diff --git a/Modules/CppRestSdk/include/mitkRESTClient.h b/Modules/CppRestSdk/include/mitkRESTClient.h index 47ca6f5f85..589b3487a8 100644 --- a/Modules/CppRestSdk/include/mitkRESTClient.h +++ b/Modules/CppRestSdk/include/mitkRESTClient.h @@ -1,92 +1,96 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKRESTCLIENT_H #define MITKRESTCLIENT_H #include "cpprest/asyncrt_utils.h" #include "cpprest/containerstream.h" #include "cpprest/filestream.h" #include "cpprest/http_client.h" #include "cpprest/json.h" #include "cpprest/producerconsumerstream.h" #include "cpprest/uri.h" +#include "mitkRESTUtil.h" #include "MitkCppRestSdkExports.h" typedef web::http::client::http_client MitkClient; typedef web::http::http_request MitkRequest; typedef web::http::http_response MitkResponse; typedef web::http::methods MitkRESTMethods; typedef web::http::uri_builder MitkUriBuilder; typedef web::http::status_codes MitkRestStatusCodes; typedef web::json::json_exception MitkJsonException; namespace mitk { class MITKCPPRESTSDK_EXPORT RESTClient { public: ; /** - * @brief Creates a new client object containing the given base url which is extended by the uri of the member methods - * - * @param url represents the base URL which is extended by the member methods and used as target for HTTP requests - */ + * @brief Creates a new client object containing the given base url which is extended by the uri of the member + * methods + * + * @param url represents the base URL which is extended by the member methods and used as target for HTTP requests + */ RESTClient(utility::string_t url); virtual ~RESTClient(); /** * @brief Executes a HTTP POST request with given uri and the file given by the filePath * * @param uri defines the URI which extends the base URL of this object resulting the target of the HTTP request * @param filePath the path to the file which shall be included in the message body as multipart * @return task to wait for */ pplx::task Post(utility::string_t uri, utility::string_t filePath); /** * @brief Executes a HTTP GET request with the given uri and stores the byte stream in a file given by the filePath * * @param filePath the file path at which the received byte stream is stored * @param uri the URI which extends the base URL of this object resulting the target of the HTTP request * @return task to wait for */ pplx::task Get(const utility::string_t filePath, utility::string_t uri); /** * @brief Executes a HTTP GET request with the given uri and returns a json object * * @param uri the URI which extends the base URL of this object resulting the target of the HTTP request * @return task with to wait for with resulting json object */ pplx::task Get(utility::string_t uri); /** * @brief Executes a HTTP PUT request to the given uri containing the given content json object - * - * @param uri the URI which extends the base URL of this object resulting the target of the HTTP request - * @param content the json body for the PUT request + * + * @param uri the URI which extends the base URL of this object resulting the target of the HTTP request + * @param content the json body for the PUT request */ pplx::task PUT(utility::string_t uri, web::json::value content); + std::string GetHost() { return mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); } + protected: MitkClient *m_Client; }; -}; +}; // namespace mitk #endif // MITKRESTCLIENT_H diff --git a/Modules/CppRestSdk/src/mitkDICOMWeb.cpp b/Modules/CppRestSdk/src/mitkDICOMWeb.cpp index 5cd68079a9..ce566ac2dd 100644 --- a/Modules/CppRestSdk/src/mitkDICOMWeb.cpp +++ b/Modules/CppRestSdk/src/mitkDICOMWeb.cpp @@ -1,135 +1,143 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkDICOMWeb.h" #include "mitkRESTUtil.h" #include mitk::DICOMWeb::DICOMWeb(utility::string_t url) : mitk::RESTClient(url) { } mitk::DICOMWeb::~DICOMWeb() { } pplx::task mitk::DICOMWeb::QidoRSInstances(std::map params) { MitkUriBuilder queryBuilder(U("rs/instances")); for (auto const& element : params) { queryBuilder.append_query(mitk::RESTUtil::convertToTString(element.first), mitk::RESTUtil::convertToTString(element.second)); } - MITK_INFO << utility::conversions::to_utf8string(queryBuilder.to_string()); + MITK_INFO << GetHost() << "/" << utility::conversions::to_utf8string(queryBuilder.to_string()); MitkRequest instances(MitkRESTMethods::GET); instances.set_request_uri(queryBuilder.to_string()); instances.headers().add(U("Accept"), U("application/json")); - return m_Client->request(instances).then([=](MitkResponse response) + return m_Client->request(instances).then([=](pplx::task taskResponse) { - auto status = response.status_code(); - MITK_INFO << " status: " << status; + try + { + MitkResponse response = taskResponse.get(); + auto status = response.status_code(); + MITK_INFO << " status: " << status; - if (status != web::http::status_codes::OK) { - MITK_ERROR << "no dicom series found for query " << utility::conversions::to_utf8string(queryBuilder.to_string()); - mitkThrow() << "no dicom series found for query " << utility::conversions::to_utf8string(queryBuilder.to_string()); - } + if (status != web::http::status_codes::OK) { + MITK_ERROR << "no dicom series found for query " << utility::conversions::to_utf8string(queryBuilder.to_string()); + mitkThrow() << "no dicom series found for query " << utility::conversions::to_utf8string(queryBuilder.to_string()); + } - return response.extract_json().get(); + return response.extract_json().get(); + } + catch (std::exception &e) + { + mitkThrow() << e.what(); + } }); } pplx::task mitk::DICOMWeb::WadoRS(utility::string_t filePath, std::string studyUID, std::string seriesUID, std::string instanceUID) { MitkUriBuilder builder(U("wado")); builder.append_query(U("requestType"), U("WADO")); builder.append_query(U("studyUID"), mitk::RESTUtil::convertToTString(studyUID)); builder.append_query(U("seriesUID"), mitk::RESTUtil::convertToTString(seriesUID)); builder.append_query(U("objectUID"), mitk::RESTUtil::convertToTString(instanceUID)); builder.append_query(U("contentType"), U("application/dicom")); return