[807] | 1 | // |
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| 2 | // ******************************************************************** |
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| 3 | // * License and Disclaimer * |
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| 4 | // * * |
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| 5 | // * The Geant4 software is copyright of the Copyright Holders of * |
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| 6 | // * the Geant4 Collaboration. It is provided under the terms and * |
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| 7 | // * conditions of the Geant4 Software License, included in the file * |
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| 8 | // * LICENSE and available at http://cern.ch/geant4/license . These * |
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| 9 | // * include a list of copyright holders. * |
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| 10 | // * * |
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| 11 | // * Neither the authors of this software system, nor their employing * |
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| 12 | // * institutes,nor the agencies providing financial support for this * |
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| 13 | // * work make any representation or warranty, express or implied, * |
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| 14 | // * regarding this software system or assume any liability for its * |
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| 15 | // * use. Please see the license in the file LICENSE and URL above * |
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| 16 | // * for the full disclaimer and the limitation of liability. * |
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| 17 | // * * |
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| 18 | // * This code implementation is the result of the scientific and * |
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| 19 | // * technical work of the GEANT4 collaboration. * |
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| 20 | // * By using, copying, modifying or distributing the software (or * |
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| 21 | // * any work based on the software) you agree to acknowledge its * |
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| 22 | // * use in resulting scientific publications, and indicate your * |
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| 23 | // * acceptance of all terms of the Geant4 Software license. * |
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| 24 | // ******************************************************************** |
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| 25 | // |
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| 26 | // The code was written by : |
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| 27 | // *Louis Archambault louis.archambault@phy.ulaval.ca, |
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| 28 | // *Luc Beaulieu beaulieu@phy.ulaval.ca |
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| 29 | // +Vincent Hubert-Tremblay at tigre.2@sympatico.ca |
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| 30 | // |
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| 31 | // |
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| 32 | // *Centre Hospitalier Universitaire de Quebec (CHUQ), |
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| 33 | // Hotel-Dieu de Quebec, departement de Radio-oncologie |
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| 34 | // 11 cote du palais. Quebec, QC, Canada, G1R 2J6 |
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| 35 | // tel (418) 525-4444 #6720 |
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| 36 | // fax (418) 691 5268 |
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| 37 | // |
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| 38 | // + Universit.Aé Laval, Québec (QC) Canada |
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| 39 | //******************************************************* |
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| 40 | // |
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| 41 | //******************************************************* |
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| 42 | // |
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| 43 | //******************************************************* |
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| 44 | // |
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| 45 | // DicomHandler.cc : |
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| 46 | // - Handling of DICM images |
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| 47 | // - Reading headers and pixels |
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| 48 | // - Transforming pixel to density and creating *.g4dcm |
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| 49 | // files |
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| 50 | // - Definitions are in DicomHandler.hh |
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| 51 | //******************************************************* |
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| 52 | |
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| 53 | #include "DicomHandler.hh" |
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| 54 | #include "globals.hh" |
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| 55 | #include "G4ios.hh" |
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| 56 | #include <fstream> |
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| 57 | |
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| 58 | #include <cctype> |
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| 59 | #include <cstring> |
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| 60 | |
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| 61 | |
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| 62 | DicomHandler::DicomHandler() |
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[1337] | 63 | : DATABUFFSIZE(8192), LINEBUFFSIZE(5020), FILENAMESIZE(512), |
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[807] | 64 | compression(0), nFiles(0), rows(0), columns(0), |
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| 65 | bitAllocated(0), maxPixelValue(0), minPixelValue(0), |
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| 66 | pixelSpacingX(0.), pixelSpacingY(0.), |
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| 67 | sliceThickness(0.), sliceLocation(0.), |
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| 68 | rescaleIntercept(0), rescaleSlope(0), |
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| 69 | littleEndian(true), implicitEndian(false), |
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| 70 | pixelRepresentation(0) { |
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| 71 | ; |
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| 72 | } |
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| 73 | |
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| 74 | DicomHandler::~DicomHandler() { |
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| 75 | ; |
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| 76 | } |
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| 77 | |
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| 78 | G4int DicomHandler::ReadFile(FILE *dicom, char * filename2) |
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| 79 | { |
