diff --git a/Modules/CppRestSdk/src/mitkRESTClient.cpp b/Modules/CppRestSdk/src/mitkRESTClient.cpp
index 440bf9066d..bedfac0beb 100644
--- a/Modules/CppRestSdk/src/mitkRESTClient.cpp
+++ b/Modules/CppRestSdk/src/mitkRESTClient.cpp
@@ -1,155 +1,157 @@
/*===================================================================
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 <mitkCommon.h>
mitk::RESTClient::RESTClient(utility::string_t url) : m_Client(url) {
}
mitk::RESTClient::~RESTClient() {}
pplx::task<void> mitk::RESTClient::Get(utility::string_t filePath, utility::string_t uri)
{
- MITK_INFO << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client "
+ MITK_DEBUG << "Calling GET with " << utility::conversions::to_utf8string(uri) << " on client "
<< utility::conversions::to_utf8string(m_Client.base_uri().to_string()) << " save into "
<< utility::conversions::to_utf8string(filePath);
auto fileBuffer = std::make_shared<concurrency::streams::streambuf<uint8_t>>();
return concurrency::streams::file_buffer<uint8_t>::open(filePath, std::ios::out).then([=](concurrency::streams::streambuf<uint8_t> outFile) -> pplx::task<MitkResponse>
{
*fileBuffer = outFile;
return m_Client.request(MitkRESTMethods::GET, uri);
})
// Write the response body into the file buffer.
.then([=](MitkResponse response) -> pplx::task<size_t>
{
- MITK_INFO << "Status code: " << response.status_code();
+ MITK_DEBUG << "Status code: " << response.status_code();
return response.body().read_to_end(*fileBuffer);
})
// Close the file buffer.
.then([=](size_t)
{
return fileBuffer->close();
});
}
pplx::task<void> mitk::RESTClient::Post(utility::string_t uri,
utility::string_t contentType,
concurrency::streams::streambuf<uint8_t> data)
{
MITK_INFO << "Calling POST with " << utility::conversions::to_utf8string(uri) << " on client "
<< utility::conversions::to_utf8string(m_Client.base_uri().to_string());
MitkRequest postRequest(MitkRESTMethods::POST);
postRequest.set_request_uri(uri);
postRequest.headers().add(U("Content-Type"), contentType);
postRequest.set_body(data);
- return m_Client.request(postRequest).then([&](MitkResponse response)
+ MITK_INFO << "Request: " << utility::conversions::to_utf8string(postRequest.to_string());
+
+ return m_Client.request(postRequest).then([=](MitkResponse response)
{
- MITK_INFO << "Status code: " << response.status_code();
+ MITK_INFO << "Response: " << utility::conversions::to_utf8string(response.to_string());
});
}
pplx::task<void> mitk::RESTClient::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"), utility::conversions::to_string_t(studyUID));
builder.append_query(U("seriesUID"), utility::conversions::to_string_t(seriesUID));
builder.append_query(U("objectUID"), utility::conversions::to_string_t(instanceUID));
builder.append_query(U("contentType"), U("application/dicom"));
return Get(filePath, builder.to_string());
}
pplx::task<std::string> mitk::RESTClient::WadoRS(const utility::string_t folderPath, std::string studyUID, std::string seriesUID)
{
// this is actually a quido-rs request, should be packed into a seperate method.. at some time..
