[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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| 63 | : DATABUFFSIZE(8192), LINEBUFFSIZE(128), FILENAMESIZE(512), |
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| 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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| 100 | G4int elementLength4; // deal with element length in 4 bytes |
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| 101 | |
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| 102 | char * data = new char[DATABUFFSIZE]; |
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| 103 | |
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| 104 | // Read information up to the pixel data |
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| 105 | while(true) { |
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| 106 | |
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| 107 | //Reading groups and elements : |
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| 108 | readGroupId = 0; |
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| 109 | readElementId = 0; |
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| 110 | // group ID |
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| 111 | std::fread(buffer, 2, 1, dicom); |
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| 112 | GetValue(buffer, readGroupId); |
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| 113 | // element ID |
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| 114 | std::fread(buffer, 2, 1, dicom); |
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| 115 | GetValue(buffer, readElementId); |
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| 116 | |
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| 117 | // Creating a tag to be identified afterward |
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| 118 | G4int tagDictionary = readGroupId*0x10000 + readElementId; |
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| 119 | |
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| 120 | |
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| 121 | // VR or element length |
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| 122 | std::fread(buffer,2,1,dicom); |
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| 123 | GetValue(buffer, elementLength2); |
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| 124 | |
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| 125 | // If value representation (VR) is OB, OW, SQ, UN, |
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| 126 | //the next length is 32 bits |
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| 127 | if((elementLength2 == 0x424f || // "OB" |
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| 128 | elementLength2 == 0x574f || // "OW" |
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| 129 | elementLength2 == 0x5153 || // "SQ" |
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| 130 | elementLength2 == 0x4e55) && // "UN" |
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| 131 | !implicitEndian ) { // explicit VR |
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| 132 | |
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| 133 | std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes |
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| 134 | |
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| 135 | // element length |
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| 136 | std::fread(buffer, 4, 1, dicom); |
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| 137 | GetValue(buffer, elementLength4); |
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| 138 | |
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| 139 | // beginning of the pixels |
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| 140 | if(tagDictionary == 0x7FE00010) break; |
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| 141 | |
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| 142 | // Reading the information with data |
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| 143 | std::fread(data, elementLength4,1,dicom); |
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| 144 | |
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| 145 | |
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| 146 | } else { // length is 16 bits : |
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| 147 | |
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| 148 | if(!implicitEndian || readGroupId == 2) { |
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| 149 | // element length (2 bytes) |
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| 150 | std::fread(buffer, 2, 1, dicom); |
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| 151 | GetValue(buffer, elementLength2); |
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| 152 | elementLength4 = elementLength2; |
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| 153 | |
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| 154 | } else { |
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| 155 | // element length (4 bytes) |
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| 156 | if(std::fseek(dicom, -2, SEEK_CUR) != 0) { |
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| 157 | G4cerr << "[DicomHandler] fseek failed" << G4endl; |
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| 158 | exit(-10); |
