Mercurial > hg > orthanc-stone
annotate Framework/Volumes/ImageBuffer3D.cpp @ 684:7719eb852dd5
new class: VolumeImageGeometry
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 16 May 2019 16:47:46 +0200 |
parents | dbc1d8bfc68a |
children | 9a474e90e832 |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
439 | 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
47 | 8 * modify it under the terms of the GNU Affero General Public License |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
0 | 11 * |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
47 | 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
15 * Affero General Public License for more details. | |
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16 * |
47 | 17 * You should have received a copy of the GNU Affero General Public License |
0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
19 **/ | |
20 | |
21 | |
22 #include "ImageBuffer3D.h" | |
23 | |
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24 #include "../Toolbox/GeometryToolbox.h" |
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25 |
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26 #include <Core/Images/ImageProcessing.h> |
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27 #include <Core/Logging.h> |
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28 #include <Core/OrthancException.h> |
0 | 29 |
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30 #include <string.h> |
0 | 31 |
32 namespace OrthancStone | |
33 { | |
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34 void ImageBuffer3D::GetAxialSliceAccessor(Orthanc::ImageAccessor& target, |
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35 unsigned int slice, |
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36 bool readOnly) const |
0 | 37 { |
38 if (slice >= depth_) | |
39 { | |
40 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
41 } | |
42 | |
43 if (readOnly) | |
44 { | |
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45 target.AssignReadOnly(format_, width_, height_, image_.GetPitch(), |
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46 image_.GetConstRow(height_ * (depth_ - 1 - slice))); |
0 | 47 } |
48 else | |
49 { | |
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50 target.AssignWritable(format_, width_, height_, image_.GetPitch(), |
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51 image_.GetRow(height_ * (depth_ - 1 - slice))); |
0 | 52 } |
53 } | |
54 | |
55 | |
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56 void ImageBuffer3D::GetCoronalSliceAccessor(Orthanc::ImageAccessor& target, |
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57 unsigned int slice, |
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58 bool readOnly) const |
0 | 59 { |
60 if (slice >= height_) | |
61 { | |
62 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
63 } | |
64 | |
65 if (readOnly) | |
66 { | |
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67 target.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_, |
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68 image_.GetConstRow(slice)); |
0 | 69 } |
70 else | |
71 { | |
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72 target.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_, |
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73 image_.GetRow(slice)); |
0 | 74 } |
75 } | |
76 | |
77 | |
78 Orthanc::Image* ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const | |
79 { | |
80 if (slice >= width_) | |
81 { | |
82 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
83 } | |
84 | |
11 | 85 std::auto_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false)); |
0 | 86 |
87 unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_); | |
88 | |
89 for (unsigned int z = 0; z < depth_; z++) | |
90 { | |
91 //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z)); | |
92 uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z)); | |
93 | |
94 for (unsigned int y = 0; y < height_; y++) | |
95 { | |
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96 const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) + |
0 | 97 bytesPerPixel * slice); |
98 | |
99 memcpy(target, source, bytesPerPixel); | |
100 target += bytesPerPixel; | |
101 } | |
102 } | |
103 | |
104 return result.release(); | |
105 } | |
106 | |
107 | |
108 ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format, | |
109 unsigned int width, | |
110 unsigned int height, | |
119
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111 unsigned int depth, |
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112 bool computeRange) : |
11 | 113 image_(format, width, height * depth, false), |
0 | 114 format_(format), |
115 width_(width), | |
116 height_(height), | |
119
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117 depth_(depth), |
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118 computeRange_(computeRange), |
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119 hasRange_(false) |
0 | 120 { |
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121 geometry_.SetSize(width, height, depth); |
105 | 122 |
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123 LOG(INFO) << "Created a 3D image of size " << width << "x" << height |
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124 << "x" << depth << " in " << Orthanc::EnumerationToString(format) |
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125 << " (" << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB)"; |
0 | 126 } |
127 | |
128 | |
129 void ImageBuffer3D::Clear() | |
130 { | |
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131 memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch()); |
0 | 132 } |
133 | |
134 | |
135 | |
136 | |
139
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137 ParallelSlices* ImageBuffer3D::GetGeometry(VolumeProjection projection) const |
0 | 138 { |
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139 const Vector dimensions = geometry_.GetVoxelDimensions(VolumeProjection_Axial); |
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140 const CoordinateSystem3D& axial = geometry_.GetAxialGeometry(); |
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141 |
0 | 142 std::auto_ptr<ParallelSlices> result(new ParallelSlices); |
143 | |
144 switch (projection) | |
145 { | |
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146 case VolumeProjection_Axial: |
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147 for (unsigned int z = 0; z < depth_; z++) |
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148 { |
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149 Vector origin = axial.GetOrigin(); |
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150 origin += static_cast<double>(z) * dimensions[2] * axial.GetNormal(); |
0 | 151 |
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152 result->AddSlice(origin, |
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153 axial.GetAxisX(), |
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154 axial.GetAxisY()); |
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155 } |
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156 break; |
0 | 157 |
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158 case VolumeProjection_Coronal: |
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159 for (unsigned int y = 0; y < height_; y++) |
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160 { |
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161 Vector origin = axial.GetOrigin(); |
