diff --git a/Modules/CppRestSdk/src/mitkRESTClient.cpp b/Modules/CppRestSdk/src/mitkRESTClient.cpp index 4b580b3d24..b12abdec29 100644 --- a/Modules/CppRestSdk/src/mitkRESTClient.cpp +++ b/Modules/CppRestSdk/src/mitkRESTClient.cpp @@ -1,146 +1,146 @@ /*=================================================================== 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 mitk::RESTClient::RESTClient(utility::string_t url) { m_Client = new MitkClient(url); } mitk::RESTClient::~RESTClient() { delete m_Client; } pplx::task mitk::RESTClient::PUT(utility::string_t uri, web::json::value content) { MITK_DEBUG << "Calling PUT with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); MitkRequest putRequest(MitkRESTMethods::PUT); putRequest.set_request_uri(uri); putRequest.set_body(content); return m_Client->request(putRequest).then([=](MitkResponse response) { auto status = response.status_code(); MITK_INFO << " status: " << status; if (status != web::http::status_codes::OK) { mitkThrow() << "response was not OK"; } return response.extract_json().get(); }); } pplx::task mitk::RESTClient::Get(utility::string_t uri) { - MITK_DEBUG << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client " + MITK_INFO << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); MitkRequest getRequest(MitkRESTMethods::GET); getRequest.set_request_uri(uri); return m_Client->request(getRequest).then([=](MitkResponse response) { auto status = response.status_code(); MITK_INFO << " status: " << status; if (status != web::http::status_codes::OK) { mitkThrow() << "response was not OK"; } return response.extract_json().get(); }); } 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 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(U("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 6e7f54e3d4..762cbc874a 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 @@ -1,579 +1,593 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #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; counter = 0; qRegisterMetaType< std::vector >("std::vector"); //m_Controls.verticalWidget->setVisible(false); m_Controls.cleanDicomBtn->setVisible(false); m_Controls.individualWidget_2->setVisible(false); m_Controls.sliderWidget->setMinimum(1); m_Controls.sliderWidget->setMaximum(100); m_Controls.sliderWidget->setTickInterval(1); m_Controls.sliderWidget->setSingleStep(1); m_Controls.radioA->setChecked(true); 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); connect(m_Controls.checkIndiv, &QCheckBox::stateChanged, this, &SegmentationReworkView::OnIndividualCheckChange); connect(m_Controls.sliderWidget, &ctkSliderWidget::valueChanged, this, &SegmentationReworkView::OnSliderWidgetChanged); m_DownloadBaseDir = mitk::IOUtil::GetTempPathA() + "segrework"; MITK_INFO << "using download base dir: " << m_DownloadBaseDir; m_UploadBaseDir = mitk::IOUtil::GetTempPathA() + "uploadSeg"; if (!itksys::SystemTools::FileIsDirectory(m_DownloadBaseDir)) { itk::FileTools::CreateDirectory(m_DownloadBaseDir); } if (!itksys::SystemTools::FileIsDirectory(m_UploadBaseDir)) { itk::FileTools::CreateDirectory(m_UploadBaseDir); } 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); connect(this, &SegmentationReworkView::InvokeProgress, this, &SegmentationReworkView::AddProgress); m_HttpHandler->SetPutCallback(std::bind(&SegmentationReworkView::RESTPutCallback, this, std::placeholders::_1)); m_HttpHandler->SetGetImageSegCallback(std::bind(&SegmentationReworkView::RESTGetCallback, this, std::placeholders::_1)); m_HttpHandler->SetGetAddSeriesCallback(std::bind(&SegmentationReworkView::RESTGetCallbackGeneric, this, std::placeholders::_1)); m_HttpHandler->Open().wait(); MITK_INFO << "Listening for requests at: " << utility::conversions::to_utf8string(address); //utility::string_t pacsURL = U("http://jip-dktk/dcm4chee-arc/aets/DCM4CHEE"); utility::string_t pacsURL = U("http://193.174.48.78:8090/dcm4chee-arc/aets/DCM4CHEE"); utility::string_t restURL = U("http://localhost:8000"); m_DICOMWeb = new mitk::DICOMWeb(pacsURL); MITK_INFO << "requests to pacs are sent to: " << utility::conversions::to_utf8string(pacsURL); m_Controls.dcm4cheeURL->setText({ (utility::conversions::to_utf8string(pacsURL).c_str()) }); m_RestService = new mitk::RESTClient(restURL); } void SegmentationReworkView::OnSliderWidgetChanged(double value) { std::map::iterator