diff --git a/Modules/DICOMReader/mitkDICOMSortByTag.cpp b/Modules/DICOMReader/mitkDICOMSortByTag.cpp index 1f56d826d1..4e691f7ddd 100644 --- a/Modules/DICOMReader/mitkDICOMSortByTag.cpp +++ b/Modules/DICOMReader/mitkDICOMSortByTag.cpp @@ -1,175 +1,176 @@ /*=================================================================== 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 "mitkDICOMSortByTag.h" mitk::DICOMSortByTag ::DICOMSortByTag(const DICOMTag& tag, DICOMSortCriterion::Pointer secondaryCriterion) :DICOMSortCriterion(secondaryCriterion) ,m_Tag(tag) { } mitk::DICOMSortByTag ::~DICOMSortByTag() { } mitk::DICOMSortByTag ::DICOMSortByTag(const DICOMSortByTag& other ) :DICOMSortCriterion(other) ,m_Tag(other.m_Tag) { } mitk::DICOMSortByTag& mitk::DICOMSortByTag ::operator=(const DICOMSortByTag& other) { if (this != &other) { DICOMSortCriterion::operator=(other); m_Tag = other.m_Tag; } return *this; } bool mitk::DICOMSortByTag ::operator==(const DICOMSortCriterion& other) const { if (const DICOMSortByTag* otherSelf = dynamic_cast(&other)) { if (!(this->m_Tag == otherSelf->m_Tag)) return false; if (this->m_SecondaryCriterion.IsNull() && otherSelf->m_SecondaryCriterion.IsNull()) return true; if (this->m_SecondaryCriterion.IsNull() || otherSelf->m_SecondaryCriterion.IsNull()) return false; return *(this->m_SecondaryCriterion) == *(otherSelf->m_SecondaryCriterion); } else { return false; } } void mitk::DICOMSortByTag ::Print(std::ostream& os) const { m_Tag.Print(os); } mitk::DICOMTagList mitk::DICOMSortByTag ::GetTagsOfInterest() const { DICOMTagList list; list.push_back(m_Tag); return list; } bool mitk::DICOMSortByTag ::IsLeftBeforeRight(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) const { return this->NumericCompare(left, right, m_Tag); } bool mitk::DICOMSortByTag ::StringCompare(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right, const DICOMTag& tag) const { assert(left); assert(right); std::string leftString = left->GetTagValueAsString(tag); std::string rightString = right->GetTagValueAsString(tag); if (leftString != rightString) { return leftString.compare(rightString) < 0; } else { return this->NextLevelIsLeftBeforeRight(left, right); } } bool mitk::DICOMSortByTag ::NumericCompare(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right, const DICOMTag& tag) const { assert(left); assert(right); std::string leftString = left->GetTagValueAsString(tag); std::string rightString = right->GetTagValueAsString(tag); std::istringstream lefti(leftString); std::istringstream righti(rightString); double leftDouble(0); double rightDouble(0); if ( (lefti >> leftDouble) && (righti >> rightDouble) && lefti.eof() && righti.eof() ) { if (leftDouble != rightDouble) // can we decide? { return leftDouble < rightDouble; } else // ask secondary criterion { return this->NextLevelIsLeftBeforeRight(left, right); } } else // no numerical conversion.. { return this->StringCompare(left,right, tag); // fallback to string compare } } double mitk::DICOMSortByTag ::NumericDistance(const mitk::DICOMDatasetAccess* from, const mitk::DICOMDatasetAccess* to) const { assert(from); assert(to); std::string fromString = from->GetTagValueAsString(m_Tag); std::string toString = to->GetTagValueAsString(m_Tag); std::istringstream fromi(fromString); std::istringstream toi(toString); double fromDouble(0); double toDouble(0); if ( (fromi >> fromDouble) && (toi >> toDouble) && fromi.eof() && toi.eof() ) { return toDouble - fromDouble; } else { + MITK_WARN << "NO NUMERIC DISTANCE between '" << fromString << "' and '" << toString << "'"; return 0; } // TODO second-level compare? } diff --git a/Modules/DICOMReader/mitkDICOMTagBasedSorter.cpp b/Modules/DICOMReader/mitkDICOMTagBasedSorter.cpp index 5475550871..34f4b8fac9 