diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h index 8bd2fc20c2..e0831af76b 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabel2DTool.h @@ -1,52 +1,52 @@ /*============================================================================ 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 #include "mitkSegWithPreviewTool.h" #include "mitkMonaiLabelTool.h" #include #include #include #include #include #include #include "mitkMonaiLabelTool.h" namespace us { class ModuleResource; } namespace mitk { - class MITKSEGMENTATION_EXPORT MonaiLabel2DTool : public MonaiLabelTool //SegWithPreviewTool + 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; protected: MonaiLabel2DTool(); ~MonaiLabel2DTool() = default; }; } #endif diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp index 66e598329e..1f2618c9e7 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp @@ -1,517 +1,535 @@ /*============================================================================ 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 "mitkInteractionPositionEvent.h" #include "mitkPointSetShapeProperty.h" #include "mitkProperties.h" #include "mitkToolManager.h" mitk::MonaiLabelTool::MonaiLabelTool() : SegWithPreviewTool(true, "PressMoveReleaseAndPointSetting") { this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); } mitk::MonaiLabelTool::~MonaiLabelTool() { itksys::SystemTools::RemoveADirectory(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::OnAddPositivePoint(StateMachineAction *, InteractionEvent *interactionEvent) { /* if ("deepgrow" != m_RequestParameters->model.type || "deepedit" != m_RequestParameters->model.type) { return; } 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; } 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) { IOUtil::Save(inputAtTimeStep, inputImagePath); PostInferRequest(hostName, port, inputImagePath, outputImagePath); } 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"; } Image::Pointer outputImage = IOUtil::Load(outputImagePath); auto outputBuffer = mitk::LabelSetImage::New(); outputBuffer->InitializeByLabeledImage(outputImage); outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); std::map labelMap = m_ResultMetadata["label_names"]; MapLabelsToSegmentation(outputBuffer, previewImage, labelMap); mitk::ImageReadAccessor newMitkImgAcc(outputBuffer.GetPointer()); previewImage->SetVolume(newMitkImgAcc.GetData(), timeStep); this->SetIsLastSuccess(true); } catch (const mitk::Exception &e) { m_IsLastSuccess = false; MITK_ERROR << e.GetDescription(); mitkThrow() << e.GetDescription(); } } void mitk::MonaiLabelTool::MapLabelsToSegmentation(const mitk::LabelSetImage *source, mitk::LabelSetImage *dest, std::map &labelMap) { std::map flippedLabelMap; for (auto const &[key, val] : labelMap) { flippedLabelMap[val] = key; } auto labelset = dest->GetLabelSet(); 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())) { Label::Pointer label = Label::New(labelId, val); std::array lookupTableColor; lookupTable->GetColor(labelId, 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); 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) { // 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 = { {"file", buffer_lf_img.str(), "post_from_mitk.nii.gz", "application/octet-stream"}}; // httplib::MultipartFormDataMap itemMap = {{"file", {"file", buffer_lf_img.str(), "spleen_58.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 (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; +} diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h index 8bac19ff22..4a953ed220 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.h @@ -1,170 +1,171 @@ /*============================================================================ 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" 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; int port; inline bool operator==(const MonaiLabelRequest &rhs) const { if (this->model == rhs.model && this->hostName == rhs.hostName && this->port == rhs.port) { 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 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 &); + void PostInferRequest(std::string&, int&, std::string&, std::string&); + 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; 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); /* * @brief Add negative seed point action of StateMachine pattern */ virtual void OnAddNegativePoint(StateMachineAction *, InteractionEvent *interactionEvent); /* * @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(); 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; PointSet::Pointer m_PointSetPositive; PointSet::Pointer m_PointSetNegative; DataNode::Pointer m_PointSetNodePositive; DataNode::Pointer m_PointSetNodeNegative; int m_PointSetCount = 0; 