diff --git a/Modules/REST/test/mitkRESTServerHttpLibTest.cpp b/Modules/REST/test/mitkRESTServerHttpLibTest.cpp index e77d14da3b..8d0f63f3e2 100644 --- a/Modules/REST/test/mitkRESTServerHttpLibTest.cpp +++ b/Modules/REST/test/mitkRESTServerHttpLibTest.cpp @@ -1,100 +1,106 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include +#include + +using namespace std::chrono_literals; class mitkRESTServerHttpLibTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkRESTServerHttpLibTestSuite); MITK_TEST(OpenListener_Succeed); MITK_TEST(OpenListenerGetRequestSamePath_ReturnExpectedJSON); CPPUNIT_TEST_SUITE_END(); std::vector> m_ft; public: void OpenListener_Succeed() { httplib::Server svr; svr.Get("/get", [](const httplib::Request &, httplib::Response &res) { res.set_content("Hello World from MITK!", "text/plain"); }); std::future ft = std::async(std::launch::async, [&]() { svr.listen("localhost", 8080); }); while (!svr.is_running()) - ; + { + std::this_thread::sleep_for(100ms); + } CPPUNIT_ASSERT_MESSAGE("Server is running", svr.is_running()); svr.stop(); } void OpenListenerGetRequestSamePath_ReturnExpectedJSON() { httplib::Server svr; std::map msgdb; msgdb[0] = "hello_MITK"; svr.Get(R"(/msg/(\d+))", [&](const httplib::Request &req, httplib::Response &res) { auto n = req.matches[1]; nlohmann::json jRes; try { jRes["id"] = std::stoi(n); jRes["msg"] = msgdb[std::stoi(n)]; res.set_content(jRes.dump(), "application/json"); } catch (const std::exception &) { res.set_content("Cannot find the requested message.", "text/plain"); } }); std::future ft = std::async(std::launch::async, [&]() { svr.listen("localhost", 8080); }); while (!svr.is_running()) - ; - + { + std::this_thread::sleep_for(100ms); + } httplib::Client cli("http://localhost:8080"); try { if (auto response = cli.Get("/msg/0")) { if (response->status == 200) { auto js = nlohmann::json::parse(response->body); std::string msg = js["msg"]; CPPUNIT_ASSERT_MESSAGE("Result is the expected JSON value", msg == msgdb[0]); } else { CPPUNIT_ASSERT_MESSAGE("A connection cannot be established", false); } } else { CPPUNIT_ASSERT_MESSAGE("A connection cannot be established", false); } } catch (const std::exception &e) { svr.stop(); CPPUNIT_ASSERT_MESSAGE(e.what(), false); } svr.stop(); } }; MITK_TEST_SUITE_REGISTRATION(mitkRESTServerHttpLib) diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp index cba066c9de..c2758a46d7 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp @@ -1,150 +1,149 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include "mitkMonaiLabel2DTool.h" +#include +#include // us -#include "mitkIOUtil.h" -#include #include #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, MonaiLabel2DTool, "MonaiLabel2D"); } void mitk::MonaiLabel2DTool::Activated() { Superclass::Activated(); this->SetLabelTransferScope(LabelTransferScope::AllLabels); } const char **mitk::MonaiLabel2DTool::GetXPM() const { return nullptr; } us::ModuleResource mitk::MonaiLabel2DTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("AI.svg"); return resource; } const char *mitk::MonaiLabel2DTool::GetName() const { return "MONAI Label 2D"; } void mitk::MonaiLabel2DTool::OnAddPositivePoint(StateMachineAction *, InteractionEvent *interactionEvent) { if ("deepgrow" == m_RequestParameters->model.type || "deepedit" == m_RequestParameters->model.type) { if ((nullptr == this->GetWorkingPlaneGeometry()) || !mitk::Equal(*(interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry()), *(this->GetWorkingPlaneGeometry()))) { this->ClearSeeds(); this->SetWorkingPlaneGeometry(interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone()); this->ResetPreviewContentAtTimeStep( - RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint()); + RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimeStep()); } if (!this->IsUpdating() && m_PointSetPositive.IsNotNull()) { const auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { m_PointSetPositive->InsertPoint(m_PointSetCount, positionEvent->GetPositionInWorld()); ++m_PointSetCount; this->UpdatePreview(); } } } } void mitk::MonaiLabel2DTool::OnAddNegativePoint(StateMachineAction *, InteractionEvent *interactionEvent) { if ("deepgrow" != m_RequestParameters->model.type) { return; } if (m_PointSetPositive->GetSize() == 0 || nullptr == this->GetWorkingPlaneGeometry() || !mitk::Equal(*(interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry()), *(this->GetWorkingPlaneGeometry()))) { return; } if (!this->IsUpdating() && m_PointSetNegative.IsNotNull()) { const auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { m_PointSetNegative->InsertPoint(m_PointSetCount, positionEvent->GetPositionInWorld()); m_PointSetCount++; this->UpdatePreview(); } } } void mitk::MonaiLabel2DTool::WriteImage(const Image *inputAtTimeStep, std::string &inputImagePath) { - mitk::Image::Pointer extendedImg = mitk::Image::New(); - unsigned int dim[] = {inputAtTimeStep->GetDimension(0), inputAtTimeStep->GetDimension(1), 1}; + Image::Pointer extendedImage = Image::New(); + std::array dim = {inputAtTimeStep->GetDimension(0), inputAtTimeStep->GetDimension(1), 1}; mitk::PixelType pt = inputAtTimeStep->GetPixelType(); - extendedImg->Initialize(pt, 3, dim); + extendedImage->Initialize(pt, 3, dim.data()); - mitk::ImageReadAccessor newMitkImgAcc(inputAtTimeStep); - extendedImg->SetVolume(newMitkImgAcc.GetData()); + ImageReadAccessor readAccessor(inputAtTimeStep); + extendedImage->SetVolume(readAccessor.GetData()); - IOUtil::Save(extendedImg.GetPointer(), inputImagePath); + IOUtil::Save(extendedImage.GetPointer(), inputImagePath); } std::stringstream mitk::MonaiLabel2DTool::GetPointsAsListString(const mitk::BaseGeometry *baseGeometry, PointSet::Pointer pointSet) { - MITK_INFO << "No.of points: " << pointSet->GetSize(); std::stringstream pointsAndLabels; pointsAndLabels << "["; - mitk::PointSet::PointsConstIterator pointSetItPos = pointSet->Begin(); + auto pointSetItPos = pointSet->Begin(); const char COMMA = ','; while (pointSetItPos != pointSet->End()) { - mitk::Point3D point3d = pointSetItPos.Value(); + auto point3d = pointSetItPos.Value(); if (baseGeometry->IsInside(point3d)) { - mitk::Point3D index3D; + Point3D index3D; baseGeometry->WorldToIndex(point3d, index3D); pointsAndLabels << "["; pointsAndLabels << static_cast(index3D[0]) << COMMA << static_cast(index3D[1]) << COMMA << 0 << "],"; } ++pointSetItPos; } if (pointsAndLabels.tellp() > 1) { pointsAndLabels.seekp(-1, pointsAndLabels.end); // remove last added comma character } pointsAndLabels << "]"; return pointsAndLabels; } void mitk::MonaiLabel2DTool::WriteBackResults(LabelSetImage *previewImage, LabelSetImage *segResults, TimeStepType timeStep) { mitk::SegTool2D::WriteSliceToVolume(previewImage, this->GetWorkingPlaneGeometry(), segResults, timeStep, false); } diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h index 9f455c88aa..e7daed9ac9 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h @@ -1,64 +1,64 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef MITKMONAILABEL2DTOOL_H -#define MITKMONAILABEL2DTOOL_H +#ifndef mitkMonaiLabel2DTool_h +#define mitkMonaiLabel2DTool_h #include "mitkSegWithPreviewTool.h" #include "mitkMonaiLabelTool.h" #include #include #include #include #include #include #include "mitkMonaiLabelTool.h" namespace us { class ModuleResource; } namespace mitk { /** \brief MonaiLabel segmentation 2D tool. