diff --git a/Modules/IGT/IO/mitkNavigationToolReader.cpp b/Modules/IGT/IO/mitkNavigationToolReader.cpp index cf30e6a5de..d7592d730b 100644 --- a/Modules/IGT/IO/mitkNavigationToolReader.cpp +++ b/Modules/IGT/IO/mitkNavigationToolReader.cpp @@ -1,220 +1,219 @@ /*=================================================================== 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. ===================================================================*/ //Poco headers #include #include //mitk headers #include "mitkNavigationToolReader.h" #include "mitkTrackingTypes.h" #include #include mitk::NavigationToolReader::NavigationToolReader() { - //TODO: maybe replace program path by a valid temp directory if there is one. See bug 17310 for the current problems. - m_ToolfilePath = mitk::IOUtil::GetProgramPath() + Poco::Path::separator() + "IGT_Toolfiles" + Poco::Path::separator(); + m_ToolfilePath = mitk::IOUtil::GetTempPath() + Poco::Path::separator() + "IGT_Toolfiles" + Poco::Path::separator(); } mitk::NavigationToolReader::~NavigationToolReader() { } mitk::NavigationTool::Pointer mitk::NavigationToolReader::DoRead(std::string filename) { //decompress all files into a temporary directory std::ifstream file( filename.c_str(), std::ios::binary ); if (!file.good()) { m_ErrorMessage = "Cannot open '" + filename + "' for reading"; return NULL; } std::string tempDirectory = m_ToolfilePath + GetFileWithoutPath(filename); Poco::Zip::Decompress unzipper( file, Poco::Path( tempDirectory ) ); unzipper.decompressAllFiles(); //use SceneSerialization to load the DataStorage mitk::SceneIO::Pointer mySceneIO = mitk::SceneIO::New(); mitk::DataStorage::Pointer loadedStorage = mySceneIO->LoadScene(tempDirectory + Poco::Path::separator() + GetFileWithoutPath(filename) + ".storage"); if (loadedStorage->GetAll()->size()==0 || loadedStorage.IsNull()) { m_ErrorMessage = "Invalid file: cannot parse tool data."; return NULL; } //convert the DataStorage back to a NavigationTool-Object mitk::DataNode::Pointer myNode = loadedStorage->GetAll()->ElementAt(0); mitk::NavigationTool::Pointer returnValue = ConvertDataNodeToNavigationTool(myNode, tempDirectory); //delete the data-storage file which is not needed any more. The toolfile must be left in the temporary directory becauses it is linked in the datatreenode of the tool std::remove((std::string(tempDirectory + Poco::Path::separator() + GetFileWithoutPath(filename) + ".storage")).c_str()); return returnValue; } mitk::NavigationTool::Pointer mitk::NavigationToolReader::ConvertDataNodeToNavigationTool(mitk::DataNode::Pointer node, std::string toolPath) { mitk::NavigationTool::Pointer returnValue = mitk::NavigationTool::New(); //DateTreeNode with Name and Surface mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(node->GetName()); newNode->SetData(node->GetData()); returnValue->SetDataNode(newNode); //Identifier std::string identifier; node->GetStringProperty("identifier",identifier); returnValue->SetIdentifier(identifier); //Serial Number std::string serial; node->GetStringProperty("serial number",serial); returnValue->SetSerialNumber(serial); //Tracking Device int device_type; node->GetIntProperty("tracking device type",device_type); returnValue->SetTrackingDeviceType(static_cast(device_type)); //Tool Type int type; node->GetIntProperty("tracking tool type",type); returnValue->SetType(static_cast(type)); //Calibration File Name std::string calibration_filename; node->GetStringProperty("toolfileName",calibration_filename); if (calibration_filename=="none") { returnValue->SetCalibrationFile("none"); } else { std::string calibration_filename_with_path = toolPath + Poco::Path::separator() + calibration_filename; returnValue->SetCalibrationFile(calibration_filename_with_path); } //Tool Landmarks mitk::PointSet::Pointer ToolRegLandmarks = mitk::PointSet::New(); mitk::PointSet::Pointer ToolCalLandmarks = mitk::PointSet::New(); std::string RegLandmarksString; std::string CalLandmarksString; node->GetStringProperty("ToolRegistrationLandmarks",RegLandmarksString); node->GetStringProperty("ToolCalibrationLandmarks",CalLandmarksString); ToolRegLandmarks = ConvertStringToPointSet(RegLandmarksString); ToolCalLandmarks = ConvertStringToPointSet(CalLandmarksString); returnValue->SetToolRegistrationLandmarks(ToolRegLandmarks); returnValue->SetToolCalibrationLandmarks(ToolCalLandmarks); //Tool Tip std::string toolTipPositionString; std::string toolTipOrientationString; bool positionSet = node->GetStringProperty("ToolTipPosition",toolTipPositionString); bool orientationSet = node->GetStringProperty("ToolTipOrientation",toolTipOrientationString); if(positionSet && orientationSet) //only define tooltip if it is set { returnValue->SetToolTipPosition(ConvertStringToPoint(toolTipPositionString)); returnValue->SetToolTipOrientation(ConvertStringToQuaternion(toolTipOrientationString)); } else if(positionSet != orientationSet) { MITK_WARN << "Tooltip definition incomplete: position and orientation have to be set! Skipping tooltip definition."; } return returnValue; } std::string