/*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ Date: $Date: 2009/05/19 15:08:36 $ Version: $Revision: 1.344 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // // -------------- 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) // or Location (0020,0050) // as the Z coordinate, // 0. for all the coordinates if nothing is found // // Image Position (Patient) (0020,0032) VM=3 // --> // The attribute Patient Orientation (0020,0020) from the General Image Module // is of type 2C and has the condition Required if image does not require // Image Orientation (0020,0037) and Image Position (0020,0032). // However, if the image does require the attributes // - Image Orientation (Patient) (0020,0037), VM=6 // - Image Position (Patient) (0020,0032), VM=3 // then attribute Patient Orientation (0020,0020) should not be present // in the images. // // Remember also : // Patient Position (0018,5100) values : // HFS = Head First-Supine, where increasing (positive axis direction) : // X -> to the direction pointed to by the patient's oustretched left arm // Y -> to the anterior-to-posterior direction in the patient's body // Z -> to the feet-to-head direction in the patient's body // HFP = Head First-Prone, where increasing (positive axis direction) : // X -> to the direction pointed to by the patient's oustretched left arm // Y -> to the anterior-to-posterior direction in the patient's body // Z -> to the feet-to-head direction in the patient's body // FFS = Feet First-Supine, where increasing (positive axis direction) : // X -> to the direction pointed to by the patient's oustretched left arm // Y -> to the anterior-to-posterion direction in the patient's body // Z -> to the feet-to-head direction in the patient's body // FFP = Feet First-Prone, where increasing (positive axis direction) : // X -> to the direction pointed to by the patient's oustretched left arm // Y -> to the posterior-to-anterior direction in the patient's body // Z -> to the feet-to-head direction in the patient's body // HFDR = Head First-Decubitus Right // HFDL = Head First-Decubitus Left // FFDR = Feet First-Decubitus Right // FFDL = Feet First-Decubitus Left // we can also find (non standard!) // SEMIERECT // SUPINE // CS 2 Patient Orientation (0020 0020) // When the coordinates of the image // are always present, this field is almost never used. // Better we don't trust it too much ... // Found Values are : // L\P // L\FP // P\F // L\F // P\FR // R\F // // (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] // --------------------------------------------------------------- // #include "gdcmFile.h" #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" #include "gdcmDataEntry.h" #include "gdcmSQItem.h" #include #include //sscanf #include // for atoi namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor used when we want to generate dicom files from scratch */ File::File(): Document() { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; BasicOffsetTableItemValue = 0; FourthDimensionLocation = TagKey(0,0); } /** * \brief Canonical destructor. */ File::~File() { if ( RLEInfo ) delete RLEInfo; if ( JPEGInfo ) delete JPEGInfo; delete[] BasicOffsetTableItemValue; } //----------------------------------------------------------------------------- // Public /** * \brief Loader * @return false if file cannot be open or no swap info was found, * or no tag was found. */ bool File::Load( ) { if ( ! this->Document::Load( ) ) return false; return DoTheLoadingJob( ); } /** * \brief Does the Loading Job (internal use only) * @return false if file cannot be open or no swap info was found, * or no tag was found. */ bool File::DoTheLoadingJob( ) { // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This entry contains the number of // the group that contains the pixel data (hence the "Pixel Data" // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). // When the "Image Location" is missing we default to group 0x7fe0. // Note: this IS the right place for the code // Image Location const std::string &imgLocation = GetEntryString(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value GrPixel = 0x7fe0; } else { GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } // sometimes Image Location value doesn't follow // the supposed processor endianness. // see gdcmData/cr172241.dcm if ( GrPixel == 0xe07f ) { GrPixel = 0x7fe0; } if ( GrPixel != 0x7fe0 ) { // This is a kludge for old dirty Philips imager. NumPixel = 0x1010; } else { NumPixel = 0x0010; } // Now, we know GrPixel and NumPixel. // Let's create a VirtualDictEntry to allow a further VR modification // and force VR to match with BitsAllocated. DocEntry *entry = GetDocEntry(GrPixel, NumPixel); if ( entry != 0 ) { // Compute the RLE or JPEG info OpenFile(); const std::string &ts = GetTransferSyntax(); Fp->seekg( entry->GetOffset(), std::ios::beg ); if ( Global::GetTS()->IsRLELossless(ts) ) ComputeRLEInfo(); else if ( Global::GetTS()->IsJPEG(ts) ) ComputeJPEGFragmentInfo(); CloseFile(); // Create a new DataEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" //==>Take it easy! //==> Just change the VR ! /* DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { VRKey PixelVR; // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'O Words' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) PixelVR = "OB"; else PixelVR = "OW"; // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) { //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, // PixelVR,"1","Pixel Data"); //DataEntry *newEntry = DataEntry::New(newDict); //newDict->Delete(); //newEntry->Copy(entry); //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); //oldEntry->SetSelfArea(false); //RemoveEntry(oldEntry); //AddEntry(newEntry); //newEntry->Delete(); } } */ VRKey PixelVR; // 8 bits allocated is a 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'OW(ords)' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) PixelVR = "OB"; else PixelVR = "OW"; // Change only made if usefull if ( PixelVR != entry->GetVR() ) { entry->SetVR(PixelVR); } } return true; } /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed * and contains the mandatory information for being considered as * a well