Mercurial > hg > orthanc-stone
annotate Framework/Volumes/ImageBuffer3D.cpp @ 119:ba83e38cf3ff wasm
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 02 Oct 2017 22:01:41 +0200 |
| parents | 2eca030792aa |
| children | e2fe9352f240 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Stone of Orthanc | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
|
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5 * Copyright (C) 2017 Osimis, 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. | |
| 16 * | |
| 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 <Core/Images/ImageProcessing.h> |
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25 #include <Core/Logging.h> |
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26 #include <Core/OrthancException.h> |
| 0 | 27 |
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28 #include <string.h> |
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29 |
| 0 | 30 namespace OrthancStone |
| 31 { | |
| 32 Orthanc::ImageAccessor ImageBuffer3D::GetAxialSliceAccessor(unsigned int slice, | |
| 33 bool readOnly) | |
| 34 { | |
| 35 if (slice >= depth_) | |
| 36 { | |
| 37 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 38 } | |
| 39 | |
| 40 Orthanc::ImageAccessor accessor; | |
| 41 | |
| 42 if (readOnly) | |
| 43 { | |
| 44 accessor.AssignReadOnly(format_, width_, height_, image_.GetPitch(), | |
| 45 image_.GetConstRow(height_ * (depth_ - 1 - slice))); | |
| 46 } | |
| 47 else | |
| 48 { | |
| 49 accessor.AssignWritable(format_, width_, height_, image_.GetPitch(), | |
| 50 image_.GetRow(height_ * (depth_ - 1 - slice))); | |
| 51 } | |
| 52 | |
| 53 return accessor; | |
| 54 } | |
| 55 | |
| 56 | |
| 57 Orthanc::ImageAccessor ImageBuffer3D::GetCoronalSliceAccessor(unsigned int slice, | |
| 58 bool readOnly) | |
| 59 { | |
| 60 if (slice >= height_) | |
| 61 { | |
| 62 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 63 } | |
| 64 | |
| 65 Orthanc::ImageAccessor accessor; | |
| 66 | |
| 67 if (readOnly) | |
| 68 { | |
| 69 accessor.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_, | |
| 70 image_.GetConstRow(slice)); | |
| 71 } | |
| 72 else | |
| 73 { | |
| 74 accessor.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_, | |
| 75 image_.GetRow(slice)); | |
| 76 } | |
| 77 | |
| 78 return accessor; | |
| 79 } | |
| 80 | |
| 81 | |
| 82 Orthanc::Image* ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const | |
| 83 { | |
| 84 if (slice >= width_) | |
| 85 { | |
| 86 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 87 } | |
| 88 | |
| 11 | 89 std::auto_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false)); |
| 0 | 90 |
| 91 unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_); | |
| 92 | |
| 93 for (unsigned int z = 0; z < depth_; z++) | |
| 94 { | |
| 95 //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z)); | |
| 96 uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z)); | |
| 97 | |
| 98 for (unsigned int y = 0; y < height_; y++) | |
| 99 { | |
| 100 const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) + | |
| 101 bytesPerPixel * slice); | |
| 102 | |
| 103 memcpy(target, source, bytesPerPixel); | |
| 104 target += bytesPerPixel; | |
| 105 } | |
| 106 } | |
| 107 | |
| 108 return result.release(); | |
| 109 } | |
| 110 | |
| 111 | |
| 112 ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format, | |
| 113 unsigned int width, | |
| 114 unsigned int height, | |
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115 unsigned int depth, |
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116 bool computeRange) : |
| 11 | 117 image_(format, width, height * depth, false), |
| 0 | 118 format_(format), |
| 119 width_(width), | |
| 120 height_(height), | |
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121 depth_(depth), |
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122 computeRange_(computeRange), |
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123 hasRange_(false) |
| 0 | 124 { |
| 125 GeometryToolbox::AssignVector(voxelDimensions_, 1, 1, 1); | |
| 105 | 126 |
| 127 LOG(INFO) << "Created an image of " | |
| 128 << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB"; | |
| 0 | 129 } |
| 130 | |
| 131 | |
| 132 void ImageBuffer3D::Clear() | |
| 133 { | |
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134 memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch()); |
| 0 | 135 } |
| 136 | |
| 137 | |
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138 void ImageBuffer3D::SetAxialGeometry(const CoordinateSystem3D& geometry) |
| 0 | 139 { |
| 140 axialGeometry_ = geometry; | |
| 141 } | |
| 142 | |
| 143 | |
| 144 void ImageBuffer3D::SetVoxelDimensions(double x, | |
| 145 double y, | |
| 146 double z) | |
| 147 { | |
| 148 if (x <= 0 || | |
| 149 y <= 0 || | |
| 150 z <= 0) | |
| 151 { | |
| 152 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 153 } | |
| 154 | |
| 155 { | |
| 156 GeometryToolbox::AssignVector(voxelDimensions_, x, y, z); | |
| 157 } | |
| 158 } | |
| 159 | |
| 160 | |
| 161 Vector ImageBuffer3D::GetVoxelDimensions(VolumeProjection projection) | |
| 162 { | |
| 163 Vector result; | |
| 164 switch (projection) | |
| 165 { | |
| 166 case VolumeProjection_Axial: | |
| 167 result = voxelDimensions_; | |
| 168 break; | |
| 169 | |
| 170 case VolumeProjection_Coronal: | |
| 171 GeometryToolbox::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]); | |
| 172 break; | |
| 173 | |
| 174 case VolumeProjection_Sagittal: | |
| 175 GeometryToolbox::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]); | |
| 176 break; | |
| 177 | |
| 178 default: | |
| 179 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 180 } | |
| 181 | |
| 182 return result; | |
| 183 } | |
| 184 | |
| 185 | |
| 186 void ImageBuffer3D::GetSliceSize(unsigned int& width, | |