Get(filePath, builder.to_string()); } pplx::task mitk::DICOMWeb::WadoRS(const utility::string_t folderPath, std::string studyUID, std::string seriesUID) { typedef std::map ParamMap; ParamMap seriesInstancesParams; seriesInstancesParams.insert(ParamMap::value_type({"StudyInstanceUID"}, studyUID)); seriesInstancesParams.insert(ParamMap::value_type({"SeriesInstanceUID"}, seriesUID)); return QidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) -> pplx::task { auto jsonListResult = jsonResult; auto resultArray = jsonListResult.as_array(); auto firstFileName = std::string(); std::vector> tasks; for (unsigned short i = 0; i < resultArray.size(); i++) { try { auto firstResult = resultArray[i]; auto sopInstanceUIDKey = firstResult.at(U("00080018")); auto sopInstanceObject = sopInstanceUIDKey.as_object(); auto valueKey = sopInstanceObject.at(U("Value")); auto valueArray = valueKey.as_array(); auto sopInstanceUID = valueArray[0].as_string(); auto fileName = utility::string_t(sopInstanceUID).append(U(".dcm")); // save first file name as result to load series if (i == 0) { firstFileName = utility::conversions::to_utf8string(fileName); } auto filePath = utility::string_t(folderPath).append(fileName); auto task = WadoRS(filePath, studyUID, seriesUID, mitk::RESTUtil::convertToUtf8(sopInstanceUID)); tasks.push_back(task); } catch (const web::json::json_exception& e) { MITK_ERROR << e.what(); } } auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto returnTask = joinTask.then([=](void) -> std::string { auto folderPathUtf8 = utility::conversions::to_utf8string(folderPath); auto result = folderPathUtf8 + firstFileName; return result; }); return returnTask; }); } pplx::task mitk::DICOMWeb::StowRS(utility::string_t filePath, std::string studyUID) { // TODO: add data MitkUriBuilder builder(U("rs/studies")); builder.append_path(mitk::RESTUtil::convertToTString(studyUID)); return Post(builder.to_string(), filePath); } \ No newline at end of file diff --git a/Modules/CppRestSdk/src/mitkRESTClient.cpp b/Modules/CppRestSdk/src/mitkRESTClient.cpp index b12abdec29..da288a73eb 100644 --- a/Modules/CppRestSdk/src/mitkRESTClient.cpp +++ b/Modules/CppRestSdk/src/mitkRESTClient.cpp @@ -1,146 +1,169 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkRESTClient.h" #include "mitkRESTUtil.h" #include mitk::RESTClient::RESTClient(utility::string_t url) { m_Client = new MitkClient(url); + web::http::client::http_client_config conf = m_Client->client_config(); + conf.set_timeout(utility::seconds(3)); } mitk::RESTClient::~RESTClient() { delete m_Client; } pplx::task mitk::RESTClient::PUT(utility::string_t uri, web::json::value content) { MITK_DEBUG << "Calling PUT with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); MitkRequest putRequest(MitkRESTMethods::PUT); putRequest.set_request_uri(uri); putRequest.set_body(content); - return m_Client->request(putRequest).then([=](MitkResponse response) + return m_Client->request(putRequest).then([=](pplx::task responseTask) { - auto status = response.status_code(); - MITK_INFO << " status: " << status; - - if (status != web::http::status_codes::OK) { - mitkThrow() << "response was not OK"; + try + { + auto response = responseTask.get(); + auto status = response.status_code(); + MITK_INFO << " status: " << status; + + if (status != web::http::status_codes::OK) + { + mitkThrow() << "response was not OK"; + } + + return response.extract_json().get(); + } + catch (std::exception &e) { + MITK_WARN << e.what(); + return web::json::value::null(); } - - return response.extract_json().get(); }); } pplx::task mitk::RESTClient::Get(utility::string_t uri) { MITK_INFO << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()); MitkRequest getRequest(MitkRESTMethods::GET); getRequest.set_request_uri(uri); - return m_Client->request(getRequest).then([=](MitkResponse response) + return m_Client->request(getRequest).then([=](pplx::task responseTask) { - auto status = response.status_code(); - MITK_INFO << " status: " << status; + try + { + auto response = responseTask.get(); - if (status != web::http::status_codes::OK) { - mitkThrow() << "response was not OK"; - } + auto status = response.status_code(); + MITK_INFO << " status: " << status; + + if (status != web::http::status_codes::OK) + { + mitkThrow() << "response was not OK"; + } - return response.extract_json().get(); + return response.extract_json().get(); + } + catch (std::exception &e) + { + MITK_WARN << e.what(); + return web::json::value::null(); + } }); } pplx::task mitk::RESTClient::Get(utility::string_t filePath, utility::string_t uri) { MITK_DEBUG << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client " << mitk::RESTUtil::convertToUtf8(m_Client->base_uri().to_string()) << " save into " << mitk::RESTUtil::convertToUtf8(filePath); auto fileBuffer = std::make_shared>(); return concurrency::streams::file_buffer::open(filePath, std::ios::out).then([=](concurrency::streams::streambuf outFile) -> pplx::task { *fileBuffer = outFile; return m_Client->request(MitkRESTMethods::GET, uri); }) // Write the response body into the file buffer. - .then([=](MitkResponse response) -> pplx::task + .then([=](pplx::task responseTask) -> pplx::task { + auto response = responseTask.get(); auto status = response.status_code(); MITK_DEBUG << "Status code: " << status; if (status != web::http::status_codes::OK) { mitkThrow() << "GET ended up with response " << mitk::RESTUtil::convertToUtf8(response.to_string()); } return response.body().read_to_end(*fileBuffer); }) // Close the file buffer. .then([=](size_t) { return fileBuffer->close(); }); } pplx::task mitk::RESTClient::Post(utility::string_t uri, utility::string_t filePath) { // this is the working stow-rs request