Mercurial > hg > orthanc-wsi
diff Framework/Inputs/OpenSlideLibrary.cpp @ 0:4a7a53257c7d
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 22 Oct 2016 21:48:33 +0200 |
parents | |
children | 7a88c614be04 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Framework/Inputs/OpenSlideLibrary.cpp Sat Oct 22 21:48:33 2016 +0200 @@ -0,0 +1,233 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics + * Department, University Hospital of Liege, Belgium + * + * This program is free software: you can redistribute it and/or + * modify it under the terms of the GNU Affero General Public License + * as published by the Free Software Foundation, either version 3 of + * the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + **/ + + +#include "OpenSlideLibrary.h" + +#include "../Orthanc/Core/Logging.h" +#include "../Orthanc/Core/Images/Image.h" + +namespace OrthancWSI +{ + static std::auto_ptr<OpenSlideLibrary> globalLibrary_; + + + OpenSlideLibrary::OpenSlideLibrary(const std::string& path) : + library_(path) + { + close_ = (FunctionClose) library_.GetFunction("openslide_close"); + getLevelCount_ = (FunctionGetLevelCount) library_.GetFunction("openslide_get_level_count"); + getLevelDimensions_ = (FunctionGetLevelDimensions) library_.GetFunction("openslide_get_level_dimensions"); + getLevelDownsample_ = (FunctionGetLevelDownsample) library_.GetFunction("openslide_get_level_downsample"); + open_ = (FunctionOpen) library_.GetFunction("openslide_open"); + readRegion_ = (FunctionReadRegion) library_.GetFunction("openslide_read_region"); + } + + + OpenSlideLibrary::Image::Level::Level() : + width_(0), + height_(0), + downsample_(1) + { + } + + + OpenSlideLibrary::Image::Level::Level(int64_t width, + int64_t height, + double downsample) : + width_(static_cast<unsigned int>(width)), + height_(static_cast<unsigned int>(height)), + downsample_(downsample) + { + if (width < 0 || + height < 0 || + downsample <= 0) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); + } + + if (static_cast<int64_t>(width_) != width || + static_cast<int64_t>(height_) != height) + { + LOG(ERROR) << "The whole-slide image is too large"; + throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); + } + } + + + void OpenSlideLibrary::Image::Initialize(const std::string& path) + { + handle_ = that_.open_(path.c_str()); + if (handle_ == NULL) + { + LOG(ERROR) << "Cannot open an image with OpenSlide: " << path; + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); + } + + try + { + LOG(INFO) << "Opening an image with OpenSlide: " << path; + + int32_t tmp = that_.getLevelCount_(handle_); + if (tmp <= 0) + { + LOG(ERROR) << "Image with no pyramid level"; + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); + } + + levels_.resize(tmp); + + for (int32_t level = 0; level < tmp; level++) + { + int64_t width, height; + that_.getLevelDimensions_(handle_, level, &width, &height); + + double downsample = that_.getLevelDownsample_(handle_, level); + + levels_[level] = Level(width, height, downsample); + } + + for (size_t i = 1; i < levels_.size(); i++) + { + if (levels_[i].width_ >= levels_[i - 1].width_ || + levels_[i].height_ >= levels_[i - 1].height_) + { + // This is not a pyramid with levels of decreasing sizes + // (level "0" must be the finest level) + LOG(ERROR) << "The pyramid does not have levels of strictly decreasing sizes"; + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); + } + } + } + catch (Orthanc::OrthancException&) + { + Close(); + throw; + } + } + + + OpenSlideLibrary::Image::Image(OpenSlideLibrary& that, + const std::string& path) : + that_(that), + handle_(NULL) + { + Initialize(path); + } + + + OpenSlideLibrary::Image::Image(const std::string& path) : + that_(OpenSlideLibrary::GetInstance()), + handle_(NULL) + { + Initialize(path); + } + + + void OpenSlideLibrary::Image::Close() + { + if (handle_ != NULL) + { + that_.close_(handle_); + handle_ = NULL; + } + } + + + void OpenSlideLibrary::Image::CheckLevel(unsigned int level) const + { + if (level >= levels_.size()) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); + } + } + + + double OpenSlideLibrary::Image::GetLevelDownsample(unsigned int level) const + { + CheckLevel(level); + return levels_[level].downsample_; + } + + + unsigned int OpenSlideLibrary::Image::GetLevelWidth(unsigned int level) const + { + CheckLevel(level); + return levels_[level].width_; + } + + + unsigned int OpenSlideLibrary::Image::GetLevelHeight(unsigned int level) const + { + CheckLevel(level); + return levels_[level].height_; + } + + + Orthanc::ImageAccessor* OpenSlideLibrary::Image::ReadRegion(unsigned int level, + uint64_t x, + uint64_t y, + unsigned int width, + unsigned int height) + { + CheckLevel(level); + + // Create a new image, with minimal pitch so as to be compatible with OpenSlide API + std::auto_ptr<Orthanc::ImageAccessor> region(new Orthanc::Image(Orthanc::PixelFormat_RGBA32, width, height, true)); + + if (region->GetWidth() != 0 && + region->GetHeight() != 0) + { + double zoom = levels_[level].downsample_; + x = static_cast<uint64_t>(zoom * static_cast<double>(x)); + y = static_cast<uint64_t>(zoom * static_cast<double>(y)); + + that_.readRegion_(handle_, reinterpret_cast<uint32_t*>(region->GetBuffer()), + x, y, level, region->GetWidth(), region->GetHeight()); + } + + return region.release(); + } + + + OpenSlideLibrary& OpenSlideLibrary::GetInstance() + { + if (globalLibrary_.get() == NULL) + { + LOG(ERROR) << "OpenSlide has not been initialized"; + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); + } + else + { + return *globalLibrary_; + } + } + + + void OpenSlideLibrary::Initialize(const std::string& path) + { + globalLibrary_.reset(new OpenSlideLibrary(path)); + } + + + void OpenSlideLibrary::Finalize() + { + globalLibrary_.reset(NULL); + } +}