Use the correct model

Author: constantinpape

example/bioimageio-core-usage.ipynb

@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c72ba149",
    "metadata": {},
    "outputs": [],
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "74613461",
    "metadata": {},
    "outputs": [],
@@ -52,43 +52,43 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "2de51dae",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# rdf_url = \"https://sandbox.zenodo.org/record/881989/files/rdf.yaml\"\n",
-    "rdf_url = \"https://sandbox.zenodo.org/record/881989/files/rdf.yaml?download=1\"\n",
-    "rdf_doi = \"10.5072/zenodo.881940\"\n",
+    "rdf_url = \"https://sandbox.zenodo.org/record/933830/files/rdf.yaml\"\n",
+    "\n",
+    "rdf_doi = \"10.5072/zenodo.933830\"\n",
+    "\n",
     "rdf_path = \"/home/pape/Downloads/dsb-nuclei-boundarymodelnew_pytorch_state_dict.zip\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "ce884f8c",
    "metadata": {},
    "outputs": [],
    "source": [
     "# load model from link to rdf.yaml\n",
-    "# TODO does not work yet\n",
-    "# model_resource = bioimageio.core.load_resource_description(rdf_url)"
+    "model_resource = bioimageio.core.load_resource_description(rdf_url)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "c1230b2d",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# TODO does not work yet\n",
-    "# model_resource = bioimageio.core.load_resource_description(rdf_doi)"
+    "# load model from doi\n",
+    "model_resource = bioimageio.core.load_resource_description(rdf_doi)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "8329315c",
    "metadata": {},
    "outputs": [],
@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "f59b1b15",
    "metadata": {},
    "outputs": [],
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "808e2ca7",
    "metadata": {},
    "outputs": [],
@@ -139,27 +139,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "4f235e9a",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/pape/Work/software/conda/miniconda3/envs/bio-core-dev/lib/python3.7/site-packages/torch/nn/functional.py:718: UserWarning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for anything important until they are released as stable. (Triggered internally at  /tmp/pip-req-build-xi8rb33b/c10/core/TensorImpl.h:1156.)\n",
-      "  return torch.max_pool2d(input, kernel_size, stride, padding, dilation, ceil_mode)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "prediction = predict_numpy(model_resource, input_image)\n",
     "show_images(input_image, prediction, names=[\"image\", \"prediction\"])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "58f6c459",
    "metadata": {},
    "outputs": [],
@@ -178,7 +169,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "id": "879618df",
    "metadata": {},
    "outputs": [],
@@ -198,18 +189,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "id": "5962d73a",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "invalid local relative path: documentation.md\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# create a new model with different post-processing\n",
     "from bioimageio.core.build_spec import build_model\n",
@@ -265,7 +248,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "id": "e0616547",
    "metadata": {},
    "outputs": [],
@@ -285,18 +268,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "id": "482a64bb",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "invalid local relative path: ./documentation.md\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from bioimageio.core.weight_converter.torch import convert_weights_to_pytorch_script\n",
     "from bioimageio.core.build_spec import add_weights\n",
@@ -309,7 +284,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "id": "b15dd990",
    "metadata": {},
    "outputs": [],
@@ -321,28 +296,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": null,
    "id": "2aa9db23",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "invalid local relative path: ./documentation.md\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'another_model.zip'"
-      ]
-     },
-     "execution_count": 18,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# saving model packages\n",
     "bioimageio.core.export_resource_package(new_model2_raw, output_path=\"another_model.zip\")"