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| 80 | G4cout << " ReadFile " << filename2 << G4endl; |
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| 81 | G4int returnvalue = 0; |
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| 82 | char * buffer = new char[LINEBUFFSIZE]; |
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| 83 | |
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| 84 | implicitEndian = false; |
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| 85 | littleEndian = true; |
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| 86 | |
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| 87 | std::fread( buffer, 1, 128, dicom ); // The first 128 bytes |
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| 88 | //are not important |
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| 89 | // Reads the "DICOM" letters |
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| 90 | std::fread( buffer, 1, 4, dicom ); |
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| 91 | // if there is no preamble, the FILE pointer is rewinded. |
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| 92 | if(std::strncmp("DICM", buffer, 4) != 0) { |
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| 93 | std::fseek(dicom, 0, SEEK_SET); |
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| 94 | implicitEndian = true; |
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| 95 | } |
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| 96 | |
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| 97 | short readGroupId; // identify the kind of input data |
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| 98 | short readElementId; // identify a particular type information |
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| 99 | short elementLength2; // deal with element length in 2 bytes |
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[1337] | 100 | //unsigned int elementLength4; // deal with element length in 4 bytes |
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[807] | 101 | G4int elementLength4; // deal with element length in 4 bytes |
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| 102 | |
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| 103 | char * data = new char[DATABUFFSIZE]; |
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| 104 | |
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[1337] | 105 | |
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[807] | 106 | // Read information up to the pixel data |
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| 107 | while(true) { |
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| 108 | |
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| 109 | //Reading groups and elements : |
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| 110 | readGroupId = 0; |
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| 111 | readElementId = 0; |
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| 112 | // group ID |
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| 113 | std::fread(buffer, 2, 1, dicom); |
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| 114 | GetValue(buffer, readGroupId); |
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| 115 | // element ID |
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| 116 | std::fread(buffer, 2, 1, dicom); |
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| 117 | GetValue(buffer, readElementId); |
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| 118 | |
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| 119 | // Creating a tag to be identified afterward |
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| 120 | G4int tagDictionary = readGroupId*0x10000 + readElementId; |
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[1337] | 121 | |
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| 122 | // beginning of the pixels |
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| 123 | if(tagDictionary == 0x7FE00010) break; |
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[807] | 124 | |
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[1337] | 125 | // VR or element length |
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[807] | 126 | std::fread(buffer,2,1,dicom); |
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| 127 | GetValue(buffer, elementLength2); |
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[1337] | 128 | |
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| 129 | // If value representation (VR) is OB, OW, SQ, UN, added OF and UT |
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[807] | 130 | //the next length is 32 bits |
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| 131 | if((elementLength2 == 0x424f || // "OB" |
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| 132 | elementLength2 == 0x574f || // "OW" |
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[1337] | 133 | elementLength2 == 0x464f || // "OF" |
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| 134 | elementLength2 == 0x5455 || // "UT" |
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| 135 | elementLength2 == 0x5153 || // "SQ" |
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[807] | 136 | elementLength2 == 0x4e55) && // "UN" |
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| 137 | !implicitEndian ) { // explicit VR |
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| 138 | |
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| 139 | std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes |
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| 140 | |
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| 141 | // element length |
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| 142 | std::fread(buffer, 4, 1, dicom); |
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| 143 | GetValue(buffer, elementLength4); |
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[1337] | 144 | |
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| 145 | if(elementLength2 == 0x5153) |
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| 146 | { |
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| 147 | if(elementLength4 == 0xFFFFFFFF) |
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| 148 | read_undefined_nested( dicom ); |
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| 149 | else{ |
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| 150 | if(read_defined_nested( dicom, elementLength4 )==0){ |
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| 151 | G4cerr << "Reading defined nested functin failed!" << G4endl; |
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| 152 | exit(-10); } |
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| 153 | } |
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| 154 | } else { |
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[807] | 155 | // Reading the information with data |
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| 156 | std::fread(data, elementLength4,1,dicom); |
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[1337] | 157 | } |
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[807] | 158 | |
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[1337] | 159 | |
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| 160 | } else { |
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[807] | 161 | |
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[1337] | 162 | if(!implicitEndian || readGroupId == 2) { // explicit with VR different than previous ones |
