diff --git a/Modules/Chart/CMakeLists.txt b/Modules/Chart/CMakeLists.txt index 09bd55d774..fe576d053f 100644 --- a/Modules/Chart/CMakeLists.txt +++ b/Modules/Chart/CMakeLists.txt @@ -1,6 +1,7 @@ MITK_CREATE_MODULE( DEPENDS MitkCore PACKAGE_DEPENDS PUBLIC Qt5|WebEngineWidgets + WARNINGS_NO_ERRORS ) add_subdirectory(test) \ No newline at end of file diff --git a/Modules/CppRestSdk/CMakeLists.txt b/Modules/CppRestSdk/CMakeLists.txt index 758d9c941d..bdefa16c79 100644 --- a/Modules/CppRestSdk/CMakeLists.txt +++ b/Modules/CppRestSdk/CMakeLists.txt @@ -1,8 +1,9 @@ if(MITK_USE_CppRestSdk) MITK_CREATE_MODULE( DEPENDS MitkCore MitkQtWidgetsExt PACKAGE_DEPENDS Qt5|Core + WARNINGS_NO_ERRORS ) endif(MITK_USE_CppRestSdk) diff --git a/Modules/CppRestSdk/include/mitkRESTServer.h b/Modules/CppRestSdk/include/mitkRESTServer.h index 9bf281ff64..adeb925f69 100644 --- a/Modules/CppRestSdk/include/mitkRESTServer.h +++ b/Modules/CppRestSdk/include/mitkRESTServer.h @@ -1,77 +1,66 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKRESTSERVER_H #define MITKRESTSERVER_H #include #include "cpprest/asyncrt_utils.h" #include "cpprest/containerstream.h" #include "cpprest/filestream.h" #include "cpprest/http_listener.h" #include "cpprest/json.h" #include "cpprest/producerconsumerstream.h" #include "cpprest/uri.h" #include #include #include "MitkCppRestSdkExports.h" typedef web::http::experimental::listener::http_listener MitkListener; typedef web::http::http_request MitkRequest; typedef web::http::http_response MitkResponse; typedef web::http::methods MitkRESTMethods; typedef web::http::status_codes MitkRestStatusCodes; typedef web::json::json_exception MitkJsonException; namespace mitk { class MITKCPPRESTSDK_EXPORT RESTServer : public QObject { public: - struct CallbackDTO { - }; - - typedef std::function CallbackType(); - typedef std::map CallbackMapType; - RESTServer(); RESTServer(utility::string_t url); virtual ~RESTServer(); pplx::task Open() { return m_Listener.open(); } pplx::task Close() { return m_Listener.close(); } - void addGETPathHandler(std::string uri, CallbackType callback) { - - } - protected: virtual void HandleGet(MitkRequest){}; virtual void HandlePut(MitkRequest){}; virtual void HandlePost(MitkRequest){}; virtual void HandleDelete(MitkRequest){}; void HandleError(pplx::task &t); MitkListener m_Listener; - //CallbackMapType uriResolverGET; }; }; #endif // MITKRESTSERVER_H diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp index d334bed42c..9012c3ef6d 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp @@ -1,131 +1,131 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "SegmentationReworkREST.h" #include #include SegmentationReworkREST::SegmentationReworkREST() {} SegmentationReworkREST::SegmentationReworkREST(utility::string_t url) : mitk::RESTServer(url) { m_Listener.support(MitkRESTMethods::PUT, std::bind(&SegmentationReworkREST::HandlePut, this, std::placeholders::_1)); m_Listener.support(MitkRESTMethods::GET, std::bind(&SegmentationReworkREST::HandleGet, this, std::placeholders::_1)); } SegmentationReworkREST::~SegmentationReworkREST() {} void SegmentationReworkREST::HandleGet(MitkRequest message) { auto messageString = message.to_string(); MITK_INFO << "Message GET incoming..."; MITK_INFO << mitk::RESTUtil::convertToUtf8(messageString); auto httpParams = web::uri::split_query(message.request_uri().query()); // IHE Invoke Image Display style auto requestType = httpParams.find(L"requestType"); if (requestType != httpParams.end() && requestType->second == L"IMAGE_SEG") { try { auto studyUID = httpParams.at(L"studyUID"); auto imageSeriesUID = httpParams.at(L"imageSeriesUID"); auto segSeriesUID = httpParams.at(L"segSeriesUID"); DicomDTO dto; dto.imageSeriesUID = mitk::RESTUtil::convertToUtf8(imageSeriesUID); dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); dto.segSeriesUIDA = mitk::RESTUtil::convertToUtf8(segSeriesUID); - m_GetCallback(dto); + m_GetImageSegCallback(dto); MitkResponse response(MitkRestStatusCodes::OK); response.set_body("Sure, i got you.. have an awesome day"); message.reply(response); } catch (std::out_of_range& e) { message.reply(MitkRestStatusCodes::BadRequest, "oh man, that was not expected: " + std::string(e.what())); } } else if (requestType != httpParams.end() && requestType->second == L"SEG_EVALUATION") { // TODO: implement PUT handling as GET } else { message.reply(MitkRestStatusCodes::BadRequest, "Oh man, i can only deal with 'requestType' = 'IMAGE+SEG'..."); } } void SegmentationReworkREST::HandlePut(MitkRequest message) { auto messageString = message.to_string(); MITK_INFO << "Message PUT incoming..."; MITK_INFO << mitk::RESTUtil::convertToUtf8(messageString); try { auto jsonMessage = message.extract_json().get(); auto messageTypeKey = jsonMessage.at(U("messageType")); if (messageTypeKey.as_string() == U("downloadData")) { auto imageStudyUIDKey = jsonMessage.at(U("studyUID")); auto srSeriesUIDKey = jsonMessage.at(U("srSeriesUID")); auto groundTruthKey = jsonMessage.at(U("groundTruth")); auto simScoreKey = jsonMessage.at(U("simScoreArray")); auto minSliceStartKey = jsonMessage.at(U("minSliceStart")); DicomDTO dto; dto.srSeriesUID = mitk::RESTUtil::convertToUtf8(srSeriesUIDKey.as_string()); dto.groundTruth = mitk::RESTUtil::convertToUtf8(groundTruthKey.as_string()); dto.studyUID = mitk::RESTUtil::convertToUtf8(imageStudyUIDKey.as_string()); dto.minSliceStart = minSliceStartKey.as_integer(); std::vector vec; web::json::array simArray = simScoreKey.as_array(); for (web::json::value score : simArray) { vec.push_back(score.as_double()); } dto.simScoreArray = vec; m_PutCallback(dto); emit InvokeUpdateChartWidget(); } else { message.reply(MitkRestStatusCodes::BadRequest, "Oh man, i can only deal with 'messageType' = 'downloadData'..."); } } catch (MitkJsonException &e) { MITK_ERROR << e.what() << ".. oh man, that was not expected"; message.reply(MitkRestStatusCodes::BadRequest, "oh man, that was not expected"); return; } MitkResponse response(MitkRestStatusCodes::OK); response.headers().add(U("Access-Control-Allow-Origin"), U("localhost:9000/*")); response.set_body("Sure, i got you.. have an awesome day"); message.reply(response); return; } \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.h b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.h index 890f9ea0f2..ede31e8ad0 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.h +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.h @@ -1,65 +1,72 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef SegmentationReworkREST_h #define SegmentationReworkREST_h #include class SegmentationReworkREST : public mitk::RESTServer { Q_OBJECT public: struct DicomDTO { std::string segSeriesUIDA; std::string segSeriesUIDB; std::string imageSeriesUID; std::string studyUID; std::string segInstanceUIDA; std::string segInstanceUIDB; std::string srSeriesUID; std::vector simScoreArray; int minSliceStart; std::string groundTruth; }; SegmentationReworkREST(); SegmentationReworkREST(utility::string_t url); ~SegmentationReworkREST(); void HandlePut(MitkRequest message); void HandleGet(MitkRequest message); void SetPutCallback(std::function callback) { m_PutCallback = callback; } - void SetGetCallback(std::function callback) + + void SetGetImageSegCallback(std::function callback) + { + m_GetImageSegCallback = callback; + } + + void SetGetEvalCallback(std::function callback) { - m_GetCallback = callback; + m_GetEvalCallback = callback; } signals: void