diff --git a/Modules/DICOMReader/mitkDICOMReaderConfigurator.cpp b/Modules/DICOMReader/mitkDICOMReaderConfigurator.cpp index eaa184d1ef..3b0e550a5e 100644 --- a/Modules/DICOMReader/mitkDICOMReaderConfigurator.cpp +++ b/Modules/DICOMReader/mitkDICOMReaderConfigurator.cpp @@ -1,333 +1,333 @@ /*=================================================================== 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 "mitkDICOMReaderConfigurator.h" #include "mitkClassicDICOMSeriesReader.h" #include "mitkDICOMTagBasedSorter.h" #include "mitkDICOMSortByTag.h" #include "mitkSortByImagePositionPatient.h" mitk::DICOMReaderConfigurator ::DICOMReaderConfigurator() { } mitk::DICOMReaderConfigurator ::~DICOMReaderConfigurator() { } mitk::DICOMFileReader::Pointer mitk::DICOMReaderConfigurator ::CreateFromConfigFile(const std::string& filename) { TiXmlDocument doc (filename); if (doc.LoadFile()) { return this->CreateFromTiXmlDocument( doc ); } else { MITK_ERROR << "Unable to load file at '" << filename <<"'"; return DICOMFileReader::Pointer(); } } mitk::DICOMFileReader::Pointer mitk::DICOMReaderConfigurator ::CreateFromUTF8ConfigString(const std::string& xmlContents) { TiXmlDocument doc; doc.Parse(xmlContents.c_str(), 0, TIXML_ENCODING_UTF8); return this->CreateFromTiXmlDocument( doc ); } mitk::DICOMFileReader::Pointer mitk::DICOMReaderConfigurator ::CreateFromTiXmlDocument(TiXmlDocument& doc) { TiXmlHandle root(doc.RootElement()); if (TiXmlElement* rootElement = root.ToElement()) { if (strcmp(rootElement->Value(), "DICOMFileReader")) // :-( no std::string methods { MITK_ERROR << "File should contain a tag at top-level! Found '" << (rootElement->Value() ? std::string(rootElement->Value()) : std::string("!nothing!")) << "' instead"; return NULL; } const char* classnameC = rootElement->Attribute("class"); if (!classnameC) { MITK_ERROR << "File should name a reader class in the class attribute: . Found nothing instead"; return NULL; } std::string classname(classnameC); if (classname == "ThreeDnTDICOMSeriesReader") { mitk::ThreeDnTDICOMSeriesReader::Pointer reader = mitk::ThreeDnTDICOMSeriesReader::New(); return ConfigureThreeDnTDICOMSeriesReader(reader, rootElement).GetPointer(); } else if (classname == "DICOMITKSeriesGDCMReader") { mitk::DICOMITKSeriesGDCMReader::Pointer reader = mitk::DICOMITKSeriesGDCMReader::New(); return ConfigureDICOMITKSeriesGDCMReader(reader, rootElement).GetPointer(); } else { MITK_ERROR << "DICOMFileReader tag names unknown class '" << classname << "'"; return NULL; } } else { MITK_ERROR << "Great confusion: no root element in XML document. Expecting a DICOMFileReader tag at top-level."; return NULL; } } #define boolStringTrue(s) \ ( s == "true" || s == "on" || s == "1" \ || s == "TRUE" || s == "ON") mitk::ThreeDnTDICOMSeriesReader::Pointer mitk::DICOMReaderConfigurator ::ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement* element) { assert(element); // use all the base class configuration if (this->ConfigureDICOMITKSeriesGDCMReader( reader.GetPointer(), element ).IsNull()) { return NULL; } // add the "group3DnT" flag bool group3DnT(true); const char* group3DnTC = element->Attribute("group3DnT"); if (group3DnTC) { std::string group3DnTS(group3DnTC); group3DnT = boolStringTrue(group3DnTS); } reader->SetGroup3DandT( group3DnT ); return reader; } mitk::DICOMITKSeriesGDCMReader::Pointer mitk::DICOMReaderConfigurator ::ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement* element) { assert(element); const char* configLabelC = element->Attribute("label"); if (configLabelC) { std::string configLabel(configLabelC); reader->SetConfigurationLabel(configLabel); } - const char* configDescriptionC = element->Attribute("label"); + const char* configDescriptionC = element->Attribute("description"); if (configDescriptionC) { std::string configDescription(configDescriptionC); reader->SetConfigurationDescription(configDescriptionC); } // "fixTiltByShearing" flag bool fixTiltByShearing(false); const char* fixTiltByShearingC = element->Attribute("fixTiltByShearing"); if (fixTiltByShearingC) { std::string fixTiltByShearingS(fixTiltByShearingC); fixTiltByShearing = boolStringTrue(fixTiltByShearingS); } reader->SetFixTiltByShearing( fixTiltByShearing ); // "distinguishing tags" mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New(); TiXmlElement* dElement = element->FirstChildElement("Distinguishing"); if (dElement) { for ( TiXmlElement* tChild = dElement->FirstChildElement(); tChild != NULL; tChild = tChild->NextSiblingElement() ) { try { mitk::DICOMTag tag = tagFromXMLElement(tChild); tagSorter->AddDistinguishingTag( tag ); } catch(...) { return NULL; } } } // "sorting tags" TiXmlElement* sElement = element->FirstChildElement("Sorting"); if (dElement) { DICOMSortCriterion::Pointer previousCriterion; DICOMSortCriterion::Pointer currentCriterion; for ( TiXmlNode* tChildNode = sElement->LastChild(); tChildNode != NULL; tChildNode = tChildNode->PreviousSibling() ) { TiXmlElement* tChild = tChildNode->ToElement(); if (!tChild) continue; if (!strcmp(tChild->Value(), "Tag")) { try { currentCriterion = this->CreateDICOMSortByTag(tChild, previousCriterion); } catch(...) { std::stringstream ss; ss << "Could not parse element at (input line " << tChild->Row() << ", col. " << tChild->Column() << ")!"; MITK_ERROR << ss.str(); return NULL; } } else if (!strcmp(tChild->Value(), "ImagePositionPatient")) { try { currentCriterion = this->CreateSortByImagePositionPatient(tChild, previousCriterion); } catch(...) { std::stringstream ss; ss << "Could not parse element at (input line " << tChild->Row() << ", col. " << tChild->Column() << ")!"; MITK_ERROR << ss.str(); return NULL; } } else { MITK_ERROR << "File contain unknown tag <" << tChild->Value() << "> tag as child to ! Cannot interpret..."; } previousCriterion = currentCriterion; } tagSorter->SetSortCriterion( currentCriterion.GetPointer() ); // TODO get ConstPointer declarations right here } reader->AddSortingElement( tagSorter ); return reader; } std::string mitk::DICOMReaderConfigurator ::requiredStringAttribute(TiXmlElement* xmlElement, const std::string& key) { assert(xmlElement); const char* gC = xmlElement->Attribute(key.c_str()); if (gC) { std::string gS(gC); return gS; } else { std::stringstream ss; ss << "Expected an attribute '" << key << "' at this position " "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!"; MITK_ERROR << ss.str(); throw std::invalid_argument( ss.str() ); } } unsigned int mitk::DICOMReaderConfigurator ::hexStringToUInt(const std::string& s) { std::stringstream converter(s); unsigned int ui; converter >> std::hex >> ui; MITK_DEBUG << "Converted string '" << s << "' to unsigned int " << ui; return ui; } mitk::DICOMTag mitk::DICOMReaderConfigurator ::tagFromXMLElement(TiXmlElement* xmlElement) { assert(xmlElement); if (strcmp(xmlElement->Value(), "Tag")) // :-( no std::string methods { std::stringstream ss; ss << "Expected a tag at this position " "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!"; MITK_ERROR << ss.str(); throw std::invalid_argument( ss.str() ); } std::string name = requiredStringAttribute(xmlElement, "name"); std::string groupS = requiredStringAttribute(xmlElement, "group"); std::string elementS = requiredStringAttribute(xmlElement, "element"); try { // convert string to int (assuming string is in hex format with leading "0x" like "0x0020") unsigned int group = hexStringToUInt(groupS); unsigned int element = hexStringToUInt(elementS); return DICOMTag(group, element); } catch(...) { std::stringstream ss; ss << "Expected group and element values in to be hexadecimal with leading 0x, e.g. '0x0020'" "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!"; MITK_ERROR << ss.str(); throw std::invalid_argument( ss.str() ); } } mitk::DICOMSortCriterion::Pointer mitk::DICOMReaderConfigurator ::CreateDICOMSortByTag(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) { mitk::DICOMTag tag = tagFromXMLElement(xmlElement); return DICOMSortByTag::New(tag, secondaryCriterion).GetPointer(); } mitk::DICOMSortCriterion::Pointer mitk::DICOMReaderConfigurator ::CreateSortByImagePositionPatient(TiXmlElement*, DICOMSortCriterion::Pointer secondaryCriterion) { return SortByImagePositionPatient::New(secondaryCriterion).GetPointer(); }