diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp index 4221df9529..e7fc4611ef 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.cpp @@ -1,164 +1,154 @@ /*============================================================================ 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" // us #include "mitkIOUtil.h" #include #include #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, MonaiLabel2DTool, "MonaiLabel2D"); } mitk::MonaiLabel2DTool::MonaiLabel2DTool() { this->ResetsToEmptyPreviewOn(); this->IsTimePointChangeAwareOff(); } void mitk::MonaiLabel2DTool::Activated() { Superclass::Activated(); this->SetLabelTransferScope(LabelTransferScope::AllLabels); - this->SetLabelTransferMode(LabelTransferMode::AddLabel); } 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 "MonaiLabel2D"; } 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()); } 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_INFO << "WriteImage: MonaiLabel2DTool"; - - for (unsigned int i = 0; i < inputAtTimeStep->GetDimension(); i++) - MITK_INFO << "Dim " << i << ":" << inputAtTimeStep->GetDimension(i); - mitk::Image::Pointer extendedImg = mitk::Image::New(); unsigned int dim[] = {inputAtTimeStep->GetDimension(0), inputAtTimeStep->GetDimension(1), 1}; mitk::PixelType pt = inputAtTimeStep->GetPixelType(); extendedImg->Initialize(pt, 3, dim); mitk::ImageReadAccessor newMitkImgAcc(inputAtTimeStep); extendedImg->SetVolume(newMitkImgAcc.GetData()); - for (unsigned int i = 0; i < extendedImg->GetDimension(); i++) - MITK_INFO << "Dim " << i << ":" << extendedImg->GetDimension(i); - IOUtil::Save(extendedImg.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(); 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 << 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); - this->SetSelectedLabels({1}); } diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp index 0e1b39b53c..aa1506ed84 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.cpp @@ -1,66 +1,102 @@ /*============================================================================ 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 namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, MonaiLabel3DTool, "MonaiLabel3D"); } mitk::MonaiLabel3DTool::MonaiLabel3DTool() { this->IsTimePointChangeAwareOff(); } void mitk::MonaiLabel3DTool::Activated() { Superclass::Activated(); this->SetLabelTransferScope(LabelTransferScope::AllLabels); - this->SetLabelTransferMode(LabelTransferMode::AddLabel); } 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 "MonaiLabel3D"; } void mitk::MonaiLabel3DTool::WriteImage(const Image *inputAtTimeStep, std::string &inputImagePath) { - MITK_INFO << "WriteImage: MonaiLabel3DTool"; IOUtil::Save(inputAtTimeStep, inputImagePath); } -void mitk::MonaiLabel3DTool::WriteBackResults(LabelSetImage *previewImage, LabelSetImage *segResults, TimeStepType) +void mitk::MonaiLabel3DTool::WriteBackResults(LabelSetImage *previewImage, + LabelSetImage *segResults, + TimeStepType timeStep) { - this->SetSelectedLabels({1}); - MITK_INFO << "MonaiLabel3DTool WriteBackResults"; + 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(); + } + } } diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h index b6f981534f..1e0cb37e7f 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel3DTool.h @@ -1,45 +1,47 @@ /*============================================================================ 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 #include "mitkMonaiLabelTool.h" #include namespace us { class ModuleResource; } namespace mitk { class MITKSEGMENTATION_EXPORT MonaiLabel3DTool : public MonaiLabelTool // SegWithPreviewTool { 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; void WriteImage(const Image *, std::string &) override; void WriteBackResults(LabelSetImage *, LabelSetImage *, TimeStepType) override; protected: MonaiLabel3DTool(); ~MonaiLabel3DTool() = default; }; } // namespace mitk #endif diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp index b5bf9c636e..f6b9055f06 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp @@ -1,601 +1,528 @@ /*============================================================================ 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 #include "mitkPointSetShapeProperty.h" #include "mitkProperties.h" #include "mitkToolManager.h" #include mitk::MonaiLabelTool::MonaiLabelTool() : SegWithPreviewTool(true, "PressMoveReleaseAndPointSetting") { this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); } mitk::MonaiLabelTool::~MonaiLabelTool() { - itksys::SystemTools::RemoveADirectory(this->GetMitkTempDir()); + std::filesystem::remove_all(this->GetMitkTempDir()); } 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)); - - this->SetLabelTransferScope(LabelTransferScope::ActiveLabel); - this->SetLabelTransferMode(LabelTransferMode::MapLabel); } void mitk::MonaiLabelTool::Deactivated() { this->ClearSeeds(); GetDataStorage()->Remove(m_PointSetNodePositive); 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::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()); - }*/ - 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::MonaiLabelTool::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::MonaiLabelTool::OnDelete(StateMachineAction *, InteractionEvent *) { if (!this->IsUpdating() && m_PointSetPositive.IsNotNull()) { PointSet::Pointer removeSet = m_PointSetPositive; decltype(m_PointSetPositive->GetMaxId().Index()) 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) { httplib::Client cli(hostName, port); while (cli.is_socket_open()) ; if (auto response = cli.Get("/info/")) { return true; } return false; } 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; - if (!m_TEST) - if (!IsMonaiServerOn(hostName, port)) - { - mitkThrow() << m_SERVER_503_ERROR_TEXT; - } + if (!IsMonaiServerOn(hostName, port)) + { + mitkThrow() << m_SERVER_503_ERROR_TEXT; + } 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"; try { m_IsLastSuccess = false; - if (!m_TEST) - { - this->WriteImage(inputAtTimeStep, inputImagePath); - PostInferRequest(hostName, port, inputImagePath, outputImagePath, inputAtTimeStep->GetGeometry()); - } - else - { - std::string metaData_test = - "{\"label_names\":{\"spleen\": 1, \"right kidney\": 2, \"left kidney\": 3, \"liver\": 6, \"stomach\": 7, " - "\"aorta\": 8, \"inferior " - "vena cava\": 9, \"background\": 0}, \"latencies\": {\"pre\": 0.64, \"infer\": 1.13, \"invert\": 0.03, " - "\"post\": 0.06, \"write\": 0.1, \"total\": 1.96, \"transform\": {\"pre\": {\"LoadImaged\": 0.1483, " - "\"EnsureChannelFirstd\": 0.0, \"Orientationd\": 0.0, \"ScaleIntensityRanged\": 0.0403, \"Resized\": 0.0401, " - "\"DiscardAddGuidanced\": 0.0297, \"EnsureTyped\": 0.3703}, \"post\": {\"EnsureTyped\": 0.0, \"Activationsd\": " - "0.0, \"AsDiscreted\": 0.0, \"SqueezeDimd\": 0.0, \"ToNumpyd\": 0.0473, \"Restored\": 0.0001}}}}"; - m_ResultMetadata = nlohmann::json::parse(metaData_test); - outputImagePath = "C:/DKFZ/MONAI_work/monai_test_python/output.nii.gz"; - } - + this->WriteImage(inputAtTimeStep, inputImagePath); + PostInferRequest(hostName, port, inputImagePath, outputImagePath, inputAtTimeStep->GetGeometry()); Image::Pointer outputImage = IOUtil::Load(outputImagePath); auto outputBuffer = mitk::LabelSetImage::New(); outputBuffer->InitializeByLabeledImage(outputImage); - outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); - if (m_AUTO_SEG_TYPE_NAME.find(m_RequestParameters->model.type) != m_AUTO_SEG_TYPE_NAME.end()) { + outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); std::map labelMap = m_ResultMetadata["label_names"]; this->MapLabelsToSegmentation(outputBuffer, previewImage, labelMap); + this->SetLabelTransferMode(LabelTransferMode::AddLabel); } else { - std::map labelMap; //{{m_RequestParameters->requestLabel, 1}}; + std::map labelMap; // empty map. this->MapLabelsToSegmentation(outputBuffer, previewImage, labelMap); + this->SetLabelTransferMode(LabelTransferMode::MapLabel); + this->SetSelectedLabels({MASK_VALUE}); } - mitk::ImageReadAccessor newMitkImgAcc(outputBuffer.GetPointer()); - previewImage->SetVolume(newMitkImgAcc.GetData(), timeStep); this->WriteBackResults(previewImage, outputBuffer.GetPointer(), timeStep); this->SetIsLastSuccess(true); MonaiStatusEvent.Send(true); } catch (const mitk::Exception &e) { m_IsLastSuccess = false; 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); - //mitk::Label::PixelType labelId = 0; for (auto const &[key, val] : flippedLabelMap) { - //if (source->ExistLabel(labelId, source->GetActiveLayer())) 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; } - // labelId++; } } 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::Client cli(hostName, port); // httplib::Client cli("localhost", 8000); + httplib::Client cli(hostName, port); 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!"; return; } m_InfoParameters = DataMapper(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, std::string &filePath, std::string &outFile, const mitk::BaseGeometry *baseGeometry) { - // std::string url = "http://localhost:8000/infer/deepedit_seg"; // + m_ModelName; 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::string filePath = "C:/DKFZ/MONAI_work/monai_test_python/la_030.nii.gz"; 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_INTERACTIVE_SEG_TYPE_NAME.find(m_RequestParameters->model.type) != m_INTERACTIVE_SEG_TYPE_NAME.end()) { 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 << foreground.str(); MITK_INFO << background.str(); MITK_INFO << paramString.str(); + paramString << "{" + << "\"foreground\":" << foreground.str() + << ",\"background\":" << background.str() + << "}"; + MITK_INFO << paramString.str(); items.push_back({"params", paramString.str()}); } - //httplib::MultipartFormDataItems items = { - //{"params", "{\"restore_label_idx\": true} "}, - //{"params", "{\"foreground\" : [[ 59, 43, 56 ]], \"background\" : []}"}, - //{"file", buffer_lf_img.str(), "post_from_mitk.nii.gz", "application/octet-stream"}}; + 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::Client cli(hostName, port); cli.set_read_timeout(60); // arbitary 1 minute time-out to avoid corner cases. - if (auto response = cli.Post(postPath, items)) // cli.Post("/infer/deepedit_seg", items); + 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; // Parse metadata JSON std::string resBody = response->body; 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; auto jsonObj = nlohmann::json::parse(metaDataPart); if (jsonObj.is_discarded() || !jsonObj.is_object()) { MITK_ERROR << "Could not parse \"" << /* jsonPath.toStdString() << */ "\" 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::ofstream output(outFile, std::ios::out | std::ios::app | std::ios::binary); output << imageDataPart; 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, const std::string &boundary) { std::vector retVal; std::string master = body; size_t found = master.find(boundary); size_t beginPos = 0; while (found != std::string::npos) { std::string part = master.substr(beginPos, found); if (!part.empty()) { retVal.push_back(part); } master.erase(beginPos, found + boundary.length()); found = master.find(boundary); } return retVal; } std::unique_ptr mitk::MonaiLabelTool::DataMapper(nlohmann::json &jsonObj) { auto object = std::make_unique(); object->name = jsonObj["name"].get(); object->description = jsonObj["description"].get(); object->labels = jsonObj["labels"].get>(); 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 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)) { autoModels.push_back(model); } } } return autoModels; } std::vector mitk::MonaiLabelTool::GetInteractiveSegmentationModels(int dim) { 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)) { interactiveModels.push_back(model); } } } return interactiveModels; } std::vector mitk::MonaiLabelTool::GetScribbleSegmentationModels(int dim) { 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)) { scribbleModels.push_back(model); } } } return scribbleModels; } mitk::MonaiModelInfo mitk::MonaiLabelTool::GetModelInfoFromName(std::string &modelName) { 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; } std::stringstream mitk::MonaiLabelTool::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/mitkMonaiLabelTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h