mitk::NavigationToolReader::GetFileWithoutPath(std::string FileWithPath) { Poco::Path myFile(FileWithPath.c_str()); return myFile.getFileName(); } mitk::PointSet::Pointer mitk::NavigationToolReader::ConvertStringToPointSet(std::string string) { mitk::PointSet::Pointer returnValue = mitk::PointSet::New(); std::string pointSeperator = "|"; std::string valueSeperator = ";"; std::vector points; split(string,pointSeperator,points); for(unsigned int i=0; i values; split(points.at(i),valueSeperator,values); if (values.size() == 4) { double index = atof(values.at(0).c_str()); mitk::Point3D point; point[0] = atof(values.at(1).c_str()); point[1] = atof(values.at(2).c_str()); point[2] = atof(values.at(3).c_str()); returnValue->SetPoint(index,point); } } return returnValue; } mitk::Point3D mitk::NavigationToolReader::ConvertStringToPoint(std::string string) { std::string valueSeperator = ";"; std::vector values; split(string,valueSeperator,values); mitk::Point3D point; if (values.size() == 3) { point[0] = atof(values.at(0).c_str()); point[1] = atof(values.at(1).c_str()); point[2] = atof(values.at(2).c_str()); } return point; } mitk::Quaternion mitk::NavigationToolReader::ConvertStringToQuaternion(std::string string) { std::string valueSeperator = ";"; std::vector values; split(string,valueSeperator,values); mitk::Quaternion quat = mitk::Quaternion(0,0,0,1); if (values.size() == 4) { quat = mitk::Quaternion(atof(values.at(0).c_str()), atof(values.at(1).c_str()), atof(values.at(2).c_str()), atof(values.at(3).c_str())); } return quat; } void mitk::NavigationToolReader::split(std::string& text, std::string& separators, std::vector& words) { int n = text.length(); int start, stop; start = text.find_first_not_of(separators); while ((start >= 0) && (start < n)) { stop = text.find_first_of(separators, start); if ((stop < 0) || (stop > n)) stop = n; words.push_back(text.substr(start, stop - start)); start = text.find_first_not_of(separators, stop+1); } } diff --git a/Modules/IGT/Testing/files.cmake b/Modules/IGT/Testing/files.cmake index 645738fc8f..cc77978970 100644 --- a/Modules/IGT/Testing/files.cmake +++ b/Modules/IGT/Testing/files.cmake @@ -1,65 +1,65 @@ set(MODULE_TESTS # IMPORTANT: If you plan to deactivate / comment out a test please write a bug number to the commented out line of code. # # Example: #mitkMyTest #this test is commented out because of bug 12345 # # It is important that the bug is open and that the test will be activated again before the bug is closed. This assures that # no test is forgotten after it was commented out. If there is no bug for your current problem, please add a new one and # mark it as critical. ################## ON THE FENCE TESTS ################################################# # none ################## DISABLED TESTS ##################################################### # mitkNavigationToolStorageDeserializerTest.cpp # This test was disabled because of bug 17303. # mitkNavigationToolStorageSerializerAndDeserializerIntegrationTest.cpp # This test was disabled because of bug 17181. # mitkNavigationToolStorageSerializerTest.cpp # This test was disabled because of bug 18671 ################# RUNNING TESTS ####################################################### mitkCameraVisualizationTest.cpp mitkClaronInterfaceTest.cpp mitkClaronToolTest.cpp mitkClaronTrackingDeviceTest.cpp mitkInternalTrackingToolTest.cpp mitkNavigationDataDisplacementFilterTest.cpp mitkNavigationDataLandmarkTransformFilterTest.cpp mitkNavigationDataObjectVisualizationFilterTest.cpp mitkNavigationDataSetTest.cpp mitkNavigationDataTest.cpp mitkNavigationDataRecorderTest.cpp mitkNavigationDataReferenceTransformFilterTest.cpp mitkNavigationDataSequentialPlayerTest.cpp mitkNavigationDataSetReaderWriterXMLTest.cpp mitkNavigationDataSetReaderWriterCSVTest.cpp mitkNavigationDataSourceTest.cpp mitkNavigationDataToMessageFilterTest.cpp mitkNavigationDataToNavigationDataFilterTest.cpp mitkNavigationDataToPointSetFilterTest.cpp mitkNavigationDataToIGTLMessageFilterTest.cpp mitkNavigationDataTransformFilterTest.cpp mitkNDIPassiveToolTest.cpp mitkNDIProtocolTest.cpp mitkNDITrackingDeviceTest.cpp mitkTimeStampTest.cpp mitkTrackingVolumeGeneratorTest.cpp mitkTrackingDeviceTest.cpp mitkTrackingToolTest.cpp mitkVirtualTrackingDeviceTest.cpp # mitkNavigationDataPlayerTest.cpp # random fails see bug 16485. # We decided to won't fix because of complete restructuring via bug 15959. mitkTrackingDeviceSourceTest.cpp mitkTrackingDeviceSourceConfiguratorTest.cpp mitkNavigationDataEvaluationFilterTest.cpp mitkTrackingTypesTest.cpp # ------------------ Navigation Tool Management Tests ------------------- mitkNavigationToolStorageTest.cpp mitkNavigationToolTest.cpp - # mitkNavigationToolReaderAndWriterTest.cpp # deactivated because of bug 18835 + mitkNavigationToolReaderAndWriterTest.cpp # ----------------------------------------------------------------------- ) set(MODULE_CUSTOM_TESTS mitkNDIAuroraHardwareTest.cpp mitkNDIPolarisHardwareTest.cpp mitkClaronTrackingDeviceHardwareTest.cpp )