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| 163 | |
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| 164 | //G4cout << "Reading DICOM files with Explicit VR"<< G4endl; |
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| 165 | // element length (2 bytes) |
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| 166 | std::fread(buffer, 2, 1, dicom); |
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| 167 | GetValue(buffer, elementLength2); |
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| 168 | elementLength4 = elementLength2; |
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| 169 | |
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| 170 | |
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| 171 | |
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| 172 | std::fread(data, elementLength4, 1, dicom); |
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| 173 | |
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| 174 | } else { // Implicit VR |
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[807] | 175 | |
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[1337] | 176 | //G4cout << "Reading DICOM files with Implicit VR"<< G4endl; |
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| 177 | |
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| 178 | // element length (4 bytes) |
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| 179 | if(std::fseek(dicom, -2, SEEK_CUR) != 0) { |
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| 180 | G4cerr << "[DicomHandler] fseek failed" << G4endl; |
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| 181 | exit(-10);} |
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[807] | 182 | |
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[1337] | 183 | std::fread(buffer, 4, 1, dicom); |
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| 184 | GetValue(buffer, elementLength4); |
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[807] | 185 | |
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[1337] | 186 | //G4cout << std::hex<< elementLength4 << G4endl; |
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| 187 | |
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| 188 | if(elementLength4 == 0xFFFFFFFF) |
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| 189 | read_undefined_nested(dicom); |
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| 190 | else { |
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| 191 | |
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| 192 | |
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| 193 | std::fread(data, elementLength4, 1, dicom); |
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| 194 | |
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| 195 | } |
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| 196 | |
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| 197 | } |
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[807] | 198 | } |
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| 199 | |
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| 200 | // NULL termination |
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| 201 | data[elementLength4] = '\0'; |
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| 202 | |
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| 203 | // analyzing information |
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| 204 | GetInformation(tagDictionary, data); |
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| 205 | } |
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| 206 | |
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| 207 | // Creating files to store information |
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| 208 | std::ofstream foutG4DCM; |
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| 209 | G4String fnameG4DCM = G4String(filename2) + ".g4dcm"; |
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| 210 | foutG4DCM.open(fnameG4DCM); |
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[1337] | 211 | G4cout << "### Writing of " << fnameG4DCM << " ### " << G4endl; |
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[807] | 212 | |
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| 213 | foutG4DCM << fMaterialIndices.size() << G4endl; |
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| 214 | //--- Write materials |
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[1337] | 215 | unsigned int ii = 0; |
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| 216 | std::map<G4float,G4String>::const_iterator ite; |
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[807] | 217 | for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++, ii++ ){ |
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| 218 | foutG4DCM << ii << " " << (*ite).second << G4endl; |
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| 219 | } |
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| 220 | //--- Write number of voxels (assume only one voxel in Z) |
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| 221 | foutG4DCM << rows/compression << " " << columns/compression << " 1 " << G4endl; |
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| 222 | //--- Write minimum and maximum extensions |
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| 223 | foutG4DCM << -pixelSpacingX*rows/2 << " " << pixelSpacingX*rows/2 << G4endl; |
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| 224 | foutG4DCM << -pixelSpacingY*columns/2 << " " << pixelSpacingY*columns/2 << G4endl; |
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| 225 | foutG4DCM << sliceLocation-sliceThickness/2. << " " << sliceLocation+sliceThickness/2. << G4endl; |
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[1337] | 226 | // foutG4DCM << compression << G4endl; |
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[807] | 227 | |
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| 228 | ReadData( dicom, filename2 ); |
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| 229 | |
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| 230 | StoreData( foutG4DCM ); |
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| 231 | |
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| 232 | foutG4DCM.close(); |
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| 233 | |
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| 234 | // |
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| 235 | delete [] buffer; |
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| 236 | delete [] data; |
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| 237 | |
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| 238 | return returnvalue; |
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| 239 | } |
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| 240 | |
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| 241 | // |
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| 242 | void DicomHandler::GetInformation(G4int & tagDictionary, char * data) { |
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| 243 | if(tagDictionary == 0x00280010 ) { // Number of Rows |
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| 244 | GetValue(data, rows); |
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| 245 | std::printf("[0x00280010] Rows -> %i\n",rows); |
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| 246 | |
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| 247 | } else if(tagDictionary == 0x00280011 ) { // Number of columns |
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| 248 | GetValue(data, columns); |
