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 d00a8d4e6d..dc62e4e1f2 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 @@ -1,156 +1,169 @@ /*=================================================================== 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 #include #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()); + MITK_INFO << mitk::RESTUtil::convertToUtf8(message.request_uri().to_string()); + auto uri = web::uri::decode(message.request_uri().to_string()); + + auto query = web::uri(uri).query(); + auto httpParams = web::uri::split_query(query); // IHE Invoke Image Display style auto requestType = httpParams.find(U("requestType")); + MITK_INFO << "parameters found: " << httpParams.size(); if (requestType != httpParams.end() && requestType->second == U("IMAGE_SEG")) { try { auto studyUID = httpParams.at(U("studyUID")); auto imageSeriesUID = httpParams.at(U("imageSeriesUID")); auto segSeriesUID = httpParams.at(U("segSeriesUID")); DicomDTO dto; dto.imageSeriesUID = mitk::RESTUtil::convertToUtf8(imageSeriesUID); dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); dto.segSeriesUIDA = mitk::RESTUtil::convertToUtf8(segSeriesUID); + MITK_INFO << "studyUID: " << dto.studyUID; + MITK_INFO << "imageSeriesUID: " << dto.imageSeriesUID; + MITK_INFO << "segSeriesUID: " << dto.segSeriesUIDA; + 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 == U("SEG_EVALUATION")) { // TODO: implement PUT handling as GET } else if (requestType != httpParams.end() && requestType->second == U("IMAGE_SEG_LIST")) { auto studyUID = httpParams.at(U("studyUID")); auto imageSeriesUID = httpParams.at(U("imageSeriesUID")); auto segSeriesUIDList = httpParams.at(U("segSeriesUIDList")); DicomDTO dto; dto.imageSeriesUID = mitk::RESTUtil::convertToUtf8(imageSeriesUID); dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); auto segSeriesUIDListUtf8 = mitk::RESTUtil::convertToUtf8(segSeriesUIDList); std::istringstream f(segSeriesUIDListUtf8); std::string s; while (getline(f, s, ',')) { dto.segSeriesUIDList.push_back(s); } + MITK_INFO << "studyUID: " << dto.studyUID; + MITK_INFO << "imageSeriesUID: " << dto.imageSeriesUID; + MITK_INFO << "segSeriesUIDList: " << segSeriesUIDListUtf8; + m_GetImageSegCallback(dto); MitkResponse response(MitkRestStatusCodes::OK); response.set_body("Sure, i got you.. have an awesome day"); message.reply(response); } else { - message.reply(MitkRestStatusCodes::BadRequest, "Oh man, i can only deal with 'requestType' = 'IMAGE+SEG'..."); + 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() * 100); } 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/SegmentationReworkView.cpp b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp index 0fac15fcb4..77709f99e5 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 @@ -1,361 +1,362 @@ /*=================================================================== 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" #include // Qt #include #include #include "QmitkNewSegmentationDialog.h" #include "mitkSegTool2D.h" #include "mitkToolManagerProvider.h" 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; counter = 0; qRegisterMetaType< std::vector >("std::vector"); m_Controls.chartWidget->setVisible(false); m_Controls.verticalWidget->setVisible(false); m_Controls.cleanDicomBtn->setVisible(false); 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); connect(m_Controls.restartConnection, &QPushButton::clicked, this, &SegmentationReworkView::RestartConnection); m_DownloadBaseDir = mitk::IOUtil::GetTempPathA() + "segrework"; - MITK_INFO << m_DownloadBaseDir; + MITK_INFO << "using download base dir: " << m_DownloadBaseDir; m_tempSegDir = "/tempSeg/"; if (!itksys::SystemTools::FileIsDirectory(m_DownloadBaseDir)) { itk::FileTools::CreateDirectory(m_DownloadBaseDir); } - std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; - - MITK_INFO << folderPathSeries; - //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->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); MITK_INFO << "requests to pacs are sent to: " << utility::conversions::to_utf8string(pacsHost); } std::string SegmentationReworkView::getNextFolderName() { counter++; std::string name = std::string("foldername") + std::to_string(counter); MITK_INFO << name; return name; } void SegmentationReworkView::RestartConnection() { auto host = m_Controls.dcm4cheeHostValue->text(); std::string url = host.toStdString() + "/dcm4chee-arc/aets/DCM4CHEE"; m_DICOMWeb = new mitk::DICOMWeb(utility::conversions::to_string_t(url)); MITK_INFO << "requests to pacs are sent to: " << url; } 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 == U("1.2.840.10008.5.1.4.1.1.66.4")) // SEG { if (segSeriesUIDA.length() == 0) { segSeriesUIDA = seriesUID; } else { segSeriesUIDB = seriesUID; } } else if (sopClassUID == U("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 ..."; std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) +"/"; std::string pathSegA = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; std::string pathSegB = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; auto folderPathSegA = utility::conversions::to_string_t(pathSegA); auto folderPathSegB = utility::conversions::to_string_t(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) { std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; MITK_INFO << folderPathSeries; std::string pathSeg = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; auto folderPathSeg = utility::conversions::to_string_t(pathSeg); MITK_INFO << pathSeg; - std::vector> tasks; - auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); - - tasks.push_back(imageSeriesTask); + try { + std::vector> tasks; + auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); - if (dto.segSeriesUIDList.size() > 0) { - for (std::string segSeriesUID : dto.segSeriesUIDList) - { - auto segTask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, segSeriesUID); - tasks.push_back(segTask); + tasks.push_back(imageSeriesTask); + + if (dto.segSeriesUIDList.size() > 0) { + for (std::string segSeriesUID : dto.segSeriesUIDList) + { + auto segTask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, segSeriesUID); + tasks.push_back(segTask); + } + } + else { + auto segATask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, dto.segSeriesUIDA); + tasks.push_back(segATask); } - } - else { - auto segATask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, dto.segSeriesUIDA); - tasks.push_back(segATask); - } - auto joinTask = pplx::when_all(begin(tasks), end(tasks)); - auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); + auto joinTask = pplx::when_all(begin(tasks), end(tasks)); + auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); + } + catch (const std::exception &exception) { + MITK_INFO << exception.what(); + } } 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); if (dataNodes->size() > 2) { 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 graph"); m_Controls.chartWidget->SetChartType("similarity graph", QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetXAxisLabel("slice number"); m_Controls.chartWidget->SetYAxisLabel("similarity in percent"); } void SegmentationReworkView::UploadNewSegmentation() { std::string folderPathSeg = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; 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() { if (m_SegA || m_SegB || m_SegC) { QMessageBox::warning(nullptr, tr("Clean dicom folder"), tr("Please remove the data in data storage before cleaning the download folder")); return; } //std::experimental::filesystem::remove_all(m_DownloadBaseDir); // TODO : use POCO //itk::FileTools::CreateDirectory(m_DownloadBaseDir); }