adapted queries to use ann_index

Author: DanielaSchacherer

notebooks/collections_demos/bonemarrowwsi_pediatricleukemia.ipynb

@@ -115,7 +115,7 @@
       "outputs": [],
       "source": [
         "idc_client = IDCClient() # set-up idc_client\n",
-        "idc_client.fetch_index('sm_instance_index')"
+        "idc_client.fetch_index('ann_index') # fetch index for ANN objects"
       ]
     },
     {
@@ -164,7 +164,7 @@
         "id": "1-ZR8MkhFqKX"
       },
       "source": [
-        "Next, let's have a look on the available annotation (ANN) files. The following query collects information about ANN files on series-level."
+        "Next, let's have a look on the available annotation (ANN) files. The following query collects information about ANN files on series-level from idc-index's `ann_index`."
       ]
     },
     {
@@ -177,18 +177,14 @@
       "source": [
         "query_anns = '''\n",
         "SELECT\n",
-        "    SeriesDescription,\n",
         "    SeriesInstanceUID,\n",
-        "    ANY_VALUE(StudyInstanceUID) AS StudyInstanceUID,\n",
-        "    ANY_VALUE(Modality) AS Modality,\n",
-        "    ANY_VALUE(ReferencedSeriesSequence[SAFE_OFFSET(0)].SeriesInstanceUID) AS referencedSeriesInstanceUID\n",
+        "    SeriesDescription,\n",
+        "    StudyInstanceUID,\n",
+        "    referencedSeriesInstanceUID\n",
         "FROM\n",
-        "    index\n",
+        "    ann_index\n",
         "WHERE\n",
-        "    collection_id = 'bonemarrowwsi_pediatricleukemia' AND Modality='ANN'\n",
-        "GROUP BY\n",
-        "    SeriesInstanceUID,\n",
-        "    SeriesDescription\n",
+        "    collection_id = 'bonemarrowwsi_pediatricleukemia'\n",
         "ORDER BY\n",
         "    referencedSeriesInstanceUID\n",
         "'''\n",
@@ -366,10 +362,9 @@
         "    SELECT\n",
         "        SeriesInstanceUID\n",
         "    FROM\n",
-        "        index\n",
+        "        ann_index\n",
         "    WHERE\n",
         "        collection_id = 'bonemarrowwsi_pediatricleukemia'\n",
-        "        AND Modality='ANN'\n",
         "        AND LOWER(SeriesDescription) LIKE '%monolayer%'\n",
         "    ORDER BY\n",
         "        SeriesInstanceUID\n",
@@ -1135,10 +1130,9 @@
         "          SELECT\n",
         "              SeriesInstanceUID,\n",
         "          FROM\n",
-        "              index\n",
+        "              ann_index\n",
         "          WHERE\n",
         "              collection_id = 'bonemarrowwsi_pediatricleukemia'\n",
-        "              AND Modality='ANN'\n",
         "              AND LOWER(SeriesDescription) LIKE '%{query_word}%'\n",
         "          ORDER BY\n",
         "              SeriesInstanceUID\n",
@@ -1149,10 +1143,9 @@
         "          SELECT\n",
         "              SeriesInstanceUID,\n",
         "          FROM\n",
-        "              index\n",
+        "              ann_index\n",
         "          WHERE\n",
         "              collection_id = 'bonemarrowwsi_pediatricleukemia'\n",
-        "              AND Modality='ANN'\n",
         "          ORDER BY\n",
         "              SeriesInstanceUID\n",
         "          LIMIT {ann_to_process}\n",