100644 --- a/Modules/DICOMReader/mitkDICOMTagBasedSorter.cpp +++ b/Modules/DICOMReader/mitkDICOMTagBasedSorter.cpp @@ -1,540 +1,559 @@ /*=================================================================== 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 "mitkDICOMTagBasedSorter.h" #include #include mitk::DICOMTagBasedSorter::CutDecimalPlaces ::CutDecimalPlaces(unsigned int precision) :m_Precision(precision) { } mitk::DICOMTagBasedSorter::CutDecimalPlaces ::CutDecimalPlaces(const CutDecimalPlaces& other) :m_Precision(other.m_Precision) { } std::string mitk::DICOMTagBasedSorter::CutDecimalPlaces ::operator()(const std::string& input) const { // be a bit tolerant for tags such as image orientation orienatation, let only the first few digits matter (http://bugs.mitk.org/show_bug.cgi?id=12263) // iterate all fields, convert each to a number, cut this number as configured, then return a concatenated string with all cut-off numbers std::ostringstream resultString; resultString.str(std::string()); resultString.clear(); resultString.setf(std::ios::fixed, std::ios::floatfield); resultString.precision(m_Precision); std::stringstream ss(input); ss.str(input); ss.clear(); std::string item; double number(0); std::istringstream converter(item); while (std::getline(ss, item, '\\')) { converter.str(item); converter.clear(); if (converter >> number && converter.eof()) { // converted to double resultString << number; } else { // did not convert to double resultString << item; // just paste the unmodified string } if (!ss.eof()) { resultString << "\\"; } } return resultString.str(); } mitk::DICOMTagBasedSorter::TagValueProcessor* mitk::DICOMTagBasedSorter::CutDecimalPlaces ::Clone() const { return new CutDecimalPlaces(*this); } unsigned int mitk::DICOMTagBasedSorter::CutDecimalPlaces ::GetPrecision() const { return m_Precision; } mitk::DICOMTagBasedSorter ::DICOMTagBasedSorter() :DICOMDatasetSorter() ,m_StrictSorting(true) { } mitk::DICOMTagBasedSorter ::~DICOMTagBasedSorter() { for(TagValueProcessorMap::iterator ti = m_TagValueProcessor.begin(); ti != m_TagValueProcessor.end(); ++ti) { delete ti->second; } } mitk::DICOMTagBasedSorter ::DICOMTagBasedSorter(const DICOMTagBasedSorter& other ) :DICOMDatasetSorter(other) ,m_DistinguishingTags( other.m_DistinguishingTags ) ,m_SortCriterion( other.m_SortCriterion ) ,m_StrictSorting( other.m_StrictSorting ) { for(TagValueProcessorMap::const_iterator ti = other.m_TagValueProcessor.begin(); ti != other.m_TagValueProcessor.end(); ++ti) { m_TagValueProcessor[ti->first] = ti->second->Clone(); } } mitk::DICOMTagBasedSorter& mitk::DICOMTagBasedSorter ::operator=(const DICOMTagBasedSorter& other) { if (this != &other) { DICOMDatasetSorter::operator=(other); m_DistinguishingTags = other.m_DistinguishingTags; m_SortCriterion = other.m_SortCriterion; m_StrictSorting = other.m_StrictSorting; for(TagValueProcessorMap::const_iterator ti = other.m_TagValueProcessor.begin(); ti != other.m_TagValueProcessor.end(); ++ti) { m_TagValueProcessor[ti->first] = ti->second->Clone(); } } return *this; } bool mitk::DICOMTagBasedSorter ::operator==(const DICOMDatasetSorter& other) const { if (const DICOMTagBasedSorter* otherSelf = dynamic_cast(&other)) { if (this->m_StrictSorting != otherSelf->m_StrictSorting) return false; bool allTagsPresentAndEqual(true); if (this->m_DistinguishingTags.size() != otherSelf->m_DistinguishingTags.size()) return false; for (DICOMTagList::const_iterator myTag = this->m_DistinguishingTags.begin(); myTag != this->m_DistinguishingTags.end(); ++myTag) { allTagsPresentAndEqual &= (std::find( otherSelf->m_DistinguishingTags.begin(), otherSelf->m_DistinguishingTags.end(), *myTag ) != otherSelf->m_DistinguishingTags.end()); // other contains