diff --git a/Modules/CppRestSdk/src/mitkRESTClient.cpp b/Modules/CppRestSdk/src/mitkRESTClient.cpp index 53b74ad845..8340dcbd79 100644 --- a/Modules/CppRestSdk/src/mitkRESTClient.cpp +++ b/Modules/CppRestSdk/src/mitkRESTClient.cpp @@ -1,144 +1,144 @@ /*=================================================================== 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 "mitkRESTClient.h" #include "mitkRESTUtil.h" -#include +#include #include mitk::RESTClient::RESTClient(utility::string_t url) { m_Client = new MitkClient(url); } mitk::RESTClient::~RESTClient() { delete m_Client; } pplx::task mitk::RESTClient::Get(utility::string_t filePath, utility::string_t uri) { MITK_DEBUG << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()) << " save into " << mitk::RESTUtil::convertToUtf8(filePath); auto fileBuffer = std::make_shared>(); return concurrency::streams::file_buffer::open(filePath, std::ios::out).then([=](concurrency::streams::streambuf outFile) -> pplx::task { *fileBuffer = outFile; return m_Client->request(MitkRESTMethods::GET, uri); }) // Write the response body into the file buffer. .then([=](MitkResponse response) -> pplx::task { auto status = response.status_code(); MITK_DEBUG << "Status code: " << status; if (status != web::http::status_codes::OK) { mitkThrow() << "GET ended up with response " << mitk::RESTUtil::convertToUtf8(response.to_string()); } return response.body().read_to_end(*fileBuffer); }) // Close the file buffer. .then([=](size_t) { return fileBuffer->close(); }); } pplx::task mitk::RESTClient::Post(utility::string_t uri, utility::string_t contentType, concurrency::streams::basic_istream fileStream) { MITK_INFO << "Calling POST with " << mitk::RESTUtil::convertToUtf8(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); // currently not working, but stream approach may be useful for later.. don't use string streams for dcm files... concurrency::streams::container_buffer inStringBuffer; return fileStream.read(inStringBuffer, fileStream.streambuf().size()).then([=](size_t bytesRead) -> pplx::task { const std::string &text = inStringBuffer.collection(); std::string body = ""; body += "\r\n--boundary"; body += "\r\nContentType: " + mitk::RESTUtil::convertToUtf8(L"application/dicom") + "\r\n\r\n"; body += text; body += "\r\n--boundary--"; auto utf8String = utility::conversions::to_utf8string(body); auto binaryVector = std::vector(utf8String.begin(), utf8String.end()); MitkRequest postRequest(MitkRESTMethods::POST); postRequest.set_request_uri(uri); postRequest.headers().add(U("Content-Type"), contentType); postRequest.set_body(binaryVector); MITK_INFO << "Request: " << mitk::RESTUtil::convertToUtf8(postRequest.to_string()); return m_Client->request(postRequest).then([fileStream](MitkResponse response) { fileStream.close(); auto status = response.status_code(); if (status != web::http::status_codes::OK) { mitkThrow() << "POST ended up with response " << mitk::RESTUtil::convertToUtf8(response.to_string()); } }); }); } pplx::task mitk::RESTClient::Post(utility::string_t uri, utility::string_t contentType, utility::string_t filePath) { // this is the working stow-rs request which supports just one dicom file packed into a multipart message std::basic_ifstream input(filePath, std::ios::binary); std::vector result; std::vector buffer((std::istreambuf_iterator(input)), (std::istreambuf_iterator())); // reuse 'content-type' variable or struct to be more flexible, in future more than one file should also be supported.. std::string head = ""; head += "\r\n--boundary"; head += "\r\nContent-Type: " + mitk::RESTUtil::convertToUtf8(L"application/dicom") + "\r\n\r\n"; std::vector bodyVector(head.begin(), head.end()); std::string tail = ""; tail += "\r\n--boundary--"; result.insert(result.end(), bodyVector.begin(), bodyVector.end()); result.insert(result.end(), buffer.begin(), buffer.end()); result.insert(result.end(), tail.begin(), tail.end()); MitkRequest postRequest(MitkRESTMethods::POST); postRequest.set_request_uri(uri); postRequest.headers().add(U("Content-Type"), "multipart/related; type=\"application/dicom\"; boundary=boundary"); postRequest.set_body(result); MITK_INFO << "Request: " << mitk::RESTUtil::convertToUtf8(postRequest.to_string()); return m_Client->request(postRequest).then([](MitkResponse response) { auto status = response.status_code(); if (status != web::http::status_codes::OK) { mitkThrow() << "POST ended up with response " << mitk::RESTUtil::convertToUtf8(response.to_string()); } MITK_INFO << "Response: " << mitk::RESTUtil::convertToUtf8(response.to_string()); }); } \ 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 775eeb6ae5..d25773b9bd 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 +1,345 @@ /*=================================================================== 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->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); - + if (dataNodes->size() == 3) { + 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); }