it; unsigned int count = 0; for (it = m_ScoreMap.begin(); it != m_ScoreMap.end(); it++) { if (it->second < value) { count++; } } QString labelsToDelete = "slices to delete: " + QString::number(count); m_Controls.slicesToDeleteLabel->setText(labelsToDelete); } void SegmentationReworkView::AddProgress(int progress, QString status) { auto futureValue = m_Controls.progressBar->value() + progress; if (futureValue >= 100) { - m_Controls.progressBar->setValue(100); + m_Controls.progressBar->setValue(0); m_Controls.progressBar->setFormat("Finished %p%"); } else { m_Controls.progressBar->setFormat(status.append(" %p%")); m_Controls.progressBar->setValue(futureValue); } } 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; m_Controls.dcm4cheeURL->setText({ (utility::conversions::to_utf8string(url).c_str()) }); } void SegmentationReworkView::OnIndividualCheckChange(int state) { if(state == Qt::Unchecked) { m_Controls.individualWidget_2->setVisible(false); } else if (state == Qt::Checked) { m_Controls.individualWidget_2->setVisible(true); } } void SegmentationReworkView::RESTPutCallback(const SegmentationReworkREST::DicomDTO &dto) { emit InvokeProgress(20, { "display graph and query structured report" }); SetSimilarityGraph(dto.simScoreArray, dto.minSliceStart); + m_SRUID = dto.srSeriesUID; + 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; } } emit InvokeProgress(10, {"load composite context of structured report"}); 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) { emit InvokeProgress(50, {"load dicom files from disk"}); InvokeLoadData(filePathList); - auto algorithmNameA = GetAlgorithmOfSegByPath(filePathList[0]); - auto algorithmNameB = GetAlgorithmOfSegByPath(filePathList[1]); - emit InvokeProgress(20, { "load meta data from disk" }); - m_Controls.labelSegA->setText(m_Controls.labelSegA->text() + " " + algorithmNameA.c_str()); - m_Controls.labelSegA->setText(m_Controls.labelSegB->text() + " " + algorithmNameB.c_str()); }); //ParamMap seriesInstancesParams; //seriesInstancesParams.insert((ParamMap::value_type({ "StudyInstanceUID" }, dto.studyUID))); //seriesInstancesParams.insert((ParamMap::value_type({ "SeriesInstanceUID" }, segSeriesUIDA))); //m_DICOMWeb->QuidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) { // emit InvokeProgress(10, {"display SEG A data"}); // auto seriesDescription = QString(utility::conversions::to_utf8string(jsonResult[0][U("0008103E")][U("Value")][0].as_string()).c_str()); // m_Controls.labelSegA->setText(m_Controls.labelSegA->text() + " " + seriesDescription); //}); //seriesInstancesParams["SeriesInstanceUID"] = segSeriesUIDB; //m_DICOMWeb->QuidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) { // emit InvokeProgress(10, { "display SEG B data" }); // auto seriesDescription = QString(utility::conversions::to_utf8string(jsonResult[0][U("0008103E")][U("Value")][0].as_string()).c_str()); // m_Controls.labelSegB->setText(m_Controls.labelSegB->text() + " " + seriesDescription ); //}); }); } catch (mitk::Exception& e) { MITK_ERROR << e.what(); } } void SegmentationReworkView::RESTGetCallbackGeneric(const SegmentationReworkREST::DicomDTO &dto) { std::vector> tasks; if (dto.seriesUIDList.size() > 0) { for (std::string segSeriesUID : dto.seriesUIDList) { std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; try { auto seriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, segSeriesUID); tasks.push_back(seriesTask); } catch (const mitk::Exception &exception) { MITK_INFO << exception.what(); return; } } } try { auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); } catch (const mitk::Exception& exception) { MITK_INFO << exception.what(); return; } } 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; try { std::vector> tasks; auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); tasks.push_back(imageSeriesTask); if (dto.seriesUIDList.size() > 0) { for (std::string segSeriesUID : dto.seriesUIDList) { 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); } auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); } catch (const mitk::Exception &exception) { MITK_INFO << exception.what(); } } std::string SegmentationReworkView::GetAlgorithmOfSegByPath(std::string path) { auto scanner = mitk::DICOMDCMTKTagScanner::New(); mitk::DICOMTagPath algorithmName; - algorithmName.AddSelection(0x0062, 