this tags // since size is equal, we don't need to check the inverse } if (!allTagsPresentAndEqual) return false; if (this->m_SortCriterion.IsNotNull() && otherSelf->m_SortCriterion.IsNotNull()) { return *(this->m_SortCriterion) == *(otherSelf->m_SortCriterion); } else { return this->m_SortCriterion.IsNull() && otherSelf->m_SortCriterion.IsNull(); } } else { return false; } } void mitk::DICOMTagBasedSorter ::PrintConfiguration(std::ostream& os, const std::string& indent) const { os << indent << "Tag based sorting:" << std::endl; for (DICOMTagList::const_iterator tagIter = m_DistinguishingTags.begin(); tagIter != m_DistinguishingTags.end(); ++tagIter) { os << indent << " Split on "; tagIter->Print(os); os << std::endl; } DICOMSortCriterion::ConstPointer crit = m_SortCriterion.GetPointer(); while (crit.IsNotNull()) { os << indent << " Sort by "; crit->Print(os); os << std::endl; crit = crit->GetSecondaryCriterion(); } } void mitk::DICOMTagBasedSorter ::SetStrictSorting(bool strict) { m_StrictSorting = strict; } bool mitk::DICOMTagBasedSorter ::GetStrictSorting() const { return m_StrictSorting; } mitk::DICOMTagList mitk::DICOMTagBasedSorter ::GetTagsOfInterest() { DICOMTagList allTags = m_DistinguishingTags; DICOMTagList sortingRelevantTags = m_SortCriterion->GetAllTagsOfInterest(); allTags.insert( allTags.end(), sortingRelevantTags.begin(), sortingRelevantTags.end() ); // append return allTags; } mitk::DICOMTagList mitk::DICOMTagBasedSorter ::GetDistinguishingTags() const { return m_DistinguishingTags; } const mitk::DICOMTagBasedSorter::TagValueProcessor* mitk::DICOMTagBasedSorter ::GetTagValueProcessorForDistinguishingTag(const DICOMTag& tag) const { TagValueProcessorMap::const_iterator loc = m_TagValueProcessor.find(tag); if (loc != m_TagValueProcessor.end()) { return loc->second; } else { return NULL; } } void mitk::DICOMTagBasedSorter ::AddDistinguishingTag( const DICOMTag& tag, TagValueProcessor* tagValueProcessor ) { m_DistinguishingTags.push_back(tag); m_TagValueProcessor[tag] = tagValueProcessor; } void mitk::DICOMTagBasedSorter ::SetSortCriterion( DICOMSortCriterion::ConstPointer criterion ) { m_SortCriterion = criterion; } mitk::DICOMSortCriterion::ConstPointer mitk::DICOMTagBasedSorter ::GetSortCriterion() const { return m_SortCriterion; } void mitk::DICOMTagBasedSorter ::Sort() { // 1. split // 2. sort each group GroupIDToListType groups = this->SplitInputGroups(); GroupIDToListType& sortedGroups = this->SortGroups( groups ); // 3. define output this->SetNumberOfOutputs(sortedGroups.size()); unsigned int outputIndex(0); for (GroupIDToListType::iterator groupIter = sortedGroups.begin(); groupIter != sortedGroups.end(); ++outputIndex, ++groupIter) { this->SetOutput(outputIndex, groupIter->second); } } std::string mitk::DICOMTagBasedSorter ::BuildGroupID( DICOMDatasetAccess* dataset ) { // just concatenate all tag values assert(dataset); std::stringstream groupID; groupID << "g"; for (DICOMTagList::iterator tagIter = m_DistinguishingTags.begin(); tagIter != m_DistinguishingTags.end(); ++tagIter) { groupID << tagIter->GetGroup() << tagIter->GetElement(); // make group/element part of the id to cover empty tags std::string rawTagValue = dataset->GetTagValueAsString(*tagIter); std::string processedTagValue; if ( m_TagValueProcessor[*tagIter] != NULL ) { processedTagValue = (*m_TagValueProcessor[*tagIter])(rawTagValue); } else { processedTagValue = rawTagValue; } groupID << processedTagValue; } // shorten ID? return groupID.str(); } mitk::DICOMTagBasedSorter::GroupIDToListType mitk::DICOMTagBasedSorter ::SplitInputGroups() { DICOMDatasetList input = GetInput(); // copy GroupIDToListType listForGroupID; for (DICOMDatasetList::iterator dsIter = input.begin(); dsIter != input.end(); ++dsIter) { DICOMDatasetAccess* dataset = *dsIter; assert(dataset); std::string groupID = this->BuildGroupID( dataset ); MITK_DEBUG << "Group ID for for " << dataset->GetFilenameIfAvailable() << ": " << groupID; listForGroupID[groupID].push_back(dataset); } MITK_DEBUG << "After tag based splitting: " << listForGroupID.size() << " groups"; return listForGroupID; } mitk::DICOMTagBasedSorter::GroupIDToListType& mitk::DICOMTagBasedSorter ::SortGroups(GroupIDToListType& groups) { if (m_SortCriterion.IsNotNull()) { /* Three steps here: 1. sort within each group - this may result in orders such as 1 2 3 4 6 7 8 10 12 13 14 2. create new groups by enforcing consecutive order within each group - resorts above example like 1 2 3 4 ; 6 7 8 ; 10 ; 12 13 14 3. sort all of the groups (not WITHIN each group) by their first frame - if earlier "distinguish" steps created groups like 6 7 8 ; 1 2 3 4 ; 10, then this step would sort them like 1 2 3 4 ; 6 7 8 ; 10 */ // Step 1: sort within the groups // for each output // sort by all configured tags, use secondary tags when equal or empty // make configurable: // - sorting order (ascending, descending) // - sort numerically // - ... ? unsigned int groupIndex(0); for (GroupIDToListType::iterator gIter = groups.begin(); gIter != groups.end(); ++groupIndex, ++gIter) { DICOMDatasetList& dsList = gIter->second; MITK_DEBUG << " --------------------------------------------------------------------------------"; MITK_DEBUG << " DICOMTagBasedSorter before sorting group : " << groupIndex; for (DICOMDatasetList::iterator oi = dsList.begin(); oi != dsList.end(); ++oi) { MITK_DEBUG << " INPUT : " << (*oi)->GetFilenameIfAvailable(); } std::sort( dsList.begin(), dsList.end(), ParameterizedDatasetSort( m_SortCriterion ) ); MITK_DEBUG << " --------------------------------------------------------------------------------"; MITK_DEBUG << " DICOMTagBasedSorter after sorting group : " << groupIndex; for (DICOMDatasetList::iterator oi = dsList.begin(); oi != dsList.end(); ++oi) { MITK_DEBUG << " OUTPUT : " << (*oi)->GetFilenameIfAvailable(); } MITK_DEBUG << " --------------------------------------------------------------------------------"; } GroupIDToListType consecutiveGroups; if (m_StrictSorting) { // Step 2: create new groups by enforcing consecutive order within each group unsigned int groupIndex(0); for (GroupIDToListType::iterator gIter = groups.begin(); gIter != groups.end(); ++gIter) { std::stringstream groupKey; groupKey << std::setfill('0') << std::setw(6) << groupIndex++; DICOMDatasetList& dsList = gIter->second; DICOMDatasetAccess* previousDS(NULL); unsigned int dsIndex(0); double constantDistance(0.0); bool constantDistanceInitialized(false); for (DICOMDatasetList::iterator dataset = dsList.begin(); dataset != dsList.end(); ++dsIndex, ++dataset) { if (dsIndex >0) // ignore the first dataset, we cannot check any distances yet.. { // for the second and every following dataset: // let the sorting criterion calculate a "distance" // if the distance is not 1, split off a new group! double currentDistance = m_SortCriterion->NumericDistance(previousDS, *dataset); if (constantDistanceInitialized) { - if (fabs(currentDistance - constantDistance) < constantDistance * 0.01) // ok, deviation of up to 1% of distance is tolerated + if (fabs(currentDistance - constantDistance) < fabs(constantDistance * 0.01)) // ok, deviation of up to 1% of distance is tolerated { // nothing to do, just ok + MITK_DEBUG << "Checking currentDistance==" << currentDistance << ": small enough"; } - else if (currentDistance < mitk::eps) // close enough to 0 - { - // no numeric comparison possible? - // rare case(?), just accept - } + //else if (currentDistance < mitk::eps) // close enough to 0 