rerun tutorials with latest package version

Author: MarcelRosier

panoptica/example_spine_matched_instance.ipynb

@@ -16,14 +16,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Requirement already satisfied: panoptica in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (0.5.0.post4.dev0+f327a0f)\n",
+      "Requirement already satisfied: panoptica in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (0.5.2)\n",
       "Requirement already satisfied: auxiliary in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.35)\n",
       "Requirement already satisfied: rich in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (13.6.0)\n",
       "Requirement already satisfied: numpy in /Users/marcelrosier/opt/anaconda3/envs/brainles/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.25.2)\n",
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -96,7 +96,7 @@
        "        106, 107, 108, 202, 203, 204, 205, 206, 207, 208], dtype=uint8))"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -118,23 +118,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "evaluate took 0.06522703170776367 seconds to execute.\n",
-      "Number of instances in prediction: 22\n",
-      "Number of instances in reference: 22\n",
-      "True Positives (tp): 19\n",
-      "False Positives (fp): 3\n",
-      "False Negatives (fn): 3\n",
-      "Recognition Quality / F1 Score (RQ): 0.8636363636363636\n",
-      "Segmentation Quality (SQ): 0.8328184295330796 ± 0.15186064004517466\n",
-      "Panoptic Quality (PQ): 0.719252280051296\n",
-      "volumetric instance-wise DICE: 0.9002926160099541 ± 0.1025356617495733\n"
+      "evaluate took 3.041011333465576 seconds to execute.\n"
      ]
     }
    ],
@@ -146,8 +137,7 @@
     "    iou_threshold=0.5,\n",
     ")\n",
     "\n",
-    "result, debug_data = evaluator.evaluate(sample)\n",
-    "print(result)"
+    "result, debug_data = evaluator.evaluate(sample)"
    ]
   },
   {
@@ -160,7 +150,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -175,7 +165,9 @@
       "Recognition Quality / F1 Score (RQ): 0.8636363636363636\n",
       "Segmentation Quality (SQ): 0.8328184295330796 ± 0.15186064004517466\n",
       "Panoptic Quality (PQ): 0.719252280051296\n",
-      "volumetric instance-wise DICE: 0.9002926160099541 ± 0.1025356617495733\n"
+      "DSC-based Segmentation Quality (DQ_DSC): 0.900292616009954 ± 0.1025356617495733\n",
+      "DSC-based Panoptic Quality (PQ_DSC): 0.7775254410995057\n",
+      "Average symmetric surface distance (ASSD): 0.25033188787922506 ± 0.07696680402317077\n"
      ]
     },
     {
@@ -205,8 +197,11 @@
        "    <span style=\"color: #008000; text-decoration-color: #008000\">'sq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.8328184295330796</span>,\n",
        "    <span style=\"color: #008000; text-decoration-color: #008000\">'sq_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.15186064004517466</span>,\n",
        "    <span style=\"color: #008000; text-decoration-color: #008000\">'pq'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.719252280051296</span>,\n",
-       "    <span style=\"color: #008000; text-decoration-color: #008000\">'instance_dice'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.9002926160099541</span>,\n",
-       "    <span style=\"color: #008000; text-decoration-color: #008000\">'instance_dice_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.1025356617495733</span>\n",
+       "    <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.900292616009954</span>,\n",
+       "    <span style=\"color: #008000; text-decoration-color: #008000\">'sq_dsc_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.1025356617495733</span>,\n",
+       "    <span style=\"color: #008000; text-decoration-color: #008000\">'pq_dsc'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.7775254410995057</span>,\n",
+       "    <span style=\"color: #008000; text-decoration-color: #008000\">'assd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.25033188787922506</span>,\n",
+       "    <span style=\"color: #008000; text-decoration-color: #008000\">'assd_sd'</span>: <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0.07696680402317077</span>\n",
        "<span style=\"font-weight: bold\">}</span>\n",
        "</pre>\n"
       ],
@@ -222,8 +217,11 @@
        "    \u001b[32m'sq'\u001b[0m: \u001b[1;36m0.8328184295330796\u001b[0m,\n",
        "    \u001b[32m'sq_sd'\u001b[0m: \u001b[1;36m0.15186064004517466\u001b[0m,\n",
        "    \u001b[32m'pq'\u001b[0m: \u001b[1;36m0.719252280051296\u001b[0m,\n",
-       "    \u001b[32m'instance_dice'\u001b[0m: \u001b[1;36m0.9002926160099541\u001b[0m,\n",
-       "    \u001b[32m'instance_dice_sd'\u001b[0m: \u001b[1;36m0.1025356617495733\u001b[0m\n",
+       "    \u001b[32m'sq_dsc'\u001b[0m: \u001b[1;36m0.900292616009954\u001b[0m,\n",
+       "    \u001b[32m'sq_dsc_sd'\u001b[0m: \u001b[1;36m0.1025356617495733\u001b[0m,\n",
+       "    \u001b[32m'pq_dsc'\u001b[0m: \u001b[1;36m0.7775254410995057\u001b[0m,\n",
+       "    \u001b[32m'assd'\u001b[0m: \u001b[1;36m0.25033188787922506\u001b[0m,\n",
+       "    \u001b[32m'assd_sd'\u001b[0m: \u001b[1;36m0.07696680402317077\u001b[0m\n",
        "\u001b[1m}\u001b[0m\n"
       ]
      },