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| 249 | std::printf("[0x00280011] Columns -> %i\n",columns); |
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| 250 | |
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| 251 | } else if(tagDictionary == 0x00280102 ) { // High bits ( not used ) |
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| 252 | short highBits; |
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| 253 | GetValue(data, highBits); |
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| 254 | std::printf("[0x00280102] High bits -> %i\n",highBits); |
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| 255 | |
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| 256 | } else if(tagDictionary == 0x00280100 ) { // Bits allocated |
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| 257 | GetValue(data, bitAllocated); |
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| 258 | std::printf("[0x00280100] Bits allocated -> %i\n", bitAllocated); |
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| 259 | |
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| 260 | } else if(tagDictionary == 0x00280101 ) { // Bits stored ( not used ) |
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| 261 | short bitStored; |
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| 262 | GetValue(data, bitStored); |
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| 263 | std::printf("[0x00280101] Bits stored -> %i\n",bitStored); |
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| 264 | |
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| 265 | } else if(tagDictionary == 0x00280106 ) { // Min. pixel value |
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| 266 | GetValue(data, minPixelValue); |
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| 267 | std::printf("[0x00280106] Min. pixel value -> %i\n", minPixelValue); |
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| 268 | |
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| 269 | } else if(tagDictionary == 0x00280107 ) { // Max. pixel value |
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| 270 | GetValue(data, maxPixelValue); |
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| 271 | std::printf("[0x00280107] Max. pixel value -> %i\n", maxPixelValue); |
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| 272 | |
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| 273 | } else if(tagDictionary == 0x00281053) { // Rescale slope |
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| 274 | rescaleSlope = atoi(data); |
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| 275 | std::printf("[0x00281053] Rescale Slope -> %d\n", rescaleSlope); |
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| 276 | |
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| 277 | } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept |
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| 278 | rescaleIntercept = atoi(data); |
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| 279 | std::printf("[0x00281052] Rescale Intercept -> %d\n", rescaleIntercept ); |
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| 280 | |
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| 281 | } else if(tagDictionary == 0x00280103 ) { |
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| 282 | // Pixel representation ( functions not design to read signed bits ) |
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| 283 | pixelRepresentation = atoi(data); // 0: unsigned 1: signed |
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| 284 | std::printf("[0x00280103] Pixel Representation -> %i\n", pixelRepresentation); |
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| 285 | if(pixelRepresentation == 1 ) { |
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| 286 | std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, "); |
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| 287 | std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE "); |
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| 288 | std::printf("ERROR !!!!!! -> \n"); |
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| 289 | } |
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| 290 | |
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| 291 | } else if(tagDictionary == 0x00080006 ) { // Modality |
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| 292 | std::printf("[0x00080006] Modality -> %s\n", data); |
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| 293 | |
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| 294 | } else if(tagDictionary == 0x00080070 ) { // Manufacturer |
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| 295 | std::printf("[0x00080070] Manufacturer -> %s\n", data); |
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| 296 | |
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| 297 | } else if(tagDictionary == 0x00080080 ) { // Institution Name |
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| 298 | std::printf("[0x00080080] Institution Name -> %s\n", data); |
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| 299 | |
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| 300 | } else if(tagDictionary == 0x00080081 ) { // Institution Address |
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| 301 | std::printf("[0x00080081] Institution Address -> %s\n", data); |
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| 302 | |
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| 303 | } else if(tagDictionary == 0x00081040 ) { // Institution Department Name |
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| 304 | std::printf("[0x00081040] Institution Department Name -> %s\n", data); |
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| 305 | |
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| 306 | } else if(tagDictionary == 0x00081090 ) { // Manufacturer's Model Name |
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| 307 | std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data); |
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| 308 | |
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| 309 | } else if(tagDictionary == 0x00181000 ) { // Device Serial Number |
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| 310 | std::printf("[0x00181000] Device Serial Number -> %s\n", data); |
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| 311 | |
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| 312 | } else if(tagDictionary == 0x00080008 ) { // Image type ( not used ) |
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| 313 | std::printf("[0x00080008] Image Types -> %s\n", data); |
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| 314 | |
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| 315 | } else if(tagDictionary == 0x00283000 ) { // Modality LUT Sequence ( not used ) |
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| 316 | std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data); |
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| 317 | |
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| 318 | } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used ) |
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| 319 | std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data); |
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| 320 | |
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| 321 | } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used ) |
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| 322 | std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data); |
