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 67fe584658..43d8933f94 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 @@ -1,357 +1,360 @@ /*=================================================================== 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"); m_Controls.chartWidget->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 = 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); + MITK_INFO << "requests to pacs are sent to: " << utility::conversions::to_utf8string(pacsHost); } -void SegmentationReworkView::RestartConnection() +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 << "Listening for requests at: " << url; + MITK_INFO << "requests to pacs are sent to: " << url; +} + +void SegmentationReworkView::OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList &nodes) { + } 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 ..."; 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); 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); } 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); 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() { 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); + //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); std::experimental::filesystem::create_directory(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 adbbfcb5b0..73d919d49c 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 @@ -1,91 +1,93 @@ /*=================================================================== 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 "SegmentationReworkREST.h" #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 UpdateChartWidget(); void LoadData(std::vector filePathList); signals: void InvokeLoadData(std::vector filePathList); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList &nodes) override; + /// \brief Called when the user clicks the GUI button void CreateNewSegmentationC(); void CleanDicomFolder(); void UploadNewSegmentation(); void RestartConnection(); Ui::SegmentationReworkViewControls m_Controls; private: void SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart); std::unique_ptr m_HttpHandler; mitk::DICOMWeb* m_DICOMWeb; std::string m_CurrentStudyUID; std::experimental::filesystem::path m_downloadBaseDir; std::experimental::filesystem::path m_tempSegDir; mitk::DataNode::Pointer m_Image; mitk::DataNode::Pointer m_SegA; mitk::DataNode::Pointer m_SegB; mitk::DataNode::Pointer m_SegC; std::string m_GroundTruth; QWidget* m_Parent; }; #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 9c75e56bd7..f23976f6a2 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 @@ -1,209 +1,209 @@ - SegmentationReworkViewControls - - - - 0 - 0 - 465 - 691 - - - - - 0 - 0 - - - - QmitkTemplate - - - - - - - - dcm4chee host - - - - - - - example input: http://193.174.48.78:8090 - - - - - - - restart dcm4chee connection - - - - - - - - - Segmentation A: - - - - - - - Segmentation B: - - - - - - - ground truth: - - - - - - - Qt::Horizontal - - - - - - - - 0 - 400 - - - + SegmentationReworkViewControls + + + + 0 + 0 + 465 + 691 + + + - 16777215 - 400 + 0 + 0 - - - - - - - Qt::Horizontal - - - - - - - false - - + + + QmitkTemplate + + - - - - 0 - 0 - - - - - 0 - 60 - - - - Select segmentation basis - - - true - - - - QLayout::SetDefaultConstraint - - - - - A - - - - - - - B - - - - - - - Individual - - - + + + + + dcm4chee host + + + + + + + example input: http://193.174.48.78:8090 + + + + + + + restart dcm4chee connection + + + - - - - Create new Segmentation - - + + + Segmentation A: + + - - - - - - - Do image processing - - - Upload Segmentation - - - - - - - Qt::Vertical - - - QSizePolicy::Expanding - - - - 20 - 220 - - - - - - - - clean dicom download folder - - - - - - - - - QmitkChartWidget - QWidget -
QmitkChartWidget.h
- 1 -
-
- - -
+ + + + Segmentation B: + + + + + + + ground truth: + + + + + + + Qt::Horizontal + + + + + + + + 0 + 400 + + + + + 16777215 + 400 + + + + + + + + Qt::Horizontal + + + + + + + false + + + + + + + 0 + 0 + + + + + 0 + 60 + + + + Select segmentation basis + + + true + + + + QLayout::SetDefaultConstraint + + + + + A + + + + + + + B + + + + + + + Individual + + + + + + + + + + Create new Segmentation + + + + + + + + + + Do image processing + + + Upload Segmentation + + + + + + + Qt::Vertical + + + QSizePolicy::Expanding + + + + 20 + 220 + + + + + + + + clean dicom download folder + + + + + + + + + QmitkChartWidget + QWidget +
QmitkChartWidget.h
+ 1 +
+
+ + + \ No newline at end of file