| 187 unsigned int& height, | |
| 188 VolumeProjection projection) | |
| 189 { | |
| 190 switch (projection) | |
| 191 { | |
| 192 case VolumeProjection_Axial: | |
| 193 width = width_; | |
| 194 height = height_; | |
| 195 break; | |
| 196 | |
| 197 case VolumeProjection_Coronal: | |
| 198 width = width_; | |
| 199 height = depth_; | |
| 200 break; | |
| 201 | |
| 202 case VolumeProjection_Sagittal: | |
| 203 width = height_; | |
| 204 height = depth_; | |
| 205 break; | |
| 206 | |
| 207 default: | |
| 208 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 209 } | |
| 210 } | |
| 211 | |
| 212 | |
| 213 ParallelSlices* ImageBuffer3D::GetGeometry(VolumeProjection projection) | |
| 214 { | |
| 215 std::auto_ptr<ParallelSlices> result(new ParallelSlices); | |
| 216 | |
| 217 switch (projection) | |
| 218 { | |
| 219 case VolumeProjection_Axial: | |
| 220 for (unsigned int z = 0; z < depth_; z++) | |
| 221 { | |
| 222 Vector origin = axialGeometry_.GetOrigin(); | |
| 223 origin += static_cast<double>(z) * voxelDimensions_[2] * axialGeometry_.GetNormal(); | |
| 224 | |
| 225 result->AddSlice(origin, | |
| 226 axialGeometry_.GetAxisX(), | |
| 227 axialGeometry_.GetAxisY()); | |
| 228 } | |
| 229 break; | |
| 230 | |
| 231 case VolumeProjection_Coronal: | |
| 232 for (unsigned int y = 0; y < height_; y++) | |
| 233 { | |
| 234 Vector origin = axialGeometry_.GetOrigin(); | |
| 235 origin += static_cast<double>(y) * voxelDimensions_[1] * axialGeometry_.GetAxisY(); | |
| 236 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal(); | |
| 237 | |
| 238 result->AddSlice(origin, | |
| 239 axialGeometry_.GetAxisX(), | |
| 240 -axialGeometry_.GetNormal()); | |
| 241 } | |
| 242 break; | |
| 243 | |
| 244 case VolumeProjection_Sagittal: | |
| 245 for (unsigned int x = 0; x < width_; x++) | |
| 246 { | |
| 247 Vector origin = axialGeometry_.GetOrigin(); | |
| 248 origin += static_cast<double>(x) * voxelDimensions_[0] * axialGeometry_.GetAxisX(); | |
| 249 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal(); | |
| 250 | |
| 251 result->AddSlice(origin, | |
| 252 axialGeometry_.GetAxisY(), | |
| 253 -axialGeometry_.GetNormal()); | |
| 254 } | |
| 255 break; | |
| 256 | |
| 257 default: | |
| 258 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 259 } | |
| 260 | |
| 261 return result.release(); | |
| 262 } | |
| 263 | |
| 264 | |
| 105 | 265 uint64_t ImageBuffer3D::GetEstimatedMemorySize() const |
| 266 { | |
| 267 return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_); | |
| 268 } | |
| 269 | |
| 270 | |
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271 void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice) |
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272 { |
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273 if (!computeRange_ || |
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274 slice.GetWidth() == 0 || |
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275 slice.GetHeight() == 0) |
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276 { |
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277 return; |
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278 } |
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279 |
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280 float sliceMin, sliceMax; |
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281 |
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282 switch (slice.GetFormat()) |
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283 { |
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284 case Orthanc::PixelFormat_Grayscale8: |
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285 case Orthanc::PixelFormat_Grayscale16: |
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286 case Orthanc::PixelFormat_Grayscale32: |
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287 case Orthanc::PixelFormat_SignedGrayscale16: |
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288 { |
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289 int64_t a, b; |
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290 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice); |
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291 sliceMin = static_cast<float>(a); |
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292 sliceMax = static_cast<float>(b); |
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293 break; |
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294 } |
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295 |
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296 case Orthanc::PixelFormat_Float32: |
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297 Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice); |
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298 break; |
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299 |
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300 default: |
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301 return; |
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302 } |
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303 |
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304 if (hasRange_) |
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305 { |
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306 minValue_ = std::min(minValue_, sliceMin); |
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307 maxValue_ = std::max(maxValue_, sliceMax); |
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308 } |
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309 else |
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310 { |
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311 hasRange_ = true; |
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312 minValue_ = sliceMin; |