//but there are many possible requests to support: http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_6.7.html
MitkUriBuilder builder(U("rs/instances"));
builder.append_query(U("StudyInstanceUID"), utility::conversions::to_string_t(studyUID));
builder.append_query(U("SeriesInstanceUID"), utility::conversions::to_string_t(seriesUID));
MITK_INFO << utility::conversions::to_utf8string(builder.to_string());
MitkRequest getSeries(MitkRESTMethods::GET);
getSeries.set_request_uri(builder.to_string());
getSeries.headers().add(U("Accept"), U("application/json"));
return m_Client.request(getSeries).then([=](MitkResponse response) -> pplx::task<std::string>
{
MITK_INFO << "search for instances in series with uid " << seriesUID
- << " status: " << response.status_code();
+ << " status: " << response.status_code();
auto jsonListResult = response.extract_json().get();
auto resultArray = jsonListResult.as_array();
- auto firstFileName = std::string();
+ auto firstFileName = std::string();
std::vector<pplx::task<void>> tasks;
for (unsigned short i = 0; i < resultArray.size(); i++)
{
- try
+ 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 = sopInstanceUID.append(U(".dcm"));
+ 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);
- }
+ // 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, utility::conversions::to_utf8string(sopInstanceUID));
tasks.push_back(task);
}
- catch (const web::json::json_exception& e)
+ catch (const web::json::json_exception& e)
{
MITK_ERROR << e.what();
}
}
auto joinTask = pplx::when_all(begin(tasks), end(tasks));
- return joinTask.then([=](void)
- {
- return firstFileName;
- });
+ return joinTask.then([=](void)
+ {
+ return utility::conversions::to_utf8string(folderPath).append(firstFileName);
+ });
});
}
pplx::task<void> mitk::RESTClient::StowRS(utility::string_t filePath, std::string studyUID)
{
// TODO: add data
MitkUriBuilder builder(U("rs/studies"));
- builder.append_query(utility::conversions::to_string_t(studyUID));
+ builder.append_path(utility::conversions::to_string_t(studyUID));
- concurrency::streams::file_buffer<uint8_t>::open(filePath, std::ios::in)
- .then([&](concurrency::streams::streambuf<uint8_t> data) {
- return Post(builder.to_string(), U("multipart/related; type='application/dicom'; boundary='boundary'"), data);
+ return concurrency::streams::file_buffer<uint8_t>::open(filePath, std::ios::in)
+ .then([=](concurrency::streams::streambuf<uint8_t> data) {
+ return Post(builder.to_string(), U("multipart/related; type='application/dicom';"), data);
});
}
\ 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 4355356664..d2d01c9eac 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
@@ -1,95 +1,90 @@
/*===================================================================
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 "SegmentationReworkREST.h"
#include <mitkCommon.h>
SegmentationReworkREST::SegmentationReworkREST() {}
SegmentationReworkREST::SegmentationReworkREST(utility::string_t url) : mitk::RESTServer(url)
{
m_Listener.support(MitkRESTMethods::PUT, std::bind(&SegmentationReworkREST::HandlePut, this, std::placeholders::_1));
}
SegmentationReworkREST::~SegmentationReworkREST() {}
void SegmentationReworkREST::SetPutCallback(std::function<void(DicomDTO& message)> callback)
{
m_PutCallback = callback;
}
void SegmentationReworkREST::HandlePut(MitkRequest message)
{
auto messageString = message.to_string();
MITK_INFO << "Message PUT incoming...";
MITK_INFO << 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 imageSeriesUIDKey = jsonMessage.at(U("imageSeriesUID"));
auto segSeriesUIDAKey = jsonMessage.at(U("segSeriesUIDA"));
auto segSeriesUIDBKey = jsonMessage.at(U("segSeriesUIDB"));
- auto segInstanceUIDAKey = jsonMessage.at(U("segInstanceUIDA"));
- auto segInstanceUIDBKey = jsonMessage.at(U("segInstanceUIDB"));
-
auto simScoreKey = jsonMessage.at(U("simScoreArray"));
auto minSliceStartKey = jsonMessage.at(U("minSliceStart"));
DicomDTO dto;
dto.segSeriesUIDA = convertToUtf8(segSeriesUIDAKey.as_string());
