diff --git a/Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp b/Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp index 7c8977956b..af65bb55da 100644 --- a/Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp +++ b/Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp @@ -1,633 +1,634 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #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 orientation, let only the first few digits matter (https://phabricator.mitk.org/T12263) // 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(m_DefaultStrictSorting) ,m_ExpectDistanceOne(m_DefaultExpectDistanceOne) { } mitk::DICOMTagBasedSorter ::~DICOMTagBasedSorter() { for(auto ti = m_TagValueProcessor.cbegin(); ti != m_TagValueProcessor.cend(); ++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 ) ,m_ExpectDistanceOne( other.m_ExpectDistanceOne ) { for(auto ti = other.m_TagValueProcessor.cbegin(); ti != other.m_TagValueProcessor.cend(); ++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; m_ExpectDistanceOne = other.m_ExpectDistanceOne; for(auto ti = other.m_TagValueProcessor.cbegin(); ti != other.m_TagValueProcessor.cend(); ++ti) { m_TagValueProcessor[ti->first] = ti->second->Clone(); } } return *this; } bool mitk::DICOMTagBasedSorter ::operator==(const DICOMDatasetSorter& other) const { if (const auto* otherSelf = dynamic_cast(&other)) { if (this->m_StrictSorting != otherSelf->m_StrictSorting) return false; if (this->m_ExpectDistanceOne != otherSelf->m_ExpectDistanceOne) return false; bool allTagsPresentAndEqual(true); if (this->m_DistinguishingTags.size() != otherSelf->m_DistinguishingTags.size()) return false; for (auto myTag = this->m_DistinguishingTags.cbegin(); myTag != this->m_DistinguishingTags.cend(); ++myTag) { allTagsPresentAndEqual &= (std::find( otherSelf->m_DistinguishingTags.cbegin(), otherSelf->m_DistinguishingTags.cend(), *myTag ) != otherSelf->m_DistinguishingTags.cend()); // 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 " << "(strict=" << (m_StrictSorting?"true":"false") << ", expectDistanceOne=" << (m_ExpectDistanceOne?"true":"false") << "):" << std::endl; for (auto 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; } void mitk::DICOMTagBasedSorter ::SetExpectDistanceOne(bool strict) { m_ExpectDistanceOne = strict; } bool mitk::DICOMTagBasedSorter ::GetExpectDistanceOne() const { return m_ExpectDistanceOne; } mitk::DICOMTagList mitk::DICOMTagBasedSorter ::GetTagsOfInterest() { DICOMTagList allTags = m_DistinguishingTags; if (m_SortCriterion.IsNotNull()) { const DICOMTagList sortingRelevantTags = m_SortCriterion->GetAllTagsOfInterest(); allTags.insert( allTags.end(), sortingRelevantTags.cbegin(), sortingRelevantTags.cend() ); // append } return allTags; } mitk::DICOMTagList mitk::DICOMTagBasedSorter ::GetDistinguishingTags() const { return m_DistinguishingTags; } const mitk::DICOMTagBasedSorter::TagValueProcessor* mitk::DICOMTagBasedSorter ::GetTagValueProcessorForDistinguishingTag(const DICOMTag& tag) const { auto loc = m_TagValueProcessor.find(tag); if (loc != m_TagValueProcessor.cend()) { return loc->second; } else { return nullptr; } } 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() { SplitReasonListType splitReasons; // 1. split GroupIDToListType groups = this->SplitInputGroups(splitReasons); // 2. sort each group (can also lead to a split due to distance) GroupIDToListType& sortedGroups = this->SortGroups( groups, splitReasons); // 3. define output this->SetNumberOfOutputs(sortedGroups.size()); unsigned int outputIndex(0); for (auto groupIter = sortedGroups.cbegin(); groupIter != sortedGroups.cend(); ++outputIndex, ++groupIter) { this->SetOutput(outputIndex, groupIter->second, splitReasons[groupIter->first]); } } std::string mitk::DICOMTagBasedSorter ::BuildGroupID( DICOMDatasetAccess* dataset ) { // just concatenate all tag values assert(dataset); std::stringstream groupID; groupID << "g"; for (auto tagIter = m_DistinguishingTags.cbegin(); tagIter != m_DistinguishingTags.cend(); ++tagIter) { groupID << tagIter->GetGroup() << tagIter->GetElement(); // make group/element part of the id to cover empty tags DICOMDatasetFinding rawTagValue = dataset->GetTagValueAsString(*tagIter); std::string processedTagValue; if ( m_TagValueProcessor[*tagIter] != nullptr && rawTagValue.isValid) { processedTagValue = (*m_TagValueProcessor[*tagIter])(rawTagValue.value); } else { processedTagValue = rawTagValue.value; } groupID << "#" << processedTagValue; } // shorten ID? return groupID.str(); } mitk::DICOMTagBasedSorter::GroupIDToListType mitk::DICOMTagBasedSorter ::SplitInputGroups(SplitReasonListType& splitReasons) { DICOMDatasetList input = GetInput(); // copy GroupIDToListType listForGroupID; for (auto dsIter = input.cbegin(); dsIter != input.cend(); ++dsIter) { DICOMDatasetAccess* dataset = *dsIter; assert(dataset); const 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"; splitReasons.clear(); if (listForGroupID.size() == 1) { //no split -> no reason splitReasons[listForGroupID.begin()->first] = IOVolumeSplitReason::New(); } else { for (auto& [key, value] : listForGroupID) { + (void)value; // Prevent unused variable error in older