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bioimage-io · Jun 10, 2024 · 23783ba · 23783ba
1 parent 51b31b9
commit 23783ba
Showing 1 changed file with 28 additions and 8 deletions.
diff --git a/notebooks/bioengine-tutorial-embl-2024.ipynb b/notebooks/bioengine-tutorial-embl-2024.ipynb
@@ -33,7 +33,7 @@
         "trusted": true
       },
       "outputs": [],
-      "execution_count": 2
+      "execution_count": 3
     },
     {
       "cell_type": "code",
@@ -42,7 +42,7 @@
         "trusted": true
       },
       "outputs": [],
-      "execution_count": 3
+      "execution_count": 4
     },
     {
       "cell_type": "markdown",
@@ -70,7 +70,7 @@
           "metadata": {}
         }
       ],
-      "execution_count": 10
+      "execution_count": 5
     },
     {
       "cell_type": "markdown",
@@ -85,7 +85,7 @@
         "trusted": true
       },
       "outputs": [],
-      "execution_count": 11
+      "execution_count": 7
     },
     {
       "cell_type": "markdown",
@@ -94,7 +94,7 @@
     },
     {
       "cell_type": "code",
-      "source": "import json\nret = await triton.execute(inputs=[{'inputs': None, \"model_id\": \"creative-panda\", 'return_rdf':True}],\n                           model_name=\"bioengine-model-runner\",\n                           serialization=\"imjoy\",\n                          )\nrdf_content = ret['result']['rdf']\nprint(json.dumps(rdf_content, indent=4))",
+      "source": "import json\nret = await triton.execute(inputs=[{'inputs': None, \"model_id\": \"creative-panda\", 'return_rdf':True}],\n                           model_name=\"bioengine-model-runner\",\n                           serialization=\"imjoy\",\n                          )\nmodel_rdf = ret['result']['rdf']\nprint(json.dumps(model_rdf, indent=4))",
       "metadata": {
         "trusted": true
       },
@@ -105,7 +105,27 @@
           "output_type": "stream"
         }
       ],
-      "execution_count": 17
+      "execution_count": 8
+    },
+    {
+      "cell_type": "markdown",
+      "source": "## Make sure the input image shape is valid",
+      "metadata": {}
+    },
+    {
+      "cell_type": "code",
+      "source": "input_image_shape = tuple(model_rdf[\"inputs\"][0][\"shape\"][1:])\nprint(\"Input image shape\", input_image_shape)\ninput_image = image[...,None]\nassert input_image.shape == input_image_shape, f\"Wrong shape ({input_image.shape}), expected: {input_image_shape}\"\nprint(\"Valid image shape, ready to go!\")",
+      "metadata": {
+        "trusted": true
+      },
+      "outputs": [
+        {
+          "name": "stdout",
+          "text": "Input image shape (512, 512, 1)\nValid image shape, ready to go!\n",
+          "output_type": "stream"
+        }
+      ],
+      "execution_count": 28
     },
     {
       "cell_type": "markdown",
@@ -114,7 +134,7 @@
     },
     {
       "cell_type": "code",
-      "source": "ret = await triton.execute(inputs=[{\"inputs\":[[image[...,None]]], \"model_id\": \"creative-panda\"}],\n                           model_name=\"bioengine-model-runner\",\n                           serialization=\"imjoy\",\n                          )\nresult = ret[\"result\"]\nmask = result['outputs'][0]\nprint('prediction: ', mask.shape)",
+      "source": "ret = await triton.execute(inputs=[{\"inputs\":[[input_image]], \"model_id\": \"creative-panda\"}],\n                           model_name=\"bioengine-model-runner\",\n                           serialization=\"imjoy\",\n                          )\nresult = ret[\"result\"]\nmask = result['outputs'][0]\nprint('prediction: ', mask.shape)",
       "metadata": {
         "trusted": true
       },
@@ -125,7 +145,7 @@
           "output_type": "stream"
         }
       ],
-      "execution_count": 13
+      "execution_count": 27
     },
     {
       "cell_type": "markdown",