Experimental use of orjson to fasten json serialization (test on chan…

…nel histogram bounds)

See tiangolo/fastapi#2615

pims/api/histograms.py

@@ -242,7 +242,8 @@ def show_channels_histogram(
 
 @router.get(
     '/image/{filepath:path}/histogram/per-channels/bounds',
-    tags=api_tags, response_model=ChannelsHistogramInfoCollection
+    tags=api_tags, response_model=ChannelsHistogramInfoCollection,
+    response_class=CustomOrJsonResponse
 )
 def show_channels_histogram_bounds(
     path: Path = Depends(imagepath_parameter),
@@ -266,14 +267,14 @@ def show_channels_histogram_bounds(
     for channel, bounds in zip(channels, channels_bounds):
         mini, maxi = bounds
         hist_info.append(
-            ChannelHistogramInfo(
+            dict(
                 channel=channel, type=htype,
                 color=in_image.channels[channel].hex_color,
                 minimum=mini, maximum=maxi
             )
         )
 
-    return response_list(hist_info)
+    return CustomOrJsonResponse(response_list(hist_info))
 
 
 @router.get(

pims/api/utils/response.py

@@ -12,9 +12,11 @@
 #  * See the License for the specific language governing permissions and
 #  * limitations under the License.
 import logging
-from typing import Optional
+from typing import Any, Optional
 
+import orjson
 from cytomine.models import Model
+from fastapi.responses import ORJSONResponse
 from pint import Quantity
 
 log = logging.getLogger("pims")
@@ -66,3 +68,16 @@ def serialize_cytomine_model(o):
         return d
     log.warning(f"The object {o} is not a Cytomine model and is thus not serialized.")
     return o
+
+
+class CustomOrJsonResponse(ORJSONResponse):
+    def render(self, content: Any) -> bytes:
+        assert orjson is not None, "orjson must be installed to use ORJSONResponse"
+
+        def default(obj):
+            """ custom parser for orjson (usually named default) """
+            raise TypeError
+
+        return orjson.dumps(
+            content, option=orjson.OPT_SERIALIZE_NUMPY, default=default
+        )

requirements.txt

@@ -123,6 +123,8 @@ numpy==1.21.4
     #   zarr
 opencv-python-headless==4.5.4.60
     # via cytomine-python-client
+orjson==3.6.5
+    # via pims (setup.py)
 packaging==21.3
     # via
     #   matplotlib

setup.py

@@ -37,6 +37,7 @@
     'uvicorn[standard]>=0.13.4',
     'fastapi>=0.65.1',
     'pydantic>=1.8.2',
+    'orjson>=3.6.5',
     'rich>=10.2.2',
     'python-dotenv>=0.17.1',
     'python-multipart>=0.0.5',