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| 159 | } |
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| 160 | std::fread(buffer, 4, 1, dicom); |
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| 161 | GetValue(buffer, elementLength4); |
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| 162 | } |
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| 163 | |
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| 164 | // beginning of the pixels |
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| 165 | if(tagDictionary == 0x7FE00010) break; |
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| 166 | |
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| 167 | std::fread(data, elementLength4, 1, dicom); |
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| 168 | } |
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| 169 | |
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| 170 | // NULL termination |
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| 171 | data[elementLength4] = '\0'; |
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| 172 | |
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| 173 | // analyzing information |
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| 174 | GetInformation(tagDictionary, data); |
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| 175 | } |
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| 176 | |
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| 177 | // Creating files to store information |
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| 178 | std::ofstream foutG4DCM; |
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| 179 | G4String fnameG4DCM = G4String(filename2) + ".g4dcm"; |
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| 180 | foutG4DCM.open(fnameG4DCM); |
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| 181 | G4cout << " opened fnameG4DCM file " << fnameG4DCM << G4endl; |
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| 182 | |
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| 183 | foutG4DCM << fMaterialIndices.size() << G4endl; |
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| 184 | //--- Write materials |
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| 185 | size_t ii = 0; |
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| 186 | std::map<G4double,G4String>::const_iterator ite; |
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| 187 | for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++, ii++ ){ |
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| 188 | foutG4DCM << ii << " " << (*ite).second << G4endl; |
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| 189 | } |
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| 190 | //--- Write number of voxels (assume only one voxel in Z) |
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| 191 | foutG4DCM << rows/compression << " " << columns/compression << " 1 " << G4endl; |
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| 192 | //--- Write minimum and maximum extensions |
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| 193 | foutG4DCM << -pixelSpacingX*rows/2 << " " << pixelSpacingX*rows/2 << G4endl; |
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| 194 | foutG4DCM << -pixelSpacingY*columns/2 << " " << pixelSpacingY*columns/2 << G4endl; |
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| 195 | foutG4DCM << sliceLocation-sliceThickness/2. << " " << sliceLocation+sliceThickness/2. << G4endl; |
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| 196 | |
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| 197 | ReadData( dicom, filename2 ); |
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| 198 | |
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| 199 | StoreData( foutG4DCM ); |
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| 200 | |
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| 201 | foutG4DCM.close(); |
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| 202 | |
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| 203 | // |
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| 204 | delete [] buffer; |
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| 205 | delete [] data; |
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| 206 | |
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| 207 | return returnvalue; |
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| 208 | } |
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| 209 | |
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| 210 | // |
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| 211 | void DicomHandler::GetInformation(G4int & tagDictionary, char * data) { |
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| 212 | if(tagDictionary == 0x00280010 ) { // Number of Rows |
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| 213 | GetValue(data, rows); |
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| 214 | std::printf("[0x00280010] Rows -> %i\n",rows); |
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| 215 | |
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| 216 | } else if(tagDictionary == 0x00280011 ) { // Number of columns |
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| 217 | GetValue(data, columns); |
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| 218 | std::printf("[0x00280011] Columns -> %i\n",columns); |
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| 219 | |