which supports just one dicom file packed into a multipart message std::basic_ifstream input(filePath, std::ios::binary); std::vector result; std::vector buffer((std::istreambuf_iterator(input)), (std::istreambuf_iterator())); // reuse 'content-type' variable or struct to be more flexible, in future more than one file should also be supported.. std::string head = ""; head += "\r\n--boundary"; head += "\r\nContent-Type: " + mitk::RESTUtil::convertToUtf8(U("application/dicom")) + "\r\n\r\n"; std::vector bodyVector(head.begin(), head.end()); std::string tail = ""; tail += "\r\n--boundary--"; result.insert(result.end(), bodyVector.begin(), bodyVector.end()); result.insert(result.end(), buffer.begin(), buffer.end()); result.insert(result.end(), tail.begin(), tail.end()); MitkRequest postRequest(MitkRESTMethods::POST); postRequest.set_request_uri(uri); postRequest.headers().add(U("Content-Type"), "multipart/related; type=\"application/dicom\"; boundary=boundary"); postRequest.set_body(result); MITK_INFO << "Request: " << mitk::RESTUtil::convertToUtf8(postRequest.to_string()); return m_Client->request(postRequest).then([](MitkResponse response) { auto status = response.status_code(); if (status != web::http::status_codes::OK) { mitkThrow() << "POST ended up with response " << mitk::RESTUtil::convertToUtf8(response.to_string()); } MITK_INFO << "Response: " << mitk::RESTUtil::convertToUtf8(response.to_string()); }); } \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp index fa8f5cc59d..c5432c1bc8 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkREST.cpp @@ -1,196 +1,196 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include "SegmentationReworkREST.h" #include #include SegmentationReworkREST::SegmentationReworkREST() {} SegmentationReworkREST::SegmentationReworkREST(utility::string_t url) : mitk::RESTServer(url) { m_Listener.support(MitkRESTMethods::PUT, std::bind(&SegmentationReworkREST::HandlePut, this, std::placeholders::_1)); m_Listener.support(MitkRESTMethods::GET, std::bind(&SegmentationReworkREST::HandleGet, this, std::placeholders::_1)); } SegmentationReworkREST::~SegmentationReworkREST() {} void SegmentationReworkREST::HandleGet(MitkRequest message) { auto messageString = message.to_string(); MITK_INFO << "Message GET incoming..."; MITK_INFO << mitk::RESTUtil::convertToUtf8(messageString); MITK_INFO << mitk::RESTUtil::convertToUtf8(message.request_uri().to_string()); auto uri = web::uri::decode(message.request_uri().to_string()); if (uri.find(U("/robots.txt")) != std::string::npos || uri.find(U("/favicon.ico")) != std::string::npos || uri == U("/-") || uri.length() == 0) { - MITK_INFO << "ignore GET request."; + MITK_INFO << "ignore GET request: " << mitk::RESTUtil::convertToUtf8(messageString); return; } auto query = web::uri(uri).query(); auto httpParams = web::uri::split_query(query); // IHE Invoke Image Display style auto requestType = httpParams.find(U("requestType")); MITK_INFO << "parameters found: " << httpParams.size(); MitkResponse responsePositive(MitkRestStatusCodes::OK); responsePositive.set_body("call to mitk was successfully!"); if (requestType != httpParams.end() && requestType->second == U("IMAGE_SEG")) { try { auto studyUID = httpParams.at(U("studyUID")); auto imageSeriesUID = httpParams.at(U("imageSeriesUID")); auto segSeriesUID = httpParams.at(U("segSeriesUID")); DicomDTO dto; dto.imageSeriesUID = mitk::RESTUtil::convertToUtf8(imageSeriesUID); dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); dto.segSeriesUIDA = mitk::RESTUtil::convertToUtf8(segSeriesUID); MITK_INFO << "studyUID: " << dto.studyUID; MITK_INFO << "imageSeriesUID: " << dto.imageSeriesUID; MITK_INFO << "segSeriesUID: " << dto.segSeriesUIDA; m_GetImageSegCallback(dto); MitkResponse response(MitkRestStatusCodes::OK); message.reply(responsePositive); } catch (std::out_of_range& e) { message.reply(MitkRestStatusCodes::BadRequest, "oh man, that was not expected: " + std::string(e.what())); } } else if (requestType != httpParams.end() && requestType->second == U("SEG_EVALUATION")) { // TODO: implement PUT handling as GET } else if (requestType != httpParams.end() && requestType->second == U("IMAGE_SEG_LIST")) { auto studyUID = httpParams.at(U("studyUID")); auto imageSeriesUID = httpParams.at(U("imageSeriesUID")); auto segSeriesUIDList = httpParams.at(U("segSeriesUIDList")); DicomDTO dto; dto.imageSeriesUID = mitk::RESTUtil::convertToUtf8(imageSeriesUID); dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); auto segSeriesUIDListUtf8 = mitk::RESTUtil::convertToUtf8(segSeriesUIDList); std::istringstream f(segSeriesUIDListUtf8); std::string s; while (getline(f, s, ',')) { dto.seriesUIDList.push_back(s); } MITK_INFO << "studyUID: " << dto.studyUID; MITK_INFO << "imageSeriesUID: " << dto.imageSeriesUID; MITK_INFO << "segSeriesUIDList: " << segSeriesUIDListUtf8; m_GetImageSegCallback(dto); message.reply(responsePositive); } else if (requestType != httpParams.end() && requestType->second == U("ADD_SERIES")) { auto studyUID = httpParams.at(U("studyUID")); auto segSeriesUIDList = httpParams.at(U("seriesUIDList")); DicomDTO dto; dto.studyUID = mitk::RESTUtil::convertToUtf8(studyUID); auto seriesUIDListUtf8 = mitk::RESTUtil::convertToUtf8(segSeriesUIDList); std::istringstream f(seriesUIDListUtf8); std::string s; while (getline(f, s, ',')) { dto.seriesUIDList.push_back(s); } MITK_INFO << "studyUID: " << dto.studyUID; MITK_INFO << "seriesUIDList: " << seriesUIDListUtf8; m_GetAddSeriesCallback(dto); message.reply(responsePositive); } else { message.reply(MitkRestStatusCodes::BadRequest, "unknown request type " + mitk::RESTUtil::convertToUtf8(requestType->second)); } } void SegmentationReworkREST::HandlePut(MitkRequest message) { auto messageString = message.to_string(); MITK_INFO << "Message PUT incoming..."; MITK_INFO << mitk::RESTUtil::convertToUtf8(messageString); try { auto jsonMessage = message.extract_json().get(); auto messageTypeKey = jsonMessage.at(U("messageType")); if (messageTypeKey.as_string() == U("downloadData")) { auto imageStudyUIDKey = jsonMessage.at(U("studyUID")); auto srSeriesUIDKey = jsonMessage.at(U("srSeriesUID")); auto groundTruthKey = jsonMessage.at(U("groundTruth")); auto simScoreKey = jsonMessage.at(U("simScoreArray")); auto minSliceStartKey = jsonMessage.at(U("minSliceStart")); DicomDTO dto; dto.srSeriesUID = mitk::RESTUtil::convertToUtf8(srSeriesUIDKey.as_string()); dto.groundTruth = mitk::RESTUtil::convertToUtf8(groundTruthKey.as_string()); dto.studyUID = mitk::RESTUtil::convertToUtf8(imageStudyUIDKey.as_string()); dto.minSliceStart = minSliceStartKey.as_integer(); std::vector vec; web::json::array simArray = simScoreKey.as_array(); for (web::json::value score : simArray) { vec.push_back(score.as_double() * 100); } dto.simScoreArray = vec; m_PutCallback(dto); emit InvokeUpdateChartWidget(); } else { message.reply(MitkRestStatusCodes::BadRequest, "Oh man, i can only deal with 'messageType' = 'downloadData'..."); } } catch (MitkJsonException &e) { MITK_ERROR << e.what() << ".. oh man, that was not expected"; message.reply(MitkRestStatusCodes::BadRequest, "oh man, that was not expected"); return; } MitkResponse response(MitkRestStatusCodes::OK); response.headers().add(U("Access-Control-Allow-Origin"), U("localhost:9000/*")); response.set_body("Sure, i got you.. have an awesome day"); message.reply(response); return; } \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp index 18225d1543..37c485b397 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.cpp @@ -1,592 +1,699 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "SegmentationReworkView.h" #include // Qt #include #include -#include #include -#include -#include +#include +#include +#include #include +#include #include -#include -#include +#include #include -#include #include +#include const std::string SegmentationReworkView::VIEW_ID = "org.mitk.views.segmentationreworkview"; void SegmentationReworkView::SetFocus() {} void SegmentationReworkView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; counter = 0; - qRegisterMetaType< std::vector >("std::vector"); + qRegisterMetaType>("std::vector"); - //m_Controls.verticalWidget->setVisible(false); + // m_Controls.verticalWidget->setVisible(false); m_Controls.cleanDicomBtn->setVisible(false); m_Controls.individualWidget_2->setVisible(false); m_Controls.sliderWidget->setMinimum(1); m_Controls.sliderWidget->setMaximum(100); m_Controls.sliderWidget->setTickInterval(1); m_Controls.sliderWidget->setSingleStep(1); m_Controls.radioA->setChecked(true); connect(m_Controls.buttonUpload, &QPushButton::clicked, this, &SegmentationReworkView::UploadNewSegmentation); connect(m_Controls.buttonNewSeg, &QPushButton::clicked, this, &SegmentationReworkView::CreateNewSegmentationC); connect(m_Controls.cleanDicomBtn, &QPushButton::clicked, this, &SegmentationReworkView::CleanDicomFolder); - connect(m_Controls.restartConnection, &QPushButton::clicked, this, &SegmentationReworkView::RestartConnection); + connect(m_Controls.restartConnection, &QPushButton::clicked, this, &SegmentationReworkView::OnRestartConnection); + connect(m_Controls.testConnection, &QPushButton::clicked, this, &SegmentationReworkView::TestConnection); connect(m_Controls.checkIndiv, &QCheckBox::stateChanged, this, &SegmentationReworkView::OnIndividualCheckChange); - connect(m_Controls.sliderWidget, &ctkSliderWidget::valueChanged, this, &SegmentationReworkView::OnSliderWidgetChanged); + connect( + m_Controls.sliderWidget, &ctkSliderWidget::valueChanged, this, &SegmentationReworkView::OnSliderWidgetChanged); m_DownloadBaseDir = mitk::IOUtil::GetTempPathA() + "segrework"; MITK_INFO << "using download base dir: " << m_DownloadBaseDir; m_UploadBaseDir = mitk::IOUtil::GetTempPathA() + "uploadSeg"; if (!itksys::SystemTools::FileIsDirectory(m_DownloadBaseDir)) { itk::FileTools::CreateDirectory(m_DownloadBaseDir); } if (!itksys::SystemTools::FileIsDirectory(m_UploadBaseDir)) { itk::FileTools::CreateDirectory(m_UploadBaseDir); } utility::string_t port = U("2020"); utility::string_t address = U("http://127.0.0.1:"); address.append(port); m_HttpHandler = std::unique_ptr(new SegmentationReworkREST(address)); connect(m_HttpHandler.get(), - &SegmentationReworkREST::InvokeUpdateChartWidget, - this, - &SegmentationReworkView::UpdateChartWidget); + &SegmentationReworkREST::InvokeUpdateChartWidget, + this, + &SegmentationReworkView::UpdateChartWidget); connect(this, &SegmentationReworkView::InvokeLoadData, this, &SegmentationReworkView::LoadData); connect(this, &SegmentationReworkView::InvokeProgress, this, &SegmentationReworkView::AddProgress); m_HttpHandler->SetPutCallback(std::bind(&SegmentationReworkView::RESTPutCallback, this, std::placeholders::_1)); - m_HttpHandler->SetGetImageSegCallback(std::bind(&SegmentationReworkView::RESTGetCallback, this, std::placeholders::_1)); - m_HttpHandler->SetGetAddSeriesCallback(std::bind(&SegmentationReworkView::RESTGetCallbackGeneric, this, std::placeholders::_1)); + m_HttpHandler->SetGetImageSegCallback( + std::bind(&SegmentationReworkView::RESTGetCallback, this, std::placeholders::_1)); + m_HttpHandler->SetGetAddSeriesCallback( + std::bind(&SegmentationReworkView::RESTGetCallbackGeneric, this, std::placeholders::_1)); m_HttpHandler->Open().wait(); MITK_INFO << "Listening for requests at: " << utility::conversions::to_utf8string(address); - //utility::string_t pacsURL = U("http://jip-dktk/dcm4chee-arc/aets/DCM4CHEE"); - utility::string_t pacsURL = U("http://193.174.48.78:8090/dcm4chee-arc/aets/DCM4CHEE"); + // utility::string_t pacsURL = U("http://jip-dktk/dcm4chee-arc/aets/DCM4CHEE"); utility::string_t restURL = U("http://localhost:8000"); - m_DICOMWeb = new mitk::DICOMWeb(pacsURL); - MITK_INFO << "requests to pacs are sent to: " << utility::conversions::to_utf8string(pacsURL); - m_Controls.dcm4cheeURL->setText({ (utility::conversions::to_utf8string(pacsURL).c_str()) }); - + RestartConnection("http://e230-pc03.inet.dkfz-heidelberg.de:8090"); m_RestService = new mitk::RESTClient(restURL); } void SegmentationReworkView::OnSliderWidgetChanged(double value) { std::map::iterator it; unsigned int count = 0; for (it = m_ScoreMap.begin(); it != m_ScoreMap.end(); it++) { if (it->second < value) { count++; } } QString labelsToDelete = "slices to delete: " + QString::number(count); m_Controls.slicesToDeleteLabel->setText(labelsToDelete); std::map thresholdMap; for (it = m_ScoreMap.begin(); it != m_ScoreMap.end(); it++) { thresholdMap.insert(std::map::value_type(it->first, value)); } m_Controls.chartWidget->RemoveData(m_thresholdLabel); m_Controls.chartWidget->AddData2D(thresholdMap, m_thresholdLabel); m_Controls.chartWidget->SetChartType(m_thresholdLabel, QmitkChartWidget::ChartType::line); m_Controls.chartWidget->Show(); } void SegmentationReworkView::AddProgress(int progress, QString status) { auto futureValue = m_Controls.progressBar->value() + progress; - if (futureValue >= 100) + if (futureValue >= 100) { m_Controls.progressBar->setValue(0); m_Controls.progressBar->setFormat(""); - } else + } + else { m_Controls.progressBar->setFormat(status.append(" %p%")); m_Controls.progressBar->setValue(futureValue); } } -void SegmentationReworkView::RestartConnection() +pplx::task SegmentationReworkView::TestConnection() +{ + typedef std::map ParamMap; + ParamMap seriesInstancesParams; + + seriesInstancesParams.insert((ParamMap::value_type({"limit"}, {"1"}))); + m_Controls.connectionStatus->setText(QString("Testing connection ...")); + return m_DICOMWeb->QidoRSInstances(seriesInstancesParams).then([=](pplx::task resultTask) { + try + { + auto result = resultTask.get(); + if (!result.is_null()) + { + m_Controls.connectionStatus->setText(QString("Connection works!")); + return true; + } + else + { + m_Controls.connectionStatus->setText(QString("Trouble with connection. Not valid!")); + return false; + } + } + catch (mitk::Exception &e) + { + MITK_WARN << e.what(); + m_Controls.connectionStatus->setText(QString("No connection possible.")); + return false; + } + }); +} + +void SegmentationReworkView::OnRestartConnection() { - auto host = m_Controls.dcm4cheeHostValue->text(); - std::string url = host.toStdString() + "/dcm4chee-arc/aets/DCM4CHEE"; + RestartConnection(); +} - m_DICOMWeb = new mitk::DICOMWeb(utility::conversions::to_string_t(url)); - MITK_INFO << "requests to pacs are sent to: " << url; - m_Controls.dcm4cheeURL->setText({ (utility::conversions::to_utf8string(url).c_str()) }); +void SegmentationReworkView::RestartConnection(std::string newHost) +{ + auto hostBefore = m_Controls.dcm4cheeURL->text(); + std::string host; + if (newHost.empty()) + { + host = m_Controls.dcm4cheeHostValue->text().toStdString(); + } + else + { + host = newHost; + } + + std::string url = host + "/dcm4chee-arc/aets/DCM4CHEE"; + + if (!host.empty()) + { + MITK_INFO << "Restarting connection to " << url << " ..."; + m_Controls.connectionStatus->setText(QString("Restarting connection...")); + m_Controls.dcm4cheeURL->setText({(utility::conversions::to_utf8string(url).c_str())}); + try + { + m_DICOMWeb = new mitk::DICOMWeb(utility::conversions::to_string_t(url)); + } + catch (std::exception &e) + { + MITK_WARN << e.what(); + m_Controls.dcm4cheeURL->setText(hostBefore); + m_Controls.connectionStatus->setText(QString("Invalid host!")); + return; + } + + if (!TestConnection().get()) + { + MITK_INFO << "Restart did not work.."; + m_Controls.connectionStatus->setText(QString("No PACS server available under given host!")); + } + else{ + MITK_INFO << "requests to pacs are sent to: " << url; + } + } + else + { + m_Controls.connectionStatus->setText(QString("Host must not be empty!")); + } } void SegmentationReworkView::OnIndividualCheckChange(int state) { - if(state == Qt::Unchecked) + if (state == Qt::Unchecked) { m_Controls.individualWidget_2->setVisible(false); } else if (state == Qt::Checked) { m_Controls.individualWidget_2->setVisible(true); } } void SegmentationReworkView::RESTPutCallback(const SegmentationReworkREST::DicomDTO &dto) { - emit InvokeProgress(20, { "display graph and query structured report" }); + emit InvokeProgress(20, {"display graph and query structured report"}); SetSimilarityGraph(dto.simScoreArray, dto.minSliceStart); m_SRUID = dto.srSeriesUID; m_GroundTruth = dto.groundTruth; typedef std::map ParamMap; ParamMap seriesInstancesParams; seriesInstancesParams.insert((ParamMap::value_type({"StudyInstanceUID"}, dto.studyUID))); seriesInstancesParams.insert((ParamMap::value_type({"SeriesInstanceUID"}, dto.srSeriesUID))); - seriesInstancesParams.insert((ParamMap::value_type({"includefield"}, {"0040A375"}))); // Current Requested Procedure Evidence Sequence - - try { - m_DICOMWeb->QidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) - { + seriesInstancesParams.insert( + (ParamMap::value_type({"includefield"}, {"0040A375"}))); // Current Requested Procedure Evidence Sequence + try + { + m_DICOMWeb->QidoRSInstances(seriesInstancesParams).then([=](web::json::value jsonResult) { auto firstResult = jsonResult[0]; - auto actualListKey = firstResult.at(U("0040A375")).as_object().at(U("Value")).as_array()[0].as_object().at(U("00081115")).as_object().at(U("Value")).as_array(); + auto actualListKey = firstResult.at(U("0040A375")) + .as_object() + .at(U("Value")) + .as_array()[0] + .as_object() + .at(U("00081115")) + .as_object() + .at(U("Value")) + .as_array(); std::string segSeriesUIDA = ""; std::string segSeriesUIDB = ""; std::string imageSeriesUID = ""; - for (unsigned int index = 0; index < actualListKey.size(); index++) { + for (unsigned int index = 0; index < actualListKey.size(); index++) + { auto element = actualListKey[index].as_object(); // get