formed and usable Dicom/Acr File. * @return true when File is the one of a reasonable Dicom/Acr file, * false otherwise. */ bool File::IsReadable() { if ( !Document::IsReadable() ) { return false; } const std::string &res = GetEntryString(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { gdcmWarningMacro("Wrong Image Dimensions" << res); return false; // Image Dimensions } bool b0028_0100 = true; if ( !GetDocEntry(0x0028, 0x0100) ) { gdcmWarningMacro("Bits Allocated (0028|0100) not found"); //return false; // "Bits Allocated" b0028_0100 = false; } bool b0028_0101 = true; if ( !GetDocEntry(0x0028, 0x0101) ) { gdcmWarningMacro("Bits Stored (0028|0101) not found"); //return false; // "Bits Stored" b0028_0101 = false; } bool b0028_0102 = true; if ( !GetDocEntry(0x0028, 0x0102) ) { gdcmWarningMacro("Hight Bit (0028|0102) not found"); //return false; // "High Bit" b0028_0102 = false; } bool b0028_0103 = true; if ( !GetDocEntry(0x0028, 0x0103) ) { gdcmWarningMacro("Pixel Representation (0028|0103) not found"); //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) b0028_0103 = false; } if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) { gdcmWarningMacro("Too much mandatory Tags missing !"); return false; } if ( !GetDocEntry(GrPixel, NumPixel) ) { gdcmWarningMacro("Pixel Dicom Element " << std::hex << GrPixel << "|" << NumPixel << "not found"); return false; // Pixel Dicom Element not found :-( } return true; } /** * \brief gets the info from 0020,0013 : Image Number else 0. * @return image number */ int File::GetImageNumber() { //0020 0013 : Image Number std::string strImNumber = GetEntryString(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); } return 0; //Hopeless } /** * \brief gets the info from 0008,0060 : Modality * @return Modality Type */ ModalityType File::GetModality() { // 0008 0060 : Modality std::string strModality = GetEntryString(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; else if ( strModality.find("AS") < strModality.length()) return AS; else if ( strModality.find("BI") < strModality.length()) return BI; else if ( strModality.find("CF") < strModality.length()) return CF; else if ( strModality.find("CP") < strModality.length()) return CP; else if ( strModality.find("CR") < strModality.length()) return CR; else if ( strModality.find("CT") < strModality.length()) return CT; else if ( strModality.find("CS") < strModality.length()) return CS; else if ( strModality.find("DD") < strModality.length()) return DD; else if ( strModality.find("DF") < strModality.length()) return DF; else if ( strModality.find("DG") < strModality.length()) return DG; else if ( strModality.find("DM") < strModality.length()) return DM; else if ( strModality.find("DS") < strModality.length()) return DS; else if ( strModality.find("DX") < strModality.length()) return DX; else if ( strModality.find("ECG") < strModality.length()) return ECG; else if ( strModality.find("EPS") < strModality.length()) return EPS; else if ( strModality.find("FA") < strModality.length()) return FA; else if ( strModality.find("FS") < strModality.length()) return FS; else if ( strModality.find("HC") < strModality.length()) return HC; else if ( strModality.find("HD") < strModality.length()) return HD; else if ( strModality.find("LP") < strModality.length()) return LP; else if ( strModality.find("LS") < strModality.length()) return LS; else if ( strModality.find("MA") < strModality.length()) return MA; else if ( strModality.find("MR") < strModality.length()) return MR; else if ( strModality.find("NM") < strModality.length()) return NM; else if ( strModality.find("OT") < strModality.length()) return OT; else if ( strModality.find("PT") < strModality.length()) return PT; else if ( strModality.find("RF") < strModality.length()) return RF; else if ( strModality.find("RG") < strModality.length()) return RG; else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; else if ( strModality.find("SM") < strModality.length()) return SM; else if ( strModality.find("ST") < strModality.length()) return ST; else if ( strModality.find("TG") < strModality.length()) return TG; else if ( strModality.find("US") < strModality.length()) return US; else if ( strModality.find("VF") < strModality.length()) return VF; else if ( strModality.find("XA") < strModality.length()) return XA; else if ( strModality.find("XC") < strModality.length()) return XC; else { /// \todo throw error return value ??? /// specified <> unknown in our database return Unknow; } } return Unknow; } /** * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. * 0 means the file is NOT USABLE. The caller will have to check */ int File::GetXSize() { DataEntry *entry = GetDataEntry(0x0028,0x0011); if( entry ) return (int)entry->GetValue(0); return 0; } /** * \brief Retrieve the number of lines of image. * \warning The defaulted value is 1 as opposed to File::GetXSize() * @return The encountered size when found, 1 by default * (The ACR-NEMA file contains a Signal, not an Image). */ int File::GetYSize() { DataEntry *entry = GetDataEntry(0x0028,0x0010); if( entry ) return (int)entry->GetValue(0); if ( IsDicomV3() ) { return 0; } // The Rows (0028,0010) entry was optional for ACR/NEMA. // (at least some images didn't have it.) // It might hence be a signal (1D image). So we default to 1: return 1; } /** * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third * dimension. When missing we consider the third dimension as * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ int File::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. DataEntry *entry = GetDataEntry(0x0028,0x0008); if( entry ) return (int)entry->GetValue(0); // We then consider the "Planes" entry as the third dimension entry = GetDataEntry(0x0028,0x0012); if( entry ) return (int)entry->GetValue(0); return 1; } // Special case: // ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing) { xspacing = yspacing = zspacing = 1.0; TS *ts = Global::GetTS(); std::string sopclassuid_used; // D 0002|0002 [UI] [Media Storage SOP Class UID] //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002); const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); //D 0008|0016 [UI] [SOP Class