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| 220 | } else if(tagDictionary == 0x00280102 ) { // High bits ( not used ) |
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| 221 | short highBits; |
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| 222 | GetValue(data, highBits); |
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| 223 | std::printf("[0x00280102] High bits -> %i\n",highBits); |
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| 224 | |
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| 225 | } else if(tagDictionary == 0x00280100 ) { // Bits allocated |
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| 226 | GetValue(data, bitAllocated); |
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| 227 | std::printf("[0x00280100] Bits allocated -> %i\n", bitAllocated); |
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| 228 | |
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| 229 | } else if(tagDictionary == 0x00280101 ) { // Bits stored ( not used ) |
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| 230 | short bitStored; |
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| 231 | GetValue(data, bitStored); |
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| 232 | std::printf("[0x00280101] Bits stored -> %i\n",bitStored); |
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| 233 | |
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| 234 | } else if(tagDictionary == 0x00280106 ) { // Min. pixel value |
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| 235 | GetValue(data, minPixelValue); |
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| 236 | std::printf("[0x00280106] Min. pixel value -> %i\n", minPixelValue); |
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| 237 | |
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| 238 | } else if(tagDictionary == 0x00280107 ) { // Max. pixel value |
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| 239 | GetValue(data, maxPixelValue); |
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| 240 | std::printf("[0x00280107] Max. pixel value -> %i\n", maxPixelValue); |
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| 241 | |
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| 242 | } else if(tagDictionary == 0x00281053) { // Rescale slope |
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| 243 | rescaleSlope = atoi(data); |
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| 244 | std::printf("[0x00281053] Rescale Slope -> %d\n", rescaleSlope); |
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| 245 | |
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| 246 | } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept |
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| 247 | rescaleIntercept = atoi(data); |
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| 248 | std::printf("[0x00281052] Rescale Intercept -> %d\n", rescaleIntercept ); |
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| 249 | |
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| 250 | } else if(tagDictionary == 0x00280103 ) { |
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| 251 | // Pixel representation ( functions not design to read signed bits ) |
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| 252 | pixelRepresentation = atoi(data); // 0: unsigned 1: signed |
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| 253 | std::printf("[0x00280103] Pixel Representation -> %i\n", pixelRepresentation); |
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| 254 | if(pixelRepresentation == 1 ) { |
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| 255 | std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, "); |
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| 256 | std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE "); |
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| 257 | std::printf("ERROR !!!!!! -> \n"); |
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| 258 | } |
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| 259 | |
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| 260 | } else if(tagDictionary == 0x00080006 ) { // Modality |
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| 261 | std::printf("[0x00080006] Modality -> %s\n", data); |
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| 262 | |
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| 263 | } else if(tagDictionary == 0x00080070 ) { // Manufacturer |
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| 264 | std::printf("[0x00080070] Manufacturer -> %s\n", data); |
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| 265 | |
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| 266 | } else if(tagDictionary == 0x00080080 ) { // Institution Name |
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| 267 | std::printf("[0x00080080] Institution Name -> %s\n", data); |
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| 268 | |
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| 269 | } else if(tagDictionary == 0x00080081 ) { // Institution Address |
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| 270 | std::printf("[0x00080081] Institution Address -> %s\n", data); |
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| 271 | |
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| 272 | } else if(tagDictionary == 0x00081040 ) { // Institution Department Name |
