- * \ingroup gdcmFile
- *
-* @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
- * @return false if write fails
- */
-bool gdcmFile::WriteBase (std::string fileName, FileType type) {
-
- FILE * fp1;
- fp1 = fopen(fileName.c_str(),"wb");
- if (fp1 == NULL) {
- printf("Failed to open (write) File [%s] \n",fileName.c_str());
- return (false);
- }
-
- if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
- char * filePreamble;
- // writing Dicom File Preamble
- filePreamble=(char*)calloc(128,1);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- free (filePreamble);
- }
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // if recognition code tells us we dealt with a LibIDO image
- // we reproduce on disk the switch between lineNumber and columnNumber
- // just before writting ...
-
- std::string rows, columns;
- if ( Header->GetFileType() == ACR_LIBIDO){
- rows = Header->GetEntryByNumber(0x0028, 0x0010);
- columns = Header->GetEntryByNumber(0x0028, 0x0011);
- Header->SetEntryByNumber(columns, 0x0028, 0x0010);
- Header->SetEntryByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
-
- // TODO : get the grPixel, numPixel values
- guint16 grPixel =0x7fe0;
- guint16 numPixel=0x0010;
-
- IterHT p;
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel);
- gdcmHeaderEntry * a;
- TagHeaderEntryHT::iterator p2;
-
- //IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel);
- // Update Pixel Data Length
- // the *last* of the 7fe0,0010, if many.
-
-/*
- // good looking, but it doesn't work
- p= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym
- p2=p.second; // iterator on the last synonym
- a=p2->second; // H Table target column (2-nd col)
- //a->SetLength(lgrTotale);
- a->SetPrintLevel(2);
- a->Print();
- // use the old -wrong if many 7fe0,0010- way
- */
- if (PixelRead==1)
- Header->SetEntryLengthByNumber(lgrTotaleRaw,grPixel, numPixel);
- else if (PixelRead==0)
- Header->SetEntryLengthByNumber(lgrTotale, grPixel, numPixel);
- // if == -1 : no Pixel Data was read : abort the method
-
- Header->Write(fp1, type);
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // ...and we restore the Header to be Dicom Compliant again
- // just after writting
-
- if (Header->GetFileType() == ACR_LIBIDO){
- Header->SetEntryByNumber(rows , 0x0028, 0x0010);
- Header->SetEntryByNumber(columns, 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
+ * \brief tells us if LUT are used
+ * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
+ * are NOT considered as LUT, since nobody knows
+ * how to deal with them
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
+ */
+bool File::HasLUT()
+{
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetDocEntry(0x0028,0x1101) )
+ {
+ return false;
+ }
+ // LutDescriptorGreen
+ if ( !GetDocEntry(0x0028,0x1102) )
+ {
+ return false;
+ }
+ // LutDescriptorBlue
+ if ( !GetDocEntry(0x0028,0x1103) )
+ {
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1201) )
+ {
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1203) )
+ {
+ return false;
+ }
+
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
+}
+
+/**
+ * \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 ]
+ * @ return bit number of each LUT item
+ */
+int File::GetLUTNbits()
+{
+ std::vector<std::string> tokens;
+ int lutNbits;
+
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
+ // = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string lutDescription = GetEntryString(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
+ return 0;
+ }
+
+ tokens.clear(); // clean any previous value
+ Util::Tokenize ( lutDescription, tokens, "\\" );
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
+
+ lutNbits = atoi( tokens[2].c_str() );
+ tokens.clear();
+
+ return lutNbits;
+}
+
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept. defaulted to 0.0 is not found or empty
+ */
+float File::GetRescaleIntercept()
+{
+ // 0028 1052 DS IMG Rescale Intercept
+ DataEntry *entry = GetDataEntry(0x0028, 0x1052);
+ if( !entry )
+ {
+ gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
+ return 0.0f;
+ }
+ return (float)entry->GetValue(0);
+
+}
+
+/**
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope. defaulted to 1.0 is not found or empty
+ */
+float File::GetRescaleSlope()
+{
+ // 0028 1053 DS IMG Rescale Slope
+ DataEntry *entry = GetDataEntry(0x0028, 0x1053);
+ if( !entry )
+ {
+ gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
+ return 1.0f;
+ }
+ return (float)entry->GetValue(0);
+}
+
+/**
+ * \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, if no LUT found ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
+ */
+int File::GetNumberOfScalarComponents()
+{
+ if ( GetSamplesPerPixel() == 3 )
+ {
+ return 3;
+ }
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
+
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
+ {
+ return 3;
+ }
+ else
+ {
+ return 1;
+ }
+ }
+
+ // beware of trailing space at end of string
+ // DICOM tags are never of odd length
+ if ( strPhotometricInterpretation == GDCM_UNFOUND ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
+ {
+ return 1;
+ }
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
+}
+
+/**
+ * \brief This function is intended to user that DOESN'T want
+ * to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * - the (vtk) user is supposed to know how deal with LUTs -
+ * \warning to be used with GetImagePixelsRaw()
+ * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
+ */
+int File::GetNumberOfScalarComponentsRaw()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryString(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
+}
+
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t File::GetPixelOffset()
+{
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
+ }
+ else
+ {
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
+ */
+size_t File::GetPixelAreaLength()
+{
+ DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+ gdcmWarningMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
+ return 0;
+ }
+}
+
+/**
+ * \brief Adds the characteristics of a new element we want to anonymize
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value new value (string) to substitute with
+ */
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
+{
+ DicomElement el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ UserAnonymizeList.push_back(el);
+}
+
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
+{
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t valLgth = 0;
+ std::string *spaces;
+ for (ListElements::iterator it = UserAnonymizeList.begin();
+ it != UserAnonymizeList.end();
+ ++it)
+ {