UID] const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); const std::string &sopclassuid = ts->GetValue(sopclassuid_str); if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) { return false; } else { if ( mediastoragesopclassuid == sopclassuid ) { sopclassuid_used = mediastoragesopclassuid; } else { gdcmWarningMacro( "Inconsistant SOP Class UID: " << mediastoragesopclassuid << " and " << sopclassuid ); return false; } } // ok we have now the correct SOP Class UID if( sopclassuid_used == "Enhanced MR Image Storage" ) { SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); if( !n ) return false; SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); DocEntry *p = item1->GetDocEntry(0x0028,0x9110); if( !p ) return false; SeqEntry *seq = dynamic_cast(p); unsigned int n1 = seq->GetNumberOfSQItems(); if( !n1 ) return false; SQItem *item2 = seq->GetFirstSQItem(); // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ] DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030); if( !p2 ) return false; DataEntry *entry = dynamic_cast(p2); std::string spacing = entry->GetString(); if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 ) { xspacing = yspacing = 1.; return false; } // D 0018|0050 [DS] [Slice Thickness] [1 ] DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050); if( !p3 ) return false; DataEntry *entry2 = dynamic_cast(p3); std::string thickness = entry2->GetString(); if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 ) { zspacing = 1.; return false; } return true; } return false; } /** * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. * User has to tell gdcm the location of this '4th Dimension component' * using SetFourthDimensionLocation() method before. * \warning The defaulted value is 1. * @return The encountered size when found, 1 by default * (The file doesn't contain a '4D image'.). */ int File::GetTSize() { if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object return 1; DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), FourthDimensionLocation.GetElement() ); if( !entry ) { gdcmWarningMacro( " FourthDimensionLocation not found at : " << std::hex << FourthDimensionLocation.GetGroup() << "|" << FourthDimensionLocation.GetElement()); return 1; } else { return (int)entry->GetValue(0); } } /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ float File::GetXSpacing() { float xspacing = 1.0; float yspacing = 1.0; float zspacing = 1.0; uint32_t nbValue; DataEntry *entry; bool ok = false; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return xspacing; } // else fallback /* From:David Clunie - view profile Date:Wed, May 24 2006 1:12 pm Email:David Clunie Groups:comp.protocols.dicom The short answer is that: - (0018,1164) describes a spacing equivalent to that which would be measured off a film in projection radiography - (0018,7022) does not describe the image pixels themselves, since detector elements may have been binned to produce pixels - (0018,7020) may be different from (0018,7022) since there may be non-sensitive material separating individual detectors (i.e. the size is smaller than the spacing between centers) Only (0018,1164) is relevant when measuring things; the detector-specific attributes are there to describe the acquisition. David PS. For ultrasound you need to use Region Calibration. */ /* It *SHOULD* first find the IOD and then deduce which tags to read Eg: Cross section this is in Pixel Spacing (0028,0030) CR is in Imager Pixel Spacing (0018,1164) US is in Pixel Aspect Ratio (0028,0034) RT is in : (3002,0011) Image Plane Pixel Spacing (3002,0012) RT Image Position and (3004,000c) for deducing Z spacing */ std::string SOPClassUID = GetEntryString(0x0008,0x0016); /// \todo check the various SOP Class /// to get the Pixel Spacing at the proper location ///\todo find images to check if it *actually* works if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") // Ultrasound Image Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") // Ultrasound Image Storage || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") // Ultrasound Multi-Frame Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) // Ultrasound Multi-FrameImage Storage { // - check if SOPClassUID contains 2 parts (e.g. "4\3") // - guess how to deduce the spacing (FOV ?, ??) entry = GetDataEntry(0x0028,0x0034); if ( entry ) { nbValue = entry->GetValueCount(); if( nbValue !=2 ) { gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " << "has a wrong number of values :" << nbValue); } xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... ok = true; } if (ok) return xspacing; } /* if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") ) // Computed Radiography Image Storage // CR is in Imager Pixel Spacing (0018,1164)// */ // go on with old method ... // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing entry = GetDataEntry(0x0018,0x1164); if( entry ) { nbValue = entry->GetValueCount(); // Can't use IsValueCountValid because of the complex heuristic. if( nbValue !=2 ) gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " << "has a wrong number of values :" << nbValue); if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; return xspacing; } else { gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } entry = GetDataEntry(0x0028,0x0030); if( entry ) { nbValue = entry->GetValueCount(); if( nbValue !