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| 273 | std::printf("[0x00081040] Institution Department Name -> %s\n", data); |
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| 274 | |
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| 275 | } else if(tagDictionary == 0x00081090 ) { // Manufacturer's Model Name |
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| 276 | std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data); |
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| 277 | |
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| 278 | } else if(tagDictionary == 0x00181000 ) { // Device Serial Number |
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| 279 | std::printf("[0x00181000] Device Serial Number -> %s\n", data); |
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| 280 | |
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| 281 | } else if(tagDictionary == 0x00080008 ) { // Image type ( not used ) |
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| 282 | std::printf("[0x00080008] Image Types -> %s\n", data); |
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| 283 | |
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| 284 | } else if(tagDictionary == 0x00283000 ) { // Modality LUT Sequence ( not used ) |
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| 285 | std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data); |
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| 286 | |
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| 287 | } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used ) |
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| 288 | std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data); |
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| 289 | |
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| 290 | } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used ) |
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| 291 | std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data); |
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| 292 | |
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| 293 | } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used ) |
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| 294 | std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data); |
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| 295 | |
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| 296 | } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used ) |
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| 297 | std::printf("[0x00283006] LUT Data US or SS -> %s\n", data); |
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| 298 | |
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| 299 | } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used ) |
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| 300 | std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data); |
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| 301 | |
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| 302 | } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value ( not used ) |
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| 303 | std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data); |
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| 304 | |
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| 305 | } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing |
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| 306 | G4String datas(data); |
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| 307 | int iss = datas.find('\\'); |
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| 308 | pixelSpacingX = atof( datas.substr(0,iss).c_str() ); |
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| 309 | pixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() ); |
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| 310 | |
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| 311 | } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used ) |
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| 312 | std::printf("[0x00200037] Image Orientation (Patient) -> %s\n", data); |
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| 313 | |
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| 314 | } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used ) |
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| 315 | std::printf("[0x00200032] Image Position (Patient,mm) -> %s\n", data); |
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| 316 | |
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| 317 | } else if(tagDictionary == 0x00180050 ) { // Slice Thickness |
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| 318 | sliceThickness = atof(data); |
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| 319 | std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", sliceThickness); |
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| 320 | |
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| 321 | } else if(tagDictionary == 0x00201041 ) { // Slice Location |
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| 322 | sliceLocation = atof(data); |
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| 323 | std::printf("[0x00201041] Slice Location -> %f\n", sliceLocation); |
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| 324 | |
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| 325 | } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation ( not used ) |