SOP class UID auto innerElement = element.at(U("00081199")).as_object().at(U("Value")).as_array()[0]; auto sopClassUID = innerElement.at(U("00081150")).as_object().at(U("Value")).as_array()[0].as_string(); - auto seriesUID = utility::conversions::to_utf8string(element.at(U("0020000E")).as_object().at(U("Value")).as_array()[0].as_string()); + auto seriesUID = utility::conversions::to_utf8string( + element.at(U("0020000E")).as_object().at(U("Value")).as_array()[0].as_string()); if (sopClassUID == U("1.2.840.10008.5.1.4.1.1.66.4")) // SEG { if (segSeriesUIDA.length() == 0) { segSeriesUIDA = seriesUID; } else { segSeriesUIDB = seriesUID; } } - else if (sopClassUID == U("1.2.840.10008.5.1.4.1.1.2")) // CT + else if (sopClassUID == U("1.2.840.10008.5.1.4.1.1.2")) // CT { imageSeriesUID = seriesUID; } } emit InvokeProgress(10, {"load composite context of structured report"}); MITK_INFO << "image series UID " << imageSeriesUID; MITK_INFO << "seg A series UID " << segSeriesUIDA; MITK_INFO << "seg B series UID " << segSeriesUIDB; MITK_INFO << "Load related dicom series ..."; - std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) +"/"; + std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; std::string pathSegA = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; std::string pathSegB = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; auto folderPathSegA = utility::conversions::to_string_t(pathSegA); auto folderPathSegB = utility::conversions::to_string_t(pathSegB); m_CurrentStudyUID = dto.studyUID; std::vector> tasks; - auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, imageSeriesUID); + auto imageSeriesTask = + m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, imageSeriesUID); auto segATask = m_DICOMWeb->WadoRS(folderPathSegA, dto.studyUID, segSeriesUIDA); auto segBTask = m_DICOMWeb->WadoRS(folderPathSegB, dto.studyUID, segSeriesUIDB); tasks.push_back(imageSeriesTask); tasks.push_back(segATask); tasks.push_back(segBTask); auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { emit InvokeProgress(50, {"load dicom files from disk"}); InvokeLoadData(filePathList); }); }); - } - catch (mitk::Exception& e) { + catch (mitk::Exception &e) + { MITK_ERROR << e.what(); } } void SegmentationReworkView::RESTGetCallbackGeneric(const SegmentationReworkREST::DicomDTO &dto) { std::vector> tasks; - if (dto.seriesUIDList.size() > 0) { + if (dto.seriesUIDList.size() > 0) + { for (std::string segSeriesUID : dto.seriesUIDList) { std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; - try { - auto seriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, segSeriesUID); + try + { + auto seriesTask = + m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, segSeriesUID); tasks.push_back(seriesTask); - } catch (const mitk::Exception &exception) + } + catch (const mitk::Exception &exception) { MITK_INFO << exception.what(); return; } } } - try + try { auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); } - catch (const mitk::Exception& exception) + catch (const mitk::Exception &exception) { MITK_INFO << exception.what(); return; } } -void SegmentationReworkView::RESTGetCallback(const SegmentationReworkREST::DicomDTO &dto) +void SegmentationReworkView::RESTGetCallback(const SegmentationReworkREST::DicomDTO &dto) { std::string folderPathSeries = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; MITK_INFO << folderPathSeries; std::string pathSeg = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_DownloadBaseDir) + "/"; auto folderPathSeg = utility::conversions::to_string_t(pathSeg); MITK_INFO << pathSeg; - try { + try + { std::vector> tasks; - auto imageSeriesTask = m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); + auto imageSeriesTask = + m_DICOMWeb->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID); tasks.push_back(imageSeriesTask); - if (dto.seriesUIDList.size() > 0) { + if (dto.seriesUIDList.size() > 0) + { for (std::string segSeriesUID : dto.seriesUIDList) { auto segTask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, segSeriesUID); tasks.push_back(segTask); } } - else { + else + { auto segATask = m_DICOMWeb->WadoRS(folderPathSeg, dto.studyUID, dto.segSeriesUIDA); tasks.push_back(segATask); } - auto joinTask = pplx::when_all(begin(tasks), end(tasks)); auto filePathList = joinTask.then([&](std::vector filePathList) { InvokeLoadData(filePathList); }); } - catch (const mitk::Exception &exception) { + catch (const mitk::Exception &exception) + { MITK_INFO << exception.what(); } } std::string SegmentationReworkView::GetAlgorithmOfSegByPath(std::string path) { auto scanner = mitk::DICOMDCMTKTagScanner::New(); mitk::DICOMTagPath algorithmName; algorithmName.AddAnySelection(0x0062, 0x0002).AddElement(0x0062, 0x0009); mitk::StringList files; files.push_back(path); scanner->SetInputFiles(files); scanner->AddTagPath(algorithmName); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); auto findings = frames.front()->GetTagValueAsString(algorithmName); if (findings.size() != 0) MITK_INFO << findings.front().value; return findings.front().value; } void SegmentationReworkView::LoadData(std::vector filePathList) { MITK_INFO << "Loading finished. Pushing data to data storage ..."; auto ds = GetDataStorage(); auto dataNodes = mitk::IOUtil::Load(filePathList, *ds); // reinit view mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(ds); // find data nodes m_Image = dataNodes->at(0); m_Image->SetName("image data"); m_SegA = dataNodes->at(1); m_SegB = dataNodes->at(2); auto algorithmNameA = GetAlgorithmOfSegByPath(filePathList[1]); auto algorithmNameB = GetAlgorithmOfSegByPath(filePathList[2]); m_SegA->SetName(algorithmNameA); m_SegB->SetName(algorithmNameB); m_Controls.labelSegAValue->setText(algorithmNameA.c_str()); m_Controls.labelSegBValue->setText(algorithmNameB.c_str()); m_Controls.labelGroundTruthValue->setText(m_GroundTruth.c_str()); - emit