compilers auto reason = IOVolumeSplitReason::New(); reason->AddReason(IOVolumeSplitReason::ReasonType::ValueSplitDifference); splitReasons[key] = reason; } } return listForGroupID; } mitk::DICOMTagBasedSorter::GroupIDToListType& mitk::DICOMTagBasedSorter ::SortGroups(GroupIDToListType& groups, SplitReasonListType& splitReasons) { 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 // - ... ? #ifdef MBILOG_ENABLE_DEBUG unsigned int groupIndex(0); #endif for (auto gIter = groups.begin(); gIter != groups.end(); #ifdef MBILOG_ENABLE_DEBUG ++groupIndex, #endif ++gIter) { DICOMDatasetList& dsList = gIter->second; #ifdef MBILOG_ENABLE_DEBUG MITK_DEBUG << " --------------------------------------------------------------------------------"; MITK_DEBUG << " DICOMTagBasedSorter before sorting group : " << groupIndex; for (auto oi = dsList.begin(); oi != dsList.cend(); ++oi) { MITK_DEBUG << " INPUT : " << (*oi)->GetFilenameIfAvailable(); } #endif // #ifdef MBILOG_ENABLE_DEBUG std::sort( dsList.begin(), dsList.end(), ParameterizedDatasetSort( m_SortCriterion ) ); #ifdef MBILOG_ENABLE_DEBUG MITK_DEBUG << " --------------------------------------------------------------------------------"; MITK_DEBUG << " DICOMTagBasedSorter after sorting group : " << groupIndex; for (auto oi = dsList.cbegin(); oi != dsList.cend(); ++oi) { MITK_DEBUG << " OUTPUT : " << (*oi)->GetFilenameIfAvailable(); } MITK_DEBUG << " --------------------------------------------------------------------------------"; #endif // MBILOG_ENABLE_DEBUG } GroupIDToListType consecutiveGroups; SplitReasonListType consecutiveReasons; if (m_StrictSorting) { // Step 2: create new groups by enforcing consecutive order within each group unsigned int groupIndex(0); for (auto gIter = groups.begin(); gIter != groups.end(); ++gIter) { std::stringstream groupKey; groupKey << std::setfill('0') << std::setw(6) << groupIndex++; std::string groupKeyStr = groupKey.str(); DICOMDatasetList& dsList = gIter->second; DICOMDatasetAccess* previousDS(nullptr); unsigned int dsIndex(0); double constantDistance(0.0); bool constantDistanceInitialized(false); for (auto dataset = dsList.cbegin(); dataset != dsList.cend(); ++dsIndex, ++dataset) { bool splitted = false; 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! const double currentDistance = m_SortCriterion->NumericDistance(previousDS, *dataset); if (constantDistanceInitialized) { 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 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++; groupKeyStr = groupKey.str(); splitted = true; } } 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 // addition to the above: when sorting by imagepositions, a distance other than 1 between the first two slices is // not unusual, actually expected... then we should not split if (m_ExpectDistanceOne) { 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 << " (special case: expected distance 1 exactly)"; groupKey.str(std::string()); groupKey.clear(); groupKey << std::setfill('0') << std::setw(6) << groupIndex++; groupKeyStr = groupKey.str(); splitted = true; } } MITK_DEBUG << "Initialize strict distance to currentDistance=" << currentDistance; constantDistance = currentDistance; constantDistanceInitialized = true; } } consecutiveGroups[groupKeyStr].push_back(*dataset); if (consecutiveReasons.find(groupKeyStr) == consecutiveReasons.end()) { auto dsReason = splitReasons[gIter->first]->Clone(); if (splitted) dsReason->AddReason(IOVolumeSplitReason::ReasonType::ValueSortDistance); consecutiveReasons[groupKeyStr] = dsReason; } 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 (auto gIter = consecutiveGroups.cbegin(); gIter != consecutiveGroups.cend(); ++gIter) { assert(!gIter->second.empty()); firstSlices.push_back(gIter->second.front()); } std::sort( firstSlices.begin(), firstSlices.end(), ParameterizedDatasetSort( m_SortCriterion ) ); GroupIDToListType sortedResultBlocks; SplitReasonListType sortedResultsReasons; for (auto& [key, group] : consecutiveGroups) { auto findSliceIterator = std::find(firstSlices.begin(), firstSlices.end(), group.front()); std::stringstream groupKey; groupKey << std::setfill('0') << std::setw(6) << std::distance(firstSlices.begin(),findSliceIterator); // try more than 999,999 groups and you are doomed (your application already is) const auto groupKeyStr = groupKey.str(); sortedResultBlocks[groupKeyStr] = group; sortedResultsReasons[groupKeyStr] = consecutiveReasons[key]; } groups = sortedResultBlocks; splitReasons = sortedResultsReasons; } #ifdef MBILOG_ENABLE_DEBUG unsigned int groupIndex( 0 ); for ( auto gIter = groups.begin(); gIter != groups.end(); ++groupIndex, ++gIter ) { DICOMDatasetList& dsList = gIter->second; MITK_DEBUG << " --------------------------------------------------------------------------------"; MITK_DEBUG << " DICOMTagBasedSorter after sorting group : " << groupIndex; for ( auto oi = dsList.begin(); oi != dsList.end(); ++oi ) { MITK_DEBUG << " OUTPUT : " << ( *oi )->GetFilenameIfAvailable(); } MITK_DEBUG << " --------------------------------------------------------------------------------"; } #endif // MBILOG_ENABLE_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); }