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::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."; }; } #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.cpp index b0a8e9c169..43fb118247 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel2DToolGUI.cpp @@ -1,5 +1,17 @@ +/*============================================================================ + +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 "QmitkMonaiLabel2DToolGUI.h" MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkMonaiLabel2DToolGUI, "") QmitkMonaiLabel2DToolGUI::QmitkMonaiLabel2DToolGUI(): QmitkMonaiLabelToolGUI(2) {} diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.cpp index 4077a3589a..15857ff290 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabel3DToolGUI.cpp @@ -1,5 +1,17 @@ +/*============================================================================ + +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 "QmitkMonaiLabel3DToolGUI.h" MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkMonaiLabel3DToolGUI, "") QmitkMonaiLabel3DToolGUI::QmitkMonaiLabel3DToolGUI(): QmitkMonaiLabelToolGUI(3) {} diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp index 18bc60eb6f..1d1ae2001b 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.cpp @@ -1,168 +1,192 @@ /*============================================================================ 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 QmitkMonaiLabelToolGUI::QmitkMonaiLabelToolGUI(int dimension) : QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc) { m_Dimension = dimension; m_EnableConfirmSegBtnFnc = [this](bool enabled) { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; } 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::OnModelChanged(const QString &modelName) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr == tool) + { + return; + } + mitk::MonaiModelInfo model = tool->GetModelInfoFromName(modelName.toStdString()); + if ("deepgrow" == model.type || "deepedit" == model.type) + { + m_Controls.responseNote->setText("Interactive model selected. Please press SHIFT + click on the render windows."); + m_Controls.previewButton->setEnabled(false); + } + else + { + m_Controls.responseNote->setText("Auto-segmentation model selected. Please click on Preview."); + m_Controls.previewButton->setEnabled(true); + } +} + void QmitkMonaiLabelToolGUI::OnFetchBtnClicked() { 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"); 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()); m_Controls.responseNote->setText(QString::fromStdString(response)); m_Controls.appBox->addItem(QString::fromStdString(response)); for (auto &model : autoModels) { m_Controls.modelBox->addItem(QString::fromStdString(model.name)); } + m_Controls.modelBox->setCurrentIndex(-1); } } catch (const mitk::Exception &e) { MITK_ERROR << e.GetDescription(); // Add GUI msg box to show } } else { MITK_ERROR << "Invalid URL entered: " << urlString.toStdString(); // set as status message on GUI } } 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) { 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)) { 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(); m_FirstPreviewComputation = false; this->SetLabelSetPreview(tool->GetPreviewSegmentation()); tool->IsTimePointChangeAwareOn(); this->ActualizePreviewLabelVisibility(); } catch (...) { MITK_ERROR << "Connection error"; //This catch is never reached when exception is thrown in UpdatePreview method } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h index 1d29f575b0..a66313cde4 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUI.h @@ -1,51 +1,52 @@ /*============================================================================ 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 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() = default; void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; void InitializeUI(QBoxLayout* mainLayout) override; void EnableWidgets(bool enabled) override; 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?"; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui index cc197b4d5a..117a286c13 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui +++ b/Modules/SegmentationUI/Qmitk/QmitkMonaiLabelToolGUIControls.ui @@ -1,180 +1,180 @@ QmitkMonaiLabelToolGUIControls 0 0 699 352 0 0 100 0 100000 100000 QmitkMonaiToolWidget 0 0 0 0 0 - - - - - 0 - 0 - - - - <html><head/><body><p>Welcome to Monai Label in MITK. [Experimental] - - - Qt::RichText - - - true - - - 0 0 Monai Server URL: - - - - http://localhost:8000 - - - - - - + + + + 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>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://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> Qt::RichText true 0 0 Models: - + + + + + 0 + 0 + + + + <html><head/><body><p>Welcome to Monai Label in MITK. [Experimental] + + + Qt::RichText + + + true + + + 0 0 100000 16777215 Preview ctkComboBox QComboBox