else { + MITK_DEBUG << "Split consecutive group at index " << dsIndex << " (current distance " << currentDistance << ", constant distance " << constantDistance << ")"; // split! this is done by simply creating a new group (key) groupKey.str(std::string()); groupKey.clear(); groupKey << std::setfill('0') << std::setw(6) << groupIndex++; } } else { // second slice: learn about the expected distance! // heuristic: if distance is an integer, we check for a special case: // if the distance is integer and not 1/-1, then we assume // a missing slice right after the first slice // ==> split off slices // in all other cases: second dataset at this position, no need to split already, we are still learning about the images if ((currentDistance - (int)currentDistance == 0.0) && fabs(currentDistance) != 1.0) // exact comparison. An integer should not be expressed as 1.000000000000000000000000001! { + MITK_DEBUG << "Split consecutive group at index " << dsIndex << " (strange special case)"; groupKey.str(std::string()); groupKey.clear(); groupKey << std::setfill('0') << std::setw(6) << groupIndex++; } + MITK_DEBUG << "Initialize strict distance to currentDistance=" << currentDistance; + constantDistance = currentDistance; constantDistanceInitialized = true; } } consecutiveGroups[groupKey.str()].push_back(*dataset); previousDS = *dataset; } } } else { consecutiveGroups = groups; } // Step 3: sort all of the groups (not WITHIN each group) by their first frame /* build a list-1 of datasets with the first dataset one of each group sort this list-1 build a new result list-2: - iterate list-1, for each dataset - find the group that contains this dataset - add this group as the next element to list-2 return list-2 as the sorted output */ DICOMDatasetList firstSlices; for (GroupIDToListType::iterator gIter = consecutiveGroups.begin(); gIter != consecutiveGroups.end(); ++gIter) { assert(!gIter->second.empty()); firstSlices.push_back(gIter->second.front()); } std::sort( firstSlices.begin(), firstSlices.end(), ParameterizedDatasetSort( m_SortCriterion ) ); GroupIDToListType sortedResultBlocks; unsigned int groupKeyValue(0); for (DICOMDatasetList::iterator firstSlice = firstSlices.begin(); firstSlice != firstSlices.end(); ++firstSlice) { for (GroupIDToListType::iterator gIter = consecutiveGroups.begin(); gIter != consecutiveGroups.end(); ++groupKeyValue, ++gIter) { if (gIter->second.front() == *firstSlice) { std::stringstream groupKey; groupKey << std::setfill('0') << std::setw(6) << groupKeyValue; // try more than 999,999 groups and you are doomed (your application already is) sortedResultBlocks[groupKey.str()] = gIter->second; } } } groups = sortedResultBlocks; } + unsigned int groupIndex(0); + for (GroupIDToListType::iterator gIter = groups.begin(); + gIter != groups.end(); + ++groupIndex, ++gIter) + { + DICOMDatasetList& dsList = gIter->second; + MITK_DEBUG << " --------------------------------------------------------------------------------"; + MITK_DEBUG << " DICOMTagBasedSorter after sorting group : " << groupIndex; + for (DICOMDatasetList::iterator oi = dsList.begin(); + oi != dsList.end(); + ++oi) + { + MITK_DEBUG << " OUTPUT : " << (*oi)->GetFilenameIfAvailable(); + } + MITK_DEBUG << " --------------------------------------------------------------------------------"; + } + + return groups; } mitk::DICOMTagBasedSorter::ParameterizedDatasetSort ::ParameterizedDatasetSort(DICOMSortCriterion::ConstPointer criterion) :m_SortCriterion(criterion) { } bool mitk::DICOMTagBasedSorter::ParameterizedDatasetSort ::operator() (const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) { assert(left); assert(right); assert(m_SortCriterion.IsNotNull()); return m_SortCriterion->IsLeftBeforeRight(left, right); }