InvokeProgress(20, { "" }); + emit InvokeProgress(20, {""}); } void SegmentationReworkView::UpdateChartWidget() { m_Controls.chartWidget->Show(); } void SegmentationReworkView::SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart) { std::string label = "similarity graph"; m_thresholdLabel = "threshold"; - //m_Controls.chartWidget->Clear(); + // m_Controls.chartWidget->Clear(); double sliceIndex = sliceMinStart; for (double score : simScoreArray) { m_ScoreMap.insert(std::map::value_type(sliceIndex, score)); sliceIndex++; } std::map thresholdMap; m_Controls.chartWidget->AddData2D(m_ScoreMap, label); m_Controls.chartWidget->AddData2D(thresholdMap, m_thresholdLabel); m_Controls.chartWidget->SetChartType(label, QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetChartType(m_thresholdLabel, QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetXAxisLabel("slice number"); m_Controls.chartWidget->SetYAxisLabel("similarity in percent"); m_Controls.chartWidget->SetTitle("Similartiy Score for Segmentation Comparison"); } void SegmentationReworkView::UploadNewSegmentation() { - AddProgress(10, { "save SEG to temp folder" }); + AddProgress(10, {"save SEG to temp folder"}); std::string folderPathSeg = mitk::IOUtil::CreateTemporaryDirectory("XXXXXX", m_UploadBaseDir) + "/"; const std::string savePath = folderPathSeg + m_SegC->GetName() + ".dcm"; const std::string mimeType = mitk::MitkDICOMQIIOMimeTypes::DICOMSEG_MIMETYPE_NAME(); mitk::IOUtil::Save(m_SegC->GetData(), mimeType, savePath); // get Series Instance UID from new SEG auto scanner = mitk::DICOMDCMTKTagScanner::New(); mitk::DICOMTagPath seriesUID(0x0020, 0x000E); mitk::StringList files; files.push_back(savePath); scanner->SetInputFiles(files); scanner->AddTagPath(seriesUID); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); auto findings = frames.front()->GetTagValueAsString(seriesUID); auto segSeriesUID = findings.front().value; AddProgress(20, {"push SEG to PACS"}); auto filePath = utility::conversions::to_string_t(savePath); - try { + try + { m_DICOMWeb->StowRS(filePath, m_CurrentStudyUID).then([=] { - emit InvokeProgress(40, {"persist reworked SEG to evaluation database"}); + emit InvokeProgress(40, {"persist reworked SEG to evaluation database"}); MitkUriBuilder queryBuilder(U("tasks/evaluations/")); queryBuilder.append_query(U("srUID"), utility::conversions::to_string_t(m_SRUID)); - //queryBuilder.append_path(U("71/")); + m_RestService->Get(queryBuilder.to_string()).then([=](web::json::value result) { MITK_INFO << "after GET"; MITK_INFO << utility::conversions::to_utf8string(result.to_string()); auto updatedContent = result.as_array()[0]; - updatedContent[U("reworkedSegmentationUID")] = web::json::value::string(utility::conversions::to_string_t(segSeriesUID)); - + updatedContent[U("reworkedSegmentationUID")] = + web::json::value::string(utility::conversions::to_string_t(segSeriesUID)); + auto id = updatedContent.at(U("id")).as_integer(); MITK_INFO << id; auto idParam = std::to_string(id).append("/"); MitkUriBuilder queryBuilder(U("tasks/evaluations")); queryBuilder.append_path(utility::conversions::to_string_t(idParam)); m_RestService->PUT(queryBuilder.to_string(), updatedContent).then([=](web::json::value result) { MITK_INFO << "successfully stored"; - emit InvokeProgress(30, { "successfully stored" }); + emit InvokeProgress(30, {"successfully stored"}); }); }); }); } catch (const std::exception &exception) { std::cout << exception.what() << std::endl; } } -std::vector SegmentationReworkView::CreateSegmentation(mitk::Image::Pointer baseSegmentation, double threshold) +std::vector SegmentationReworkView::CreateSegmentation(mitk::Image::Pointer baseSegmentation, + double threshold) { MITK_INFO << "handle individual segmentation creation"; std::map::iterator it; std::vector sliceIndices; unsigned int count = 0; for (it = m_ScoreMap.begin(); it != m_ScoreMap.end(); it++) { if (it->second < threshold) { auto index = it->first; - try + try { mitk::ImagePixelWriteAccessor imageAccessor(baseSegmentation); for (unsigned int x = 0; x < baseSegmentation->GetDimension(0); x++) { for (unsigned int y = 0; y < baseSegmentation->GetDimension(1); y++) { - imageAccessor.SetPixelByIndex({ { x, y, int(index) } }, 0); + imageAccessor.SetPixelByIndex({{x, y, int(index)}}, 0); } } } - catch (mitk::Exception& e) { + catch (mitk::Exception &e) + { MITK_ERROR << e.what(); } count++; sliceIndices.push_back(index); - MITK_INFO << "slice " << it->first << " removed "; - } + MITK_INFO << "slice " << it->first << " removed "; + } } MITK_INFO << "slices deleted " << count; return sliceIndices; } -void SegmentationReworkView::CreateNewSegmentationC() +void SegmentationReworkView::CreateNewSegmentationC() { - mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); + mitk::ToolManager *toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); toolManager->InitializeTools(); toolManager->SetReferenceData(m_Image); - + mitk::Image::Pointer baseImage; - if (m_Controls.radioA->isChecked()) { - baseImage = dynamic_cast(m_SegA->GetData())->Clone(); + if (m_Controls.radioA->isChecked()) + { + baseImage = dynamic_cast(m_SegA->GetData())->Clone(); } - else if (m_Controls.radioB->isChecked()) { - baseImage = dynamic_cast(m_SegB->GetData())->Clone(); + else if (m_Controls.radioB->isChecked()) + { + baseImage = dynamic_cast(m_SegB->GetData())->Clone(); } if (m_Controls.checkIndiv->isChecked()) { auto sliceIndices = CreateSegmentation(baseImage, m_Controls.sliderWidget->value()); } - QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent); // needs a QWidget as parent, "this" is not QWidget + QmitkNewSegmentationDialog *dialog = + new QmitkNewSegmentationDialog(m_Parent); // needs a QWidget as parent, "this" is not QWidget int dialogReturnValue = dialog->exec(); if (dialogReturnValue == QDialog::Rejected) { // user clicked cancel or pressed Esc or something