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| 326 | std::printf("[0x00280004] Photometric Interpretation -> %s\n", data); |
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| 327 | |
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| 328 | } else if(tagDictionary == 0x00020010) { // Endian |
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| 329 | if(strcmp(data, "1.2.840.10008.1.2") == 0) |
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| 330 | implicitEndian = true; |
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| 331 | else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0) |
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| 332 | littleEndian = false; |
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| 333 | //else 1.2.840..10008.1.2.1 (explicit little endian) |
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| 334 | |
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| 335 | std::printf("[0x00020010] Endian -> %s\n", data); |
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| 336 | } |
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| 337 | |
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| 338 | // others |
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| 339 | else { |
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| 340 | std::printf("[0x%x] -> %s\n", tagDictionary, data); |
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| 341 | |
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| 342 | } |
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| 343 | |
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| 344 | } |
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| 345 | |
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| 346 | void DicomHandler::StoreData(std::ofstream& foutG4DCM) |
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| 347 | { |
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| 348 | G4int mean; |
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| 349 | G4double density; |
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| 350 | G4bool overflow = false; |
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| 351 | G4int cpt=1; |
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| 352 | |
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| 353 | //----- Print indices of material |
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| 354 | if(compression == 1) { // no compression: each pixel has a density value) |
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| 355 | for( G4int ww = 0; ww < rows; ww++) { |
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| 356 | for( G4int xx = 0; xx < columns; xx++) { |
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| 357 | mean = tab[ww][xx]; |
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| 358 | density = Pixel2density(mean); |
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| 359 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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| 360 | } |
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| 361 | foutG4DCM << G4endl; |
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| 362 | } |
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| 363 | |
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| 364 | } else { |
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| 365 | // density value is the average of a square region of |
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| 366 | // compression*compression pixels |
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| 367 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
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| 368 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
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| 369 | overflow = false; |
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| 370 | mean = 0; |
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| 371 | for(int sumx = 0; sumx < compression; sumx++) { |
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| 372 | for(int sumy = 0; sumy < compression; sumy++) { |
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| 373 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
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| 374 | mean += tab[ww+sumy][xx+sumx]; |
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| 375 | } |
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| 376 | if(overflow) break; |
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| 377 | } |
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| 378 | mean /= compression*compression; |
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| 379 | cpt = 1; |
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| 380 | |
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| 381 | if(!overflow) { |
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| 382 | G4double density = Pixel2density(mean); |
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| 383 | foutG4DCM << GetMaterialIndex( density ) << " "; |
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| 384 | } |
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| 385 | } |
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| 386 | foutG4DCM << G4endl; |
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| 387 | } |
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| 388 | |