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162 origin += static_cast<double>(y) * dimensions[1] * axial.GetAxisY(); |
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163 origin += static_cast<double>(depth_ - 1) * dimensions[2] * axial.GetNormal(); |
0 | 164 |
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165 result->AddSlice(origin, |
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166 axial.GetAxisX(), |
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167 -axial.GetNormal()); |
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168 } |
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169 break; |
0 | 170 |
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171 case VolumeProjection_Sagittal: |
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172 for (unsigned int x = 0; x < width_; x++) |
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173 { |
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174 Vector origin = axial.GetOrigin(); |
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175 origin += static_cast<double>(x) * dimensions[0] * axial.GetAxisX(); |
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176 origin += static_cast<double>(depth_ - 1) * dimensions[2] * axial.GetNormal(); |
0 | 177 |
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178 result->AddSlice(origin, |
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179 axial.GetAxisY(), |
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180 -axial.GetNormal()); |
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181 } |
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182 break; |
0 | 183 |
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184 default: |
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185 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 186 } |
187 | |
188 return result.release(); | |
189 } | |
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190 |
0 | 191 |
105 | 192 uint64_t ImageBuffer3D::GetEstimatedMemorySize() const |
193 { | |
194 return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_); | |
195 } | |
196 | |
197 | |
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198 void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice) |
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199 { |
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200 if (!computeRange_ || |
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201 slice.GetWidth() == 0 || |
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202 slice.GetHeight() == 0) |
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203 { |
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204 return; |
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205 } |
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206 |
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207 float sliceMin, sliceMax; |
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208 |
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209 switch (slice.GetFormat()) |
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210 { |
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211 case Orthanc::PixelFormat_Grayscale8: |
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212 case Orthanc::PixelFormat_Grayscale16: |
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213 case Orthanc::PixelFormat_Grayscale32: |
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214 case Orthanc::PixelFormat_SignedGrayscale16: |
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215 { |
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216 int64_t a, b; |
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217 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice); |
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218 sliceMin = static_cast<float>(a); |
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219 sliceMax = static_cast<float>(b); |
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220 break; |
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221 } |
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222 |
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223 case Orthanc::PixelFormat_Float32: |
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224 Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice); |
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225 break; |
119
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226 |
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227 default: |
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228 return; |
119
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229 } |
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230 |
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231 if (hasRange_) |
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232 { |
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233 minValue_ = std::min(minValue_, sliceMin); |
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234 maxValue_ = std::max(maxValue_, sliceMax); |
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235 } |
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236 else |
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237 { |
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238 hasRange_ = true; |
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239 minValue_ = sliceMin; |
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240 maxValue_ = sliceMax; |
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241 } |
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242 } |
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243 |
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244 |
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245 bool ImageBuffer3D::GetRange(float& minValue, |
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246 float& maxValue) const |
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247 { |
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248 if (hasRange_) |
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249 { |
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250 minValue = minValue_; |
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251 maxValue = maxValue_; |
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252 return true; |
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253 } |
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254 else |
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255 { |
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256 return false; |
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257 } |
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258 } |
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259 |
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260 |
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261 bool ImageBuffer3D::FitWindowingToRange(RenderStyle& style, |
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262 const DicomFrameConverter& converter) const |
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263 { |
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264 if (hasRange_) |
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265 { |
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266 style.windowing_ = ImageWindowing_Custom; |
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267 style.customWindowCenter_ = converter.Apply((minValue_ + maxValue_) / 2.0); |