dto.segSeriesUIDB = convertToUtf8(segSeriesUIDBKey.as_string());
dto.imageSeriesUID = convertToUtf8(imageSeriesUIDKey.as_string());
- dto.segInstanceUIDA = convertToUtf8(segInstanceUIDAKey.as_string());
- dto.segInstanceUIDB = convertToUtf8(segInstanceUIDBKey.as_string());
dto.studyUID = convertToUtf8(imageStudyUIDKey.as_string());
dto.minSliceStart = minSliceStartKey.as_integer();
std::vector<double> vec;
web::json::array simArray = simScoreKey.as_array();
for (web::json::value score : simArray) {
vec.push_back(score.as_double());
}
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 a1673c0a5a..a7bb73fb57 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
@@ -1,177 +1,186 @@
/*===================================================================
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 <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Qmitk
#include "SegmentationReworkView.h"
// Qt
#include <QMessageBox>
#include <mitkIOUtil.h>
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);
+ qRegisterMetaType< std::vector<std::string> >("std::vector<std::string>");
+
connect(m_Controls.buttonUpload, &QPushButton::clicked, this, &SegmentationReworkView::UploadNewSegmentation);
utility::string_t port = U("2020");
utility::string_t address = U("http://127.0.0.1:");
address.append(port);
m_HttpHandler = std::unique_ptr<SegmentationReworkREST>(new SegmentationReworkREST(address));
connect(m_HttpHandler.get(),
- &SegmentationReworkREST::InvokeUpdateChartWidget,
- this,
- &SegmentationReworkView::UpdateChartWidget);
+ &SegmentationReworkREST::InvokeUpdateChartWidget,
+ this,
+ &SegmentationReworkView::UpdateChartWidget);
+ connect(this, &SegmentationReworkView::InvokeLoadData, this, &SegmentationReworkView::LoadData);
m_HttpHandler->SetPutCallback(std::bind(&SegmentationReworkView::RESTPutCallback, this, std::placeholders::_1));
m_HttpHandler->Open().wait();
MITK_INFO << "Listening for requests at: " << utility::conversions::to_utf8string(address);
utility::string_t pacsHost = U("http://193.174.48.78:8090/dcm4chee-arc/aets/DCM4CHEE");
m_RestClient = new mitk::RESTClient(pacsHost);
}
void SegmentationReworkView::RESTPutCallback(const SegmentationReworkREST::DicomDTO &dto)
{
SetSimilarityGraph(dto.simScoreArray, dto.minSliceStart);
- MITK_INFO << "Loading image series";
+ MITK_INFO << "Load related dicom series ...";
std::string folderPathSeries = "/temp/downloadSeries/";
+ auto folderPathSegA = U("/temp/segA/");
+ auto folderPathSegB = U("/temp/segB/");
m_CurrentStudyUID = dto.studyUID;
- m_RestClient->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID)
- .then([&](std::string fileName) {
- MITK_INFO << "Loading image series into data storage";
- auto folderPath = folderPathSeries;
- auto firstFilePath = folderPath.append(fileName);
- mitk::IOUtil::Load(firstFilePath, *this->GetDataStorage());
-
- MITK_INFO << "Loading segmentations...";
-
- auto filePathSegA = U("/temp/segA.dcm");
- auto filePathSegB = U("/temp/segB.dcm");
-
- m_RestClient->WadoRS(filePathSegA, dto.studyUID, dto.segSeriesUIDA, dto.segInstanceUIDA).then([&] {
- mitk::IOUtil::Load(utility::conversions::to_utf8string(filePathSegA), *this->GetDataStorage());
- });
+ std::vector<pplx::task<std::string>> tasks;
+ auto imageSeriesTask = m_RestClient->WadoRS(utility::conversions::to_string_t(folderPathSeries), dto.studyUID, dto.imageSeriesUID);
+ auto segATask = m_RestClient->WadoRS(folderPathSegA, dto.studyUID, dto.segSeriesUIDA);
+ auto segBTask = m_RestClient->WadoRS(folderPathSegB, dto.studyUID, dto.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<std::string> filePathList) {
+ InvokeLoadData(filePathList);
+ });
+}
- m_RestClient->WadoRS(filePathSegB, dto.studyUID, dto.segSeriesUIDB, dto.segInstanceUIDB).then([&] {
- mitk::IOUtil::Load(utility::conversions::to_utf8string(filePathSegB), *this->GetDataStorage());
- });
- });
+void SegmentationReworkView::LoadData(std::vector<std::string> filePathList)
+{
+ MITK_INFO << "Loading finished. Pushing data to data storage ...";
+ mitk::IOUtil::Load(filePathList, *this->GetDataStorage());
}