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| 389 | } |
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| 390 | |
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| 391 | //----- Print densities |
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| 392 | if(compression == 1) { // no compression: each pixel has a density value) |
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| 393 | for( G4int ww = 0; ww < rows; ww++) { |
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| 394 | for( G4int xx = 0; xx < columns; xx++) { |
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| 395 | mean = tab[ww][xx]; |
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| 396 | density = Pixel2density(mean); |
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| 397 | foutG4DCM << density << " "; |
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| 398 | if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
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| 399 | } |
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| 400 | } |
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| 401 | |
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| 402 | } else { |
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| 403 | // density value is the average of a square region of |
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| 404 | // compression*compression pixels |
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| 405 | for(G4int ww = 0; ww < rows ;ww += compression ) { |
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| 406 | for(G4int xx = 0; xx < columns ;xx +=compression ) { |
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| 407 | overflow = false; |
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| 408 | mean = 0; |
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| 409 | for(int sumx = 0; sumx < compression; sumx++) { |
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| 410 | for(int sumy = 0; sumy < compression; sumy++) { |
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| 411 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
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| 412 | mean += tab[ww+sumy][xx+sumx]; |
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| 413 | } |
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| 414 | if(overflow) break; |
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| 415 | } |
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| 416 | mean /= compression*compression; |
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| 417 | cpt = 1; |
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| 418 | |
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| 419 | if(!overflow) { |
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| 420 | G4double density = Pixel2density(mean); |
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| 421 | foutG4DCM << density << " "; |
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| 422 | if( xx/compression%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading |
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| 423 | } |
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| 424 | } |
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| 425 | } |
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| 426 | |
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| 427 | } |
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| 428 | |
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| 429 | } |
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| 430 | |
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| 431 | void DicomHandler::ReadMaterialIndices( std::ifstream& finData) |
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| 432 | { |
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| 433 | size_t nMate; |
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| 434 | G4String mateName; |
---|
| 435 | G4double densityMax; |
---|
| 436 | finData >> nMate; |
---|
| 437 | if( finData.eof() ) return; |
---|
| 438 | |
---|
| 439 | G4cout << " ReadMaterialIndices " << nMate << G4endl; |
---|
| 440 | for( size_t ii = 0; ii < nMate; ii++ ){ |
---|
| 441 | finData >> mateName >> densityMax; |
---|
| 442 | fMaterialIndices[densityMax] = mateName; |
---|
| 443 | G4cout << ii << " ReadMaterialIndices " << mateName << " " << densityMax << G4endl; |
---|
| 444 | } |
---|
| 445 | |
---|
| 446 | } |
---|
| 447 | |
---|
| 448 | size_t DicomHandler::GetMaterialIndex( G4double density ) |
---|
| 449 | { |
---|
| 450 | size_t mateID; |
---|
| 451 | std::map<G4double,G4String>::reverse_iterator ite; |
---|
| 452 | G4int ii = fMaterialIndices.size(); |
---|
| 453 | for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend(); ite++, ii-- ) { |
---|
| 454 | if( density >= (*ite).first ) { |
---|
| 455 | break; |
---|
| 456 | } |
---|
| 457 | } |
---|
| 458 | //- G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl; |
---|
| 459 | return ii; |
---|
| 460 | |
---|
| 461 | } |
---|
| 462 | |
---|
| 463 | // |
---|
| 464 | G4int DicomHandler::ReadData(FILE *dicom,char * filename2) |
---|
| 465 | { |
---|
| 466 | G4int returnvalue = 0; |
---|
| 467 | |
---|
| 468 | // READING THE PIXELS : |
---|
| 469 | G4int w = 0; |
---|
| 470 | G4int len = 0; |
---|
| 471 | |
---|
| 472 | tab = new G4int*[rows]; |
---|
| 473 | for ( G4int i = 0; i < rows; i ++ ) { |
---|
| 474 | tab[i] = new G4int[columns]; |