index b28032a505..52b9969219 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h @@ -1,180 +1,180 @@ /*============================================================================ 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 #include "mitkSegWithPreviewTool.h" #include #include #include #include #include #include #include "mitkPointSet.h" #include "mitkInteractionPositionEvent.h" namespace us { class ModuleResource; } namespace mitk { struct MonaiModelInfo { std::string name; std::string type; std::unordered_map labels; int dimension; std::string description; std::unordered_map config; //TODO: find the full extent 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; } }; struct MonaiAppMetadata { std::string hostName; int port; std::string origin; std::string name; std::string description; std::string version; std::vector labels; std::vector models; }; /** * Parameters that goes into infer POST */ 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; } }; class MITKSEGMENTATION_EXPORT MonaiLabelTool : public SegWithPreviewTool { public: mitkClassMacro(MonaiLabelTool, SegWithPreviewTool); itkCloneMacro(Self); - bool m_TEST = false; // cleanup later void Activated() override; void Deactivated() override; void UpdatePrepare() override; virtual void WriteImage(const Image*, std::string&) = 0; void GetOverallInfo(std::string&, int&); std::unique_ptr m_InfoParameters; //contains all parameters from Server to serve the GUI std::unique_ptr m_RequestParameters; std::vector GetAutoSegmentationModels(int dim = -1); std::vector GetInteractiveSegmentationModels(int dim = -1); std::vector GetScribbleSegmentationModels(int dim = -1); void PostInferRequest(std::string &, int &, std::string &, std::string &, const mitk::BaseGeometry *); MonaiModelInfo GetModelInfoFromName(std::string&); 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(IsLastSuccess, bool); itkGetConstMacro(IsLastSuccess, bool); /** * @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); + virtual void OnAddPositivePoint(StateMachineAction *, InteractionEvent *interactionEvent) = 0; /* * @brief Add negative seed point action of StateMachine pattern */ - virtual void OnAddNegativePoint(StateMachineAction *, InteractionEvent *interactionEvent); + 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(); virtual std::stringstream GetPointsAsListString(const mitk::BaseGeometry*, PointSet::Pointer); 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::vector getPartsBetweenBoundary(const std::string &, const std::string &); std::unique_ptr mitk::MonaiLabelTool::DataMapper(nlohmann::json&); void MapLabelsToSegmentation(const mitk::LabelSetImage*, mitk::LabelSetImage*, std::map&); bool IsMonaiServerOn(std::string &, int &); bool m_IsLastSuccess = false; 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 = {"deepedit", "deepgrow"}; + 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/QmitkMonaiLabelToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp index 26ee3cda1d..6c8c9e071e 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp @@ -1,277 +1,267 @@ /*============================================================================ 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 "mitkMonaiLabelTool.h" #include "usServiceReference.h" #include +#include #include #include -#include -#include -#include -#include - QmitkMonaiLabelToolGUI::QmitkMonaiLabelToolGUI(int dimension) : QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc) { m_Dimension = dimension; m_EnableConfirmSegBtnFnc = [this](bool enabled) { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; } QmitkMonaiLabelToolGUI::~QmitkMonaiLabelToolGUI() { auto tool = this->GetConnectedToolAs(); if (nullptr != tool) { - tool->MonaiStatusEvent -= mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); + tool->MonaiStatusEvent -= + mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); } } void QmitkMonaiLabelToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) { Superclass::ConnectNewTool(newTool); newTool->IsTimePointChangeAwareOff(); 