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| 323 | |
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| 324 | } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used ) |
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| 325 | std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data); |
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| 326 | |
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| 327 | } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used ) |
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| 328 | std::printf("[0x00283006] LUT Data US or SS -> %s\n", data); |
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| 329 | |
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| 330 | } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used ) |
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| 331 | std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data); |
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| 332 | |
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| 333 | } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value ( not used ) |
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| 334 | std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data); |
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| 335 | |
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| 336 | } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing |
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| 337 | G4String datas(data); |
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| 338 | int iss = datas.find('\\'); |
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| 339 | pixelSpacingX = atof( datas.substr(0,iss).c_str() ); |
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| 340 | pixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() ); |
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| 341 | |
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| 342 | } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used ) |
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| 343 | std::printf("[0x00200037] Image Orientation (Patient) -> %s\n", data); |
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| 344 | |
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| 345 | } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used ) |
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| 346 | std::printf("[0x00200032] Image Position (Patient,mm) -> %s\n", data); |
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| 347 | |
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| 348 | } else if(tagDictionary == 0x00180050 ) { // Slice Thickness |
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| 349 | sliceThickness = atof(data); |
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| 350 | std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", sliceThickness); |
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| 351 | |
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| 352 | } else if(tagDictionary == 0x00201041 ) { // Slice Location |
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| 353 | sliceLocation = atof(data); |
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| 354 | std::printf("[0x00201041] Slice Location -> %f\n", sliceLocation); |
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| 355 | |
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| 356 | } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation ( not used ) |
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| 357 | std::printf("[0x00280004] Photometric Interpretation -> %s\n", data); |
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| 358 | |
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| 359 | } else if(tagDictionary == 0x00020010) { // Endian |
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| 360 | if(strcmp(data, "1.2.840.10008.1.2") == 0) |
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| 361 | implicitEndian = true; |
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| 362 | else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0) |
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| 363 | littleEndian = false; |
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| 364 | //else 1.2.840..10008.1.2.1 (explicit little endian) |
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| 365 | |
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| 366 | std::printf("[0x00020010] Endian -> %s\n", data); |
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| 367 | } |
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| 368 | |
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| 369 | // others |
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| 370 | else { |
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| 371 | std::printf("[0x%x] -> %s\n", tagDictionary, data); |
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| 372 | |
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| 373 | } |
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| 374 | |
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| 375 | } |
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| 376 | |
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| 377 | void DicomHandler::StoreData(std::ofstream& foutG4DCM) |
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| 378 | { |
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| 379 | G4int mean; |
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| 380 | G4double density; |
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| 381 | G4bool overflow = false; |
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| 382 | G4int cpt=1; |
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| 383 | |
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| 384 | //----- Print indices of material |
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| 385 | if(compression == 1) { // no compression: each pixel has a density value) |
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| 386 | for( G4int ww = 0; ww < rows; ww++) { |
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| 387 | for( G4int xx = 0; xx < columns; xx++) { |
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| 388 | mean = tab[ww][xx]; |
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| 389 | density = Pixel2density(mean); |
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| 390 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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| 391 | } |
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| 392 | foutG4DCM << G4endl; |
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| 393 | } |
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| 394 | |
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| 395 | } else { |
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| 396 | // density value is the average of a square region of |
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| 397 | // compression*compression pixels |
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| 398 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
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| 399 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
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| 400 | overflow = false; |
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| 401 | mean = 0; |
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| 402 | for(int sumx = 0; sumx < compression; sumx++) { |
