GetZSpacing() { } } +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept + */ float gdcmHeaderHelper::GetRescaleIntercept() { float resInter = 0.; std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept @@ -256,7 +268,12 @@ float gdcmHeaderHelper::GetRescaleIntercept() { return resInter; } -float gdcmHeaderHelper::GetRescaleSlope() { +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ + float gdcmHeaderHelper::GetRescaleSlope() { float resSlope = 1.; std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope if (StrRescSlope != GDCM_UNFOUND) { @@ -265,19 +282,18 @@ float gdcmHeaderHelper::GetRescaleSlope() { // bug in the element 0x0028,0x1053 } } - return resSlope; + return resSlope; } /** * \ingroup gdcmHeaderHelper - * \brief This function is intended to user who doesn't whan + * \brief This function is intended to user who doesn't want * \ to have to manage a LUT and expects to get an RBG Pixel image * \ (or a monochrome one ...) * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) */ int gdcmHeaderHelper::GetNumberOfScalarComponents() { - if (GetSamplesPerPixel() ==3) return 3; @@ -328,22 +344,48 @@ int gdcmHeaderHelper::GetNumberOfScalarComponentsRaw() { return GetSamplesPerPixel(); } -std::string gdcmHeaderHelper::GetStudyUID(){ +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0020,000d : Study Instance UID + *\todo ? : return the ACR-NEMA element value if DICOM one is not found + * @return Study Instance UID + */ + std::string gdcmHeaderHelper::GetStudyUID(){ return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID } -std::string gdcmHeaderHelper::GetSeriesUID(){ +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0020,000e : Series Instance UID + *\todo ? : return the ACR-NEMA element value if DICOM one is not found + * @return Series Instance UID + */ + std::string gdcmHeaderHelper::GetSeriesUID(){ return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID } -std::string gdcmHeaderHelper::GetClassUID(){ +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0008,0016 : SOP Class UID + *\todo ? : return the ACR-NEMA element value if DICOM one is not found + * @return SOP Class UID + */ + std::string gdcmHeaderHelper::GetClassUID(){ return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID } -std::string gdcmHeaderHelper::GetInstanceUID(){ +/** + *\ingroup gdcmHeaderHelper + *\brief gets the info from 0008,0018 : SOP Instance UID + *\todo ? : return the ACR-NEMA element value if DICOM one is not found + * @return SOP Instance UID + */ + std::string gdcmHeaderHelper::GetInstanceUID(){ return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID } - +// +// -------------- Remember ! ---------------------------------- +// // Image Position Patient (0020,0032): // If not found (ACR_NEMA) we try Image Position (0020,0030) // If not found (ACR-NEMA), we consider Slice Location (0020,1041) @@ -353,13 +395,18 @@ std::string gdcmHeaderHelper::GetInstanceUID(){ // TODO : find a way to inform the caller nothing was found // TODO : How to tell the caller a wrong number of values was found? +// +// --------------------------------------------------------------- +// + /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0032 : Image Position Patient *\ else from 0020,0030 : Image Position (RET) *\ else 0. - * @return up-left image corner position + * @return up-left image corner X position */ + float gdcmHeaderHelper::GetXOrigin() { float xImPos, yImPos, zImPos; std::string StrImPos = GetEntryByNumber(0x0020,0x0032); @@ -383,7 +430,7 @@ float gdcmHeaderHelper::GetXOrigin() { * \brief gets the info from 0020,0032 : Image Position Patient * \ else from 0020,0030 : Image Position (RET) * \ else 0. - * @return up-left image corner position + * @return up-left image corner Y position */ float gdcmHeaderHelper::GetYOrigin() { float xImPos, yImPos, zImPos; @@ -410,7 +457,7 @@ float gdcmHeaderHelper::GetYOrigin() { * \ else from 0020,1041 : Slice Location * \ else from 0020,0050 : Location * \ else 0. - * @return up-left image corner position + * @return up-left image corner Z position */ float