Merge ec2-107-20-88-134.compute-1.amazonaws.com:flann

examples/flann_example_mpi.cpp

 
 #include <flann/flann_mpi.hpp>
+#include <flann/flann.hpp>
 #include <flann/io/hdf5.h>
 
 #include <stdio.h>
@@ -48,43 +49,48 @@ int main(int argc, char** argv)
 	boost::mpi::environment env(argc, argv);
 	boost::mpi::communicator world;
 
-    int nn = 1;
+	int nn = 1;
 
-//    flann::Matrix<float> dataset;
-    flann::Matrix<float> query;
-    flann::Matrix<int> match;
+	//flann::Matrix<float> dataset;
+	flann::Matrix<float> query;
+	flann::Matrix<int> match;
+	flann::Matrix<float> gt_dists;
 
-    IF_RANK0 start_timer("Loading data...\n");
-    flann::load_from_file(query, "sift100K.h5","query");
-    flann::load_from_file(match, "sift100K.h5","match");
-    flann::Matrix<int> indices(new int[query.rows*nn], query.rows, nn);
-    flann::Matrix<float> dists(new float[query.rows*nn], query.rows, nn);
+	IF_RANK0 start_timer("Loading data...\n");
+	//flann::load_from_file(dataset, "sift100K.h5","dataset");
+	flann::load_from_file(query, "sift100K.h5","query");
+	flann::load_from_file(match, "sift100K.h5","match");
+	flann::load_from_file(gt_dists, "sift100K.h5","dists");
+	flann::Matrix<int> indices(new int[query.rows*nn], query.rows, nn);
+	flann::Matrix<float> dists(new float[query.rows*nn], query.rows, nn);
 
-    // construct an randomized kd-tree index using 4 kd-trees
-    flann::mpi::Index<flann::L2<float> > index("sift100K.h5", "dataset", flann::KDTreeIndexParams(4));
-    IF_RANK0 printf("Loading data done (%g seconds)\n", stop_timer());
+	// construct an randomized kd-tree index using 4 kd-trees
+	flann::mpi::Index<flann::L2<float> > index("sift100K.h5", "dataset", flann::KDTreeIndexParams(4));
+	//flann::Index<flann::L2<float>	> index( dataset, flann::KDTreeIndexParams(4));
+	IF_RANK0 printf("Loading data done (%g seconds)\n", stop_timer());
 
-    IF_RANK0 printf("Index size: (%d,%d)\n", index.size(), index.veclen());
+	IF_RANK0 printf("Index size: (%d,%d)\n", index.size(), index.veclen());
 
-    start_timer("Building index...\n");
-    index.buildIndex();                                                                                               
+	start_timer("Building index...\n");
+	index.buildIndex();                                                                                               
 	printf("Building index done (%g seconds)\n", stop_timer());
+    
+    world.barrier();
 
-    // do a knn search, using 128 checks
+	// do a knn search, using 128 checks
 	IF_RANK0 start_timer("Performing search...\n");
-    index.knnSearch(query, indices, dists, nn, flann::SearchParams(128));
-    IF_RANK0 printf("Search done (%g seconds)\n", stop_timer());
-
-    IF_RANK0 {
-    	printf("Indices size: (%d,%d)\n", indices.rows, indices.cols);
-    	printf("Checking results\n");
-    	float precision = compute_precision(match, indices);
-    	printf("Precision is: %g\n", precision);
-    }
-    delete[] query.data;
-    delete[] indices.data;
-    delete[] dists.data;
-    delete[] match.data;
-    
-    return 0;
+	index.knnSearch(query, indices, dists, nn, flann::SearchParams(128));
+	IF_RANK0 printf("Search done (%g seconds)\n", stop_timer());
+	IF_RANK0 {
+		printf("Indices size: (%d,%d)\n", (int)indices.rows, (int)indices.cols);
+		printf("Checking results\n");
+		float precision = compute_precision(match, indices);
+		printf("Precision is: %g\n", precision);
+	}
+	delete[] query.data;
+	delete[] indices.data;
+	delete[] dists.data;
+	delete[] match.data;
+
+	return 0;
 }

src/cpp/flann/flann_mpi.hpp

@@ -52,6 +52,7 @@ struct SearchResults
         ar& indices.rows;
         ar& indices.cols;
         if (Archive::is_loading::value) {
+            indices.stride = indices.cols;
             indices.data = new int[indices.rows*indices.cols];
         }
         ar& boost::serialization::make_array(indices.data, indices.rows*indices.cols);
@@ -61,6 +62,7 @@ struct SearchResults
         ar& dists.rows;
         ar& dists.cols;
         if (Archive::is_loading::value) {
+            dists.stride = dists.cols;
             dists.data = new DistanceType[dists.rows*dists.cols];
         }
         ar& boost::serialization::make_array(dists.data, dists.rows*dists.cols);
@@ -76,12 +78,8 @@ struct ResultsMerger
     SearchResults<DistanceType> operator()(SearchResults<DistanceType> a, SearchResults<DistanceType> b)
     {
         SearchResults<DistanceType> results;
-        results.indices.rows = a.indices.rows;
-        results.indices.cols = a.indices.cols;
-        results.indices.data = new int[results.indices.rows*results.indices.cols];
-        results.dists.rows = a.dists.rows;
-        results.dists.cols = a.dists.cols;
-        results.dists.data = new DistanceType[results.dists.rows*results.dists.cols];
+        results.indices = flann::Matrix<int>(new int[a.indices.rows*a.indices.cols],a.indices.rows,a.indices.cols);
+        results.dists = flann::Matrix<DistanceType>(new DistanceType[a.dists.rows*a.dists.cols],a.dists.rows,a.dists.cols);
 
 
         for (size_t i = 0; i < results.dists.rows; ++i) {
@@ -103,7 +101,6 @@ struct ResultsMerger
                 }
             }
         }
-
         delete[] a.indices.data;
         delete[] a.dists.data;
         delete[] b.indices.data;

src/cpp/flann/io/hdf5.h

@@ -211,13 +211,11 @@ void load_from_file(flann::Matrix<T>& dataset, const std::string& filename, cons
 
     H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
 
-    dataset.rows = count[0];
-    dataset.cols = count[1];
-    dataset.data = new T[dataset.rows*dataset.cols];
+    dataset = flann::Matrix<T>(new T[count[0]*count[1]], count[0], count[1]);
 
     plist_id = H5Pcreate(H5P_DATASET_XFER);
     H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
-    status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset.data);
+    status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset[0]);
     CHECK_ERROR(status, "Error reading dataset");
 
     H5Pclose(plist_id);

src/python/pyflann/bindings/flann_ctypes.py

@@ -146,6 +146,11 @@ def load_flann_library():
                 return flannlib
             except Exception,e:
                 pass
+            try:
+                flannlib = cdll[os.path.join(root_dir,"build",libdir,libname)]
+                return flannlib
+            except Exception,e:
+                pass
         tmp = os.path.dirname(root_dir)
         if tmp == root_dir:
             root_dir = None