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| 403 | for(int sumy = 0; sumy < compression; sumy++) { |
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| 404 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
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| 405 | mean += tab[ww+sumy][xx+sumx]; |
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| 406 | } |
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| 407 | if(overflow) break; |
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| 408 | } |
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| 409 | mean /= compression*compression; |
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| 410 | cpt = 1; |
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| 411 | |
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| 412 | if(!overflow) { |
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| 413 | G4double density = Pixel2density(mean); |
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| 414 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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| 415 | } |
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| 416 | } |
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| 417 | foutG4DCM << G4endl; |
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| 418 | } |
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| 419 | |
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| 420 | } |
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| 421 | |
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| 422 | //----- Print densities |
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| 423 | if(compression == 1) { // no compression: each pixel has a density value) |
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| 424 | for( G4int ww = 0; ww < rows; ww++) { |
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| 425 | for( G4int xx = 0; xx < columns; xx++) { |
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| 426 | mean = tab[ww][xx]; |
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| 427 | density = Pixel2density(mean); |
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| 428 | foutG4DCM << density << " "; |
---|
| 429 | if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
---|
| 430 | } |
---|
| 431 | } |
---|
| 432 | |
---|
| 433 | } else { |
---|
| 434 | // density value is the average of a square region of |
---|
| 435 | // compression*compression pixels |
---|
| 436 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
---|
| 437 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
---|
| 438 | overflow = false; |
---|
| 439 | mean = 0; |
---|
| 440 | for(int sumx = 0; sumx < compression; sumx++) { |
---|
| 441 | for(int sumy = 0; sumy < compression; sumy++) { |
---|
| 442 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
---|
| 443 | mean += tab[ww+sumy][xx+sumx]; |
---|
| 444 | } |
---|
| 445 | if(overflow) break; |
---|
| 446 | } |
---|
| 447 | mean /= compression*compression; |
---|
| 448 | cpt = 1; |
---|
| 449 | |
---|
| 450 | if(!overflow) { |
---|
| 451 | G4double density = Pixel2density(mean); |
---|
| 452 | foutG4DCM << density << " "; |
---|
| 453 | if( xx/compression%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
---|
| 454 | } |
---|
| 455 | } |
---|
| 456 | } |
---|
| 457 | |
---|
| 458 | } |
---|
| 459 | |
---|
| 460 | } |
---|
| 461 | |
---|
| 462 | void DicomHandler::ReadMaterialIndices( std::ifstream& finData) |
---|
| 463 | { |
---|
[1337] | 464 | unsigned int nMate; |
---|
[807] | 465 | G4String mateName; |
---|
[1337] | 466 | G4float densityMax; |
---|
[807] | 467 | finData >> nMate; |
---|
| 468 | if( finData.eof() ) return; |
---|
| 469 | |
---|
| 470 | G4cout << " ReadMaterialIndices " << nMate << G4endl; |
---|
[1337] | 471 | for( unsigned int ii = 0; ii < nMate; ii++ ){ |
---|
[807] | 472 | finData >> mateName >> densityMax; |
---|
| 473 | fMaterialIndices[densityMax] = mateName; |
---|
| 474 | G4cout << ii << " ReadMaterialIndices " << mateName << " " << densityMax << G4endl; |
---|
| 475 | } |
---|
| 476 | |
---|
| 477 | } |
---|
| 478 | |
---|
[1337] | 479 | unsigned int DicomHandler::GetMaterialIndex( G4float density ) |
---|
[807] | 480 | { |
---|
[1337] | 481 | std::map<G4float,G4String>::reverse_iterator ite; |
---|
[807] | 482 | G4int ii = fMaterialIndices.size(); |
---|
| 483 | for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend(); ite++, ii-- ) { |
---|
| 484 | if( density >= (*ite).first ) { |
---|
| 485 | break; |
---|
| 486 | } |
---|
| 487 | } |
---|
| 488 | //- G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl; |
---|
| 489 | return ii; |
---|
| 490 | |
---|
| 491 | } |
---|
| 492 | |
---|
| 493 | // |
---|
| 494 | G4int DicomHandler::ReadData(FILE *dicom,char * filename2) |
---|
| 495 | { |
---|
| 496 | G4int returnvalue = 0; |
---|
| 497 | |
---|
| 498 | // READING THE PIXELS : |
---|
| 499 | G4int w = 0; |
---|
| 500 | G4int len = 0; |
---|
| 501 | |
---|
| 502 | tab = new G4int*[rows]; |
---|
| 503 | for ( G4int i = 0; i < rows; i ++ ) { |
---|
| 504 | tab[i] = new G4int[columns]; |
---|
| 505 | } |
---|
| 506 | |
---|
| 507 | if(bitAllocated == 8) { // Case 8 bits : |
---|
| 508 | |
---|
| 509 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 510 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 511 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 512 | |
---|
| 513 | unsigned char ch = 0; |
---|
| 514 | |
---|
| 515 | len = rows*columns; |
---|
| 516 | for(G4int j = 0; j < rows; j++) { |
---|
| 517 | for(G4int i = 0; i < columns; i++) { |
---|
| 518 | w++; |
---|
| 519 | std::fread( &ch, 1, 1, dicom); |
---|
| 520 | tab[j][i] = ch*rescaleSlope + rescaleIntercept; |
---|
| 521 | } |
---|
| 522 | } |
---|
| 523 | returnvalue = 1; |
---|
| 524 | |
---|
| 525 | } else { // from 12 to 16 bits : |
---|
| 526 | char sbuff[2]; |
---|
| 527 | short pixel; |
---|
| 528 | len = rows*columns; |
---|
| 529 | for( G4int j = 0; j < rows; j++) { |
---|
| 530 | for( G4int i = 0; i < columns; i++) { |
---|
| 531 | w++; |
---|
| 532 | std::fread(sbuff, 2, 1, dicom); |
---|
| 533 | GetValue(sbuff, pixel); |
---|
| 534 | tab[j][i] = pixel*rescaleSlope + rescaleIntercept; |
---|
| 535 | } |
---|
| 536 | } |
---|
| 537 | } |
---|
| 538 | |
---|
| 539 | // Creation of .g4 files wich contains averaged density data |
---|
| 540 | char * nameProcessed = new char[FILENAMESIZE]; |
---|
[1337] | 541 | FILE* fileOut; |
---|
[807] | 542 | |
---|
[1337] | 543 | std::sprintf(nameProcessed,"%s.g4dcmb",filename2); |
---|
| 544 | fileOut = std::fopen(nameProcessed,"w+b"); |
---|
[807] | 545 | std::printf("### Writing of %s ###\n",nameProcessed); |
---|
| 546 | |
---|
[1337] | 547 | unsigned int nMate = fMaterialIndices.size(); |
---|
| 548 | std::fwrite(&nMate, sizeof(unsigned int), 1, fileOut); |
---|
| 549 | //--- Write materials |
---|
| 550 | std::map<G4float,G4String>::const_iterator ite; |
---|
| 551 | for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++ ){ |
---|
| 552 | G4String mateName = (*ite).second; |
---|
| 553 | for( G4int ii = (*ite).second.length(); ii < 40; ii++ ) { |
---|
| 554 | mateName += " "; |
---|
| 555 | } //mateName = const_cast<char*>(((*ite).second).c_str()); |
---|
[807] | 556 | |
---|
[1337] | 557 | const char* mateNameC = mateName.c_str(); |
---|
| 558 | std::fwrite(mateNameC, sizeof(char),40, fileOut); |
---|
| 559 | } |
---|
| 560 | |
---|
| 561 | unsigned int rowsC = rows/compression; |
---|
| 562 | unsigned int columnsC = columns/compression; |
---|
| 563 | unsigned int planesC = 1; |
---|