0x0002, 0).AddSelection(0xfffe, 0xe000, 0).AddElement(0x0062, 0x0009); + algorithmName.AddAnySelection(0x0062, 0x0002).AddElement(0x0062, 0x0009); mitk::StringList files; files.push_back(path); scanner->SetInputFiles(files); scanner->AddTagPath(algorithmName); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); auto findings = frames.front()->GetTagValueAsString(algorithmName); - MITK_INFO << findings.front().value; + if (findings.size() != 0) + MITK_INFO << findings.front().value; return findings.front().value; } 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_Image->SetName("image data"); m_SegA = dataNodes->at(1); m_SegB = dataNodes->at(2); + + auto algorithmNameA = GetAlgorithmOfSegByPath(filePathList[1]); + auto algorithmNameB = GetAlgorithmOfSegByPath(filePathList[2]); + m_SegA->SetName(algorithmNameA); + m_SegB->SetName(algorithmNameB); + m_Controls.labelSegA->setText(m_Controls.labelSegA->text() + " " + algorithmNameA.c_str()); + m_Controls.labelSegB->setText(m_Controls.labelSegB->text() + " " + algorithmNameB.c_str()); + emit InvokeProgress(20, { "" }); } void SegmentationReworkView::UpdateChartWidget() { m_Controls.chartWidget->Show(); } void SegmentationReworkView::SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart) { std::string label = "similarity graph"; if (m_Controls.chartWidget->GetData()->size() > 0) { m_Controls.chartWidget->Clear(); } double sliceIndex = sliceMinStart; for (double score : simScoreArray) { m_ScoreMap.insert(std::map::value_type(sliceIndex, score)); sliceIndex++; } m_Controls.chartWidget->AddData2D(m_ScoreMap, label); m_Controls.chartWidget->SetChartType(label, QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetXAxisLabel("slice number"); m_Controls.chartWidget->SetYAxisLabel("similarity in percent"); } void SegmentationReworkView::UploadNewSegmentation() { AddProgress(10, { "save SEG to temp folder" }); std::string folderPathSeg = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_UploadBaseDir) + "/"; const std::string savePath = folderPathSeg + m_SegC->GetName() + ".dcm"; const std::string mimeType = mitk::MitkDICOMQIIOMimeTypes::DICOMSEG_MIMETYPE_NAME(); mitk::IOUtil::Save(m_SegC->GetData(), mimeType, savePath); // get Series Instance UID from new SEG auto scanner = mitk::DICOMDCMTKTagScanner::New(); mitk::DICOMTagPath seriesUID(0x0020, 0x000E); mitk::StringList files; files.push_back(savePath); scanner->SetInputFiles(files); scanner->AddTagPath(seriesUID); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); auto findings = frames.front()->GetTagValueAsString(seriesUID); auto segSeriesUID = findings.front().value; AddProgress(20, {"push SEG to PACS"}); auto filePath = utility::conversions::to_string_t(savePath); try { m_DICOMWeb->StowRS(filePath, m_CurrentStudyUID).then([=] { - emit AddProgress(40, {"persist reworked SEG to evaluation database"}); + emit InvokeProgress(40, {"persist reworked SEG to evaluation database"}); - MitkUriBuilder queryBuilder(U("tasks/evaluations")); - queryBuilder.append_path(U("3/")); // replace with evaluation UID + MitkUriBuilder queryBuilder(U("tasks/evaluations/")); + queryBuilder.append_query(U("srUID"), utility::conversions::to_string_t(m_SRUID)); + //queryBuilder.append_path(U("71/")); m_RestService->Get(queryBuilder.to_string()).then([=](web::json::value result) { - auto updatedContent = result; + MITK_INFO << "after GET"; + MITK_INFO << utility::conversions::to_utf8string(result.to_string()); + auto updatedContent = result.as_array()[0]; updatedContent[U("reworkedSegmentationUID")] = web::json::value::string(utility::conversions::to_string_t(segSeriesUID)); + + auto id = updatedContent.at(U("id")).as_integer(); + MITK_INFO << id; + auto idParam = std::to_string(id).append("/"); + + MitkUriBuilder queryBuilder(U("tasks/evaluations")); + queryBuilder.append_path(utility::conversions::to_string_t(idParam)); + m_RestService->PUT(queryBuilder.to_string(), updatedContent).then([=](web::json::value result) { - MITK_INFO << utility::conversions::to_utf8string(result.to_string()); MITK_INFO << "successfully stored"; - emit AddProgress(30, { "" }); + emit InvokeProgress(30, { "successfully stored" }); }); - }); - }); } catch (const std::exception &exception) { std::cout << exception.what() << std::endl; } } std::vector SegmentationReworkView::CreateSegmentation(mitk::Image::Pointer