Checkpoint

server/common/rest.py

@@ -4,6 +4,7 @@ import sys
 from http import HTTPStatus
 import zlib
 import json
+import numpy as np
 
 from flask import make_response, jsonify, current_app, abort, send_file
 from werkzeug.urls import url_unquote
@@ -419,7 +420,8 @@ def spatial_image_get(request, data_adaptor):
         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])
+    img = np.flipud(spatial[library_id]["images"][resolution])
+    matplotlib.pyplot.imsave(response_image, img)
     response_image.seek(0)
 
     try:

server/data_common/data_adaptor.py

@@ -361,6 +361,8 @@ class DataAdaptor(metaclass=ABCMeta):
         translate = 0.5 - ((max - min) / scale / 2)
         normalized_layout = normalized_layout + translate
 
+        print(f"scale {scale}, translate {translate}")
+
         normalized_layout = normalized_layout.astype(dtype=np.float32)
         return normalized_layout
 
@@ -388,6 +390,8 @@ class DataAdaptor(metaclass=ABCMeta):
                 df = pd.concat(layout_data, axis=1, copy=False)
             else:
                 df = pd.DataFrame()
+            # print("##########DF")
+            # print(df)
             fbs = encode_matrix_fbs(df, col_idx=df.columns, row_idx=None)
 
         return fbs