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annotate OrthancFramework/Sources/Images/NumpyWriter.cpp @ 4835:f3f93695d6df

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fix numpy for SignedGrasycale16
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 27 Nov 2021 12:27:01 +0100
parents bec432ee1094
children 6f780611fc03
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rev   line source
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #include "NumpyWriter.h"
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25
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26 #if ORTHANC_ENABLE_ZLIB == 1
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27 # include "../Compression/ZipWriter.h"
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28 #endif
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29
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30 #if ORTHANC_SANDBOXED == 0
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31 # include "../SystemToolbox.h"
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32 #endif
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33
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34 #include "../OrthancException.h"
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35 #include "../Toolbox.h"
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36
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37 #include <boost/lexical_cast.hpp>
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38
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39 namespace Orthanc
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40 {
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41 void NumpyWriter::WriteHeader(ChunkedBuffer& target,
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42 unsigned int depth,
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43 unsigned int width,
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44 unsigned int height,
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45 PixelFormat format)
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46 {
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47 // https://numpy.org/devdocs/reference/generated/numpy.lib.format.html
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48 static const unsigned char VERSION[] = {
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49 0x93, 'N', 'U', 'M', 'P', 'Y',
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50 0x01 /* major version: 1 */,
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51 0x00 /* minor version: 0 */
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52 };
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53
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54 std::string datatype;
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55
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56 switch (Toolbox::DetectEndianness())
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57 {
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58 case Endianness_Little:
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59 datatype = "<";
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60 break;
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61
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62 case Endianness_Big:
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63 datatype = ">";
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64 break;
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65
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66 default:
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67 throw OrthancException(ErrorCode_InternalError);
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68 }
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69
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70 unsigned int channels;
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71
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72 switch (format)
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73 {
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74 case PixelFormat_Grayscale8:
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75 datatype += "u1";
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76 channels = 1;
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77 break;
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78
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79 case PixelFormat_Grayscale16:
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80 datatype += "u2";
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81 channels = 1;
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82 break;
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83
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84 case PixelFormat_SignedGrayscale16:
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85 datatype += "i2";
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86 channels = 1;
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87 break;
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88
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89 case PixelFormat_RGB24:
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90 datatype += "u1";
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91 channels = 3;
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92 break;
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93
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94 case PixelFormat_Float32:
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95 datatype += "f4";
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96 channels = 1;
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97 break;
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98
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99 default:
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100 throw OrthancException(ErrorCode_NotImplemented);
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101 }
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102
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103 std::string depthString;
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104 if (depth != 0)
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105 {
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106 depthString = boost::lexical_cast<std::string>(depth) + ", ";
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107 }
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108
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109 const std::string info = ("{'descr': '" + datatype + "', 'fortran_order': False, " +
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110 "'shape': (" + depthString + boost::lexical_cast<std::string>(height) +
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111 "," + boost::lexical_cast<std::string>(width) +
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112 "," + boost::lexical_cast<std::string>(channels) + "), }");
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113
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114 const uint16_t minimumLength = sizeof(VERSION) + sizeof(uint16_t) + info.size() + 1 /* trailing '\n' */;
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115
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116 // The length of the header must be evenly divisible by 64. This
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117 // loop could be optimized by a "ceil()" operation, but we keep
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118 // the code as simple as possible
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119 uint16_t length = 64;
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120 while (length < minimumLength)
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121 {
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122 length += 64;
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123 }
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124
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125 uint16_t countZeros = length - minimumLength;
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126 uint16_t headerLength = info.size() + countZeros + 1 /* trailing '\n' */;
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127 uint8_t highByte = headerLength / 256;
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128 uint8_t lowByte = headerLength % 256;
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129
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130 target.AddChunk(VERSION, sizeof(VERSION));
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131 target.AddChunk(&lowByte, 1);
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132 target.AddChunk(&highByte, 1);
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133 target.AddChunk(info);
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134 target.AddChunk(std::string(countZeros, ' '));
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135 target.AddChunk("\n");
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136 }
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137
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138
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139 void NumpyWriter::WritePixels(ChunkedBuffer& target,
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140 const ImageAccessor& image)
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141 {
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142 size_t rowSize = image.GetBytesPerPixel() * image.GetWidth();
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143
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144 for (unsigned int y = 0; y < image.GetHeight(); y++)
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145 {
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146 target.AddChunk(image.GetConstRow(y), rowSize);
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147 }
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148 }
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149
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150
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151 void NumpyWriter::Finalize(std::string& target,
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152 ChunkedBuffer& source,
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153 bool compress)
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154 {
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155 if (compress)
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156 {
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157 #if ORTHANC_ENABLE_ZLIB == 1
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158 // This is the default name of the first array if arrays are
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159 // specified as positional arguments in "numpy.savez()"
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160 // https://numpy.org/doc/stable/reference/generated/numpy.savez.html
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161 const char* ARRAY_NAME = "arr_0";
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162
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163 std::string uncompressed;
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164 source.Flatten(uncompressed);
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165
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166 const bool isZip64 = (uncompressed.size() >= 1lu * 1024lu * 1024lu * 1024lu);
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167
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168 ZipWriter writer;
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169 writer.SetMemoryOutput(target, isZip64);
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170 writer.Open();
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171 writer.OpenFile(ARRAY_NAME);
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172 writer.Write(uncompressed);
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173 writer.Close();
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174 #else
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175 throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
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176 #endif
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177 }
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178 else
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179 {
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180 source.Flatten(target);
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181 }
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182 }
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183
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184
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185 #if ORTHANC_SANDBOXED == 0
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186 void NumpyWriter::WriteToFileInternal(const std::string& filename,
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187 unsigned int width,
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188 unsigned int height,
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189 unsigned int pitch,
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190 PixelFormat format,
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191 const void* buffer)
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192 {
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193 std::string content;
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194 WriteToMemoryInternal(content, width, height, pitch, format, buffer);
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195
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196 SystemToolbox::WriteFile(content, filename);
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197 }
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198 #endif
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199
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200
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201 void NumpyWriter::WriteToMemoryInternal(std::string& content,
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202 unsigned int width,
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203 unsigned int height,
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204 unsigned int pitch,
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205 PixelFormat format,
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206 const void* buffer)
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207 {
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208 ChunkedBuffer chunks;
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209 WriteHeader(chunks, 0 /* no depth */, width, height, format);
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210
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211 ImageAccessor image;
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212 image.AssignReadOnly(format, width, height, pitch, buffer);
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213 WritePixels(chunks, image);
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214
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215 Finalize(content, chunks, compressed_);
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216 }
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217
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218
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219 NumpyWriter::NumpyWriter()
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220 {
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221 compressed_ = false;
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222 }
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223
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224
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225 void NumpyWriter::SetCompressed(bool compressed)
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226 {
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227 #if ORTHANC_ENABLE_ZLIB == 1
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228 compressed_ = compressed;
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229 #else
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230 if (compressed)
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231 {
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232 throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
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233 }
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234 #endif
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235 }
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236 }