---|
| 475 | } |
---|
| 476 | |
---|
| 477 | if(bitAllocated == 8) { // Case 8 bits : |
---|
| 478 | |
---|
| 479 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 480 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 481 | std::printf("@@@ Error! Picture != 16 bits...\n"); |
---|
| 482 | |
---|
| 483 | unsigned char ch = 0; |
---|
| 484 | |
---|
| 485 | len = rows*columns; |
---|
| 486 | for(G4int j = 0; j < rows; j++) { |
---|
| 487 | for(G4int i = 0; i < columns; i++) { |
---|
| 488 | w++; |
---|
| 489 | std::fread( &ch, 1, 1, dicom); |
---|
| 490 | tab[j][i] = ch*rescaleSlope + rescaleIntercept; |
---|
| 491 | } |
---|
| 492 | } |
---|
| 493 | returnvalue = 1; |
---|
| 494 | |
---|
| 495 | } else { // from 12 to 16 bits : |
---|
| 496 | char sbuff[2]; |
---|
| 497 | short pixel; |
---|
| 498 | len = rows*columns; |
---|
| 499 | for( G4int j = 0; j < rows; j++) { |
---|
| 500 | for( G4int i = 0; i < columns; i++) { |
---|
| 501 | w++; |
---|
| 502 | std::fread(sbuff, 2, 1, dicom); |
---|
| 503 | GetValue(sbuff, pixel); |
---|
| 504 | tab[j][i] = pixel*rescaleSlope + rescaleIntercept; |
---|
| 505 | } |
---|
| 506 | } |
---|
| 507 | } |
---|
| 508 | |
---|
| 509 | // Creation of .g4 files wich contains averaged density data |
---|
| 510 | |
---|
| 511 | char * nameProcessed = new char[FILENAMESIZE]; |
---|
| 512 | FILE* processed; |
---|
| 513 | |
---|
| 514 | std::sprintf(nameProcessed,"%s.g4",filename2); |
---|
| 515 | processed = std::fopen(nameProcessed,"w+b"); |
---|
| 516 | std::printf("### Writing of %s ###\n",nameProcessed); |
---|
| 517 | |
---|
| 518 | std::fwrite(&rows, 2, 1, processed); |
---|
| 519 | std::fwrite(&columns, 2, 1, processed); |
---|
| 520 | std::fwrite(&pixelSpacingX, 8, 1, processed); |
---|
| 521 | std::fwrite(&pixelSpacingY, 8, 1, processed); |
---|
| 522 | std::fwrite(&sliceThickness, 8, 1, processed); |
---|
| 523 | std::fwrite(&sliceLocation, 8, 1, processed); |
---|
| 524 | std::fwrite(&compression, 2, 1, processed); |
---|
| 525 | |
---|
| 526 | std::printf("%8i %8i\n",rows,columns); |
---|
| 527 | std::printf("%8f %8f\n",pixelSpacingX,pixelSpacingY); |
---|
| 528 | std::printf("%8f\n", sliceThickness); |
---|
| 529 | std::printf("%8f\n", sliceLocation); |
---|
| 530 | std::printf("%8i\n", compression); |
---|
| 531 | |
---|
| 532 | G4int compSize = compression; |
---|
| 533 | G4int mean; |
---|
| 534 | G4double density; |
---|
| 535 | G4bool overflow = false; |
---|
| 536 | G4int cpt=1; |
---|
| 537 | |
---|
| 538 | if(compSize == 1) { // no compression: each pixel has a density value) |
---|
| 539 | for( G4int ww = 0; ww < rows; ww++) { |
---|
| 540 | for( G4int xx = 0; xx < columns; xx++) { |
---|
| 541 | mean = tab[ww][xx]; |
---|
| 542 | density = Pixel2density(mean); |
---|
| 543 | std::fwrite(&density, sizeof(G4double), 1, processed); |
---|
| 544 | } |
---|
| 545 | } |
---|
| 546 | |
---|
| 547 | } else { |
---|
| 548 | // density value is the average of a square region of |
---|
| 549 | // compression*compression pixels |
---|
| 550 | for(G4int ww = 0; ww < rows ;ww += compSize ) { |
---|
| 551 | for(G4int xx = 0; xx < columns ;xx +=compSize ) { |
---|
| 552 | overflow = false; |
---|
| 553 | mean = 0; |
---|
| 554 | for(int sumx = 0; sumx < compSize; sumx++) { |
---|
| 555 | for(int sumy = 0; sumy < compSize; sumy++) { |
---|
| 556 | if(ww+sumy >= rows || xx+sumx >= columns) overflow = true; |
---|
| 557 | mean += tab[ww+sumy][xx+sumx]; |
---|
| 558 | } |
---|
| 559 | if(overflow) break; |
---|
| 560 | } |
---|
| 561 | mean /= compSize*compSize; |
---|
| 562 | cpt = 1; |
---|
| 563 | |
---|
| 564 | if(!overflow) { |
---|
| 565 | G4double density = Pixel2density(mean); |
---|
| 566 | std::fwrite(&density, sizeof(G4double), 1, processed); |
---|
| 567 | } |
---|
| 568 | } |
---|
| 569 | |
---|
| 570 | } |
---|
| 571 | } |
---|
| 572 | std::fclose(processed); |
---|
| 573 | |
---|
| 574 | delete [] nameProcessed; |
---|
| 575 | |
---|
| 576 | /* for ( G4int i = 0; i < rows; i ++ ) { |
---|
| 577 | delete [] tab[i]; |
---|
| 578 | } |
---|
| 579 | delete [] tab; |
---|
| 580 | */ |
---|
| 581 | |
---|
| 582 | return returnvalue; |
---|
| 583 | } |
---|
| 584 | |
---|
| 585 | /* |
---|
| 586 | G4int DicomHandler::displayImage(char command[300]) |
---|
| 587 | { |
---|
| 588 | // Display DICOM images using ImageMagick |
---|
| 589 | char commandName[500]; |
---|
| 590 | std::sprintf(commandName,"display %s",command); |
---|
| 591 | std::printf(commandName); |
---|
| 592 | G4int i = system(commandName); |
---|
| 593 | return (G4int )i; |
---|
| 594 | } |
---|
| 595 | */ |
---|
| 596 | |
---|
| 597 | G4double DicomHandler::Pixel2density(G4int pixel) |
---|
| 598 | { |
---|
| 599 | G4double density = -1.; |
---|
| 600 | G4int nbrequali = 0; |
---|
| 601 | G4double deltaCT = 0; |
---|
| 602 | G4double deltaDensity = 0; |
---|
| 603 | |
---|
| 604 | // CT2Density.dat contains the calibration curve to convert CT (Hounsfield) |
---|
| 605 | // number to physical density |
---|
| 606 | std::ifstream calibration("CT2Density.dat"); |
---|
| 607 | calibration >> nbrequali; |
---|
| 608 | |
---|
| 609 | G4double * valuedensity = new G4double[nbrequali]; |
---|
| 610 | G4double * valueCT = new G4double[nbrequali]; |
---|
| 611 | |
---|
| 612 | if(!calibration) { |
---|
| 613 | G4cerr << "@@@ No value to transform pixels in density!" << G4endl; |
---|
| 614 | exit(1); |
---|
| 615 | |
---|
| 616 | } else { // calibration was successfully opened |
