add BruteforceFPS class

algos.yaml

@@ -2,14 +2,14 @@ bit:
   jaccard:
     Bruteforce:
       disabled: false
-      docker-tag: ann-benchmarks-sklearn
-      singularity-tag: ann-bench-sklearn
+      docker-tag: ann-benchmarks-chemfp
+      singularity-tag: ann-bench-chemfp
       module: ann_benchmarks.algorithms.bruteforce
-      constructor: BruteForceBLAS
+      constructor: BruteForceFPS
       base-args: ["@metric"]
       run-groups:
-        base:
-          args: {}
+        empty:
+          args: []
     Balltree(Sklearn):
       disabled: false
       docker-tag: ann-benchmarks-sklearn

ann_benchmarks/algorithms/bruteforce.py

@@ -96,3 +96,43 @@ def fix(index):
             ev = v
             return (index, pd[self._metric]['distance'](ep, ev))
         return map(fix, indices)
+
+class BruteForceFPS(BaseANN):
+    def __init__(self, metric):
+        if metric != 'jaccard':
+            raise NotImplementedError("BruteForce doesn't support metric %s" % metric)
+        self._metric = metric
+        self.name = 'BruteForceFPS()'
+
+
+    def fit(self, X):
+        self.index = X
+
+    def query(self, v, n):
+        import operator
+        import chemfp
+        dist_dict = {}
+        for j in range(self.index.shape[0]):
+            dist_dict[j] = chemfp.bitops.byte_tanimoto(self._queries.get_fingerprint(0), self._target.get_fingerprint(j))
+        sorted_dict = sorted(dist_dict.items(), key=operator.itemgetter(1), reverse=True)[:n]
+        return [sorted_dict[j][0] for j in range(n)]
+
+    @staticmethod
+    def matrToArena(X):
+        import chemfp
+        from bitarray import bitarray
+        # convert X to Chemfp fingerprintArena in memory
+        fps = []
+        for row in range(X.shape[0]):
+            fp = bitarray(endian='big')
+            fp.extend(X[row])
+            fps.append((row,fp.tobytes()))
+        return chemfp.load_fingerprints(fps,chemfp.Metadata(num_bits=X.shape[1]),reorder=False)
+
+    def pre_fit(self, X):
+        self._target = BruteForceFPS.matrToArena(X)
+
+
+    def pre_query(self, v, n):
+        queryMatr = numpy.array([v])
+        self._queries = BruteForceFPS.matrToArena(queryMatr)

ann_benchmarks/runner.py

@@ -35,7 +35,7 @@ def run_individual_query(algoname, algo, X_train, X_test, distance, count, run_c
 
         def single_query(v):
             # special code for the Risc, DivideSkip, and Chemfp
-            if algoname in ['Risc', 'DivideSkip', 'Chemfp']:
+            if algoname in ['Risc', 'DivideSkip', 'Chemfp', 'Bruteforce']:
                 algo.pre_query(v, count)
 
             start = time.time()
@@ -130,7 +130,7 @@ def run(definition, dataset, count, run_count, batch, rq):
             print(X_train.shape)
             algo.pre_fit(X_train)
         # special code for Chemfp
-        if definition.algorithm in 'Chemfp':
+        if definition.algorithm in ['Chemfp', 'Bruteforce']:
             algo.pre_fit(X_train)
 
         t0 = time.time()
@@ -302,7 +302,7 @@ def run_singularity(definition, dataset, count, runs, timeout, batch, rq, radius
     print('String of command', strCmd)
 
     # Chemfp uses Python2 while others use Python3
-    if definition.algorithm in 'Chemfp':
+    if definition.algorithm in ['Chemfp', 'Bruteforce']:
         subprocess.check_call('singularity exec %s/%s.sif python run_algorithm.py %s' %(sif_dir, definition.singularity_tag, strCmd), shell=True)
     else:
         subprocess.check_call('singularity exec %s/%s.sif python3 run_algorithm.py %s' %(sif_dir, definition.singularity_tag, strCmd), shell=True)