InvokeUpdateChartWidget(); private: std::function m_PutCallback; - std::function m_GetCallback; + std::function m_GetImageSegCallback; + std::function m_GetEvalCallback; }; #endif // SegmentationReworkREST_h diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp index d2efdff9c6..775eeb6ae5 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp @@ -1,344 +1,344 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "SegmentationReworkView.h" // Qt #include #include #include "QmitkNewSegmentationDialog.h" #include "mitkSegTool2D.h" #include "mitkToolManagerProvider.h" #include "mitkIOMimeTypes.h" #include // uuid class #include // generators #include #include const std::string SegmentationReworkView::VIEW_ID = "org.mitk.views.segmentationreworkview"; void SegmentationReworkView::SetFocus() {} void SegmentationReworkView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; qRegisterMetaType< std::vector >("std::vector"); connect(m_Controls.buttonUpload, &QPushButton::clicked, this, &SegmentationReworkView::UploadNewSegmentation); connect(m_Controls.buttonNewSeg, &QPushButton::clicked, this, &SegmentationReworkView::CreateNewSegmentationC); connect(m_Controls.cleanDicomBtn, &QPushButton::clicked, this, &SegmentationReworkView::CleanDicomFolder); m_downloadBaseDir = std::experimental::filesystem::path("/temp/"); m_tempSegDir = std::experimental::filesystem::path("/tempSeg/"); if (!std::experimental::filesystem::exists(m_downloadBaseDir)) { std::experimental::filesystem::create_directory(m_downloadBaseDir); } if (!std::experimental::filesystem::exists(m_tempSegDir)) { std::experimental::filesystem::create_directory(m_tempSegDir); } utility::string_t port = U("2020"); utility::string_t address = U("http://127.0.0.1:"); address.append(port); m_HttpHandler = std::unique_ptr(new SegmentationReworkREST(address)); connect(m_HttpHandler.get(), &SegmentationReworkREST::InvokeUpdateChartWidget, this, &SegmentationReworkView::UpdateChartWidget); connect(this, &SegmentationReworkView::InvokeLoadData, this, &SegmentationReworkView::LoadData); m_HttpHandler->SetPutCallback(std::bind(&SegmentationReworkView::RESTPutCallback, this, std::placeholders::_1)); - m_HttpHandler->SetGetCallback(std::bind(&SegmentationReworkView::RESTGetCallback, this, std::placeholders::_1)); + m_HttpHandler->SetGetImageSegCallback(std::bind(&SegmentationReworkView::RESTGetCallback, this, std::placeholders::_1)); m_HttpHandler->Open().wait(); MITK_INFO << "Listening for requests at: " << utility::conversions::to_utf8string(address); utility::string_t pacsHost = U("http://193.174.48.78:8090/dcm4chee-arc/aets/DCM4CHEE"); m_DICOMWeb = new mitk::DICOMWeb(pacsHost); } void SegmentationReworkView::RESTPutCallback(const SegmentationReworkREST::DicomDTO &dto) { SetSimilarityGraph(dto.simScoreArray, dto.minSliceStart); typedef std::map ParamMap; ParamMap seriesInstancesParams; seriesInstancesParams.insert((ParamMap::value_type({"StudyInstanceUID"}, dto.studyUID))); seriesInstancesParams.insert((ParamMap::value_type({"SeriesInstanceUID"}, dto.srSeriesUID))); seriesInstancesParams.insert((ParamMap::value_type({"includefield"}, {"0040A375"}))); // Current Requested Procedure Evidence Sequence try { m_DICOMWeb->QuidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) { auto firstResult = jsonResult[0]; auto actualListKey = firstResult.at(U("0040A375")).as_object().at(U("Value")).as_array()[0].as_object().at(U("00081115")).as_object().at(U("Value")).as_array(); std::string segSeriesUIDA = ""; std::string segSeriesUIDB = ""; std::string imageSeriesUID = ""; for (unsigned int index = 0; index < actualListKey.size(); index++) { auto element = actualListKey[index].as_object(); // get SOP class UID auto innerElement = element.at(U("00081199")).as_object().at(U("Value")).as_array()[0]; auto sopClassUID = innerElement.at(U("00081150")).as_object().at(U("Value")).as_array()[0].as_string(); auto seriesUID = utility::conversions::to_utf8string(element.at(U("0020000E")).as_object().at(U("Value")).as_array()[0].as_string()); if (sopClassUID == L"1.2.840.10008.5.1.4.1.1.66.4") // SEG { if (segSeriesUIDA.length() == 0) { segSeriesUIDA = seriesUID; } else { segSeriesUIDB = seriesUID; } } else if (sopClassUID == L"1.2.840.10008.5.1.4.1.1.2") // CT { imageSeriesUID = seriesUID; } } MITK_INFO << "image series UID " << imageSeriesUID; MITK_INFO << "seg A series UID " << segSeriesUIDA; MITK_INFO << "seg B series UID " << segSeriesUIDB; MITK_INFO << "Load related dicom series ..."; boost::uuids::random_generator generator; std::string folderPathSeries = std::experimental::filesystem::path(m_downloadBaseDir).append(boost::uuids::to_string(generator())).string() + "/"; std::experimental::filesystem::create_directory(folderPathSeries); std::string pathSegA = std::experimental::filesystem::path(m_downloadBaseDir).append(boost::uuids::to_string(generator())).string() + "/"; std::string pathSegB = std::experimental::filesystem::path(m_downloadBaseDir).append(boost::uuids::to_string(generator())).string() + "/"; auto folderPathSegA = utility::conversions::to_string_t(pathSegA); auto folderPathSegB = utility::conversions::to_string_t(pathSegB); std::experimental::filesystem::create_directory(pathSegA); std::experimental::filesystem::create_directory(pathSegB); m_CurrentStudyUID = dto.studyUID; std::vector> tasks; auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, imageSeriesUID); auto segATask = m_DICOMWeb->WadoRS(folderPathSegA, dto.studyUID, segSeriesUIDA); auto segBTask = m_DICOMWeb->WadoRS(folderPathSegB, dto.studyUID, segSeriesUIDB); tasks.push_back(imageSeriesTask); tasks.push_back(segATask); tasks.push_back(segBTask); auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { auto fileNameA = std::experimental::filesystem::path(filePathList[1]).filename(); auto fileNameB = std::experimental::filesystem::path(filePathList[2]).filename(); m_Controls.labelSegA->setText(m_Controls.labelSegA->text() + " " + QString::fromUtf8(fileNameA.string().c_str())); m_Controls.labelSegB->setText(m_Controls.labelSegB->text() + " " + QString::fromUtf8(fileNameB.string().c_str())); InvokeLoadData(filePathList); }); }); } catch (mitk::Exception& e) { MITK_ERROR << e.what(); } } void SegmentationReworkView::RESTGetCallback(const SegmentationReworkREST::DicomDTO &dto) { boost::uuids::random_generator generator; std::string folderPathSeries = std::experimental::filesystem::path(m_downloadBaseDir).append(boost::uuids::to_string(generator())).string() + "/"; std::experimental::filesystem::create_directory(folderPathSeries); std::string pathSeg = std::experimental::filesystem::path(m_downloadBaseDir).append(boost::uuids::to_string(generator())).string() + "/"; auto folderPathSeg = utility::conversions::to_string_t(pathSeg); std::experimental::filesystem::create_directory(pathSeg); std::vector> tasks; auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); auto segATask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, dto.segSeriesUIDA); tasks.push_back(imageSeriesTask); tasks.push_back(segATask); auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); } void SegmentationReworkView::LoadData(std::vector filePathList) { MITK_INFO << "Loading finished. Pushing data to data storage ..."; auto ds = GetDataStorage(); auto dataNodes = mitk::IOUtil::Load(filePathList, *ds); // reinit view mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(ds); // find data nodes m_Image = dataNodes->at(0); m_SegA = dataNodes->at(1); m_SegB = dataNodes->at(2); } void SegmentationReworkView::UpdateChartWidget() { m_Controls.chartWidget->Show(); } void SegmentationReworkView::SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart) { std::map map; double sliceIndex = sliceMinStart; for (double score : simScoreArray) { map.insert(std::map::value_type(sliceIndex, score)); sliceIndex++; } m_Controls.chartWidget->AddData2D(map, "similarity score"); m_Controls.chartWidget->SetChartType("similarity score", QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetXAxisLabel("slice number"); m_Controls.chartWidget->SetYAxisLabel("similarity score"); } void SegmentationReworkView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { // iterate all selected objects, adjust warning visibility foreach(mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_Controls.labelWarning->setVisible(false); return; } } m_Controls.labelWarning->setVisible(true); } void SegmentationReworkView::UploadNewSegmentation() { boost::uuids::random_generator generator; std::string folderPathSeg = std::experimental::filesystem::path(m_tempSegDir).append(boost::uuids::to_string(generator())).string() + "/"; std::experimental::filesystem::create_directory(folderPathSeg); const std::string savePath = folderPathSeg + m_SegC->GetName() + ".dcm"; const std::string mimeType = mitk::IOMimeTypes::DICOM_MIMETYPE_NAME(); mitk::IOUtil::Save(m_SegC->GetData(), mimeType, savePath); auto filePath = utility::conversions::to_string_t(savePath); try { m_DICOMWeb->StowRS(filePath, m_CurrentStudyUID).wait(); } catch (const std::exception &exception) { std::cout << exception.what() << std::endl; } } void SegmentationReworkView::CreateNewSegmentationC() { mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); toolManager->InitializeTools(); toolManager->SetReferenceData(m_Image); mitk::Image::Pointer baseImage; if (m_Controls.radioA->isChecked()) { baseImage = dynamic_cast(m_SegA->GetData()); } else if (m_Controls.radioB->isChecked()) { baseImage = dynamic_cast(m_SegB->GetData()); } QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent); // needs a QWidget as parent, "this" is not QWidget int dialogReturnValue = dialog->exec(); if (dialogReturnValue == QDialog::Rejected) { // user clicked cancel or pressed Esc or something similar return; } // ask the user about an organ type and name, add this information to the image's (!) propertylist // create a new image of the same dimensions and smallest possible pixel type mitk::Tool* firstTool = toolManager->GetToolById(0); if (firstTool) { try { std::string newNodeName = dialog->GetSegmentationName().toStdString(); if (newNodeName.empty()) { newNodeName = "no_name"; } mitk::DataNode::Pointer newSegmentation = firstTool->CreateSegmentationNode(baseImage, newNodeName, dialog->GetColor()); // initialize showVolume to false to prevent recalculating the volume while working on the segmentation newSegmentation->SetProperty("showVolume", mitk::BoolProperty::New(false)); if (!newSegmentation) { return; // could be aborted by user } if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)) { mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)->SetSelected(false); } newSegmentation->SetSelected(true); this->GetDataStorage()->Add(newSegmentation, toolManager->GetReferenceData(0)); // add as a child, because the segmentation "derives" from the original m_SegC = newSegmentation; } catch (std::bad_alloc) { QMessageBox::warning(nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation")); } } else { MITK_INFO << "no tools..."; } } void SegmentationReworkView::CleanDicomFolder() { std::experimental::filesystem::remove_all(m_downloadBaseDir); std::experimental::filesystem::create_directory(m_downloadBaseDir); }