| 564 | G4float pixelLocationXM = -pixelSpacingX*rows/2.; |
---|
| 565 | G4float pixelLocationXP = pixelSpacingX*rows/2.; |
---|
| 566 | G4float pixelLocationYM = -pixelSpacingY*rows/2.; |
---|
| 567 | G4float pixelLocationYP = pixelSpacingY*rows/2.; |
---|
| 568 | G4float sliceLocationZM = sliceLocation-sliceThickness/2.; |
---|
| 569 | G4float sliceLocationZP = sliceLocation+sliceThickness/2.; |
---|
| 570 | //--- Write number of voxels (assume only one voxel in Z) |
---|
| 571 | std::fwrite(&rowsC, sizeof(unsigned int), 1, fileOut); |
---|
| 572 | std::fwrite(&columnsC, sizeof(unsigned int), 1, fileOut); |
---|
| 573 | std::fwrite(&planesC, sizeof(unsigned int), 1, fileOut); |
---|
| 574 | //--- Write minimum and maximum extensions |
---|
| 575 | std::fwrite(&pixelLocationXM, sizeof(G4float), 1, fileOut); |
---|
| 576 | std::fwrite(&pixelLocationXP, sizeof(G4float), 1, fileOut); |
---|
| 577 | std::fwrite(&pixelLocationYM, sizeof(G4float), 1, fileOut); |
---|
| 578 | std::fwrite(&pixelLocationYP, sizeof(G4float), 1, fileOut); |
---|
| 579 | std::fwrite(&sliceLocationZM, sizeof(G4float), 1, fileOut); |
---|
| 580 | std::fwrite(&sliceLocationZP, sizeof(G4float), 1, fileOut); |
---|
| 581 | // std::fwrite(&compression, sizeof(unsigned int), 1, fileOut); |
---|
| 582 | |
---|
[807] | 583 | std::printf("%8i %8i\n",rows,columns); |
---|
| 584 | std::printf("%8f %8f\n",pixelSpacingX,pixelSpacingY); |
---|
| 585 | std::printf("%8f\n", sliceThickness); |
---|
| 586 | std::printf("%8f\n", sliceLocation); |
---|
| 587 | std::printf("%8i\n", compression); |
---|
| 588 | |
---|
| 589 | G4int compSize = compression; |
---|
| 590 | G4int mean; |
---|
[1337] | 591 | G4float density; |
---|
[807] | 592 | G4bool overflow = false; |
---|
| 593 | G4int cpt=1; |
---|
| 594 | |
---|
[1337] | 595 | //----- Write index of material for each pixel |
---|
[807] | 596 | if(compSize == 1) { // no compression: each pixel has a density value) |
---|
[1337] | 597 | for( G4int ww = 0; ww < rows; ww++) { |
---|
| 598 | for( G4int xx = 0; xx < columns; xx++) { |
---|
| 599 | mean = tab[ww][xx]; |
---|
| 600 | density = Pixel2density(mean); |
---|
| 601 | unsigned int mateID = GetMaterialIndex( density ); |
---|
| 602 | std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut); |
---|
| 603 | } |
---|
| 604 | } |
---|
[807] | 605 | |
---|
| 606 | } else { |
---|
[1337] | 607 | // density value is the average of a square region of |
---|
| 608 | // compression*compression pixels |
---|
| 609 | for(G4int ww = 0; ww < rows ;ww += compSize ) { |
---|
| 610 | for(G4int xx = 0; xx < columns ;xx +=compSize ) { |
---|
| 611 | overflow = false; |
---|
| 612 | mean = 0; |
---|
| 613 | for(int sumx = 0; sumx < compSize; sumx++) { |
---|
| 614 | for(int sumy = 0; sumy < compSize; sumy++) { |
---|
| 615 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
---|
| 616 | mean += tab[ww+sumy][xx+sumx]; |
---|
[807] | 617 | } |
---|
[1337] | 618 | if(overflow) break; |
---|
| 619 | } |
---|
| 620 | mean /= compSize*compSize; |
---|
| 621 | cpt = 1; |
---|
| 622 | |
---|
| 623 | if(!overflow) { |
---|
| 624 | density = Pixel2density(mean); |
---|
| 625 | unsigned int mateID = GetMaterialIndex( density ); |
---|
| 626 | std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut); |
---|
| 627 | } |
---|
| 628 | } |
---|
| 629 | |
---|
| 630 | } |
---|
| 631 | } |
---|
[807] | 632 | |
---|
[1337] | 633 | //----- Write density for each pixel |
---|
| 634 | if(compSize == 1) { // no compression: each pixel has a density value) |
---|
| 635 | for( G4int ww = 0; ww < rows; ww++) { |
---|
| 636 | for( G4int xx = 0; xx < columns; xx++) { |
---|
| 637 | mean = tab[ww][xx]; |
---|
| 638 | density = Pixel2density(mean); |
---|
| 639 | std::fwrite(&density, sizeof(G4float), 1, fileOut); |
---|
[807] | 640 | } |
---|
[1337] | 641 | } |
---|
| 642 | |
---|
| 643 | } else { |
---|
| 644 | // density value is the average of a square region of |
---|
| 645 | // compression*compression pixels |
---|
| 646 | for(G4int ww = 0; ww < rows ;ww += compSize ) { |
---|
| 647 | for(G4int xx = 0; xx < columns ;xx +=compSize ) { |
---|
| 648 | overflow = false; |
---|
| 649 | mean = 0; |
---|
| 650 | for(int sumx = 0; sumx < compSize; sumx++) { |
---|
| 651 | for(int sumy = 0; sumy < compSize; sumy++) { |
---|
| 652 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
---|
| 653 | mean += tab[ww+sumy][xx+sumx]; |
---|
| 654 | } |
---|
| 655 | if(overflow) break; |
---|
| 656 | } |
---|
| 657 | mean /= compSize*compSize; |
---|
| 658 | cpt = 1; |
---|
| 659 | |
---|
| 660 | if(!overflow) { |
---|
| 661 | density = Pixel2density(mean); |
---|
| 662 | std::fwrite(&density, sizeof(G4float), 1, fileOut); |
---|
| 663 | } |
---|
| 664 | } |
---|
| 665 | |
---|
| 666 | } |
---|
[807] | 667 | } |
---|
[1337] | 668 | |
---|
| 669 | std::fclose(fileOut); |
---|
| 670 | |
---|
[807] | 671 | delete [] nameProcessed; |
---|
| 672 | |
---|
| 673 | /* for ( G4int i = 0; i < rows; i ++ ) { |
---|
| 674 | delete [] tab[i]; |
---|
| 675 | } |
---|
| 676 | delete [] tab; |
---|
| 677 | */ |
---|
| 678 | |
---|
| 679 | return returnvalue; |
---|
| 680 | } |
---|
| 681 | |
---|
| 682 | /* |
---|
| 683 | G4int DicomHandler::displayImage(char command[300]) |
---|
| 684 | { |
---|
| 685 | // Display DICOM images using ImageMagick |
---|
| 686 | char commandName[500]; |
---|
| 687 | std::sprintf(commandName,"display %s",command); |
---|
| 688 | std::printf(commandName); |
---|
| 689 | G4int i = system(commandName); |
---|
| 690 | return (G4int )i; |
---|
| 691 | } |
---|
| 692 | */ |
---|
| 693 | |
---|
[1337] | 694 | G4float DicomHandler::Pixel2density(G4int pixel) |
---|
[807] | 695 | { |
---|
[1337] | 696 | G4float density = -1.; |
---|
[807] | 697 | G4int nbrequali = 0; |
---|
| 698 | G4double deltaCT = 0; |
---|
| 699 | G4double deltaDensity = 0; |
---|
| 700 | |
---|
| 701 | // CT2Density.dat contains the calibration curve to convert CT (Hounsfield) |
---|
| 702 | // number to physical density |
---|
| 703 | std::ifstream calibration("CT2Density.dat"); |
---|
| 704 | calibration >> nbrequali; |
---|
| 705 | |
---|
| 706 | G4double * valuedensity = new G4double[nbrequali]; |
---|
| 707 | G4double * valueCT = new G4double[nbrequali]; |
---|
| 708 | |
---|
| 709 | if(!calibration) { |
---|
| 710 | G4cerr << "@@@ No value to transform pixels in density!" << G4endl; |
---|
| 711 | exit(1); |
---|
| 712 | |
---|
| 713 | } else { // calibration was successfully opened |
---|
| 714 | for(G4int i = 0; i < nbrequali; i++) { // Loop to store all the pts in CT2Density.dat |
---|
| 715 | calibration >> valueCT[i] >> valuedensity[i]; |
---|
| 716 | } |
---|
| 717 | } |
---|
| 718 | calibration.close(); |
---|
| 719 | |
---|
| 720 | for(G4int j = 1; j < nbrequali; j++) { |
---|
| 721 | if( pixel >= valueCT[j-1] && pixel < valueCT[j]) { |
---|
| 722 | |
---|
| 723 | deltaCT = valueCT[j] - valueCT[j-1]; |
---|
| 724 | deltaDensity = valuedensity[j] - valuedensity[j-1]; |
---|
| 725 | |
---|
| 726 | // interpolating linearly |
---|
| 727 | density = valuedensity[j] - ((valueCT[j] - pixel)*deltaDensity/deltaCT ); |
---|
| 728 | break; |
---|
| 729 | } |
---|
| 730 | } |
---|
| 731 | |
---|
| 732 | if(density < 0.) { |
---|
| 733 | std::printf("@@@ Error density = %f && Pixel = %i (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel, deltaDensity/deltaCT); |
---|
| 734 | } |
---|
| 735 | |
---|
| 736 | delete [] valuedensity; |
---|
| 737 | delete [] valueCT; |
---|
| 738 | |
---|
| 739 | return density; |
---|
| 740 | } |
---|
| 741 | |
---|
| 742 | |
---|
| 743 | void DicomHandler::CheckFileFormat() |
---|
| 744 | { |
---|