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313 maxValue_ = sliceMax; |
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314 } |
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315 } |
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316 |
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317 |
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318 bool ImageBuffer3D::GetRange(float& minValue, |
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319 float& maxValue) const |
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320 { |
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321 if (hasRange_) |
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322 { |
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323 minValue = minValue_; |
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324 maxValue = maxValue_; |
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325 return true; |
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326 } |
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327 else |
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328 { |
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329 return false; |
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330 } |
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331 } |
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332 |
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333 |
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334 bool ImageBuffer3D::FitWindowingToRange(RenderStyle& style, |
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335 const DicomFrameConverter& converter) const |
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336 { |
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337 if (hasRange_) |
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338 { |
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339 style.windowing_ = ImageWindowing_Custom; |
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340 style.customWindowCenter_ = converter.Apply((minValue_ + maxValue_) / 2.0); |
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341 style.customWindowWidth_ = converter.Apply(maxValue_ - minValue_); |
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342 |
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343 if (style.customWindowWidth_ > 1) |
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344 { |
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345 return true; |
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346 } |
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347 } |
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348 |
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349 style.windowing_ = ImageWindowing_Custom; |
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350 style.customWindowCenter_ = 128.0; |
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351 style.customWindowWidth_ = 256.0; |
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352 return false; |
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353 } |
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354 |
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355 |
| 0 | 356 ImageBuffer3D::SliceReader::SliceReader(ImageBuffer3D& that, |
| 357 VolumeProjection projection, | |
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358 unsigned int slice) |
| 0 | 359 { |
| 360 switch (projection) | |
| 361 { | |
| 362 case VolumeProjection_Axial: | |
| 363 accessor_ = that.GetAxialSliceAccessor(slice, true); | |
| 364 break; | |
| 365 | |
| 366 case VolumeProjection_Coronal: | |
| 367 accessor_ = that.GetCoronalSliceAccessor(slice, true); | |
| 368 break; | |
| 369 | |
| 370 case VolumeProjection_Sagittal: | |
| 371 sagittal_.reset(that.ExtractSagittalSlice(slice)); | |
| 372 accessor_ = *sagittal_; | |
| 373 break; | |
| 374 | |
| 375 default: | |
| 376 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 377 } | |
| 378 } | |
| 379 | |
| 380 | |
| 381 void ImageBuffer3D::SliceWriter::Flush() | |
| 382 { | |
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383 if (modified_) |
| 0 | 384 { |
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385 if (sagittal_.get() != NULL) |
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386 { |
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387 // TODO |
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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389 } |
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390 |
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391 // Update the dynamic range of the underlying image, if |
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392 // "computeRange_" is set to true |
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393 that_.ExtendImageRange(accessor_); |
| 0 | 394 } |
| 395 } | |
| 396 | |
| 397 | |
| 398 ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that, | |
| 399 VolumeProjection projection, | |
| 400 unsigned int slice) : | |
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401 that_(that), |
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402 modified_(false) |
| 0 | 403 { |
| 404 switch (projection) | |
| 405 { | |
| 406 case VolumeProjection_Axial: | |
| 407 accessor_ = that.GetAxialSliceAccessor(slice, false); | |
| 408 break; | |
| 409 | |
| 410 case VolumeProjection_Coronal: | |
| 411 accessor_ = that.GetCoronalSliceAccessor(slice, false); | |
| 412 break; | |
| 413 | |
| 414 case VolumeProjection_Sagittal: | |
| 415 sagittal_.reset(that.ExtractSagittalSlice(slice)); | |
| 416 accessor_ = *sagittal_; | |
| 417 break; | |
| 418 | |
| 419 default: | |
| 420 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 421 } | |
| 422 } | |
| 423 } |