minor changes in text and code

Author: DanielaSchacherer

notebooks/collections_demos/RMS-Mutation-Prediction-Expert-Annotations_exploration.ipynb

@@ -235,34 +235,11 @@
         "id": "xhNohZuPm_hq",
         "outputId": "2d3aae96-d2b4-43a1-ebc6-397006b93b56"
       },
-      "outputs": [
-        {
-          "data": {
-            "text/html": [
-              "\n",
-              "        <iframe\n",
-              "            width=\"1600\"\n",
-              "            height=\"900\"\n",
-              "            src=\"https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.155017484756498730492136597238994838876\"\n",
-              "            frameborder=\"0\"\n",
-              "            allowfullscreen\n",
-              "            \n",
-              "        ></iframe>\n",
-              "        "
-            ],
-            "text/plain": [
-              "<IPython.lib.display.IFrame at 0x7f6f352e9690>"
-            ]
-          },
-          "execution_count": 12,
-          "metadata": {},
-          "output_type": "execute_result"
-        }
-      ],
+      "outputs": [],
       "source": [
         "viewer_url = idc_client.get_viewer_URL(studyInstanceUID=rms_srs['StudyInstanceUID'].iloc[0], viewer_selector='slim')\n",
         "from IPython.display import IFrame\n",
-        "IFrame(viewer_url, width=1600, height=900)\n"
+        "IFrame(viewer_url, width=1600, height=900)"
       ]
     },
     {
@@ -1352,26 +1329,7 @@
         "id": "996QfHpuHrmI",
         "outputId": "6083da12-80bd-44f5-ff17-14e8449e9e95"
       },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "Finding type: Embryonal rhabdomyosarcoma\n",
-            "ROI GraphicTypeValues3D.POLYGON\n",
-            "[[13.92508507 40.25288391  0.        ]\n",
-            " [13.73841286 39.99548721  0.        ]\n",
-            " [13.66768551 39.51605225  0.        ]\n",
-            " ...\n",
-            " [13.87456512 40.24278259  0.        ]\n",
-            " [13.86446095 40.23772812  0.        ]\n",
-            " [13.92508507 40.25288391  0.        ]]\n",
-            "ROI refers to FrameOfReferenceUID: 1.3.6.1.4.1.5962.99.1.2774652108.856667456.1686401864908.7.0\n",
-            "\n",
-            "\n"
-          ]
-        }
-      ],
+      "outputs": [],
       "source": [
         "# Extract different attributes from the measurement group\n",
         "for m_group in planar_measurement_groups_example1[:3]:\n",
@@ -1415,7 +1373,7 @@
         "    planar_measurement_groups = extract_planar_measurements_groups(dcm_sr_path)\n",
         "    for m_group in planar_measurement_groups:\n",
         "        study_instance_uid = hd.sr.srread(dcm_sr_path).StudyInstanceUID\n",
-        "        slim_viewer_url = get_slim_viewer_url(study_instance_uid)\n",
+        "        slim_viewer_url = idc_client.get_viewer_URL(studyInstanceUID=study_instance_uid, viewer_selector='slim')\n",
         "        measurements_and_rois[(dcm_sr_path, slim_viewer_url)][m_group.finding_type.meaning].append(m_group.roi)\n",
         "\n",
         "df_measurements_and_rois = pd.DataFrame.from_dict(measurements_and_rois, orient='index')"