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation */ class MITKSEGMENTATION_EXPORT MonaiLabel2DTool : public MonaiLabelTool { public: mitkClassMacro(MonaiLabel2DTool, MonaiLabelTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char *GetName() const override; const char **GetXPM() const override; us::ModuleResource GetIconResource() const override; void Activated() override; void WriteImage(const Image *, std::string &) override; std::stringstream GetPointsAsListString(const mitk::BaseGeometry *, PointSet::Pointer) override; void OnAddPositivePoint(StateMachineAction *, InteractionEvent *) override; void OnAddNegativePoint(StateMachineAction *, InteractionEvent *) override; void WriteBackResults(LabelSetImage *, LabelSetImage *, TimeStepType) override; protected: MonaiLabel2DTool() = default; ~MonaiLabel2DTool() = default; }; } #endif diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp index a395be4274..e4556c0c4a 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp @@ -1,127 +1,127 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkMonaiLabel3DTool.h" -#include "mitkIOUtil.h" +#include #include #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, MonaiLabel3DTool, "MonaiLabel3D"); } void mitk::MonaiLabel3DTool::Activated() { Superclass::Activated(); this->SetLabelTransferScope(LabelTransferScope::AllLabels); } const char **mitk::MonaiLabel3DTool::GetXPM() const { return nullptr; } us::ModuleResource mitk::MonaiLabel3DTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("AI.svg"); return resource; } const char *mitk::MonaiLabel3DTool::GetName() const { return "MONAI Label 3D"; } void mitk::MonaiLabel3DTool::WriteImage(const Image *inputAtTimeStep, std::string &inputImagePath) { IOUtil::Save(inputAtTimeStep, inputImagePath); } void mitk::MonaiLabel3DTool::WriteBackResults(LabelSetImage *previewImage, LabelSetImage *segResults, TimeStepType timeStep) { mitk::ImageReadAccessor newMitkImgAcc(segResults); previewImage->SetVolume(newMitkImgAcc.GetData(), timeStep); } void mitk::MonaiLabel3DTool::OnAddPositivePoint(StateMachineAction *, InteractionEvent *interactionEvent) { if ("deepgrow" == m_RequestParameters->model.type || "deepedit" == m_RequestParameters->model.type) { if (!this->IsUpdating() && m_PointSetPositive.IsNotNull()) { const auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { m_PointSetPositive->InsertPoint(m_PointSetCount, positionEvent->GetPositionInWorld()); ++m_PointSetCount; this->UpdatePreview(); } } } } void mitk::MonaiLabel3DTool::OnAddNegativePoint(StateMachineAction *, InteractionEvent *interactionEvent) { if ("deepgrow" != m_RequestParameters->model.type) { return; } if (!this->IsUpdating() && m_PointSetNegative.IsNotNull()) { const auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { m_PointSetNegative->InsertPoint(m_PointSetCount, positionEvent->GetPositionInWorld()); m_PointSetCount++; this->UpdatePreview(); } } } std::stringstream mitk::MonaiLabel3DTool::GetPointsAsListString(const mitk::BaseGeometry *baseGeometry, PointSet::Pointer pointSet) { MITK_INFO << "No.of points: " << pointSet->GetSize(); std::stringstream pointsAndLabels; pointsAndLabels << "["; mitk::PointSet::PointsConstIterator pointSetItPos = pointSet->Begin(); const char COMMA = ','; while (pointSetItPos != pointSet->End()) { mitk::Point3D point3d = pointSetItPos.Value(); if (baseGeometry->IsInside(point3d)) { mitk::Point3D index3D; baseGeometry->WorldToIndex(point3d, index3D); pointsAndLabels << "["; pointsAndLabels << static_cast(index3D[0]) << COMMA << static_cast(index3D[1]) << COMMA << static_cast(index3D[2]) << "],"; } ++pointSetItPos; } if (pointsAndLabels.tellp() > 1) { pointsAndLabels.seekp(-1, pointsAndLabels.end); // remove last added comma character } pointsAndLabels << "]"; return pointsAndLabels; } diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h index 60a9c69041..117afdf80d 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h @@ -1,55 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef MITKMONAILABEL3DTOOL_H -#define MITKMONAILABEL3DTOOL_H +#ifndef mitkMonaiLabel3DTool_h +#define mitkMonaiLabel3DTool_h #include "mitkMonaiLabelTool.h" #include namespace us { class ModuleResource; } namespace mitk { /** \brief MonaiLabel segmentation 3D tool. \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MITKSEGMENTATION_EXPORT MonaiLabel3DTool : public MonaiLabelTool { public: mitkClassMacro(MonaiLabel3DTool, MonaiLabelTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char *GetName() const override; const char **GetXPM() const override; us::ModuleResource GetIconResource() const override; void Activated() override; void OnAddPositivePoint(StateMachineAction *, InteractionEvent *) override; void OnAddNegativePoint(StateMachineAction *, InteractionEvent *) override; std::stringstream GetPointsAsListString(const mitk::BaseGeometry *, PointSet::Pointer) override; void WriteImage(const Image *, std::string &) override; void WriteBackResults(LabelSetImage *, LabelSetImage *, TimeStepType) override; protected: MonaiLabel3DTool() = default; ~MonaiLabel3DTool() = default; }; } // namespace mitk #endif diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp index 088ab26175..9f7d8a7ac9 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp @@ -1,503 +1,515 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkMonaiLabelTool.h" -#include "mitkIOUtil.h" +#include #include #include -#include "mitkPointSetShapeProperty.h" -#include "mitkProperties.h" -#include "mitkToolManager.h" +#include +#include +#include #include mitk::MonaiLabelTool::MonaiLabelTool() : SegWithPreviewTool(true, "PressMoveReleaseAndPointSetting") { this->ResetsToEmptyPreviewOn(); this->IsTimePointChangeAwareOff(); } mitk::MonaiLabelTool::~MonaiLabelTool() { - std::filesystem::remove_all(this->GetMitkTempDir()); + std::filesystem::remove_all(this->GetTempDir()); } void mitk::MonaiLabelTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("ShiftSecondaryButtonPressed", OnAddNegativePoint); CONNECT_FUNCTION("ShiftPrimaryButtonPressed", OnAddPositivePoint); CONNECT_FUNCTION("DeletePoint", OnDelete); } void mitk::MonaiLabelTool::Activated() { Superclass::Activated(); m_PointSetPositive = mitk::PointSet::New(); m_PointSetNodePositive = mitk::DataNode::New(); m_PointSetNodePositive->SetData(m_PointSetPositive); m_PointSetNodePositive->SetName(std::string(this->GetName()) + "_PointSetPositive"); m_PointSetNodePositive->SetBoolProperty("helper object", true); m_PointSetNodePositive->SetColor(0.0, 1.0, 0.0); m_PointSetNodePositive->SetVisibility(true); m_PointSetNodePositive->SetProperty("Pointset.2D.shape", mitk::PointSetShapeProperty::New(mitk::PointSetShapeProperty::CIRCLE)); m_PointSetNodePositive->SetProperty("Pointset.2D.fill shape", mitk::BoolProperty::New(true)); this->GetDataStorage()->Add(m_PointSetNodePositive, this->GetToolManager()->GetWorkingData(0)); m_PointSetNegative = mitk::PointSet::New(); m_PointSetNodeNegative = mitk::DataNode::New(); m_PointSetNodeNegative->SetData(m_PointSetNegative); m_PointSetNodeNegative->SetName(std::string(this->GetName()) + "_PointSetNegative"); m_PointSetNodeNegative->SetBoolProperty("helper object", true); m_PointSetNodeNegative->SetColor(1.0, 0.0, 0.0); m_PointSetNodeNegative->SetVisibility(true); m_PointSetNodeNegative->SetProperty("Pointset.2D.shape", mitk::PointSetShapeProperty::New(mitk::PointSetShapeProperty::CIRCLE)); m_PointSetNodeNegative->SetProperty("Pointset.2D.fill shape", mitk::BoolProperty::New(true)); this->GetDataStorage()->Add(m_PointSetNodeNegative, this->GetToolManager()->GetWorkingData(0)); } void mitk::MonaiLabelTool::Deactivated() { this->ClearSeeds(); - GetDataStorage()->Remove(m_PointSetNodePositive); - GetDataStorage()->Remove(m_PointSetNodeNegative); + this->GetDataStorage()->Remove(m_PointSetNodePositive); + this->GetDataStorage()->Remove(m_PointSetNodeNegative); m_PointSetNodePositive = nullptr; m_PointSetNodeNegative = nullptr; m_PointSetPositive = nullptr; m_PointSetNegative = nullptr; Superclass::Deactivated(); } void mitk::MonaiLabelTool::UpdatePrepare() { Superclass::UpdatePrepare(); auto preview = this->GetPreviewSegmentation(); for (LabelSetImage::GroupIndexType i = 0; i < preview->GetNumberOfLayers(); ++i) { preview->GetLabelSet(i)->RemoveAllLabels(); } } void mitk::MonaiLabelTool::OnDelete(StateMachineAction *, InteractionEvent *) { if (!this->IsUpdating() && m_PointSetPositive.IsNotNull()) { PointSet::Pointer removeSet = m_PointSetPositive; - decltype(m_PointSetPositive->GetMaxId().Index()) maxId = 0; + itk::IdentifierType maxId = 0; if (m_PointSetPositive->GetSize() > 0) { maxId = m_PointSetPositive->GetMaxId().Index(); } if (m_PointSetNegative->GetSize() > 0 && (maxId < m_PointSetNegative->GetMaxId().Index())) { removeSet = m_PointSetNegative; } removeSet->RemovePointAtEnd(0); --m_PointSetCount; this->UpdatePreview(); } } void mitk::MonaiLabelTool::ClearPicks() { this->ClearSeeds(); this->UpdatePreview(); } bool mitk::MonaiLabelTool::HasPicks() const { return this->m_PointSetPositive.IsNotNull() && this->m_PointSetPositive->GetSize() > 0; } void mitk::MonaiLabelTool::ClearSeeds() { if (this->m_PointSetPositive.IsNotNull()) { m_PointSetCount -= m_PointSetPositive->GetSize(); this->m_PointSetPositive = mitk::PointSet::New(); // renew pointset this->m_PointSetNodePositive->SetData(this->m_PointSetPositive); } if (this->m_PointSetNegative.IsNotNull()) { m_PointSetCount -= m_PointSetNegative->GetSize(); this->m_PointSetNegative = mitk::PointSet::New(); // renew pointset this->m_PointSetNodeNegative->SetData(this->m_PointSetNegative); } } -bool mitk::MonaiLabelTool::IsMonaiServerOn(std::string &hostName, int &port) +bool mitk::MonaiLabelTool::IsMonaiServerOn(const std::string &hostName, const int &port) const { httplib::SSLClient cli(hostName, port); cli.enable_server_certificate_verification(false); while (cli.is_socket_open()); - if (auto response = cli.Get("/info/")) - { - return true; - } - return false; + return cli.Get("/info/"); } void mitk::MonaiLabelTool::DoUpdatePreview(const Image *inputAtTimeStep, const Image * /*oldSegAtTimeStep*/, LabelSetImage *previewImage, TimeStepType timeStep) { - std::string &hostName = m_RequestParameters->hostName; - int port = m_RequestParameters->port; + const std::string &hostName = m_RequestParameters->hostName; + const int port = m_RequestParameters->port; if (!IsMonaiServerOn(hostName, port)) { mitkThrow() << m_SERVER_503_ERROR_TEXT; } - if (this->m_MitkTempDir.empty()) + if (this->m_TempDir.empty()) { - this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); + this->SetTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); } - std::string inDir, outDir, inputImagePath, outputImagePath; - inDir = IOUtil::CreateTemporaryDirectory("monai-in-XXXXXX", this->GetMitkTempDir()); - std::ofstream tmpStream; - inputImagePath = IOUtil::CreateTemporaryFile(tmpStream, m_TEMPLATE_FILENAME, inDir + IOUtil::GetDirectorySeparator()); - tmpStream.close(); - std::size_t found = inputImagePath.find_last_of(IOUtil::GetDirectorySeparator()); - std::string fileName = inputImagePath.substr(found + 1); - std::string token = fileName.substr(0, fileName.find("_")); - outDir = IOUtil::CreateTemporaryDirectory("monai-out-XXXXXX", this->GetMitkTempDir()); - outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; + + std::string inputImagePath, outputImagePath; + std::tie(inputImagePath, outputImagePath) = this->CreateTempDirs(m_TEMPLATE_FILENAME); + try { this->WriteImage(inputAtTimeStep, inputImagePath); this->PostInferRequest(hostName, port, inputImagePath, outputImagePath, inputAtTimeStep->GetGeometry()); Image::Pointer outputImage = IOUtil::Load(outputImagePath); auto outputBuffer = mitk::LabelSetImage::New(); outputBuffer->InitializeByLabeledImage(outputImage); std::map labelMap; // empty map if (m_RequestParameters->model.IsInteractive()) { this->SetLabelTransferMode(LabelTransferMode::MapLabel); this->SetSelectedLabels({MASK_VALUE}); } else { outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); labelMap = m_ResultMetadata["label_names"]; this->SetLabelTransferMode(LabelTransferMode::AddLabel); } this->MapLabelsToSegmentation(outputBuffer, previewImage, labelMap); this->WriteBackResults(previewImage, outputBuffer.GetPointer(), timeStep); MonaiStatusEvent.Send(true); } catch (const mitk::Exception &e) { MITK_ERROR << e.GetDescription(); mitkThrow() << e.GetDescription(); MonaiStatusEvent.Send(false); } } void mitk::MonaiLabelTool::MapLabelsToSegmentation(const mitk::LabelSetImage *source, mitk::LabelSetImage *dest, std::map &labelMap) { auto labelset = dest->GetLabelSet(); if (labelMap.empty()) { auto label = LabelSetImageHelper::CreateNewLabel(dest, "object"); label->SetValue(1); labelset->AddLabel(label, false); return; } std::map flippedLabelMap; for (auto const &[key, val] : labelMap) { flippedLabelMap[val] = key; } auto lookupTable = mitk::LookupTable::New(); lookupTable->SetType(mitk::LookupTable::LookupTableType::MULTILABEL); for (auto const &[key, val] : flippedLabelMap) { if (source->ExistLabel(key, source->GetActiveLayer())) { Label::Pointer