void SegmentationReworkView::UpdateChartWidget()
{
m_Controls.chartWidget->Show();
}
void SegmentationReworkView::SetSimilarityGraph(std::vector<double> simScoreArray, int sliceMinStart)
{
std::map<double, double> map;
- MITK_INFO << simScoreArray.size();
double sliceIndex = sliceMinStart;
for (double score : simScoreArray)
{
map.insert(std::map<double, double>::value_type(sliceIndex, score));
sliceIndex++;
}
m_Controls.chartWidget->AddData2D(map, "similarity score");
m_Controls.chartWidget->SetChartType("similarity score", QmitkChartWidget::ChartType::line);
m_Controls.chartWidget->SetXAxisLabel("slice number");
m_Controls.chartWidget->SetYAxisLabel("similarity score");
}
void SegmentationReworkView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer> &nodes)
+ const QList<mitk::DataNode::Pointer> &nodes)
{
// iterate all selected objects, adjust warning visibility
- foreach (mitk::DataNode::Pointer node, nodes)
+ foreach(mitk::DataNode::Pointer node, nodes)
{
if (node.IsNotNull() && dynamic_cast<mitk::Image *>(node->GetData()))
{
m_Controls.labelWarning->setVisible(false);
return;
}
}
m_Controls.labelWarning->setVisible(true);
}
-void SegmentationReworkView::UploadNewSegmentation()
+void SegmentationReworkView::UploadNewSegmentation()
{
- auto filePath = U("path/to/dicomSeg.dcm");
- m_RestClient->StowRS(filePath, m_CurrentStudyUID).then([]
+ auto filePath = U("/temp/segA/1.2.276.0.7230010.3.1.4.296485376.8.1533635734.141264.dcm");
+ m_CurrentStudyUID = "1.2.840.113654.2.70.1.159145727925405623564217141386659468090";
+ try {
+ m_RestClient->StowRS(filePath, m_CurrentStudyUID).then([]
+ {
+ MITK_INFO << "SEG uploaded";
+ });
+ }
+ catch (std::exception &exception)
{
- MITK_INFO << "SEG uploaded";
- });
+ MITK_ERROR << exception.what();
+ }
}
void SegmentationReworkView::DoImageProcessing()
{
QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
if (nodes.empty())
return;
mitk::DataNode *node = nodes.front();
if (!node)
{
// Nothing selected. Inform the user and return
QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing.");
return;
}
// here we have a valid mitk::DataNode
// a node itself is not very useful, we need its data item (the image)
mitk::BaseData *data = node->GetData();
if (data)
{
// test if this data item is an image or not (could also be a surface or something totally different)
mitk::Image *image = dynamic_cast<mitk::Image *>(data);
if (image)
{
std::stringstream message;
std::string name;
message << "Performing image processing for image ";
if (node->GetName(name))
{
// a property called "name" was found for this DataNode
message << "'" << name << "'";
}
message << ".";
MITK_INFO << message.str();
// actually do something here...
}
}
}
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 844fe96189..8a8f5bfca4 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
@@ -1,76 +1,80 @@
/*===================================================================
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 <berryISelectionListener.h>
#include <QmitkAbstractView.h>
#include "ui_SegmentationReworkViewControls.h"
#include "SegmentationReworkRest.h"
#include <mitkRESTClient.h>
/**
\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 UpdateChartWidget();
+ void LoadData(std::vector<std::string> filePathList);
+
+signals:
+ void InvokeLoadData(std::vector<std::string> filePathList);
protected:
virtual void CreateQtPartControl(QWidget *parent) override;
virtual void SetFocus() override;
/// \brief called by QmitkFunctionality when DataManager's selection has changed
virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
const QList<mitk::DataNode::Pointer> &nodes) override;
/// \brief Called when the user clicks the GUI button
void DoImageProcessing();
void UploadNewSegmentation();
Ui::SegmentationReworkViewControls m_Controls;
private:
void SetSimilarityGraph(std::vector<double> simScoreArray, int sliceMinStart);
std::unique_ptr<SegmentationReworkREST> m_HttpHandler;
mitk::RESTClient* m_RestClient;
std::string m_CurrentStudyUID;
};
#endif // SegmentationReworkView_h