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); 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(); - //Superclass::DisplayWidgets(false); m_FirstPreviewComputation = false; } void QmitkMonaiLabelToolGUI::DisplayWidgets(bool enabled) { Superclass::DisplayWidgets(enabled); m_Controls.previewButton->setVisible(enabled); } void QmitkMonaiLabelToolGUI::OnModelChanged(const QString &modelName) { auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } m_Controls.labelListLabel->clear(); mitk::MonaiModelInfo model = tool->GetModelInfoFromName(modelName.toStdString()); if ("deepgrow" == model.type || "deepedit" == model.type) { 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. Label selection will be ignored.\n"); + this->WriteStatusMessage( + "Auto-segmentation model selected. Please click on Preview. Label selection will be ignored.\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) { 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(',')); break; } } - tool->MonaiStatusEvent += mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); + tool->MonaiStatusEvent += + mitk::MessageDelegate1(this, &QmitkMonaiLabelToolGUI::StatusMessageListener); } void QmitkMonaiLabelToolGUI::OnFetchBtnClicked() { + QMessageBox::StandardButton reply; + reply = QMessageBox::question(this, "Confirm", m_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(); m_Controls.modelBox->clear(); m_Controls.appBox->clear(); QString urlString = m_Controls.urlBox->text(); QUrl url(urlString); if (url.isValid() && !url.isLocalFile() && !url.hasFragment() && !url.hasQuery()) // sanity check { QString hostName = url.host(); int port = url.port(); try { - tool->GetOverallInfo(hostName.toStdString(), port); // tool->GetOverallInfo("localhost",8000"); + tool->GetOverallInfo(hostName.toStdString(), port); // tool->GetOverallInfo("localhost",8000"); 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); autoModels.insert(autoModels.end(), interactiveModels.begin(), interactiveModels.end()); this->WriteStatusMessage(QString::fromStdString(response)); m_Controls.appBox->addItem(QString::fromStdString(response)); for (auto &model : autoModels) { - m_Controls.modelBox->addItem(QString::fromStdString(model.name)); + QString modelName = QString::fromStdString(model.name); + if (SUPPORTED_MODELS.contains(modelName)) + { + m_Controls.modelBox->addItem(modelName); + } } m_Controls.modelBox->setCurrentIndex(-1); } } catch (const mitk::Exception &e) { - MITK_ERROR << e.GetDescription(); // Add GUI msg box to show + MITK_ERROR << e.GetDescription(); + this->WriteErrorMessage(e.GetDescription()); } } else { - MITK_ERROR << "Invalid URL entered: " << urlString.toStdString(); // set as status message on GUI + 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; } - QMessageBox::StandardButton reply; - reply = QMessageBox::question(this, "Confirm", m_CONFIRM_QUESTION_TEXT, QMessageBox::Yes | QMessageBox::No); - if (reply == QMessageBox::No) - { - MITK_INFO << "Didn't went ahead with Monai Label inferencing"; - return; - } - - bool test = false; - if (!test) + std::string selectedModel = m_Controls.modelBox->currentText().toStdString(); + for (const mitk::MonaiModelInfo &modelObject : tool->m_InfoParameters->models) { - std::string selectedModel = m_Controls.modelBox->currentText().toStdString(); - for (const mitk::MonaiModelInfo &modelObject : tool->m_InfoParameters->models) + if (modelObject.name == selectedModel) { - if (modelObject.name == selectedModel) + auto requestObject = std::make_unique(); + requestObject->model = modelObject; + requestObject->hostName = tool->m_InfoParameters->hostName; + requestObject->port = tool->m_InfoParameters->port; + if (!m_FirstPreviewComputation && tool->GetIsLastSuccess() && *requestObject == *(tool->m_RequestParameters)) { - auto requestObject = std::make_unique(); - requestObject->model = modelObject; - requestObject->hostName = tool->m_InfoParameters->hostName; - requestObject->port = tool->m_InfoParameters->port; - if (!m_FirstPreviewComputation && tool->GetIsLastSuccess() && *requestObject == *(tool->m_RequestParameters)) - { - MITK_INFO << "won't do segmentation..."; - return; - } - else - { - tool->m_RequestParameters = std::move(requestObject); - } - break; + MITK_INFO << "won't do segmentation..."; + return; + } + else + { + tool->m_RequestParameters = std::move(requestObject); } + break; } } - else - { - MITK_INFO << " RUNNING ON TEST parameters..."; - tool->m_RequestParameters = std::make_unique(); - mitk::MonaiModelInfo modelObject; - modelObject.name = "deepedit_seg"; - tool->m_RequestParameters->model = modelObject; - tool->m_RequestParameters->hostName = "localhost"; - tool->m_RequestParameters->port = 8000; - } 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::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) { this->setCursor(Qt::ArrowCursor); QMessageBox *messageBox = new QMessageBox(icon, nullptr, message.c_str()); messageBox->exec(); delete messageBox; MITK_WARN << message; } diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h index c1f93d252e..8e36d35797 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h @@ -1,75 +1,86 @@ /*============================================================================ 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 #include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" #include "ui_QmitkMonaiLabelToolGUIControls.h" #include #include class MITKSEGMENTATIONUI_EXPORT QmitkMonaiLabelToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitkMonaiLabelToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); itkCloneMacro(Self); -protected slots : +protected slots: void OnPreviewBtnClicked(); void OnFetchBtnClicked(); - void OnModelChanged(const QString&); + void OnModelChanged(const QString &); protected: QmitkMonaiLabelToolGUI(int); ~QmitkMonaiLabelToolGUI(); - void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; - void InitializeUI(QBoxLayout* mainLayout) override; + 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); - + /** * @brief Function to listen to tool class status emitters. */ void StatusMessageListener(const bool); - + private: 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 SUPPORTED_MODELS = { + "deepgrow_2d", + "deepgrow_3d", + "deepedit_seg", + "localization_vertebra", + "segmentation", + "segmentation_spleen", + "segmentation_vertebra", + "deepgrow_pipeline", + "vertebra_pipeline," + }; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui index 483c30a236..acab0cf818 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui @@ -1,209 +1,209 @@ QmitkMonaiLabelToolGUIControls 0 0 699 352 0 0 100 0 100000 100000 QmitkMonaiToolWidget 0 0 0 0 0 0 0 Monai Server URL: http://localhost:8000 0 0 Available Apps: 0 0 - <html><head/><body><p>Welcome to MONAI Label App in MITK. [Experimental]</p><p>Please note that this is only an interface to MONAI Label. MITK does not ship with any apps. Make sure to have a started a MONAI Label server beforehand. </p><p>Refer to <a href="https://github.com/MIC-DKFZ/nnUNet"><span style=" text-decoration: underline; color:#0000ff;">https://docs.monai.io/projects/label/en/latest/</span></a> to learn everything about the MONAI Label App.</p><p><br/></p><p>Provide a valid URL (eg. http://localhost:8000) to the server &amp; start the workflow.</p><p><br/></p></body></html> + <html><head/><body><p>Welcome to MONAI Label App in MITK. [Experimental]</p><p>Please note that this is only an interface to MONAI Label. MITK does not ship with any apps. Make sure to have a started a MONAI Label server beforehand. </p><p>Refer to <a href="https://docs.monai.io/projects/label/en/latest/"><span style=" text-decoration: underline; color:#0000ff;">https://docs.monai.io/projects/label/en/latest/</span></a> to learn everything about the MONAI Label App.</p><p><br/></p><p>Provide a valid URL (eg. http://localhost:8000) to the server &amp; start the workflow.</p><p><br/></p></body></html> Qt::RichText true 0 0 Models: 0 0 Supported Labels: 0 0 Qt::RichText true 0 0 <html><head/><body><p>Welcome to Monai Label in MITK. [Experimental]</p></body></html> Qt::RichText true 0 0 100000 16777215 Preview ctkComboBox QComboBox
ctkComboBox.h
1