label = Label::New(key, val); std::array lookupTableColor; lookupTable->GetColor(key, lookupTableColor.data()); Color color; color.SetRed(lookupTableColor[0]); color.SetGreen(lookupTableColor[1]); color.SetBlue(lookupTableColor[2]); label->SetColor(color); labelset->AddLabel(label, false); } else { MITK_INFO << "Label not found for " << val; } } } void mitk::MonaiLabelTool::GetOverallInfo(std::string &hostName, int &port) { - MITK_INFO << "URL..." << hostName << ":" << port; if (!IsMonaiServerOn(hostName, port)) { Tool::ErrorMessage.Send(m_SERVER_503_ERROR_TEXT); mitkThrow() << m_SERVER_503_ERROR_TEXT; } httplib::SSLClient cli(hostName, port); cli.enable_server_certificate_verification(false); if (auto response = cli.Get("/info/")) { if (response->status == 200) { auto jsonObj = nlohmann::json::parse(response->body); if (jsonObj.is_discarded() || !jsonObj.is_object()) { - MITK_ERROR << "Could not parse \"" << /* jsonPath.toStdString() << */ "\" as JSON object!"; + MITK_ERROR << "Could not parse response from MONAILabel server as JSON object!"; return; } - m_InfoParameters = DataMapper(jsonObj); + m_InfoParameters = MapJSONToObject(jsonObj); if (nullptr != m_InfoParameters) { m_InfoParameters->hostName = hostName; m_InfoParameters->port = port; } } } else { Tool::ErrorMessage.Send(httplib::to_string(response.error()) + " error occured."); } } -void mitk::MonaiLabelTool::PostInferRequest(std::string &hostName, - int &port, +void mitk::MonaiLabelTool::PostInferRequest(const std::string &hostName, + const int &port, std::string &filePath, std::string &outFile, const mitk::BaseGeometry *baseGeometry) { std::string &modelName = m_RequestParameters->model.name; // Get this from args as well. std::string postPath = "/infer/"; // make this separate class of constants postPath.append(modelName); std::ifstream input(filePath, std::ios::binary); if (!input) { MITK_WARN << "could not read file to POST"; } std::stringstream buffer_lf_img; buffer_lf_img << input.rdbuf(); input.close(); httplib::MultipartFormDataItems items; if (m_RequestParameters->model.IsInteractive()) { std::stringstream foreground = this->GetPointsAsListString(baseGeometry, m_PointSetPositive); std::stringstream background = this->GetPointsAsListString(baseGeometry, m_PointSetNegative); std::stringstream paramString; paramString << "{" << "\"foreground\":" << foreground.str() << ",\"background\":" << background.str() << "}"; - MITK_INFO << paramString.str(); + MITK_DEBUG << paramString.str(); items.push_back({"params", paramString.str(), "", ""}); } else // Auto models { items.push_back({"params", "{\"restore_label_idx\": true}", "", ""}); } items.push_back({"file", buffer_lf_img.str(), "post_from_mitk.nii.gz", "application/octet-stream"}); httplib::SSLClient cli(hostName, port); cli.set_read_timeout(60); // arbitary 1 minute time-out to avoid corner cases. cli.enable_server_certificate_verification(false); if (auto response = cli.Post(postPath, items)) { if (response->status == 200) { // Find boundary - httplib::Headers headers = response->headers; - std::string contentType = headers.find("content-type")->second; - std::string delimiter = "boundary="; - std::string boundaryString = - contentType.substr(contentType.find(delimiter) + delimiter.length(), std::string::npos); - boundaryString.insert(0, "--"); - MITK_INFO << "boundary hash: " << boundaryString; + std::string boundaryString = this->GetBoundaryString(response); + MITK_DEBUG << "boundary hash: " << boundaryString; // Parse metadata JSON std::string resBody = response->body; - std::vector multiPartResponse = this->getPartsBetweenBoundary(resBody, boundaryString); + std::vector multiPartResponse = this->GetPartsBetweenBoundary(resBody, boundaryString); std::string metaData = multiPartResponse[0]; std::string contentTypeJson = "Content-Type: application/json"; size_t ctPos = metaData.find(contentTypeJson) + contentTypeJson.length(); std::string metaDataPart = metaData.substr(ctPos); - MITK_INFO << metaDataPart; + MITK_DEBUG << metaDataPart; auto jsonObj = nlohmann::json::parse(metaDataPart); if (jsonObj.is_discarded() || !jsonObj.is_object()) { - MITK_ERROR << "Could not parse \"" << /* jsonPath.toStdString() << */ "\" as JSON object!"; + MITK_ERROR << "Could not parse response from MONAILabel server as JSON object!"; return; } else // use the metadata { m_ResultMetadata = jsonObj; } // Parse response image string std::string imagePart = multiPartResponse[1]; - std::string contentTypeStream = "Content-Type: application/octet-stream"; - ctPos = imagePart.find(contentTypeStream) + contentTypeStream.length(); - std::string imageDataPart = imagePart.substr(ctPos); - - MITK_INFO << imageDataPart.substr(0, 50); - std::string whitespaces = " \n\r"; - imageDataPart.erase(0, imageDataPart.find_first_not_of(whitespaces)); // clean up + std::string imageData = GetResponseImageString(imagePart); std::ofstream output(outFile, std::ios::out | std::ios::app | std::ios::binary); - output << imageDataPart; + output << imageData; output.unsetf(std::ios::skipws); output.flush(); - output.close(); // necessary to close? RAII } else { auto err = response.error(); MITK_ERROR << "An HTTP POST error: " << httplib::to_string(err) << " occured."; mitkThrow() << "An HTTP POST error: " << httplib::to_string(err) << " occured."; } } } -std::vector mitk::MonaiLabelTool::getPartsBetweenBoundary(const std::string &body, +std::string mitk::MonaiLabelTool::GetBoundaryString(httplib::Result& response) +{ + httplib::Headers headers = response->headers; + std::string contentType = headers.find("content-type")->second; + std::string delimiter = "boundary="; + std::string boundaryString = contentType.substr(contentType.find(delimiter) + delimiter.length(), std::string::npos); + boundaryString.insert(0, "--"); + return boundaryString; +} + +std::string mitk::MonaiLabelTool::GetResponseImageString(std::string &imagePart) +{ + std::string contentTypeStream = "Content-Type: application/octet-stream"; + size_t ctPos = imagePart.find(contentTypeStream) + contentTypeStream.length(); + std::string imageDataPart = imagePart.substr(ctPos); + std::string whitespaces = " \n\r"; + imageDataPart.erase(0, imageDataPart.find_first_not_of(whitespaces)); // clean up + return imageDataPart; +} + +std::vector mitk::MonaiLabelTool::GetPartsBetweenBoundary(const std::string &body, const std::string &boundary) { std::vector retVal; std::string master = body; - size_t found = master.find(boundary); + size_t boundaryPos = master.find(boundary); size_t beginPos = 0; - while (found != std::string::npos) + while (boundaryPos != std::string::npos) { - std::string part = master.substr(beginPos, found); + std::string part = master.substr(beginPos, boundaryPos); if (!part.empty()) { retVal.push_back(part); } - master.erase(beginPos, found + boundary.length()); - found = master.find(boundary); + master.erase(beginPos, boundaryPos + boundary.length()); + boundaryPos = master.find(boundary); } return retVal; } -std::unique_ptr mitk::MonaiLabelTool::DataMapper(nlohmann::json &jsonObj) +std::unique_ptr mitk::MonaiLabelTool::MapJSONToObject(nlohmann::json &jsonObj) { - auto object = std::make_unique(); - object->name = jsonObj["name"].get(); - object->description = jsonObj["description"].get(); - object->labels = jsonObj["labels"].get>(); - + mitk::MonaiAppMetadata appData{ + jsonObj["name"].template get(), + jsonObj["description"].template get(), + jsonObj["labels"].template get>() + }; + auto object = std::make_unique(appData); auto modelJsonMap = jsonObj["models"].get>(); + for (const auto &[_name, _jsonObj] : modelJsonMap) { if (_jsonObj.is_discarded() || !