gdcmHeaderHelper::GetZOrigin() { float xImPos, yImPos, zImPos; @@ -477,7 +524,7 @@ int gdcmHeaderHelper::GetImageNumber() { /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0008,0060 : Modality - * @return ModalityType + * @return Modality Type */ ModalityType gdcmHeaderHelper::GetModality(void) { std::string StrModality = GetEntryByNumber(0x0008,0x0060); //0008 0060 CS ID Modality @@ -536,6 +583,7 @@ ModalityType gdcmHeaderHelper::GetModality(void) { /** * \ingroup gdcmHeaderHelper * \brief gets the info from 0020,0037 : Image Orientation Patient + * @param iop adress of the (6)float aray to receive values * @return cosines of image orientation patient */ void gdcmHeaderHelper::GetImageOrientationPatient( float* iop ) { @@ -599,6 +647,7 @@ gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper(){ /** * \ingroup gdcmHeaderHelper * \brief add a gdcmFile to the list based on file name + * @param filename Name of the file to deal with */ void gdcmSerieHeaderHelper::AddFileName(std::string filename) { gdcmHeaderHelper *GdcmFile = new gdcmHeaderHelper( filename.c_str() ); @@ -608,6 +657,7 @@ void gdcmSerieHeaderHelper::AddFileName(std::string filename) { /** * \ingroup gdcmHeaderHelper * \brief add a gdcmFile to the list + * @param file gdcmHeaderHelper to add */ void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper *file){ this->CoherentGdcmFileList.push_back( file ); @@ -615,7 +665,8 @@ void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper *file){ /** * \ingroup gdcmHeaderHelper - * \brief \todo + * \brief Sets the Directory + * @param dir Name of the directory to deal with */ void gdcmSerieHeaderHelper::SetDirectory(std::string dir){ gdcmDirList filenames_list(dir); //OS specific @@ -628,24 +679,29 @@ void gdcmSerieHeaderHelper::SetDirectory(std::string dir){ } } -//This could be implemented in a 'Strategy Pattern' approach -//But as I don't know how to do it, I leave it this way -//BTW, this is also a Strategy, I don't know this is the best approach :) +/** + * \ingroup gdcmHeaderHelper + * \brief Sorts the File List + * \warning This could be implemented in a 'Strategy Pattern' approach + * But as I don't know how to do it, I leave it this way + * BTW, this is also a Strategy, I don't know this is the best approach :) +*/ void gdcmSerieHeaderHelper::OrderGdcmFileList(){ - if( ImagePositionPatientOrdering() ) - { + if( ImagePositionPatientOrdering() ) { return ; } - else if( ImageNumberOrdering() ) - { + else if( ImageNumberOrdering() ) { return ; - } - else - { + } else { FileNameOrdering(); } } +/** + * \ingroup gdcmHeaderHelper + * \brief Gets the *coherent* File List + * @return the *coherent* File List +*/ std::list &gdcmSerieHeaderHelper::GetGdcmFileList() { return CoherentGdcmFileList; } @@ -657,11 +713,12 @@ std::list &gdcmSerieHeaderHelper::GetGdcmFileList() { // Private /** * \ingroup gdcmHeaderHelper - * \brief + * \brief sorts the images, according to their Patient Position * We may order, considering : * -# Image Number * -# Image Position Patient * -# More to come :) + * @return false only if the header is bugged ! */ bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering() //based on Jolinda's algorithm @@ -723,7 +780,6 @@ bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering() delete[] cosines; return false; } - distlist.push_back( dist ); @@ -772,7 +828,11 @@ bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering() return true; } -//Based on Image Number +/** + * \ingroup gdcmHeaderHelper + * \brief sorts the images, according to their Image Number + * @return false only if the header is bugged ! + */ bool gdcmSerieHeaderHelper::ImageNumberOrdering() { int min, max, pos; @@ -824,7 +884,13 @@ bool gdcmSerieHeaderHelper::ImageNumberOrdering() { return (mult!=0); } -bool gdcmSerieHeaderHelper::FileNameOrdering() { + +/** + * \ingroup gdcmHeaderHelper + * \brief sorts the images, according to their File Name + * @return false only if the header is bugged ! + */ + bool gdcmSerieHeaderHelper::FileNameOrdering() { //using the sort //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end()); return true;