ctkComboBox.h
1 + diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake index 8c2bdfdad8..4ed19de407 100644 --- a/Modules/SegmentationUI/files.cmake +++ b/Modules/SegmentationUI/files.cmake @@ -1,129 +1,130 @@ set(CPP_FILES Qmitk/QmitkSegWithPreviewToolGUIBase.cpp Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUI.cpp Qmitk/QmitkBinaryThresholdULToolGUI.cpp Qmitk/QmitkConfirmSegmentationDialog.cpp Qmitk/QmitkCopyToClipBoardDialog.cpp Qmitk/QmitkDrawPaintbrushToolGUI.cpp Qmitk/QmitkErasePaintbrushToolGUI.cpp Qmitk/QmitkEditableContourToolGUIBase.cpp Qmitk/QmitkGrowCutToolGUI.cpp Qmitk/QmitkLiveWireTool2DGUI.cpp Qmitk/QmitkLassoToolGUI.cpp Qmitk/QmitkOtsuTool3DGUI.cpp Qmitk/QmitkPaintbrushToolGUI.cpp Qmitk/QmitkPickingToolGUI.cpp Qmitk/QmitkSlicesInterpolator.cpp Qmitk/QmitkToolGUI.cpp Qmitk/QmitkToolGUIArea.cpp Qmitk/QmitkToolSelectionBox.cpp Qmitk/QmitknnUNetFolderParser.cpp Qmitk/QmitknnUNetToolGUI.cpp Qmitk/QmitknnUNetWorker.cpp Qmitk/QmitknnUNetGPU.cpp Qmitk/QmitkSurfaceStampWidget.cpp Qmitk/QmitkMaskStampWidget.cpp Qmitk/QmitkStaticDynamicSegmentationDialog.cpp Qmitk/QmitkSimpleLabelSetListWidget.cpp Qmitk/QmitkSegmentationTaskListWidget.cpp Qmitk/QmitkTotalSegmentatorToolGUI.cpp Qmitk/QmitkSetupVirtualEnvUtil.cpp Qmitk/QmitkMultiLabelInspector.cpp Qmitk/QmitkMultiLabelManager.cpp Qmitk/QmitkMultiLabelTreeModel.cpp Qmitk/QmitkMultiLabelTreeView.cpp Qmitk/QmitkMultiLabelPresetHelper.cpp Qmitk/QmitkLabelColorItemDelegate.cpp Qmitk/QmitkLabelToggleItemDelegate.cpp Qmitk/QmitkFindSegmentationTaskDialog.cpp Qmitk/QmitkMonaiLabelToolGUI.cpp Qmitk/QmitkMonaiLabel2DToolGUI.cpp Qmitk/QmitkMonaiLabel3DToolGUI.cpp SegmentationUtilities/QmitkBooleanOperationsWidget.cpp SegmentationUtilities/QmitkContourModelToImageWidget.cpp SegmentationUtilities/QmitkImageMaskingWidget.cpp SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/QmitkSurfaceToImageWidget.cpp SegmentationUtilities/QmitkDataSelectionWidget.cpp ) set(H_FILES Qmitk/QmitkMultiLabelPresetHelper.h ) set(MOC_H_FILES Qmitk/QmitkSegWithPreviewToolGUIBase.h Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUI.h Qmitk/QmitkBinaryThresholdULToolGUI.h Qmitk/QmitkConfirmSegmentationDialog.h Qmitk/QmitkCopyToClipBoardDialog.h Qmitk/QmitkDrawPaintbrushToolGUI.h Qmitk/QmitkErasePaintbrushToolGUI.h Qmitk/QmitkEditableContourToolGUIBase.h Qmitk/QmitkGrowCutToolGUI.h Qmitk/QmitkLiveWireTool2DGUI.h Qmitk/QmitkLassoToolGUI.h Qmitk/QmitkOtsuTool3DGUI.h Qmitk/QmitkPaintbrushToolGUI.h Qmitk/QmitkPickingToolGUI.h Qmitk/QmitkSlicesInterpolator.h Qmitk/QmitkToolGUI.h Qmitk/QmitkToolGUIArea.h Qmitk/QmitkToolSelectionBox.h Qmitk/QmitknnUNetFolderParser.h Qmitk/QmitknnUNetToolGUI.h Qmitk/QmitknnUNetGPU.h Qmitk/QmitknnUNetWorker.h Qmitk/QmitknnUNetEnsembleLayout.h Qmitk/QmitkSurfaceStampWidget.h Qmitk/QmitkMaskStampWidget.h Qmitk/QmitkStaticDynamicSegmentationDialog.h Qmitk/QmitkSimpleLabelSetListWidget.h Qmitk/QmitkSegmentationTaskListWidget.h Qmitk/QmitkTotalSegmentatorToolGUI.h Qmitk/QmitkSetupVirtualEnvUtil.h Qmitk/QmitkMultiLabelInspector.h Qmitk/QmitkMultiLabelManager.h Qmitk/QmitkMultiLabelTreeModel.h Qmitk/QmitkMultiLabelTreeView.h Qmitk/QmitkLabelColorItemDelegate.h Qmitk/QmitkLabelToggleItemDelegate.h Qmitk/QmitkFindSegmentationTaskDialog.h Qmitk/QmitkMonaiLabelToolGUI.h Qmitk/QmitkMonaiLabel2DToolGUI.h Qmitk/QmitkMonaiLabel3DToolGUI.h SegmentationUtilities/QmitkBooleanOperationsWidget.h SegmentationUtilities/QmitkContourModelToImageWidget.h SegmentationUtilities/QmitkImageMaskingWidget.h SegmentationUtilities/QmitkMorphologicalOperationsWidget.h SegmentationUtilities/QmitkSurfaceToImageWidget.h SegmentationUtilities/QmitkDataSelectionWidget.h ) set(UI_FILES Qmitk/QmitkConfirmSegmentationDialog.ui Qmitk/QmitkGrowCutToolWidgetControls.ui Qmitk/QmitkOtsuToolWidgetControls.ui Qmitk/QmitkSurfaceStampWidgetGUIControls.ui Qmitk/QmitkMaskStampWidgetGUIControls.ui Qmitk/QmitknnUNetToolGUIControls.ui Qmitk/QmitkEditableContourToolGUIControls.ui Qmitk/QmitkSegmentationTaskListWidget.ui Qmitk/QmitkTotalSegmentatorGUIControls.ui Qmitk/QmitkMultiLabelInspectorControls.ui Qmitk/QmitkMultiLabelManagerControls.ui Qmitk/QmitkFindSegmentationTaskDialog.ui + Qmitk/QmitkMonaiLabelToolGUIControls.ui SegmentationUtilities/QmitkBooleanOperationsWidgetControls.ui SegmentationUtilities/QmitkContourModelToImageWidgetControls.ui SegmentationUtilities/QmitkImageMaskingWidgetControls.ui SegmentationUtilities/QmitkMorphologicalOperationsWidgetControls.ui SegmentationUtilities/QmitkSurfaceToImageWidgetControls.ui SegmentationUtilities/QmitkDataSelectionWidgetControls.ui ) set(QRC_FILES resources/SegmentationUI.qrc )