_jsonObj.is_object()) { MITK_ERROR << "Could not parse JSON object."; } MonaiModelInfo modelInfo; modelInfo.name = _name; try { auto labels = _jsonObj["labels"].get>(); modelInfo.labels = labels; } catch (const std::exception &) { auto labels = _jsonObj["labels"].get>(); for (const auto &label : labels) { modelInfo.labels[label] = -1; // Hardcode -1 as label id } } modelInfo.type = _jsonObj["type"].get(); modelInfo.dimension = _jsonObj["dimension"].get(); modelInfo.description = _jsonObj["description"].get(); object->models.push_back(modelInfo); } return object; } -std::vector mitk::MonaiLabelTool::GetAutoSegmentationModels(int dim) +std::vector mitk::MonaiLabelTool::GetAutoSegmentationModels(int dim) const { std::vector autoModels; - bool checkDims = dim > -1; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { - if (m_AUTO_SEG_TYPE_NAME.find(model.type) != m_AUTO_SEG_TYPE_NAME.end() - && (!checkDims || model.dimension == dim)) + if (m_AUTO_SEG_TYPE_NAME.find(model.type) != m_AUTO_SEG_TYPE_NAME.end() && (!(dim > -1) || + model.dimension == dim)) { autoModels.push_back(model); } } } return autoModels; } -std::vector mitk::MonaiLabelTool::GetInteractiveSegmentationModels(int dim) +std::vector mitk::MonaiLabelTool::GetInteractiveSegmentationModels(int dim) const { std::vector interactiveModels; - bool checkDims = dim > -1; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { - if (m_INTERACTIVE_SEG_TYPE_NAME.find(model.type) != m_INTERACTIVE_SEG_TYPE_NAME.end() - && (!checkDims || model.dimension == dim)) + if (m_INTERACTIVE_SEG_TYPE_NAME.find(model.type) != m_INTERACTIVE_SEG_TYPE_NAME.end() && + (!(dim > -1) || model.dimension == dim)) { interactiveModels.push_back(model); } } } return interactiveModels; } -std::vector mitk::MonaiLabelTool::GetScribbleSegmentationModels(int dim) +std::vector mitk::MonaiLabelTool::GetScribbleSegmentationModels(int dim) const { std::vector scribbleModels; bool checkDims = dim > -1; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { - if (m_SCRIBBLE_SEG_TYPE_NAME.find(model.type) != m_SCRIBBLE_SEG_TYPE_NAME.end() - && (!checkDims || model.dimension == dim)) + if (m_SCRIBBLE_SEG_TYPE_NAME.find(model.type) != m_SCRIBBLE_SEG_TYPE_NAME.end() && + (!(dim > -1) || model.dimension == dim)) { scribbleModels.push_back(model); } } } return scribbleModels; } -mitk::MonaiModelInfo mitk::MonaiLabelTool::GetModelInfoFromName(std::string &modelName) +mitk::MonaiModelInfo mitk::MonaiLabelTool::GetModelInfoFromName(std::string &modelName) const { if (nullptr == m_InfoParameters) { mitkThrow() << "No model information found."; } mitk::MonaiModelInfo retVal; for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { if (model.name == modelName) { retVal = model; break; } } return retVal; } void mitk::MonaiLabelTool::WriteImage(const Image*, std::string&) {} + +std::pair mitk::MonaiLabelTool::CreateTempDirs(const std::string &filePattern) +{ + std::string inDir, outDir, inputImagePath, outputImagePath; + inDir = IOUtil::CreateTemporaryDirectory("monai-in-XXXXXX", this->GetTempDir()); + std::ofstream tmpStream; + inputImagePath = IOUtil::CreateTemporaryFile(tmpStream, filePattern, inDir + IOUtil::GetDirectorySeparator()); + tmpStream.close(); + std::size_t found = inputImagePath.find_last_of(IOUtil::GetDirectorySeparator()); + std::string fileName = inputImagePath.substr(found + 1); + std::string token = fileName.substr(0, fileName.find("_")); + outDir = IOUtil::CreateTemporaryDirectory("monai-out-XXXXXX", this->GetTempDir()); + outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; + return std::make_pair(inputImagePath, outputImagePath); +} diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h index 5d62b6d78b..8a3f5d9121 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h @@ -1,293 +1,292 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef MITKMONAILABELTOOL_H -#define MITKMONAILABELTOOL_H +#ifndef mitkMonaiLabelTool_h +#define mitkMonaiLabelTool_h #define CPPHTTPLIB_OPENSSL_SUPPORT #include "mitkSegWithPreviewTool.h" #include #include #include #include #include #include -#include "mitkPointSet.h" -#include "mitkInteractionPositionEvent.h" +#include +#include namespace us { class ModuleResource; } namespace mitk { /** * @brief Struct to hold featured models individual info * */ struct MonaiModelInfo { std::string name; std::string type; std::unordered_map labels; int dimension; std::string description; std::unordered_map config; inline bool operator==(const MonaiModelInfo &rhs) const { - if (this->name == rhs.name && this->type == rhs.type) // Comparing only name and type, for now. - { - return true; - } - return false; + return (this->name == rhs.name && this->type == rhs.type); // Comparing only name and type, for now. } inline bool IsInteractive() const { - if ("deepgrow" == type || "deepedit" == type) - { - return true; - } - return false; + return ("deepgrow" == type || "deepedit" == type); } }; /** * @brief Struct to store MonaiLabel server metadata including all model infos * */ struct MonaiAppMetadata { - std::string hostName; - int port; - std::string origin; std::string name; std::string description; - std::string version; std::vector labels; + std::string version; + std::string hostName; + int port; + std::string origin; std::vector models; }; /** * @brief Request class to pack model and other necessary server information * from GUI. * */ struct MonaiLabelRequest { MonaiModelInfo model; std::string hostName; std::string requestLabel; int port; inline bool operator==(const MonaiLabelRequest &rhs) const { - if (this->model == rhs.model && this->hostName == rhs.hostName && this->port == rhs.port && this->requestLabel == rhs.requestLabel) - { - return true; - } - return false; + return (this->model == rhs.model && this->hostName == rhs.hostName && this->port == rhs.port && + this->requestLabel == rhs.requestLabel); } }; /** \brief MonaiLabel segmentation tool base class. \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MITKSEGMENTATION_EXPORT