Mercurial > hg > orthanc-stone
view Framework/Radiography/RadiographyScene.cpp @ 421:f87f28624b96 cache-in-radiography
tentative to make SmartLoader and RadiographyScene work together (not really working)
author | am@osimis.io |
---|---|
date | Tue, 20 Nov 2018 16:35:29 +0100 |
parents | c23df8b3433b |
children |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2018 Osimis S.A., 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 "RadiographyScene.h" #include "../Toolbox/DicomFrameConverter.h" #include <Core/Images/Image.h> #include <Core/Images/ImageProcessing.h> #include <Core/Images/PamReader.h> #include <Core/Images/PamWriter.h> #include <Core/Images/PngWriter.h> #include <Core/OrthancException.h> #include <Core/Toolbox.h> #include <Plugins/Samples/Common/DicomDatasetReader.h> #include <Plugins/Samples/Common/FullOrthancDataset.h> #include <boost/math/special_functions/round.hpp> namespace OrthancStone { RadiographyScene::LayerAccessor::LayerAccessor(RadiographyScene& scene, size_t index) : scene_(scene), index_(index) { Layers::iterator layer = scene.layers_.find(index); if (layer == scene.layers_.end()) { layer_ = NULL; } else { assert(layer->second != NULL); layer_ = layer->second; } } RadiographyScene::LayerAccessor::LayerAccessor(RadiographyScene& scene, double x, double y) : scene_(scene), index_(0) // Dummy initialization { if (scene.LookupLayer(index_, x, y)) { Layers::iterator layer = scene.layers_.find(index_); if (layer == scene.layers_.end()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } else { assert(layer->second != NULL); layer_ = layer->second; } } else { layer_ = NULL; } } RadiographyScene& RadiographyScene::LayerAccessor::GetScene() const { if (IsValid()) { return scene_; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } size_t RadiographyScene::LayerAccessor::GetIndex() const { if (IsValid()) { return index_; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } RadiographyLayer& RadiographyScene::LayerAccessor::GetLayer() const { if (IsValid()) { return *layer_; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } class RadiographyScene::AlphaLayer : public RadiographyLayer { private: const RadiographyScene& scene_; std::auto_ptr<Orthanc::ImageAccessor> alpha_; // Grayscale8 bool useWindowing_; float foreground_; public: AlphaLayer(const RadiographyScene& scene) : scene_(scene), useWindowing_(true), foreground_(0) { } void SetForegroundValue(float foreground) { useWindowing_ = false; foreground_ = foreground; } void SetAlpha(Orthanc::ImageAccessor* image) { std::auto_ptr<Orthanc::ImageAccessor> raii(image); if (image == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } if (image->GetFormat() != Orthanc::PixelFormat_Grayscale8) { throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); } SetSize(image->GetWidth(), image->GetHeight()); alpha_ = raii; } void LoadText(const Orthanc::Font& font, const std::string& utf8) { SetAlpha(font.RenderAlpha(utf8)); } virtual bool GetDefaultWindowing(float& center, float& width) const { return false; } virtual void Render(Orthanc::ImageAccessor& buffer, const AffineTransform2D& viewTransform, ImageInterpolation interpolation) const { if (alpha_.get() == NULL) { return; } if (buffer.GetFormat() != Orthanc::PixelFormat_Float32) { throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); } unsigned int cropX, cropY, cropWidth, cropHeight; GetCrop(cropX, cropY, cropWidth, cropHeight); const AffineTransform2D t = AffineTransform2D::Combine( viewTransform, GetTransform(), AffineTransform2D::CreateOffset(cropX, cropY)); Orthanc::ImageAccessor cropped; alpha_->GetRegion(cropped, cropX, cropY, cropWidth, cropHeight); Orthanc::Image tmp(Orthanc::PixelFormat_Grayscale8, buffer.GetWidth(), buffer.GetHeight(), false); t.Apply(tmp, cropped, interpolation, true /* clear */); // Blit const unsigned int width = buffer.GetWidth(); const unsigned int height = buffer.GetHeight(); float value = foreground_; if (useWindowing_) { float center, width; if (scene_.GetWindowing(center, width)) { value = center + width / 2.0f; } } for (unsigned int y = 0; y < height; y++) { float *q = reinterpret_cast<float*>(buffer.GetRow(y)); const uint8_t *p = reinterpret_cast<uint8_t*>(tmp.GetRow(y)); for (unsigned int x = 0; x < width; x++, p++, q++) { float a = static_cast<float>(*p) / 255.0f; *q = (a * value + (1.0f - a) * (*q)); } } } virtual bool GetRange(float& minValue, float& maxValue) const { if (useWindowing_) { return false; } else { minValue = 0; maxValue = 0; if (foreground_ < 0) { minValue = foreground_; } if (foreground_ > 0) { maxValue = foreground_; } return true; } } }; class RadiographyScene::DicomLayer : public RadiographyLayer { private: boost::shared_ptr<Orthanc::ImageAccessor> source_; // Content of PixelData std::auto_ptr<DicomFrameConverter> converter_; std::auto_ptr<Orthanc::ImageAccessor> converted_; // Float32 static OrthancPlugins::DicomTag ConvertTag(const Orthanc::DicomTag& tag) { return OrthancPlugins::DicomTag(tag.GetGroup(), tag.GetElement()); } void ApplyConverter() { if (source_.get() != NULL && converter_.get() != NULL) { converted_.reset(converter_->ConvertFrame(*source_)); } } public: void SetDicomTags(const OrthancPlugins::FullOrthancDataset& dataset) { converter_.reset(new DicomFrameConverter); converter_->ReadParameters(dataset); ApplyConverter(); std::string tmp; Vector pixelSpacing; if (dataset.GetStringValue(tmp, ConvertTag(Orthanc::DICOM_TAG_PIXEL_SPACING)) && LinearAlgebra::ParseVector(pixelSpacing, tmp) && pixelSpacing.size() == 2) { SetPixelSpacing(pixelSpacing[0], pixelSpacing[1]); } //SetPan(-0.5 * GetPixelSpacingX(), -0.5 * GetPixelSpacingY()); OrthancPlugins::DicomDatasetReader reader(dataset); unsigned int width, height; if (!reader.GetUnsignedIntegerValue(width, ConvertTag(Orthanc::DICOM_TAG_COLUMNS)) || !reader.GetUnsignedIntegerValue(height, ConvertTag(Orthanc::DICOM_TAG_ROWS))) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } else { SetSize(width, height); } } void SetSourceImage(boost::shared_ptr<Orthanc::ImageAccessor> image) { if (image.get() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } SetSize(image->GetWidth(), image->GetHeight()); source_ = image; ApplyConverter(); } virtual void Render(Orthanc::ImageAccessor& buffer, const AffineTransform2D& viewTransform, ImageInterpolation interpolation) const { if (converted_.get() != NULL) { if (converted_->GetFormat() != Orthanc::PixelFormat_Float32) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } unsigned int cropX, cropY, cropWidth, cropHeight; GetCrop(cropX, cropY, cropWidth, cropHeight); AffineTransform2D t = AffineTransform2D::Combine( viewTransform, GetTransform(), AffineTransform2D::CreateOffset(cropX, cropY)); Orthanc::ImageAccessor cropped; converted_->GetRegion(cropped, cropX, cropY, cropWidth, cropHeight); t.Apply(buffer, cropped, interpolation, false); } } virtual bool GetDefaultWindowing(float& center, float& width) const { if (converter_.get() != NULL && converter_->HasDefaultWindow()) { center = static_cast<float>(converter_->GetDefaultWindowCenter()); width = static_cast<float>(converter_->GetDefaultWindowWidth()); return true; } else { return false; } } virtual bool GetRange(float& minValue, float& maxValue) const { if (converted_.get() != NULL) { if (converted_->GetFormat() != Orthanc::PixelFormat_Float32) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } Orthanc::ImageProcessing::GetMinMaxFloatValue(minValue, maxValue, *converted_); return true; } else { return false; } } }; RadiographyLayer& RadiographyScene::RegisterLayer(RadiographyLayer* layer) { if (layer == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } std::auto_ptr<RadiographyLayer> raii(layer); size_t index = countLayers_++; raii->SetIndex(index); layers_[index] = raii.release(); EmitMessage(GeometryChangedMessage(*this)); EmitMessage(ContentChangedMessage(*this)); return *layer; } RadiographyScene::RadiographyScene(MessageBroker& broker) : IObserver(broker), IObservable(broker), countLayers_(0), hasWindowing_(false), windowingCenter_(0), // Dummy initialization windowingWidth_(0) // Dummy initialization { } RadiographyScene::~RadiographyScene() { for (Layers::iterator it = layers_.begin(); it != layers_.end(); it++) { assert(it->second != NULL); delete it->second; } } bool RadiographyScene::GetWindowing(float& center, float& width) const { if (hasWindowing_) { center = windowingCenter_; width = windowingWidth_; return true; } else { return false; } } void RadiographyScene::GetWindowingWithDefault(float& center, float& width) const { if (!GetWindowing(center, width)) { center = 128; width = 256; } } void RadiographyScene::SetWindowing(float center, float width) { hasWindowing_ = true; windowingCenter_ = center; windowingWidth_ = width; } RadiographyLayer& RadiographyScene::LoadText(const Orthanc::Font& font, const std::string& utf8) { std::auto_ptr<AlphaLayer> alpha(new AlphaLayer(*this)); alpha->LoadText(font, utf8); return RegisterLayer(alpha.release()); } RadiographyLayer& RadiographyScene::LoadTestBlock(unsigned int width, unsigned int height) { std::auto_ptr<Orthanc::Image> block(new Orthanc::Image(Orthanc::PixelFormat_Grayscale8, width, height, false)); for (unsigned int padding = 0; (width > 2 * padding) && (height > 2 * padding); padding++) { uint8_t color; if (255 > 10 * padding) { color = 255 - 10 * padding; } else { color = 0; } Orthanc::ImageAccessor region; block->GetRegion(region, padding, padding, width - 2 * padding, height - 2 * padding); Orthanc::ImageProcessing::Set(region, color); } std::auto_ptr<AlphaLayer> alpha(new AlphaLayer(*this)); alpha->SetAlpha(block.release()); return RegisterLayer(alpha.release()); } RadiographyLayer& RadiographyScene::LoadDicomFrame(OrthancApiClient& orthanc, const std::string& instance, unsigned int frame, bool httpCompression) { RadiographyLayer& layer = RegisterLayer(new DicomLayer); { IWebService::HttpHeaders headers; std::string uri = "/instances/" + instance + "/tags"; orthanc.GetBinaryAsync( uri, headers, new Callable<RadiographyScene, OrthancApiClient::BinaryResponseReadyMessage> (*this, &RadiographyScene::OnTagsReceived), NULL, new Orthanc::SingleValueObject<size_t>(layer.GetIndex())); } { IWebService::HttpHeaders headers; headers["Accept"] = "image/x-portable-arbitrarymap"; if (httpCompression) { headers["Accept-Encoding"] = "gzip"; } std::string uri = ("/instances/" + instance + "/frames/" + boost::lexical_cast<std::string>(frame) + "/image-uint16"); orthanc.GetBinaryAsync( uri, headers, new Callable<RadiographyScene, OrthancApiClient::BinaryResponseReadyMessage> (*this, &RadiographyScene::OnFrameReceived), NULL, new Orthanc::SingleValueObject<size_t>(layer.GetIndex())); } return layer; } RadiographyLayer& RadiographyScene::LoadDicomWebFrame(IWebService& web) { RadiographyLayer& layer = RegisterLayer(new DicomLayer); return layer; } RadiographyLayer& RadiographyScene::SetFrame(IVolumeSlicer* slice) { RadiographyLayer& layer = RegisterLayer(new DicomLayer); layersIndexBySlice_[slice] = layer.GetIndex(); slice->RegisterObserverCallback(new Callable<RadiographyScene, IVolumeSlicer::TagsReadyMessage> (*this, &RadiographyScene::OnTagsReady)); slice->RegisterObserverCallback(new Callable<RadiographyScene, IVolumeSlicer::FrameReadyMessage> (*this, &RadiographyScene::OnImageReady)); // TODO: register failures return layer; } void RadiographyScene::OnTagsReady(const IVolumeSlicer::TagsReadyMessage &message) { size_t layerIndex = layersIndexBySlice_[&(message.GetOrigin())]; Layers::iterator layer = layers_.find(layerIndex); if (layer != layers_.end()) { assert(layer->second != NULL); const OrthancPlugins::FullOrthancDataset& dicom = message.GetDicomTags(); dynamic_cast<DicomLayer*>(layer->second)->SetDicomTags(dicom); float c, w; if (!hasWindowing_ && layer->second->GetDefaultWindowing(c, w)) { hasWindowing_ = true; windowingCenter_ = c; windowingWidth_ = w; } EmitMessage(GeometryChangedMessage(*this)); CoordinateSystem3D dummy; message.GetOrigin().ScheduleLayerCreation(dummy); } } void RadiographyScene::OnTagsReceived(const OrthancApiClient::BinaryResponseReadyMessage& message) { size_t index = dynamic_cast<const Orthanc::SingleValueObject<size_t>&> (message.GetPayload()).GetValue(); LOG(INFO) << "JSON received: " << message.GetUri().c_str() << " (" << message.GetAnswerSize() << " bytes) for layer " << index; Layers::iterator layer = layers_.find(index); if (layer != layers_.end()) { assert(layer->second != NULL); OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer(), message.GetAnswerSize()); dynamic_cast<DicomLayer*>(layer->second)->SetDicomTags(dicom); float c, w; if (!hasWindowing_ && layer->second->GetDefaultWindowing(c, w)) { hasWindowing_ = true; windowingCenter_ = c; windowingWidth_ = w; } EmitMessage(GeometryChangedMessage(*this)); } } void RadiographyScene::OnImageReady(const IVolumeSlicer::FrameReadyMessage &message) { size_t layerIndex = layersIndexBySlice_[&(message.GetOrigin())]; Layers::iterator layer = layers_.find(layerIndex); if (layer != layers_.end()) { assert(layer->second != NULL); dynamic_cast<DicomLayer*>(layer->second)->SetSourceImage(message.GetImage()); EmitMessage(ContentChangedMessage(*this)); } } void RadiographyScene::OnFrameReceived(const OrthancApiClient::BinaryResponseReadyMessage& message) { size_t index = dynamic_cast<const Orthanc::SingleValueObject<size_t>&>(message.GetPayload()).GetValue(); LOG(INFO) << "DICOM frame received: " << message.GetUri().c_str() << " (" << message.GetAnswerSize() << " bytes) for layer " << index; Layers::iterator layer = layers_.find(index); if (layer != layers_.end()) { assert(layer->second != NULL); std::string content; if (message.GetAnswerSize() > 0) { content.assign(reinterpret_cast<const char*>(message.GetAnswer()), message.GetAnswerSize()); } boost::shared_ptr<Orthanc::PamReader> reader(new Orthanc::PamReader); reader->ReadFromMemory(content); dynamic_cast<DicomLayer*>(layer->second)->SetSourceImage(reader); EmitMessage(ContentChangedMessage(*this)); } } Extent2D RadiographyScene::GetSceneExtent() const { Extent2D extent; for (Layers::const_iterator it = layers_.begin(); it != layers_.end(); ++it) { assert(it->second != NULL); extent.Union(it->second->GetExtent()); } return extent; } void RadiographyScene::Render(Orthanc::ImageAccessor& buffer, const AffineTransform2D& viewTransform, ImageInterpolation interpolation) const { Orthanc::ImageProcessing::Set(buffer, 0); // Render layers in the background-to-foreground order for (size_t index = 0; index < countLayers_; index++) { Layers::const_iterator it = layers_.find(index); if (it != layers_.end()) { assert(it->second != NULL); it->second->Render(buffer, viewTransform, interpolation); } } } bool RadiographyScene::LookupLayer(size_t& index /* out */, double x, double y) const { // Render layers in the foreground-to-background order for (size_t i = countLayers_; i > 0; i--) { index = i - 1; Layers::const_iterator it = layers_.find(index); if (it != layers_.end()) { assert(it->second != NULL); if (it->second->Contains(x, y)) { return true; } } } return false; } void RadiographyScene::DrawBorder(CairoContext& context, unsigned int layer, double zoom) { Layers::const_iterator found = layers_.find(layer); if (found != layers_.end()) { context.SetSourceColor(255, 0, 0); found->second->DrawBorders(context, zoom); } } void RadiographyScene::GetRange(float& minValue, float& maxValue) const { bool first = true; for (Layers::const_iterator it = layers_.begin(); it != layers_.end(); it++) { assert(it->second != NULL); float a, b; if (it->second->GetRange(a, b)) { if (first) { minValue = a; maxValue = b; first = false; } else { minValue = std::min(a, minValue); maxValue = std::max(b, maxValue); } } } if (first) { minValue = 0; maxValue = 0; } } // Export using PAM is faster than using PNG, but requires Orthanc // core >= 1.4.3 void RadiographyScene::ExportDicom(OrthancApiClient& orthanc, const Orthanc::DicomMap& dicom, double pixelSpacingX, double pixelSpacingY, bool invert, ImageInterpolation interpolation, bool usePam) { if (pixelSpacingX <= 0 || pixelSpacingY <= 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } LOG(INFO) << "Exporting DICOM"; Extent2D extent = GetSceneExtent(); int w = std::ceil(extent.GetWidth() / pixelSpacingX); int h = std::ceil(extent.GetHeight() / pixelSpacingY); if (w < 0 || h < 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } Orthanc::Image layers(Orthanc::PixelFormat_Float32, static_cast<unsigned int>(w), static_cast<unsigned int>(h), false); AffineTransform2D view = AffineTransform2D::Combine( AffineTransform2D::CreateScaling(1.0 / pixelSpacingX, 1.0 / pixelSpacingY), AffineTransform2D::CreateOffset(-extent.GetX1(), -extent.GetY1())); Render(layers, view, interpolation); Orthanc::Image rendered(Orthanc::PixelFormat_Grayscale16, layers.GetWidth(), layers.GetHeight(), false); Orthanc::ImageProcessing::Convert(rendered, layers); std::string base64; { std::string content; if (usePam) { Orthanc::PamWriter writer; writer.WriteToMemory(content, rendered); } else { Orthanc::PngWriter writer; writer.WriteToMemory(content, rendered); } Orthanc::Toolbox::EncodeBase64(base64, content); } std::set<Orthanc::DicomTag> tags; dicom.GetTags(tags); Json::Value json = Json::objectValue; json["Tags"] = Json::objectValue; for (std::set<Orthanc::DicomTag>::const_iterator tag = tags.begin(); tag != tags.end(); ++tag) { const Orthanc::DicomValue& value = dicom.GetValue(*tag); if (!value.IsNull() && !value.IsBinary()) { json["Tags"][tag->Format()] = value.GetContent(); } } json["Tags"][Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION.Format()] = (invert ? "MONOCHROME1" : "MONOCHROME2"); // WARNING: The order of PixelSpacing is Y/X. We use "%0.8f" to // avoid floating-point numbers to grow over 16 characters, // which would be invalid according to DICOM standard // ("dciodvfy" would complain). char buf[32]; sprintf(buf, "%0.8f\\%0.8f", pixelSpacingY, pixelSpacingX); json["Tags"][Orthanc::DICOM_TAG_PIXEL_SPACING.Format()] = buf; float center, width; if (GetWindowing(center, width)) { json["Tags"][Orthanc::DICOM_TAG_WINDOW_CENTER.Format()] = boost::lexical_cast<std::string>(boost::math::iround(center)); json["Tags"][Orthanc::DICOM_TAG_WINDOW_WIDTH.Format()] = boost::lexical_cast<std::string>(boost::math::iround(width)); } // This is Data URI scheme: https://en.wikipedia.org/wiki/Data_URI_scheme json["Content"] = ("data:" + std::string(usePam ? Orthanc::MIME_PAM : Orthanc::MIME_PNG) + ";base64," + base64); orthanc.PostJsonAsyncExpectJson( "/tools/create-dicom", json, new Callable<RadiographyScene, OrthancApiClient::JsonResponseReadyMessage> (*this, &RadiographyScene::OnDicomExported), NULL, NULL); } void RadiographyScene::OnDicomExported(const OrthancApiClient::JsonResponseReadyMessage& message) { LOG(INFO) << "DICOM export was successful: " << message.GetJson().toStyledString(); } void RadiographyScene::OnDicomWebReceived(const IWebService::HttpRequestSuccessMessage& message) { LOG(INFO) << "DICOMweb WADO-RS received: " << message.GetAnswerSize() << " bytes"; const IWebService::HttpHeaders& h = message.GetAnswerHttpHeaders(); for (IWebService::HttpHeaders::const_iterator it = h.begin(); it != h.end(); ++it) { printf("[%s] = [%s]\n", it->first.c_str(), it->second.c_str()); } } }