Add backend endpoint

server/app/app.py

@@ -190,6 +190,11 @@ class SummarizeVarAPI(Resource):
     def post(self, data_adaptor):
         return common_rest.summarize_var_post(request, data_adaptor)
 
+class SpatialImageAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return common_rest.spatial_image_get(request, data_adaptor)
+
 
 def get_api_base_resources(bp_base):
     """Add resources that are accessed from the api url"""
@@ -222,6 +227,8 @@ def get_api_dataroot_resources(bp_dataroot):
     # Computation routes
     add_resource(DiffExpObsAPI, "/diffexp/obs")
     add_resource(LayoutObsAPI, "/layout/obs")
+    # Spatial routes
+    add_resource(SpatialImageAPI, "/spatial/image")
     return api
 
 

server/common/rest.py

@@ -5,7 +5,7 @@ from http import HTTPStatus
 import zlib
 import json
 
-from flask import make_response, jsonify, current_app, abort
+from flask import make_response, jsonify, current_app, abort, send_file
 from werkzeug.urls import url_unquote
 
 from server.common.config.client_config import get_client_config
@@ -397,3 +397,39 @@ def summarize_var_post(request, data_adaptor):
 
     key = request.args.get("key", default=None)
     return summarize_var_helper(request, data_adaptor, key, request.get_data())
+
+def spatial_image_get(request, data_adaptor):
+    import io
+    import matplotlib.pyplot    
+
+    resolution = "hires"
+    spatial = data_adaptor.get_spatial()
+
+    if len(list(spatial)) == 0:
+        return abort_and_log(HTTPStatus.BAD_REQUEST, "uns does not have spatial information")
+
+    library_id = list(spatial)[0]
+    if len(spatial) > 1:
+        current_app.logger.warning(f"More than one library found under uns.spatial, using library '{library_id}'")
+
+    if "images" not in spatial[library_id]:
+        return abort_and_log(HTTPStatus.BAD_REQUEST, "spatial information does not contain images")
+
+    if resolution not in spatial[library_id]["images"]:
+        return abort_and_log(HTTPStatus.BAD_REQUEST, f"spatial information does not contain requested resolution '{resolution}'")
+
+    response_image = io.BytesIO()
+    matplotlib.pyplot.imsave(response_image, spatial[library_id]["images"][resolution])
+    response_image.seek(0)
+
+    try:
+        return send_file(response_image, attachment_filename=f"{library_id}-{resolution}.png", mimetype="image/png")
+    except (KeyError, DatasetAccessError) as e:
+        return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
+    except PrepareError:
+        return abort_and_log(
+            HTTPStatus.NOT_IMPLEMENTED,
+            f"No spatial image available {request.path}",
+            loglevel=logging.ERROR,
+            include_exc_info=True,
+        ) 

server/data_anndata/anndata_adaptor.py

@@ -274,6 +274,9 @@ class AnndataAdaptor(DataAdaptor):
             df = df[fields]
         return encode_matrix_fbs(df, col_idx=df.columns)
 
+    def get_spatial(self):
+        return self.data.uns["spatial"]
+
     def get_embedding_names(self):
         """
         Return pre-computed embeddings.

server/requirements.txt

@@ -14,6 +14,7 @@ flatten-dict>=0.2.0
 fsspec>=0.4.4,<0.8.0
 gunicorn>=20.0.4
 h5py>=3.0.0
+matplotlib>=3.5.0
 numba>=0.51.2
 numpy>=1.17.5
 packaging>=20.0