MonaiLabelTool : public SegWithPreviewTool { public: mitkClassMacro(MonaiLabelTool, SegWithPreviewTool); itkCloneMacro(Self); void Activated() override; void Deactivated() override; void UpdatePrepare() override; /** * @brief Writes image to disk as the tool desires. * Default implementation does nothing. */ virtual void WriteImage(const Image*, std::string&); /** * @brief Method does the GET Rest call to fetch MonaiLabel * server metadata including all models' info. */ void GetOverallInfo(std::string&, int&); /** * @brief Holds all parameters of the server to serve the UI * */ std::unique_ptr m_InfoParameters; /** * @brief Variable to set selected model's and other data needed * for the POST call. */ std::unique_ptr m_RequestParameters; /** * @brief Get the Auto Segmentation Models info for the given - * dimension. - * - * @param dim - * @return std::vector + * dimension. */ - std::vector GetAutoSegmentationModels(int dim = -1); + std::vector GetAutoSegmentationModels(int dim = -1) const; /** * @brief Get the Interactive Segmentation Models info for the given * dimension. - * - * @param dim - * @return std::vector */ - std::vector GetInteractiveSegmentationModels(int dim = -1); + std::vector GetInteractiveSegmentationModels(int dim = -1) const; /** * @brief Get the Scribble Segmentation Models info for the given * dimension. - * - * @param dim - * @return std::vector */ - std::vector GetScribbleSegmentationModels(int dim = -1); + std::vector GetScribbleSegmentationModels(int dim = -1) const; /** * @brief Function to prepare the Rest request and does the POST call. * Writes the POST responses back to disk. */ - void PostInferRequest(std::string &, int &, std::string &, std::string &, const mitk::BaseGeometry *); - + void PostInferRequest(const std::string &hostName, const int &port, std::string &filePath, std::string &outFile, + const mitk::BaseGeometry *baseGeometry); /** - * @brief Helper function to get full model info object from model name. - * - * @return MonaiModelInfo + * @brief Helper function to get full model info object from model name. */ - MonaiModelInfo GetModelInfoFromName(std::string&); + MonaiModelInfo GetModelInfoFromName(std::string&) const; itkSetMacro(ModelName, std::string); itkGetConstMacro(ModelName, std::string); itkSetMacro(URL, std::string); itkGetConstMacro(URL, std::string); - itkSetMacro(MitkTempDir, std::string); - itkGetConstMacro(MitkTempDir, std::string); + itkSetMacro(TempDir, std::string); + itkGetConstMacro(TempDir, std::string); /** * @brief Clears all picks and updates the preview. */ void ClearPicks(); /** * @brief Checks if any point exists in the either * of the pointsets * * @return bool */ bool HasPicks() const; Message1 MonaiStatusEvent; protected: MonaiLabelTool(); ~MonaiLabelTool(); void DoUpdatePreview(const Image* inputAtTimeStep, const Image* oldSegAtTimeStep, LabelSetImage* previewImage, TimeStepType timeStep) override; void ConnectActionsAndFunctions() override; /* * @brief Add positive seed point action of StateMachine pattern. */ virtual void OnAddPositivePoint(StateMachineAction *, InteractionEvent *interactionEvent) = 0; /* * @brief Add negative seed point action of StateMachine pattern */ virtual void OnAddNegativePoint(StateMachineAction *, InteractionEvent *interactionEvent) = 0; /* * @brief Delete action of StateMachine pattern */ virtual void OnDelete(StateMachineAction *, InteractionEvent *); /* * @brief Clear all seed points and call UpdatePreview to reset the segmentation Preview */ void ClearSeeds(); /** * @brief Get the Points from given pointset as csv string. * * @param baseGeometry * @param pointSet * @return std::stringstream */ virtual std::stringstream GetPointsAsListString(const mitk::BaseGeometry*, PointSet::Pointer) = 0; /** * @brief Writes back segmentation results in 3D or 2D shape to preview LabelSetImage. - * */ virtual void WriteBackResults(LabelSetImage *, LabelSetImage *, TimeStepType) = 0; PointSet::Pointer m_PointSetPositive; PointSet::Pointer m_PointSetNegative; DataNode::Pointer m_PointSetNodePositive; DataNode::Pointer m_PointSetNodeNegative; int m_PointSetCount = 0; private: - std::string m_MitkTempDir; + std::string m_TempDir; + + /** + * @brief Helper function to create temp directory for writing/reading images + * Returns input and output file names expected as a pair. + * @return std::vector + */ + std::pair CreateTempDirs(const std::string &filePattern); /** * @brief Helper function to get the Parts of the POST response * * @return std::vector */ - std::vector getPartsBetweenBoundary(const std::string &, const std::string &); - + std::vector GetPartsBetweenBoundary(const std::string &body, const std::string &boundary); /** * @brief Converts the json GET response from the MonaiLabel server to MonaiAppMetadata object * * @return std::unique_ptr */ - std::unique_ptr DataMapper(nlohmann::json&); + std::unique_ptr MapJSONToObject(nlohmann::json&); /** * @brief Applies the give std::map lookup table on the preview segmentation LabelSetImage. * */ - void MapLabelsToSegmentation(const mitk::LabelSetImage*, mitk::LabelSetImage*, std::map&); + void MapLabelsToSegmentation(const mitk::LabelSetImage *source, mitk::LabelSetImage *dest, + std::map &labelMap); /** * @brief Checks if MonaiLabel server is alive * * @return bool */ - bool IsMonaiServerOn(std::string &, int &); + bool IsMonaiServerOn(const std::string &hostName, const int &port) const; + + /** + * @brief Returns boundary string from Httplib response + * + * @return std::string + */ + std::string GetBoundaryString(httplib::Result &response); + + /** + * @brief Returns image data string from monai label overall response + * + * @return std::string + */ + std::string GetResponseImageString(std::string &imagePart); + std::string m_ModelName; std::string m_URL; nlohmann::json m_ResultMetadata; const std::set m_AUTO_SEG_TYPE_NAME = {"segmentation"}; const std::set m_SCRIBBLE_SEG_TYPE_NAME = {"scribbles"}; const std::set m_INTERACTIVE_SEG_TYPE_NAME = {"deepgrow"}; // deepedit not supported yet const std::string m_TEMPLATE_FILENAME = "XXXXXX_000_0000.nii.gz"; const std::string m_SERVER_503_ERROR_TEXT = "A connection to MonaiLabel server cannot be established."; const Label::PixelType MASK_VALUE = 1; }; } #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.h index 606db53d4e..9f5bd5c824 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.h @@ -1,21 +1,33 @@ -#ifndef QmitkMonaiLabelTool2DGUI_h_Included -#define QmitkMonaiLabelTool2DGUI_h_Included +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef QmitkMonaiLabelTool2DGUI_h +#define QmitkMonaiLabelTool2DGUI_h #include #include "QmitkMonaiLabelToolGUI.h" class MITKSEGMENTATIONUI_EXPORT QmitkMonaiLabel2DToolGUI : public QmitkMonaiLabelToolGUI { Q_OBJECT public: mitkClassMacro(QmitkMonaiLabel2DToolGUI, QmitkMonaiLabelToolGUI); itkFactorylessNewMacro(Self); itkCloneMacro(Self); protected: QmitkMonaiLabel2DToolGUI(); ~QmitkMonaiLabel2DToolGUI() = default; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.h index 4e19edd2c9..20254534d3 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.h @@ -1,31 +1,32 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef QmitkMonaiLabelTool3DGUI_h_Included -#define QmitkMonaiLabelTool3DGUI_h_Included + +#ifndef QmitkMonaiLabelTool3DGUI_h +#define QmitkMonaiLabelTool3DGUI_h #include #include "QmitkMonaiLabelToolGUI.h" class MITKSEGMENTATIONUI_EXPORT QmitkMonaiLabel3DToolGUI : public QmitkMonaiLabelToolGUI { Q_OBJECT public: mitkClassMacro(QmitkMonaiLabel3DToolGUI, QmitkMonaiLabelToolGUI); itkFactorylessNewMacro(Self); itkCloneMacro(Self); protected: QmitkMonaiLabel3DToolGUI(); ~QmitkMonaiLabel3DToolGUI() = default; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp index e5f233d87a..e14536477c 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp @@ -1,311 +1,327 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkMonaiLabelToolGUI.h" #include #include #include #include #include #include namespace { mitk::IPreferences *GetPreferences() { auto *preferencesService = mitk::CoreServices::GetPreferencesService(); return preferencesService->GetSystemPreferences()->Node("org.mitk.views.segmentation"); } -} // namespace +} + +const QString QmitkMonaiLabelToolGUI::CONFIRM_QUESTION_TEXT = + "Data will be sent to the processing server devoid of any patient information. Are you sure you want continue?"; + +const QStringList QmitkMonaiLabelToolGUI::WHITELISTED_MODELS = { + "deepgrow_2d", + "deepgrow_3d", + "deepedit_seg", + "localization_vertebra", + "segmentation", + "segmentation_spleen", + "segmentation_vertebra", + "deepgrow_pipeline", + "vertebra_pipeline" +}; +const QStringList QmitkMonaiLabelToolGUI::BLACKLISTED_MODELS = { + "deepedit", + "localization_spine", +}; QmitkMonaiLabelToolGUI::QmitkMonaiLabelToolGUI(int dimension) - : QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc) + : QmitkMultiLabelSegWithPreviewToolGUIBase(), + m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc), + m_Dimension(dimension) { - m_Dimension = dimension; m_EnableConfirmSegBtnFnc = [this](bool enabled) { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; m_Preferences = GetPreferences(); m_Preferences->OnPropertyChanged += mitk::MessageDelegate1( this, &QmitkMonaiLabelToolGUI::OnPreferenceChangedEvent); } QmitkMonaiLabelToolGUI::~QmitkMonaiLabelToolGUI() { auto tool = this->GetConnectedToolAs(); if (nullptr != tool) { tool->MonaiStatusEvent -= mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); } m_Preferences->OnPropertyChanged -= mitk::MessageDelegate1( this, &QmitkMonaiLabelToolGUI::OnPreferenceChangedEvent); } void QmitkMonaiLabelToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) { Superclass::ConnectNewTool(newTool); m_FirstPreviewComputation = true; } void QmitkMonaiLabelToolGUI::InitializeUI(QBoxLayout *mainLayout) { m_Controls.setupUi(this); mainLayout->addLayout(m_Controls.verticalLayout); connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewBtnClicked())); connect(m_Controls.fetchUrl, SIGNAL(clicked()), this, SLOT(OnFetchBtnClicked())); connect(m_Controls.modelBox, QOverload::of(&QComboBox::activated), [=](int index) { OnModelChanged(m_Controls.modelBox->itemText(index)); }); QIcon refreshIcon = QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/view-refresh.svg")); m_Controls.fetchUrl->setIcon(refreshIcon); m_Controls.previewButton->setEnabled(false); Superclass::InitializeUI(mainLayout); } void QmitkMonaiLabelToolGUI::EnableWidgets(bool enabled) { Superclass::EnableWidgets(enabled); } void QmitkMonaiLabelToolGUI::StatusMessageListener(const bool status) { if (!status) { return; } auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } this->SetLabelSetPreview(tool->GetPreviewSegmentation()); this->ActualizePreviewLabelVisibility(); m_FirstPreviewComputation = false; } void QmitkMonaiLabelToolGUI::DisplayWidgets(bool enabled) { Superclass::DisplayTransferWidgets(enabled); m_Controls.previewButton->setVisible(enabled); } void QmitkMonaiLabelToolGUI::OnModelChanged(const QString &modelName) { auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } m_Controls.labelListLabel->clear(); - std::string _modelName = modelName.toStdString(); - mitk::MonaiModelInfo model = tool->GetModelInfoFromName(_modelName); + mitk::MonaiModelInfo model = tool->GetModelInfoFromName(modelName.toStdString()); if (model.IsInteractive()) { this->WriteStatusMessage("Interactive model selected. Please press SHIFT + click on the render windows.\n"); m_Controls.previewButton->setEnabled(false); this->DisplayWidgets(false); } else { this->WriteStatusMessage("Auto-segmentation model selected. Please click on Preview.\n"); m_Controls.previewButton->setEnabled(true); this->DisplayWidgets(true); } - std::string selectedModel = m_Controls.modelBox->currentText().toStdString(); - for (const mitk::MonaiModelInfo &modelObject : tool->m_InfoParameters->models) + auto selectedModel = m_Controls.modelBox->currentText().toStdString(); + for (const auto &modelObject : tool->m_InfoParameters->models) { if (modelObject.name == selectedModel) { auto requestObject = std::make_unique(); requestObject->model = modelObject; requestObject->hostName = tool->m_InfoParameters->hostName; requestObject->port = tool->m_InfoParameters->port; tool->m_RequestParameters = std::move(requestObject); QStringList supportedLabels; for (const auto &label : modelObject.labels) { supportedLabels << QString::fromStdString(label.first); } m_Controls.labelListLabel->setText(supportedLabels.join(QChar(',') + QChar::Space)); break; } } tool->MonaiStatusEvent += mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); } void QmitkMonaiLabelToolGUI::OnFetchBtnClicked() { m_Controls.previewButton->setEnabled(false); m_Controls.labelListLabel->clear(); - QMessageBox::StandardButton reply; - reply = QMessageBox::question(this, "Confirm", m_CONFIRM_QUESTION_TEXT, QMessageBox::Yes | QMessageBox::No); + auto reply = QMessageBox::question(this, "Confirm", CONFIRM_QUESTION_TEXT, QMessageBox::Yes | QMessageBox::No); if (reply == QMessageBox::No) { MITK_INFO << "Didn't went ahead with Monai Label inferencing"; return; } auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } tool->m_InfoParameters.reset(); QString urlString = m_Controls.urlBox->text(); QUrl url(urlString); if (url.isValid() && !url.isLocalFile() && !url.hasFragment() && !url.hasQuery()) // sanity check { std::string hostName = url.host().toStdString(); int port = url.port(); try { tool->GetOverallInfo(hostName, port); bool allowAllModels = m_Preferences->GetBool("monailabel allow all models", false); this->PopulateUI(allowAllModels); } catch (const