vqdang#133 UPD: fix tile format for metric

samjmolyneux · Jun 20, 2021 · a0f80c7 · a0f80c7
1 parent 9515afa
commit a0f80c7
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/compute_stats.py b/compute_stats.py
@@ -15,6 +15,7 @@
     get_fast_dice_2,
     get_fast_pq,
     remap_label,
+    pair_coordinates
 )
 
 

diff --git a/infer/tile.py b/infer/tile.py
@@ -175,11 +175,17 @@ def proc_callback(results):
             """
             img_name, pred_map, pred_inst, inst_info_dict, overlaid_img = results
 
-            inst_type = [[k, v["type"]] for k, v in inst_info_dict.items()]
-            inst_type = np.array(inst_type)
+            nuc_val_list = list(inst_info_dict.values())
+            # need singleton to make matlab happy
+            nuc_uid_list = np.array(list(inst_info_dict.keys()))[:,None]
+            nuc_type_list = np.array([v["type"] for v in nuc_val_list])[:,None]
+            nuc_coms_list = np.array([v["centroid"] for v in nuc_val_list])
+
             mat_dict = {
-                "inst_map": pred_inst,
-                "inst_type": inst_type,
+                "inst_map" : pred_inst,
+                "inst_uid" : nuc_uid_list,
+                "inst_type": nuc_type_list,
+                "inst_centroid": nuc_coms_list
             }
             if self.nr_types is None: # matlab does not have None type array
                 mat_dict.pop("inst_type", None) 

diff --git a/metrics/stats_utils.py b/metrics/stats_utils.py
@@ -409,7 +409,6 @@ def pair_coordinates(setA, setB, radius):
     """
     # * Euclidean distance as the cost matrix
     pair_distance = scipy.spatial.distance.cdist(setA, setB, metric='euclidean')
-    print(setA.shape, setB.shape)
 
     # * Munkres pairing with scipy library
     # the algorithm return (row indices, matched column indices)