baseSegmentation, double threshold) { MITK_INFO << "handle individual segmentation creation"; std::map::iterator it; std::vector sliceIndices; unsigned int count = 0; for (it = m_ScoreMap.begin(); it != m_ScoreMap.end(); it++) { if (it->second < threshold) { auto index = it->first; try { mitk::ImagePixelWriteAccessor imageAccessor(baseSegmentation); for (unsigned int x = 0; x < baseSegmentation->GetDimension(0); x++) { for (unsigned int y = 0; y < baseSegmentation->GetDimension(1); y++) { imageAccessor.SetPixelByIndex({ { x, y, int(index) } }, 0); } } } catch (mitk::Exception& e) { MITK_ERROR << e.what(); } count++; sliceIndices.push_back(index); MITK_INFO << "slice " << it->first << " removed "; } } MITK_INFO << "slices deleted " << count; return sliceIndices; } 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())->Clone(); } else if (m_Controls.radioB->isChecked()) { baseImage = dynamic_cast(m_SegB->GetData())->Clone(); } if (m_Controls.checkIndiv->isChecked()) { auto sliceIndices = CreateSegmentation(baseImage, m_Controls.sliderWidget->value()); } 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; auto referencedImages = m_Image->GetData()->GetProperty("files"); m_SegC->GetData()->SetProperty("referenceFiles", referencedImages); } 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); } diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h index 171a13dfb1..9eaf7ee2de 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h @@ -1,105 +1,106 @@ /*=================================================================== 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 SegmentationReworkView_h #define SegmentationReworkView_h #include #include #include "ui_SegmentationReworkViewControls.h" #include "SegmentationReworkREST.h" #include #include #include /** \brief SegmentationReworkView \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class SegmentationReworkView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; void RESTPutCallback(const SegmentationReworkREST::DicomDTO& dto); void RESTGetCallback(const SegmentationReworkREST::DicomDTO& dto); void RESTGetCallbackGeneric(const SegmentationReworkREST::DicomDTO& dto); void UpdateChartWidget(); void ClearChartWidget(); void LoadData(std::vector filePathList); void OnSliderWidgetChanged(double value); void AddProgress(int, QString status); signals: void InvokeLoadData(std::vector filePathList); void InvokeProgress(int, QString status); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; /// \brief Called when the user clicks the GUI button void CreateNewSegmentationC(); void CleanDicomFolder(); void UploadNewSegmentation(); void RestartConnection(); void OnIndividualCheckChange(int state); Ui::SegmentationReworkViewControls m_Controls; private: std::vector CreateSegmentation(mitk::Image::Pointer baseSegmentation, double threshold); void InterpolateSegmentation(mitk::Image::Pointer baseSegmentation, std::vector sliceIndices); std::string GetAlgorithmOfSegByPath(std::string path); void SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart); std::unique_ptr m_HttpHandler; mitk::DICOMWeb* m_DICOMWeb; mitk::RESTClient* m_RestService; std::string m_CurrentStudyUID; + std::string m_SRUID; std::string m_DownloadBaseDir; std::string m_UploadBaseDir; mitk::DataNode::Pointer m_Image; mitk::DataNode::Pointer m_SegA; mitk::DataNode::Pointer m_SegB; mitk::DataNode::Pointer m_SegC; std::map m_ScoreMap; std::string m_GroundTruth; QWidget* m_Parent; int counter; }; #endif // SegmentationReworkView_h diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui index 3af39f0897..cac8ae1eda 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui @@ -1,263 +1,266 @@ SegmentationReworkViewControls 0 0 465 821 0 0 QmitkTemplate dcm4chee host example input: http://193.174.48.78:8090 restart dcm4chee connection 0 Qt::AlignCenter true - - - - - - - + + + + + + + Qt::AlignCenter + + + Segmentation A: Segmentation B: ground truth: 0 400 16777215 400 false 0 0 0 60 Select segmentation basis true QLayout::SetDefaultConstraint A B Individual 0 0 Slices to delete: Create new Segmentation Qt::Horizontal Do image processing Upload Segmentation Qt::Vertical QSizePolicy::Expanding 20 220 clean dicom download folder QmitkChartWidget QWidget
QmitkChartWidget.h
1
ctkSliderWidget QWidget
ctksliderwidget.h
1