Merge aa34f87 into 774d8e3

redis_consumer/consumers.py

@@ -935,12 +935,12 @@ def _get_tracker(self, redis_hash, hvalues, raw, segmented):
         features = {'appearance', 'distance', 'neighborhood', 'regionprop'}
         tracker = tracking.cell_tracker(raw, segmented,
                                         tracking_model,
-                                        max_distance=50,
-                                        track_length=5,
-                                        division=0.5,
-                                        birth=0.9,
-                                        death=0.9,
-                                        neighborhood_scale_size=30,
+                                        max_distance=settings.MAX_DISTANCE,
+                                        track_length=settings.TRACK_LENGTH,
+                                        division=settings.DIVISION,
+                                        birth=settings.BIRTH,
+                                        death=settings.DEATH,
+                                        neighborhood_scale_size=settings.NEIGHBORHOOD_SCALE_SIZE,
                                         features=features)
 
         self.logger.debug('Created tracker!')
@@ -1007,10 +1007,10 @@ def _load_data(self, hvalues, subdir, fname):
                     'identity_upload': self.hostname,
                     'input_file_name': upload_file_name,
                     'original_name': segment_fname,
-                    'model_name': 'HeLaS3watershed',
-                    'model_version': 2,
-                    'postprocess_function': 'watershed',
-                    'cuts': 0,
+                    'model_name': settings.MODEL_NAME,
+                    'model_version': settings.MODEL_VERSION,
+                    'postprocess_function': settings.POSTPROCESS_FUNCTION,
+                    'cuts': settings.CUTS,
                     'status': 'new',
                     'created_at': current_timestamp,
                     'updated_at': current_timestamp,

redis_consumer/grpc_clients.py

@@ -56,6 +56,7 @@ class GrpcClient(object):
     Arguments:
         host: string, the hostname and port of the server (`localhost:8080`)
     """
+
     def __init__(self, host):
         self.logger = logging.getLogger(self.__class__.__name__)
         self.host = host
@@ -87,6 +88,7 @@ class PredictClient(GrpcClient):
         model_name: string, name of model served by tensorflow-serving
         model_version: integer, version of the named model
     """
+
     def __init__(self, host, model_name, model_version):
         super(PredictClient, self).__init__(host)
         self.model_name = model_name
@@ -157,6 +159,7 @@ class ProcessClient(GrpcClient):
         process_type: string, pre or post processing
         function_name: string, name of processing function
     """
+
     def __init__(self, host, process_type, function_name):
         super(ProcessClient, self).__init__(host)
         self.process_type = process_type
@@ -297,6 +300,7 @@ class TrackingClient(GrpcClient):
         model_name: string, name of model served by tensorflow-serving
         model_version: integer, version of the named model
     """
+
     def __init__(self, host, redis_hash, model_name, model_version, progress_callback):
         super(TrackingClient, self).__init__(host)
         self.redis_hash = redis_hash
@@ -328,7 +332,6 @@ def _predict(self, data, request_timeout=100):
         num_preds = data[0].shape[0]
 
         predictions = []
-        self.logger.debug('Sending %i requests...', num_preds)
         for data_i in range(num_preds):
             request = PredictRequest()
             request.model_spec.name = self.model_name  # pylint: disable=E1101
@@ -341,7 +344,8 @@ def _predict(self, data, request_timeout=100):
                 tensor_proto = make_tensor_proto(model_input, 'DT_FLOAT')
                 request.inputs["input{}".format(i)].CopyFrom(tensor_proto)
 
-            predictions.append(self._single_request(stub, request))
+            # Select only last dimension in order to drop batch axis
+            predictions.append(self._single_request(stub, request)[-1])
 
         self.logger.info('Predicting everything took: %s seconds',
                          timeit.default_timer() - t)

redis_consumer/redis_test.py

@@ -70,6 +70,13 @@ def sentinel_slaves(self, _):
         n = random.randint(1, 4)
         return [{'ip': 'slave', 'port': 6379} for i in range(n)]
 
+    def sentinel_masters(self):
+        return {'mymaster': {'ip': 'master', 'port': 6379}}
+
+    def sentinel_slaves(self, _):
+        n = random.randint(1, 4)
+        return [{'ip': 'slave', 'port': 6379} for i in range(n)]
+
 
 class TestRedis(object):
 

redis_consumer/settings.py

@@ -127,3 +127,17 @@ def _strip(x):
         'retinanet': processing.retinanet_to_label_image,
     },
 }
+
+# Tracking settings
+MODEL_NAME = config('MODEL_NAME', default='HeLaS3watershed')
+MODEL_VERSION = config('MODEL_VERSION', default=2)
+POSTPROCESS_FUNCTION = config('POSTPROCESS_FUNCTION', default='watershed')
+CUTS = config('CUTS', default=0)
+
+# tracking.cell_tracker settings
+MAX_DISTANCE = config('MAX_DISTANCE', default=50)
+TRACK_LENGTH = config('TRACK_LENGTH', default=5)
+DIVISION = config('DIVISION', default=0.9)
+BIRTH = config('BIRTH', default=0.95)
+DEATH = config('DEATH', default=0.95)
+NEIGHBORHOOD_SCALE_SIZE = config('NEIGHBORHOOD_SCALE_SIZE', default=30)

redis_consumer/utils.py

@@ -127,7 +127,6 @@ def make_tensor_proto(data, dtype):
         },
         number_to_dtype_value[dtype]: values
     }
-
     dict_to_protobuf.dict_to_protobuf(tensor_proto_dict, tensor_proto)
 
     return tensor_proto