---|
| 617 | for(G4int i = 0; i < nbrequali; i++) { // Loop to store all the pts in CT2Density.dat |
---|
| 618 | calibration >> valueCT[i] >> valuedensity[i]; |
---|
| 619 | } |
---|
| 620 | } |
---|
| 621 | calibration.close(); |
---|
| 622 | |
---|
| 623 | for(G4int j = 1; j < nbrequali; j++) { |
---|
| 624 | if( pixel >= valueCT[j-1] && pixel < valueCT[j]) { |
---|
| 625 | |
---|
| 626 | deltaCT = valueCT[j] - valueCT[j-1]; |
---|
| 627 | deltaDensity = valuedensity[j] - valuedensity[j-1]; |
---|
| 628 | |
---|
| 629 | // interpolating linearly |
---|
| 630 | density = valuedensity[j] - ((valueCT[j] - pixel)*deltaDensity/deltaCT ); |
---|
| 631 | break; |
---|
| 632 | } |
---|
| 633 | } |
---|
| 634 | |
---|
| 635 | if(density < 0.) { |
---|
| 636 | std::printf("@@@ Error density = %f && Pixel = %i (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel, deltaDensity/deltaCT); |
---|
| 637 | } |
---|
| 638 | |
---|
| 639 | delete [] valuedensity; |
---|
| 640 | delete [] valueCT; |
---|
| 641 | |
---|
| 642 | return density; |
---|
| 643 | } |
---|
| 644 | |
---|
| 645 | |
---|
| 646 | void DicomHandler::CheckFileFormat() |
---|
| 647 | { |
---|
| 648 | std::ifstream checkData("Data.dat"); |
---|
| 649 | char * oneLine = new char[128]; |
---|
| 650 | |
---|
| 651 | if(!(checkData.is_open())) { //Check existance of Data.dat |
---|
| 652 | |
---|
| 653 | G4cout << "\nDicomG4 needs Data.dat :\n\tFirst line: number of image pixel for a " |
---|
| 654 | << "voxel (G4Box)\n\tSecond line: number of images (CT slices) to " |
---|
| 655 | << "read\n\tEach following line contains the name of a Dicom image except " |
---|
| 656 | << "for the .dcm extension\n"; |
---|
| 657 | exit(0); |
---|
| 658 | } |
---|
| 659 | |
---|
| 660 | checkData >> compression; |
---|
| 661 | checkData >> nFiles; |
---|
| 662 | G4String oneName; |
---|
| 663 | checkData.getline(oneLine,100); |
---|
| 664 | std::ifstream testExistence; |
---|
| 665 | G4bool existAlready = true; |
---|
| 666 | for(G4int rep = 0; rep < nFiles; rep++) { |
---|
| 667 | checkData.getline(oneLine,100); |
---|
| 668 | oneName = oneLine; |
---|
| 669 | oneName += ".g4dcm"; // create dicomFile.g4dcm |
---|
| 670 | G4cout << nFiles << " test file " << oneName << G4endl; |
---|
| 671 | testExistence.open(oneName.data()); |
---|
| 672 | if(!(testExistence.is_open())) { |
---|
| 673 | existAlready = false; |
---|
| 674 | testExistence.clear(); |
---|
| 675 | testExistence.close(); |
---|
| 676 | } |
---|
| 677 | testExistence.clear(); |
---|
| 678 | testExistence.close(); |
---|
| 679 | } |
---|
| 680 | |
---|
| 681 | ReadMaterialIndices( checkData ); |
---|
| 682 | |
---|
| 683 | checkData.close(); |
---|
| 684 | delete [] oneLine; |
---|
| 685 | |
---|
| 686 | if( existAlready == false ) { // The files *.g4dcm have to be created |
---|
| 687 | |
---|
| 688 | G4cout << "\nAll the necessary images were not found in processed form, starting " |
---|
| 689 | << "with .dcm images\n"; |
---|
| 690 | |
---|
| 691 | FILE * dicom; |
---|
| 692 | FILE * lecturePref; |
---|
| 693 | char * compressionc = new char[LINEBUFFSIZE]; |
---|
| 694 | char * maxc = new char[LINEBUFFSIZE]; |
---|
| 695 | //char name[300], inputFile[300]; |
---|
| 696 | char * name = new char[FILENAMESIZE]; |
---|
| 697 | char * inputFile = new char[FILENAMESIZE]; |
---|
| 698 | |
---|
| 699 | lecturePref = std::fopen("Data.dat","r"); |
---|
| 700 | std::fscanf(lecturePref,"%s",compressionc); |
---|
| 701 | compression = atoi(compressionc); |
---|
| 702 | std::fscanf(lecturePref,"%s",maxc); |
---|
| 703 | nFiles = atoi(maxc); |
---|
| 704 | G4cout << " nFiles " << nFiles << G4endl; |
---|
| 705 | |
---|
| 706 | for( G4int i = 1; i <= nFiles; i++ ) { // Begin loop on filenames |
---|
| 707 | |
---|
| 708 | std::fscanf(lecturePref,"%s",inputFile); |
---|
| 709 | std::sprintf(name,"%s.dcm",inputFile); |
---|
| 710 | std::cout << "check 1: " << name << std::endl; |
---|
| 711 | // Open input file and give it to gestion_dicom : |
---|
| 712 | std::printf("### Opening %s and reading :\n",name); |
---|
| 713 | dicom = std::fopen(name,"rb"); |
---|
| 714 | // Reading the .dcm in two steps: |
---|
| 715 | // 1. reading the header |
---|
| 716 | // 2. reading the pixel data and store the density in Moyenne.dat |
---|
| 717 | if( dicom != 0 ) { |
---|
| 718 | ReadFile(dicom,inputFile); |
---|
| 719 | } else { |
---|
| 720 | G4cout << "\nError opening file : " << name << G4endl; |
---|
| 721 | } |
---|
| 722 | std::fclose(dicom); |
---|
| 723 | } |
---|
| 724 | std::fclose(lecturePref); |
---|
| 725 | |
---|
| 726 | delete [] compressionc; |
---|
| 727 | delete [] maxc; |
---|
| 728 | delete [] name; |
---|
| 729 | delete [] inputFile; |
---|
| 730 | |
---|
| 731 | } |
---|
| 732 | |
---|
| 733 | } |
---|
| 734 | |
---|
| 735 | |
---|
| 736 | template <class Type> |
---|
| 737 | void DicomHandler::GetValue(char * _val, Type & _rval) { |
---|
| 738 | |
---|
| 739 | #if BYTE_ORDER == BIG_ENDIAN |
---|
| 740 | if(littleEndian) { // little endian |
---|
| 741 | #else // BYTE_ORDER == LITTLE_ENDIAN |
---|
| 742 | if(!littleEndian) { // big endian |
---|
| 743 | #endif |
---|
| 744 | const int SIZE = sizeof(_rval); |
---|
| 745 | char ctemp; |
---|
| 746 | for(int i = 0; i < SIZE/2; i++) { |
---|
| 747 | ctemp = _val[i]; |
---|
| 748 | _val[i] = _val[SIZE - 1 - i]; |
---|
| 749 | _val[SIZE - 1 - i] = ctemp; |
---|
| 750 | } |
---|
| 751 | } |
---|
| 752 | _rval = *(Type *)_val; |
---|
| 753 | } |
---|