=2 ) gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " << "has a wrong number of values :" << nbValue); if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; return xspacing; } else { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return xspacing; } /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ float File::GetYSpacing() { float xspacing = 1., yspacing = 1.0, zspacing = 1.; uint32_t nbValue; DataEntry *entry; bool ok = false; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return yspacing; } // else fallback std::string SOPClassUID = GetEntryString(0x0008,0x0016); /// \todo check the various SOP Class /// to get the Pixel Spacing at the proper location ///\todo find images to check if it *actually* works if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") // Ultrasound Image Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") // Ultrasound Image Storage || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") // Ultrasound Multi-Frame Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) // Ultrasound Multi-FrameImage Storage { // - check if SOPClassUID contains 2 parts (e.g. "4\3") // - no way to deduce the spacing/ entry = GetDataEntry(0x0028,0x0034); if ( entry ) { nbValue = entry->GetValueCount(); if( nbValue ==2 ) { yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1); //std::cout << "ys " << yspacing << std::endl; ok = true; } else { gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " << "has a wrong number of values :" << nbValue); if (nbValue == 0 ) { ok = false; } else if (nbValue == 1 ) { yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... ok = true; } } } if (ok) return yspacing; } // go on with old method ... // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing entry = GetDataEntry(0x0018,0x1164); if( entry ) { yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) yspacing = 1.0; return yspacing; } else { gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } entry = GetDataEntry(0x0028,0x0030); if( entry ) { yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) yspacing = 1.0; return yspacing; } else { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return yspacing; } /** * \brief gets the info from 0018,0088 : Space Between Slices * else from 0018,0050 : Slice Thickness * else 1.0 * * When an element is missing, we suppose slices join together * (no overlapping, no interslice gap) but we have no way to check it ! * For *Dicom* images, ZSpacing *should be* calculated using * XOrigin, YOrigin, ZOrigin (of the top left image corner) * of 2 consecutive images, and the Orientation * Computing ZSpacing on a single image is not really meaningfull ! * @return Z dimension of a voxel-to be */ float File::GetZSpacing() { float xspacing = 1.0; float yspacing = 1.0; float zspacing = 1.0; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return zspacing; } // Spacing Between Slices : distance between the middle of 2 slices // Slices may be : // jointives (Spacing between Slices = Slice Thickness) // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal // It only concerns the MRI guys, not people wanting to visualize volumes // If Spacing Between Slices is missing, // we suppose slices joint together DataEntry *entry = GetDataEntry(0x0018,0x0088); if( entry ) { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } else gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) entry = GetDataEntry(0x0018,0x0050); if( entry ) { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) entry = GetDataEntry(0x3004,0x000c); if( entry ) { float z1 = (float)entry->GetValue(0); float z2 = (float)entry->GetValue(1); zspacing = z2 - z1; // can be negative... if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } return zspacing; } /** * \brief gets the info from 0020,0032 : Image Position Patient * else from 0020,0030 : Image Position (RET) * else 0. * @return up-left image corner X position */ float File::GetXOrigin() { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); entry = GetDataEntry(0x0020,0x0030); if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.0f; } } if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); } return 0.0f; } /** * \brief gets the info from 0020,0032 : Image Position Patient * else from 0020,0030 : Image Position (RET) * else 0. * @return up-left image corner Y position */ float File::GetYOrigin() { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); entry = GetDataEntry(0x0020,0x0030); if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.0f; } } if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(1); } return 0.0f; } /** * \brief gets the info from 0020,0032 : Image Position Patient * else from 0020,0030 : Image Position (RET) * else from 0020,1041 : Slice Location * else from 0020,0050 : Location * else 0. * @return up-left image corner Z position */ float File::GetZOrigin() { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( entry ) { if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.0f; } entry = GetDataEntry(0x0020,0x0030); if( entry ) { if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.0f; } // for *very* old ACR-NEMA images entry = GetDataEntry(0x0020,0x1041); if( entry ) { if( entry->GetValueCount() == 1 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); // VM=1 ! } gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); return 0.0f; } entry = GetDataEntry(0x0020,0x0050); if( entry ) { if( entry->GetValueCount() == 1 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); } gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.0f; } return 0.; // Hopeless } /** * \brief gets the info from 0020,0037 : Image Orientation Patient * or from 0020 0035 : Image Orientation (RET) * * (needed to organize DICOM files based on their x,y,z position) * * @param iop adress of the (6)float array to receive values. * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff- * is found. * @return true when one of the tag -with consistent values- is found * false when nothing or inconsistent stuff - is found */ bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] iop[0] = iop[4] = 1.; iop[1] = iop[2] = iop[3] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)." << " Less than 6 values were found." ); return false; } return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). " << "Less than 6 values were found." ); return false; } return true; } return false; } /** * \brief gets the cosine of image X axis, against patient X axis * (Sorry, but Python needs it :-( ) * @return cosine of image X axis, against patient X axis */ float File::GetXCosineOnX() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[0]); } /** * \brief gets the cosine of image X axis, against patient Y axis * (Sorry, but Python needs it :-( ) * @return cosine of image X axis, against patient Y axis */ float File::GetXCosineOnY() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[1]); } /** * \brief gets the cosine of image X axis, against patient Z axis * (Sorry, but Python needs it :-( ) * @return cosine of image X axis, against patient Z axis */ float File::GetXCosineOnZ() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[2]); } /** * \brief gets the cosine of image Y axis, against patient X axis * (Sorry, but Python needs it :-( ) * @return cosine of image Y axis, against patient X axis */ float File::GetYCosineOnX() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[3]); } /** * \brief gets the cosine of image Y axis, against patient Y axis * (Sorry, but Python needs it :-( ) * @return cosine of image Y axis, against patient Y axis */ float File::GetYCosineOnY() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[4]); } /** * \brief gets the cosine of image Y axis, against patient Z axis * (Sorry, but Python needs it :-( ) * @return cosine of image Y axis, against patient Z axis */ float File::GetYCosineOnZ() { float iop[6]; GetImageOrientationPatient( iop ); return(iop[5]); } /** * \brief gets the info from 0020,0032 : Image Position Patient * or from 0020 0030 : Image Position (RET) * * @param ipp adress of the (3)float array to receive values. * (defaulted as 0.,0.,0. if nothing -or inconsistent stuff- * is found. * @return true when one of the tag -with consistent values- is found * false when nothing or inconsistent stuff - is found */ bool File::GetImagePositionPatient( float ipp[3] ) { std::string strImPosiPat; //ipp is supposed to be float[3] ipp[0] = ipp[1] = ipp[2] = 0.; // 0020 0032 DS REL Image Position (Patient) strImPosiPat = GetEntryString(0x0020,0x0032); if ( strImPosiPat != GDCM_UNFOUND ) { if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", &ipp[0], &ipp[1], &ipp[2]) != 3 ) { gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)." << " Less than 3 values were found." ); return false; } return true; } //For ACR-NEMA // 0020 0030 DS REL Image Position (RET) else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND ) { if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", &ipp[0], &ipp[1], &ipp[2]) != 3 ) { gdcmWarningMacro( "wrong Image Position Patient (0020,0030). " << "Less than 3 values were found." ); return false; } return true; } return false; } /** * \brief Retrieve the number of Bits Stored (actually used) * (as opposed 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 ! */ int File::GetBitsStored() { DataEntry *entry = GetDataEntry(0x0028,0x0101); if( !entry ) { gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); } /** * \brief Retrieve the number of Bits Allocated * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,) * @return The encountered Number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ int File::GetBitsAllocated() { DataEntry *entry = GetDataEntry(0x0028,0x0100); if( !entry ) { gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); } /** * \brief Retrieve the high bit position. * \warning The method defaults to 0 when information is missing. * The responsability of checking this value is left to the caller. * @return The high bit position when present. 0 when missing. */ int File::GetHighBitPosition() { DataEntry *entry = GetDataEntry(0x0028,0x0102); if( !entry ) { gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); } /** * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-) * @return The encountered number of Samples Per Pixel, 1 by default. * (we assume Gray level Pixels) */ int File::GetSamplesPerPixel() { DataEntry *entry = GetDataEntry(0x0028,0x0002); if( !entry ) { gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } return (int)entry->GetValue(0); } /** * \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 File::GetPlanarConfiguration() { DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { return 0; } return (int)entry->GetValue(0); } /** * \brief Return the size (in bytes) of a single pixel of data. * @return The size in bytes of a single pixel of data; 0 by default * 0 means the file is NOT USABLE; the caller will have to check */ int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old ACR-NEMA RGB images) assert( !(GetEntryString(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) { return 1; } if ( pixelType == "16U" || pixelType == "16S") { return 2; } if ( pixelType == "32U" || pixelType == "32S") { return 4; } if ( pixelType == "FD" ) { return 8; } gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; } /** * \brief Build the Pixel Type of the image. * Possible values are: * - 8U unsigned 8 bit, * - 8S signed 8 bit, * - 16U unsigned 16 bit, * - 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 + photochromatic interp ="RGB " * + Planar Configuration = 0 * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() { std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory"); bitsAlloc = "16"; // default and arbitrary value, not to polute the output } else if ( bitsAlloc == "64" ) { return "FD"; } // useless since we have to bypass a bug ( >8 && < 16) else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; } else if ( bitsAlloc == "24" ) { // (in order no to be messed up by old RGB images) bitsAlloc = "8"; } int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers if ( i > 8 && i < 16 ) { bitsAlloc = "16"; } std::string sign; if( IsSignedPixelData() ) { sign = "S"; } else { sign = "U"; } return bitsAlloc + sign; } /** * \brief Check whether the pixels are signed (1) or UNsigned (0) data. * \warning The method defaults to false (UNsigned) when tag 0028|0103 * is missing. * The responsability of checking this value is left to the caller * (NO transformation is performed on the pixels to make then >0) * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() { DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" if( !entry ) { gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be " << "mandatory"); return false; } return entry->GetValue(0) != 0; } /** * \brief Check whether this a monochrome picture (gray levels) or not, * using "Photometric Interpretation" tag (0x0028,0x0004). * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ bool File::IsMonochrome() { const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " << "mandatory"); // to deal with old ACR-NEMA images if (GetNumberOfScalarComponents() == 1) return true; } return false; } /** * \brief Check whether this a MONOCHROME1 picture (high values = dark) * or not using "Photometric Interpretation" tag (0x0028,0x0004). * @return true when "MONOCHROME1" . False otherwise. */ bool File::IsMonochrome1() { const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to" << " be mandatory! "); } return false; } /** * \brief Check whether this a "PALETTE COLOR" picture or not by accessing * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). * @return true when "PALETTE COLOR". False otherwise. */ bool File::IsPaletteColor() { std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; } // MONOCHROME + [Enhanced CT Image Storage] actually have Palettes std::string sopClassUid = GetEntryString( 0x0008, 0x0016 ); if (Util::DicomStringEqual( sopClassUid, "1.2.840.10008.5.1.4.1.1.2.1")) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; } /** * \brief Check whether this a "YBR_FULL" color picture or not by accessing * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). * @return true when "YBR_FULL". False otherwise. */ bool File::IsYBRFull() { std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; } /** * \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 bool segmented; segmented = GetDocEntry(0x0028,0x1221) && GetDocEntry(0x0028,0x1222) && GetDocEntry(0x0028,0x1223); if( segmented ) return true; 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 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; } // Special case: // ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; bool File::GetRescaleSlopeIntercept(double &slope, double &intercept) { slope = 1.0; intercept = 0.0; TS *ts = Global::GetTS(); std::string sopclassuid_used; // D 0002|0002 [UI] [Media Storage SOP Class UID] const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); //D 0008|0016 [UI] [SOP Class UID] const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); const std::string &sopclassuid = ts->GetValue(sopclassuid_str); if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) { return false; } else { if( mediastoragesopclassuid == sopclassuid ) { sopclassuid_used = mediastoragesopclassuid; } else { gdcmWarningMacro( "Inconsistant SOP Class UID: " << mediastoragesopclassuid << " and " << sopclassuid ); return false; } } // ok we have now the correc SOP Class UID if( sopclassuid_used == "Enhanced MR Image Storage" ) { SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); if( !n ) return false; SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); DocEntry *p = item1->GetDocEntry(0x0028,0x9145); if( !p ) return false; SeqEntry *seq = dynamic_cast(p); unsigned int n1 = seq->GetNumberOfSQItems(); if( !n1 ) return false; SQItem *item2 = seq->GetFirstSQItem(); // D 0028|1052 [DS] [Rescale Intercept] [0 ] DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052); if( !p2 ) return false; DataEntry *entry = dynamic_cast(p2); std::string intercept_str = entry->GetString(); if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 ) { intercept = 0.; return false; } // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085] DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053); if( !p3 ) return false; DataEntry *entry2 = dynamic_cast(p3); std::string slope_str = entry2->GetString(); if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 ) { slope = 1.; return false; } return true; } return false; } /** *\brief gets the info from 0028,1052 : Rescale Intercept * @return Rescale Intercept. defaulted to 0.0 if not found or empty */ double 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 if not found or empty */ double File::GetRescaleSlope() { double resInter = 0.; double resSlope = 1.; if ( GetRescaleSlopeIntercept(resSlope, resInter) ) { return resSlope; } //0028 1053 DS IMG Rescale Slope std::string strRescSlope = GetEntryString(0x0028,0x1053); if ( strRescSlope != GDCM_UNFOUND ) { if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 ) { // bug in the element 0x0028,0x1053 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } return resSlope; } /** * \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_NAME_SPACE::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) { //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<< // (*it).Elem // << "[" << (*it).Value << "] "<< std::dec << std::endl; d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; if ( dynamic_cast(d) ) { gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } valLgth = (*it).Value.size(); if (valLgth == 0) continue; offset = d->GetOffset(); lgth = d->GetLength(); //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl; if (valLgth < lgth) { spaces = new std::string( lgth-valLgth, ' '); (*it).Value = (*it).Value + *spaces; //std::cout << "[" << (*it).Value << "] " << lgth << std::endl; delete spaces; } fp->seekp( offset, std::ios::beg ); fp->write( (*it).Value.c_str(), lgth ); } fp->close(); delete fp; } /** * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() * \note You cannot Anonymize a DataEntry (to be fixed) */ bool File::AnonymizeFile() { // If Anonymisation list is empty, let's perform some basic anonymization if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) { // If exist, replace by spaces SetEntryString(" ",0x0010, 0x2154); // Telephone SetEntryString(" ",0x0010, 0x1040); // Adress SetEntryString(" ",0x0010, 0x0020); // Patient ID DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { SetEntryString(studyInstanceUID, 0x0010, 0x0010); } else { SetEntryString("anonymized", 0x0010, 0x0010); } } } else { GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) { d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; if ( dynamic_cast(d) ) { gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } /* if ( dynamic_cast(d) ) { gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); continue; } */ else SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } } // In order to make definitively impossible any further identification // remove or replace all the stuff that contains a Date //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date //0008 0021 DA ID Series Date //0008 0022 DA ID Acquisition Date //0008 0023 DA ID Content Date //0008 0024 DA ID Overlay Date //0008 0025 DA ID Curve Date //0008 002a DT ID Acquisition Datetime //0018 