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268 style.customWindowWidth_ = converter.Apply(maxValue_ - minValue_); |
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269 |
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270 if (style.customWindowWidth_ > 1) |
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271 { |
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272 return true; |
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273 } |
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274 } |
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275 |
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276 style.windowing_ = ImageWindowing_Custom; |
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277 style.customWindowCenter_ = 128.0; |
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278 style.customWindowWidth_ = 256.0; |
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279 return false; |
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280 } |
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281 |
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282 |
192
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283 ImageBuffer3D::SliceReader::SliceReader(const ImageBuffer3D& that, |
0 | 284 VolumeProjection projection, |
87
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285 unsigned int slice) |
0 | 286 { |
287 switch (projection) | |
288 { | |
289 case VolumeProjection_Axial: | |
316
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290 that.GetAxialSliceAccessor(accessor_, slice, true); |
0 | 291 break; |
292 | |
293 case VolumeProjection_Coronal: | |
316
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294 that.GetCoronalSliceAccessor(accessor_, slice, true); |
0 | 295 break; |
296 | |
297 case VolumeProjection_Sagittal: | |
298 sagittal_.reset(that.ExtractSagittalSlice(slice)); | |
316
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299 sagittal_->GetReadOnlyAccessor(accessor_); |
0 | 300 break; |
301 | |
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302 default: |
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303 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 304 } |
305 } | |
306 | |
307 | |
308 void ImageBuffer3D::SliceWriter::Flush() | |
309 { | |
87
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310 if (modified_) |
0 | 311 { |
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312 if (sagittal_.get() != NULL) |
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313 { |
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314 // TODO |
318
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315 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
87
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316 } |
119
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317 |
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318 // Update the dynamic range of the underlying image, if |
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319 // "computeRange_" is set to true |
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320 that_.ExtendImageRange(accessor_); |
0 | 321 } |
322 } | |
323 | |
324 | |
325 ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that, | |
326 VolumeProjection projection, | |
327 unsigned int slice) : | |
119
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328 that_(that), |
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329 modified_(false) |
0 | 330 { |
331 switch (projection) | |
332 { | |
333 case VolumeProjection_Axial: | |
316
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334 that.GetAxialSliceAccessor(accessor_, slice, false); |
0 | 335 break; |
336 | |
337 case VolumeProjection_Coronal: | |
316
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338 that.GetCoronalSliceAccessor(accessor_, slice, false); |
0 | 339 break; |
340 | |
341 case VolumeProjection_Sagittal: | |
342 sagittal_.reset(that.ExtractSagittalSlice(slice)); | |
316
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343 sagittal_->GetWriteableAccessor(accessor_); |
0 | 344 break; |
345 | |
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346 default: |
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347 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 348 } |
349 } | |
139
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350 |
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351 |
143 | 352 uint8_t ImageBuffer3D::GetVoxelGrayscale8(unsigned int x, |
141
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353 unsigned int y, |
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354 unsigned int z) const |
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355 { |
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356 if (format_ != Orthanc::PixelFormat_Grayscale8) |
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357 { |
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358 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); |
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359 } |
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360 |
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361 if (x >= width_ || |
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362 y >= height_ || |
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363 z >= depth_) |
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364 { |
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365 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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366 } |
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367 |
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368 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z)); |
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369 return reinterpret_cast<const uint8_t*>(p) [x]; |
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370 } |
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371 |
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372 |
143 | 373 uint16_t ImageBuffer3D::GetVoxelGrayscale16(unsigned int x, |
139
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374 unsigned int y, |
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375 unsigned int z) const |
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376 { |
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377 if (format_ != Orthanc::PixelFormat_Grayscale16) |
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378 { |
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379 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); |
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380 } |
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381 |
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382 if (x >= width_ || |
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383 y >= height_ || |
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384 z >= depth_) |
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385 { |
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386 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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387 } |
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388 |
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389 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z)); |
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390 return reinterpret_cast<const uint16_t*>(p) [x]; |
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391 } |
0 | 392 } |