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Merge pull request #18211 from pemmanuelviel:pev--handle-dna-vectors

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* DNA-mode: update miniflann to handle DNA

* DNA-mode: update hierarchical kmeans to handle DNA sequences
This commit is contained in:
pemmanuelviel
2020-09-01 22:38:21 +02:00
committed by GitHub
parent 698b2bf729
commit 31dc3e9256
2 changed files with 244 additions and 3 deletions
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modules/flann/src/miniflann.cpp
+23 -2
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@@ -345,6 +345,7 @@ typedef ::cvflann::Hamming<uchar> HammingDistance;
#else
typedef ::cvflann::HammingLUT HammingDistance;
#endif
typedef ::cvflann::DNAmming2<uchar> DNAmmingDistance;
Index::Index()
{
@@ -397,6 +398,9 @@ void Index::build(InputArray _data, const IndexParams& params, flann_distance_t
buildIndex< ::cvflann::L1<float> >(index, data, params);
break;
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
buildIndex< DNAmmingDistance >(index, data, params);
break;
case FLANN_DIST_MAX:
buildIndex< ::cvflann::MaxDistance<float> >(index, data, params);
break;
@@ -452,6 +456,9 @@ void Index::release()
deleteIndex< ::cvflann::L1<float> >(index);
break;
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
deleteIndex< DNAmmingDistance >(index);
break;
case FLANN_DIST_MAX:
deleteIndex< ::cvflann::MaxDistance<float> >(index);
break;
@@ -573,7 +580,8 @@ void Index::knnSearch(InputArray _query, OutputArray _indices,
CV_INSTRUMENT_REGION();
Mat query = _query.getMat(), indices, dists;
int dtype = distType == FLANN_DIST_HAMMING ? CV_32S : CV_32F;
int dtype = (distType == FLANN_DIST_HAMMING)
|| (distType == FLANN_DIST_DNAMMING) ? CV_32S : CV_32F;
createIndicesDists( _indices, _dists, indices, dists, query.rows, knn, knn, dtype );
@@ -589,6 +597,9 @@ void Index::knnSearch(InputArray _query, OutputArray _indices,
runKnnSearch< ::cvflann::L1<float> >(index, query, indices, dists, knn, params);
break;
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
runKnnSearch<DNAmmingDistance>(index, query, indices, dists, knn, params);
break;
case FLANN_DIST_MAX:
runKnnSearch< ::cvflann::MaxDistance<float> >(index, query, indices, dists, knn, params);
break;
@@ -617,7 +628,8 @@ int Index::radiusSearch(InputArray _query, OutputArray _indices,
CV_INSTRUMENT_REGION();
Mat query = _query.getMat(), indices, dists;
int dtype = distType == FLANN_DIST_HAMMING ? CV_32S : CV_32F;
int dtype = (distType == FLANN_DIST_HAMMING)
|| (distType == FLANN_DIST_DNAMMING) ? CV_32S : CV_32F;
CV_Assert( maxResults > 0 );
createIndicesDists( _indices, _dists, indices, dists, query.rows, maxResults, INT_MAX, dtype );
@@ -634,6 +646,8 @@ int Index::radiusSearch(InputArray _query, OutputArray _indices,
case FLANN_DIST_L1:
return runRadiusSearch< ::cvflann::L1<float> >(index, query, indices, dists, radius, params);
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
return runRadiusSearch< DNAmmingDistance >(index, query, indices, dists, radius, params);
case FLANN_DIST_MAX:
return runRadiusSearch< ::cvflann::MaxDistance<float> >(index, query, indices, dists, radius, params);
case FLANN_DIST_HIST_INTERSECT:
@@ -697,6 +711,9 @@ void Index::save(const String& filename) const
saveIndex< ::cvflann::L1<float> >(this, index, fout);
break;
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
saveIndex< DNAmmingDistance >(this, index, fout);
break;
case FLANN_DIST_MAX:
saveIndex< ::cvflann::MaxDistance<float> >(this, index, fout);
break;
@@ -778,6 +795,7 @@ bool Index::load(InputArray _data, const String& filename)
distType = (flann_distance_t)idistType;
if( !((distType == FLANN_DIST_HAMMING && featureType == CV_8U) ||
(distType == FLANN_DIST_DNAMMING && featureType == CV_8U) ||
(distType != FLANN_DIST_HAMMING && featureType == CV_32F)) )
{
fprintf(stderr, "Reading FLANN index error: unsupported feature type %d for the index type %d\n", featureType, algo);
@@ -797,6 +815,9 @@ bool Index::load(InputArray _data, const String& filename)
loadIndex< ::cvflann::L1<float> >(this, index, data, fin);
break;
#if MINIFLANN_SUPPORT_EXOTIC_DISTANCE_TYPES
case FLANN_DIST_DNAMMING:
loadIndex< DNAmmingDistance >(this, index, data, fin);
break;
case FLANN_DIST_MAX:
loadIndex< ::cvflann::MaxDistance<float> >(this, index, data, fin);
break;