9074 DT ACQ Frame Acquisition Datetime //0018 9151 DT ACQ Frame Reference Datetime //0018 a002 DT ACQ Contribution Date Time //0020 3403 SH REL Modified Image Date (RET) //0032 0032 DA SDY Study Verified Date //0032 0034 DA SDY Study Read Date //0032 1000 DA SDY Scheduled Study Start Date //0032 1010 DA SDY Scheduled Study Stop Date //0032 1040 DA SDY Study Arrival Date //0032 1050 DA SDY Study Completion Date //0038 001a DA VIS Scheduled Admission Date //0038 001c DA VIS Scheduled Discharge Date //0038 0020 DA VIS Admitting Date //0038 0030 DA VIS Discharge Date //0040 0002 DA PRC Scheduled Procedure Step Start Date //0040 0004 DA PRC Scheduled Procedure Step End Date //0040 0244 DA PRC Performed Procedure Step Start Date //0040 0250 DA PRC Performed Procedure Step End Date //0040 2004 DA PRC Issue Date of Imaging Service Request //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time //0040 4011 DT PRC Expected Completion Date and Time //0040 a030 DT PRC Verification Date Time //0040 a032 DT PRC Observation Date Time //0040 a120 DT PRC DateTime //0040 a121 DA PRC Date //0040 a13a DT PRC Referenced Datetime //0070 0082 DA ??? Presentation Creation Date //0100 0420 DT ??? SOP Autorization Date and Time //0400 0105 DT ??? Digital Signature DateTime //2100 0040 DA PJ Creation Date //3006 0008 DA SSET Structure Set Date //3008 0024 DA ??? Treatment Control Point Date //3008 0054 DA ??? First Treatment Date //3008 0056 DA ??? Most Recent Treatment Date //3008 0162 DA ??? Safe Position Exit Date //3008 0166 DA ??? Safe Position Return Date //3008 0250 DA ??? Treatment Date //300a 0006 DA RT RT Plan Date //300a 022c DA RT Air Kerma Rate Reference Date //300e 0004 DA RT Review Date return true; } /** * \brief Performs some consistency checking on various 'File related' * (as opposed to 'DicomDir related') entries * then writes in a file all the (Dicom Elements) included the Pixels * @param fileName file name to write to * @param writetype type of the file to be written * (ACR, ExplicitVR, ImplicitVR) */ bool File::Write(std::string fileName, FileType writetype) { gdcmDebugMacro(" File::Write "); std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if (*fp == NULL) { gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); return false; } // Entry : 0002|0000 = group length -> recalculated DataEntry *e0000 = GetDataEntry(0x0002,0x0000); if ( e0000 ) { std::ostringstream sLen; sLen << ComputeGroup0002Length( ); e0000->SetString(sLen.str()); } /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx if( writetype != JPEG && writetype != JPEG2000) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); if (i_lgPix != -2) /// \todo wtf "-2" ?!? { // no (GrPixel, NumPixel) element std::string s_lgPix = Util::Format("%d", i_lgPix+12); s_lgPix = Util::DicomString( s_lgPix.c_str() ); InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); } } Document::WriteContent(fp, writetype,false,false); fp->close(); delete fp; return true; } //----------------------------------------------------------------------------- // Protected //----------------------------------------------------------------------------- // Private /** * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. * Compute the RLE extra information and store it in RLEInfo * for later pixel retrieval usage. */ void File::ComputeRLEInfo() { std::string ts = GetTransferSyntax(); if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } // Encoded pixel data: for the time being we are only concerned with // Jpeg or RLE Pixel data encodings. // As stated in PS 3.5-2003, section 8.2 p44: // "If sent in Encapsulated Format (i.e. other than the Native Format) the // value representation OB is used". // Hence we expect an OB value representation. Concerning OB VR, // the section PS 3.5-2003, section A.4.c p 58-59, states: // "For the Value Representations OB and OW, the encoding shall meet the // following specifications depending on the Data element tag:" // [...snip...] // - the first item in the sequence of items before the encoded pixel // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" ReadEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) // Loop on the individual frame[s] and store the information // on the RLE fragments in a RLEFramesInfo. // Note: - when only a single frame is present, this is a // classical image. // - when more than one frame are present, then we are in // the case of a multi-frame image. long frameLength; int i=0; uint32_t sum = 0; while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { // Since we have read the basic offset table, let's check the value were correct // or else produce a warning: if ( BasicOffsetTableItemValue ) { // If a BasicOffsetTableItemValue was read uint32_t individualLength = BasicOffsetTableItemValue[i]; assert( individualLength == sum ); // REMOVE that if this is a problem if( individualLength != sum ) { gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" ); } sum += frameLength + 8; i++; } // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). long frameOffset = Fp->tellg(); // once per fragment uint32_t nbRleSegments = ReadInt32(); if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) gdcmWarningMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); } // Deduce from both RLE Header and frameLength // the fragment length, and again store this info // in a RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) { for(unsigned int k = 1; k <= nbRleSegments-1; k++) { rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - rleSegmentOffsetTable[k]; SkipBytes(rleSegmentLength[k]); } } rleSegmentLength[nbRleSegments] = frameLength - rleSegmentOffsetTable[nbRleSegments]; SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info RLEFrame *newFrame = new RLEFrame; newFrame->SetNumberOfFragments(nbRleSegments); for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) { newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]); newFrame->SetLength(uk,rleSegmentLength[uk]); } RLEInfo->AddFrame(newFrame); } // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } } /** * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. * Compute the jpeg extra information (fragment[s] offset[s] and * length) and store it[them] in JPEGInfo for later pixel * retrieval usage. */ void File::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). std::string ts = GetTransferSyntax(); if ( ! Global::GetTS()->IsJPEG(ts) ) { return; } ReadEncapsulatedBasicOffsetTable(); // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; int i=0; uint32_t sum = 0; while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { // Since we have read the basic offset table, let's check the value were correct // or else produce a warning: // A.4 Transfer syntaxes for encapsulation of encoded pixel data: // When the Item Value is present, the Basic Offset Table Item Value shall contain // concatenated 32-bit unsigned integer values that are byte offsets to the first // byte of the Item Tag of the first fragment for each frame in the Sequence of // Items. These offsets are measured from the first byte of the first Item Tag // following the Basic Offset Table item (See Table A.4-2). if ( BasicOffsetTableItemValue ) { // If a BasicOffsetTableItemValue was read uint32_t individualLength = BasicOffsetTableItemValue[i]; //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ?? if( individualLength != sum ) { gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" << individualLength << " != " << sum ); } sum += fragmentLength + 8; i++; } long fragmentOffset = Fp->tellg(); // Once per fragment // Store the collected info JPEGFragment *newFragment = new JPEGFragment; newFragment->SetOffset(fragmentOffset); newFragment->SetLength(fragmentLength); JPEGInfo->AddFragment(newFragment); SkipBytes(fragmentLength); } // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } } /** * \brief Assuming the internal file pointer Document::Fp * is placed at the beginning of a tag, check whether this * tag is (TestGroup, TestElem). * \warning On success the internal file pointer Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElem) the internal file pointer * Document::Fp is restored to its original position. * @param testGroup The expected group of the tag. * @param testElem The expected Element of the tag. * @return True on success, false otherwise. */ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { long positionOnEntry = Fp->tellg(); // Only when reading fragments //long currentPosition = positionOnEntry; // On debugging purposes // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; uint16_t itemTagElem; try { itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } catch ( FormatError ) { gdcmErrorMacro( "Can not read tag at 0x(" << std::hex << positionOnEntry << "). We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" ) ; return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) { // in order not to pollute output we don't warn on 'delimitors' if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" << " at address: " << " 0x(" << std::hex << (unsigned int)positionOnEntry << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; } return true; } /** * \brief Assuming the internal file pointer Document::Fp * is placed at the beginning of a tag (TestGroup, TestElement), * read the length associated to the Tag. * \warning On success the internal file pointer Document::Fp * is modified to point after the tag and its length. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer * Document::Fp is restored to its original position. * @param testGroup The expected Group of the tag. * @param testElem The expected Element of the tag. * @return On success returns the length associated to the tag. On failure * returns 0. */ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) { if ( !ReadTag(testGroup, testElem) ) { // Avoid polutting output if ( testGroup != 0xfffe ) gdcmErrorMacro( "ReadTag did not succeed for (" << DictEntry::TranslateToKey(testGroup,testElem) << ")..." ); return 0; } //// Then read the associated Item Length // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); gdcmDebugMacro( "Basic Item Length is: " << itemLength // << " at address: " << std::hex << (unsigned int)currentPosition ); return itemLength; } /** * \brief When parsing the Pixel Data of an encapsulated file, read * the basic offset table (when present, and BTW dump it). */ void File::ReadEncapsulatedBasicOffsetTable() { //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); // When present, read the basic offset table itself. // Notes: - since the presence of this basic offset table is optional // we can't rely on it for the implementation, and we will simply // trash its content (when present). // - still, when present, we could add some further checks on the // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { char *charBasicOffsetTableItemValue = new char[itemLength]; Fp->read(charBasicOffsetTableItemValue, itemLength); unsigned int nbEntries = itemLength/4; assert( nbEntries*4 == itemLength); // Make sure this is a multiple BasicOffsetTableItemValue = new uint32_t[nbEntries]; for (unsigned int i=0; i < nbEntries; i++ ) { BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i])); #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) uint32_t val = BasicOffsetTableItemValue[i]; BasicOffsetTableItemValue[i] = ( (val<<24) | ((val<<8) & 0x00ff0000) | ( (val>>8) & 0x0000ff00) | (val>>24) ); #endif gdcmDebugMacro( "Read one length for: " << std::hex << BasicOffsetTableItemValue[i] ); } delete[] charBasicOffsetTableItemValue; } } // These are the deprecated method that one day should be removed (after the next release) //#ifndef GDCM_LEGACY_REMOVE /* * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) * @ param fileName file to be open for parsing * @ return false if file cannot be open or no swap info was found, * or no tag was found. * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ /* bool File::Load( std::string const &fileName ) { GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", File::Load()); SetFileName( fileName ); if ( ! this->Document::Load( ) ) return false; return DoTheLoadingJob( ); } #endif */ //----------------------------------------------------------------------------- // Print //----------------------------------------------------------------------------- } // end namespace gdcm