similar return; } // ask the user about an organ type and name, add this information to the image's (!) propertylist // create a new image of the same dimensions and smallest possible pixel type - mitk::Tool* firstTool = toolManager->GetToolById(0); + mitk::Tool *firstTool = toolManager->GetToolById(0); if (firstTool) { try { std::string newNodeName = dialog->GetSegmentationName().toStdString(); if (newNodeName.empty()) { newNodeName = "no_name"; } - mitk::DataNode::Pointer newSegmentation = firstTool->CreateSegmentationNode(baseImage, newNodeName, dialog->GetColor()); + mitk::DataNode::Pointer newSegmentation = + firstTool->CreateSegmentationNode(baseImage, newNodeName, dialog->GetColor()); // initialize showVolume to false to prevent recalculating the volume while working on the segmentation newSegmentation->SetProperty("showVolume", mitk::BoolProperty::New(false)); if (!newSegmentation) { return; // could be aborted by user } if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)) { mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)->SetSelected(false); } newSegmentation->SetSelected(true); - this->GetDataStorage()->Add(newSegmentation, toolManager->GetReferenceData(0)); // add as a child, because the segmentation "derives" from the original - + this->GetDataStorage()->Add( + newSegmentation, + toolManager->GetReferenceData(0)); // add as a child, because the segmentation "derives" from the original + m_SegC = newSegmentation; auto referencedImages = m_Image->GetData()->GetProperty("files"); m_SegC->GetData()->SetProperty("referenceFiles", referencedImages); - } catch (std::bad_alloc) { - QMessageBox::warning(nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation")); + QMessageBox::warning( + nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation")); } } - else { + else + { MITK_INFO << "no tools..."; } } -void SegmentationReworkView::CleanDicomFolder() +void SegmentationReworkView::CleanDicomFolder() { - if (m_SegA || m_SegB || m_SegC) { - QMessageBox::warning(nullptr, tr("Clean dicom folder"), tr("Please remove the data in data storage before cleaning the download folder")); + if (m_SegA || m_SegB || m_SegC) + { + QMessageBox::warning(nullptr, + tr("Clean dicom folder"), + tr("Please remove the data in data storage before cleaning the download folder")); return; } - //std::experimental::filesystem::remove_all(m_DownloadBaseDir); + // std::experimental::filesystem::remove_all(m_DownloadBaseDir); // TODO : use POCO - //itk::FileTools::CreateDirectory(m_DownloadBaseDir); + // itk::FileTools::CreateDirectory(m_DownloadBaseDir); } diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h index bb8dc07e34..a3851ae860 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkView.h @@ -1,107 +1,108 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef SegmentationReworkView_h #define SegmentationReworkView_h #include #include #include "ui_SegmentationReworkViewControls.h" #include "SegmentationReworkREST.h" #include #include #include /** \brief SegmentationReworkView \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class SegmentationReworkView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; void RESTPutCallback(const SegmentationReworkREST::DicomDTO& dto); void RESTGetCallback(const SegmentationReworkREST::DicomDTO& dto); void RESTGetCallbackGeneric(const SegmentationReworkREST::DicomDTO& dto); void UpdateChartWidget(); void ClearChartWidget(); void LoadData(std::vector filePathList); void OnSliderWidgetChanged(double value); void AddProgress(int, QString status); signals: void InvokeLoadData(std::vector filePathList); void InvokeProgress(int, QString status); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; /// \brief Called when the user clicks the GUI button void CreateNewSegmentationC(); void CleanDicomFolder(); void UploadNewSegmentation(); - void RestartConnection(); + void RestartConnection(std::string = ""); + void OnRestartConnection(); + pplx::task TestConnection(); void OnIndividualCheckChange(int state); Ui::SegmentationReworkViewControls m_Controls; private: std::vector CreateSegmentation(mitk::Image::Pointer baseSegmentation, double threshold); - void InterpolateSegmentation(mitk::Image::Pointer baseSegmentation, std::vector sliceIndices); std::string GetAlgorithmOfSegByPath(std::string path); void SetSimilarityGraph(std::vector simScoreArray, int sliceMinStart); std::unique_ptr m_HttpHandler; mitk::DICOMWeb* m_DICOMWeb; mitk::RESTClient* m_RestService; std::string m_CurrentStudyUID; std::string m_SRUID; std::string m_DownloadBaseDir; std::string m_UploadBaseDir; mitk::DataNode::Pointer m_Image; mitk::DataNode::Pointer m_SegA; mitk::DataNode::Pointer m_SegB; mitk::DataNode::Pointer m_SegC; std::map m_ScoreMap; std::string m_GroundTruth; std::string m_thresholdLabel; QWidget* m_Parent; int counter; }; #endif // SegmentationReworkView_h diff --git a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui index aa68327398..b48e922c52 100644 --- a/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation.rework/src/internal/SegmentationReworkViewControls.ui @@ -1,291 +1,313 @@ SegmentationReworkViewControls 0 0 465 - 821 + 856 0 0 QmitkTemplate dcm4chee host example input: http://193.174.48.78:8090 - - - - restart dcm4chee connection - - - - + 0 Qt::AlignCenter true + + + + + + restart connection + + + + + + + + + + + + + + + + + + + + + Qt::AlignCenter + + + + + + + test connection + + + + + - - - - - - - Qt::AlignCenter - - - Segmentation B: Segmentation A: Ground Truth: 0 400 16777215 400 false 0 0 0 60 Select segmentation basis true QLayout::SetDefaultConstraint A B Individual 0 0 Slices to delete: Create new Segmentation Qt::Horizontal Do image processing Upload Segmentation Qt::Vertical QSizePolicy::Expanding 20 220 clean dicom download folder QmitkChartWidget QWidget
QmitkChartWidget.h
1 ctkSliderWidget QWidget
ctksliderwidget.h
1