mitk::Exception &e) { MITK_ERROR << e.GetDescription(); this->WriteErrorMessage(e.GetDescription()); } } else { std::string invalidURLMessage = "Invalid URL entered: " + urlString.toStdString(); MITK_ERROR << invalidURLMessage; this->ShowErrorMessage(invalidURLMessage); } } void QmitkMonaiLabelToolGUI::OnPreviewBtnClicked() { auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } std::string selectedModel = m_Controls.modelBox->currentText().toStdString(); - for (const mitk::MonaiModelInfo &modelObject : tool->m_InfoParameters->models) + for (const auto &modelObject : tool->m_InfoParameters->models) { if (modelObject.name == selectedModel) { auto requestObject = std::make_unique(); requestObject->model = modelObject; requestObject->hostName = tool->m_InfoParameters->hostName; requestObject->port = tool->m_InfoParameters->port; tool->m_RequestParameters = std::move(requestObject); break; } } try { tool->UpdatePreview(); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "STATUS: Error while processing parameters for TotalSegmentator segmentation. Reason: " << e.what(); this->ShowErrorMessage(errorMsg.str()); this->WriteErrorMessage(QString::fromStdString(errorMsg.str())); m_Controls.previewButton->setEnabled(true); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation TotalSegmentator segmentation."; this->ShowErrorMessage(errorMsg); m_Controls.previewButton->setEnabled(true); return; } } void QmitkMonaiLabelToolGUI::PopulateUI(bool allowAllModels) { auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } m_Controls.appBox->clear(); if (nullptr != tool->m_InfoParameters) { - std::string response = tool->m_InfoParameters->name; - std::vector autoModels = tool->GetAutoSegmentationModels(m_Dimension); - std::vector interactiveModels = tool->GetInteractiveSegmentationModels(m_Dimension); + auto response = tool->m_InfoParameters->name; + auto autoModels = tool->GetAutoSegmentationModels(m_Dimension); + auto interactiveModels = tool->GetInteractiveSegmentationModels(m_Dimension); autoModels.insert(autoModels.end(), interactiveModels.begin(), interactiveModels.end()); this->WriteStatusMessage(QString::fromStdString(response)); m_Controls.appBox->addItem(QString::fromStdString(response)); this->PopulateModelBox(autoModels, allowAllModels); m_Controls.modelBox->setCurrentIndex(-1); } } void QmitkMonaiLabelToolGUI::PopulateModelBox(std::vector models, bool allowAllModels) { m_Controls.modelBox->clear(); - for (auto &model : models) + for (const auto &model : models) { QString modelName = QString::fromStdString(model.name); if (allowAllModels) { if (!BLACKLISTED_MODELS.contains(modelName)) { m_Controls.modelBox->addItem(modelName); } } else { if (WHITELISTED_MODELS.contains(modelName)) { m_Controls.modelBox->addItem(modelName); } } } } void QmitkMonaiLabelToolGUI::WriteStatusMessage(const QString &message) { m_Controls.responseNote->setText(message); m_Controls.responseNote->setStyleSheet("font-weight: bold; color: white"); qApp->processEvents(); } void QmitkMonaiLabelToolGUI::WriteErrorMessage(const QString &message) { m_Controls.responseNote->setText(message); m_Controls.responseNote->setStyleSheet("font-weight: bold; color: red"); qApp->processEvents(); } -void QmitkMonaiLabelToolGUI::ShowErrorMessage(const std::string &message, QMessageBox::Icon icon) +void QmitkMonaiLabelToolGUI::ShowErrorMessage(const std::string &message) { this->setCursor(Qt::ArrowCursor); - QMessageBox *messageBox = new QMessageBox(icon, nullptr, message.c_str()); - messageBox->exec(); - delete messageBox; + QMessageBox::critical(nullptr, "MONAI Label", message.c_str()); MITK_WARN << message; } void QmitkMonaiLabelToolGUI::OnPreferenceChangedEvent(const mitk::IPreferences::ChangeEvent& event) { - if (QString::fromStdString(event.GetProperty()).startsWith("monai")) + if (event.GetProperty().rfind("monai", 0) == 0) { bool allowAllModels = m_Preferences->GetBool("monailabel allow all models", false); this->PopulateUI(allowAllModels); } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h index 29a608c15d..327b596ec1 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h @@ -1,108 +1,94 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef QmitkMonaiLabelToolGUI_h_Included -#define QmitkMonaiLabelToolGUI_h_Included +#ifndef QmitkMonaiLabelToolGUI_h +#define QmitkMonaiLabelToolGUI_h #include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" #include "ui_QmitkMonaiLabelToolGUIControls.h" #include #include #include #include class MITKSEGMENTATIONUI_EXPORT QmitkMonaiLabelToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitkMonaiLabelToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); itkCloneMacro(Self); protected slots: void OnPreviewBtnClicked(); void OnFetchBtnClicked(); void OnModelChanged(const QString &); protected: QmitkMonaiLabelToolGUI(int); ~QmitkMonaiLabelToolGUI(); void ConnectNewTool(mitk::SegWithPreviewTool *newTool) override; void InitializeUI(QBoxLayout *mainLayout) override; void EnableWidgets(bool enabled) override; virtual void DisplayWidgets(bool enabled); /** * @brief Writes any message in white on the tool pane. */ void WriteStatusMessage(const QString &); /** * @brief Writes any message in red on the tool pane. */ void WriteErrorMessage(const QString &); /** * @brief Creates a QMessage object and shows on screen. */ - void ShowErrorMessage(const std::string &, QMessageBox::Icon = QMessageBox::Critical); + void ShowErrorMessage(const std::string &message); /** * @brief Function to listen to tool class status emitters. */ void StatusMessageListener(const bool); /** * @brief Function to listen to Preference changes */ void OnPreferenceChangedEvent(const mitk::IPreferences::ChangeEvent &); /** * @brief Helper function to write MONAI model info in to model combo box */ void PopulateModelBox(std::vector models, bool allowAllModels); /** * @brief Helper function to populate required server metadata into UI */ - void PopulateUI(bool); + void PopulateUI(bool allowAllModels); private: mitk::IPreferences *m_Preferences; Ui_QmitkMonaiLabelToolGUIControls m_Controls; bool m_FirstPreviewComputation = true; EnableConfirmSegBtnFunctionType m_SuperclassEnableConfirmSegBtnFnc; int m_Dimension; - QString m_CONFIRM_QUESTION_TEXT = - "Data will be sent to the processing server devoid of any patient information. Are you sure you want continue?"; - const QStringList WHITELISTED_MODELS = { - "deepgrow_2d", - "deepgrow_3d", - "deepedit_seg", - "localization_vertebra", - "segmentation", - "segmentation_spleen", - "segmentation_vertebra", - "deepgrow_pipeline", - "vertebra_pipeline," - }; - const QStringList BLACKLISTED_MODELS = { - "deepedit", - "localization_spine", - }; + static const QString CONFIRM_QUESTION_TEXT; + static const QStringList WHITELISTED_MODELS; + static const QStringList BLACKLISTED_MODELS; }; #endif