| 745 | std::ifstream checkData("Data.dat"); |
---|
| 746 | char * oneLine = new char[128]; |
---|
| 747 | |
---|
| 748 | if(!(checkData.is_open())) { //Check existance of Data.dat |
---|
| 749 | |
---|
| 750 | G4cout << "\nDicomG4 needs Data.dat :\n\tFirst line: number of image pixel for a " |
---|
| 751 | << "voxel (G4Box)\n\tSecond line: number of images (CT slices) to " |
---|
| 752 | << "read\n\tEach following line contains the name of a Dicom image except " |
---|
| 753 | << "for the .dcm extension\n"; |
---|
| 754 | exit(0); |
---|
| 755 | } |
---|
| 756 | |
---|
| 757 | checkData >> compression; |
---|
| 758 | checkData >> nFiles; |
---|
| 759 | G4String oneName; |
---|
| 760 | checkData.getline(oneLine,100); |
---|
| 761 | std::ifstream testExistence; |
---|
| 762 | G4bool existAlready = true; |
---|
| 763 | for(G4int rep = 0; rep < nFiles; rep++) { |
---|
| 764 | checkData.getline(oneLine,100); |
---|
| 765 | oneName = oneLine; |
---|
| 766 | oneName += ".g4dcm"; // create dicomFile.g4dcm |
---|
| 767 | G4cout << nFiles << " test file " << oneName << G4endl; |
---|
| 768 | testExistence.open(oneName.data()); |
---|
| 769 | if(!(testExistence.is_open())) { |
---|
| 770 | existAlready = false; |
---|
| 771 | testExistence.clear(); |
---|
| 772 | testExistence.close(); |
---|
| 773 | } |
---|
| 774 | testExistence.clear(); |
---|
| 775 | testExistence.close(); |
---|
| 776 | } |
---|
| 777 | |
---|
| 778 | ReadMaterialIndices( checkData ); |
---|
| 779 | |
---|
| 780 | checkData.close(); |
---|
| 781 | delete [] oneLine; |
---|
| 782 | |
---|
| 783 | if( existAlready == false ) { // The files *.g4dcm have to be created |
---|
| 784 | |
---|
| 785 | G4cout << "\nAll the necessary images were not found in processed form, starting " |
---|
| 786 | << "with .dcm images\n"; |
---|
| 787 | |
---|
| 788 | FILE * dicom; |
---|
| 789 | FILE * lecturePref; |
---|
| 790 | char * compressionc = new char[LINEBUFFSIZE]; |
---|
| 791 | char * maxc = new char[LINEBUFFSIZE]; |
---|
| 792 | //char name[300], inputFile[300]; |
---|
| 793 | char * name = new char[FILENAMESIZE]; |
---|
| 794 | char * inputFile = new char[FILENAMESIZE]; |
---|
| 795 | |
---|
| 796 | lecturePref = std::fopen("Data.dat","r"); |
---|
| 797 | std::fscanf(lecturePref,"%s",compressionc); |
---|
| 798 | compression = atoi(compressionc); |
---|
| 799 | std::fscanf(lecturePref,"%s",maxc); |
---|
| 800 | nFiles = atoi(maxc); |
---|
| 801 | G4cout << " nFiles " << nFiles << G4endl; |
---|
| 802 | |
---|
| 803 | for( G4int i = 1; i <= nFiles; i++ ) { // Begin loop on filenames |
---|
| 804 | |
---|
| 805 | std::fscanf(lecturePref,"%s",inputFile); |
---|
| 806 | std::sprintf(name,"%s.dcm",inputFile); |
---|
| 807 | std::cout << "check 1: " << name << std::endl; |
---|
| 808 | // Open input file and give it to gestion_dicom : |
---|
| 809 | std::printf("### Opening %s and reading :\n",name); |
---|
| 810 | dicom = std::fopen(name,"rb"); |
---|
| 811 | // Reading the .dcm in two steps: |
---|
| 812 | // 1. reading the header |
---|
| 813 | // 2. reading the pixel data and store the density in Moyenne.dat |
---|
| 814 | if( dicom != 0 ) { |
---|
| 815 | ReadFile(dicom,inputFile); |
---|
| 816 | } else { |
---|
| 817 | G4cout << "\nError opening file : " << name << G4endl; |
---|
| 818 | } |
---|
| 819 | std::fclose(dicom); |
---|
| 820 | } |
---|
| 821 | std::fclose(lecturePref); |
---|
| 822 | |
---|
| 823 | delete [] compressionc; |
---|
| 824 | delete [] maxc; |
---|
| 825 | delete [] name; |
---|
| 826 | delete [] inputFile; |
---|
| 827 | |
---|
| 828 | } |
---|
| 829 | |
---|
| 830 | } |
---|
| 831 | |
---|
| 832 | |
---|
| 833 | template <class Type> |
---|
| 834 | void DicomHandler::GetValue(char * _val, Type & _rval) { |
---|
| 835 | |
---|
| 836 | #if BYTE_ORDER == BIG_ENDIAN |
---|
| 837 | if(littleEndian) { // little endian |
---|
| 838 | #else // BYTE_ORDER == LITTLE_ENDIAN |
---|
| 839 | if(!littleEndian) { // big endian |
---|
| 840 | #endif |
---|
| 841 | const int SIZE = sizeof(_rval); |
---|
| 842 | char ctemp; |
---|
| 843 | for(int i = 0; i < SIZE/2; i++) { |
---|
| 844 | ctemp = _val[i]; |
---|
| 845 | _val[i] = _val[SIZE - 1 - i]; |
---|
| 846 | _val[SIZE - 1 - i] = ctemp; |
---|
| 847 | } |
---|
| 848 | } |
---|
| 849 | _rval = *(Type *)_val; |
---|
| 850 | } |
---|
[1337] | 851 | |
---|
| 852 | G4int DicomHandler::read_defined_nested(FILE * nested,G4int SQ_Length) |
---|
| 853 | { |
---|
| 854 | // VARIABLES |
---|
| 855 | unsigned short item_GroupNumber; |
---|
| 856 | unsigned short item_ElementNumber; |
---|
| 857 | G4int item_Length; |
---|
| 858 | G4int items_array_length=0; |
---|
| 859 | char * buffer= new char[LINEBUFFSIZE]; |
---|
| 860 | |
---|
| 861 | |
---|
| 862 | while(items_array_length < SQ_Length) |
---|
| 863 | { |
---|
| 864 | std::fread(buffer, 2, 1, nested); |
---|
| 865 | GetValue(buffer, item_GroupNumber); |
---|
| 866 | |
---|
| 867 | std::fread(buffer, 2, 1, nested); |
---|
| 868 | GetValue(buffer, item_ElementNumber); |
---|
| 869 | |
---|
| 870 | std::fread(buffer, 4, 1, nested); |
---|
| 871 | GetValue(buffer, item_Length); |
---|
| 872 | |
---|
| 873 | std::fread(buffer, item_Length, 1, nested); |
---|
| 874 | |
---|
| 875 | items_array_length= items_array_length+8+item_Length; |
---|
| 876 | } |
---|
| 877 | |
---|
| 878 | delete []buffer; |
---|
| 879 | |
---|
| 880 | if(SQ_Length>items_array_length) |
---|
| 881 | return 0; |
---|
| 882 | else |
---|
| 883 | return 1; |
---|
| 884 | |
---|
| 885 | } |
---|
| 886 | |
---|
| 887 | void DicomHandler::read_undefined_nested(FILE * nested) |
---|
| 888 | { |
---|
| 889 | // VARIABLES |
---|
| 890 | unsigned short item_GroupNumber; |
---|
| 891 | unsigned short item_ElementNumber; |
---|
| 892 | G4int item_Length; |
---|
| 893 | char * buffer= new char[LINEBUFFSIZE]; |
---|
| 894 | |
---|
| 895 | |
---|
| 896 | do |
---|
| 897 | { |
---|
| 898 | std::fread(buffer, 2, 1, nested); |
---|
| 899 | GetValue(buffer, item_GroupNumber); |
---|
| 900 | |
---|
| 901 | std::fread(buffer, 2, 1, nested); |
---|
| 902 | GetValue(buffer, item_ElementNumber); |
---|
| 903 | |
---|
| 904 | std::fread(buffer, 4, 1, nested); |
---|
| 905 | GetValue(buffer, item_Length); |
---|
| 906 | |
---|
| 907 | if(item_Length!=0xffffffff) |
---|
| 908 | std::fread(buffer, item_Length, 1, nested); |
---|
| 909 | else |
---|
| 910 | read_undefined_item(nested); |
---|
| 911 | |
---|
| 912 | |
---|
| 913 | }while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE0DD || item_Length!=0); |
---|
| 914 | |
---|
| 915 | delete [] buffer; |
---|
| 916 | |
---|
| 917 | } |
---|
| 918 | |
---|
| 919 | void DicomHandler::read_undefined_item(FILE * nested) |
---|
| 920 | { |
---|
| 921 | // VARIABLES |
---|
| 922 | unsigned short item_GroupNumber; |
---|
| 923 | unsigned short item_ElementNumber; |
---|
| 924 | G4int item_Length; |
---|
| 925 | char *buffer= new char[LINEBUFFSIZE]; |
---|
| 926 | |
---|
| 927 | do |
---|
| 928 | { |
---|
| 929 | std::fread(buffer, 2, 1, nested); |
---|
| 930 | GetValue(buffer, item_GroupNumber); |
---|
| 931 | |
---|
| 932 | std::fread(buffer, 2, 1, nested); |
---|
| 933 | GetValue(buffer, item_ElementNumber); |
---|
| 934 | |
---|
| 935 | std::fread(buffer, 4, 1, nested); |
---|
| 936 | GetValue(buffer, item_Length); |
---|
| 937 | |
---|
| 938 | |
---|
| 939 | if(item_Length!=0) |
---|
| 940 | std::fread(buffer,item_Length,1,nested); |
---|
| 941 | |
---|
| 942 | } |
---|
| 943 | while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE00D || item_Length!=0); |
---|
| 944 | |
---|
| 945 | delete []buffer; |
---|
| 946 | |
---|
| 947 | } |
---|