upd usage files

berenslab · Jan 31, 2025 · d9c813f · d9c813f
1 parent 6870ee3
commit d9c813f
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Showing 6 changed files with 17 additions and 60 deletions.
diff --git a/0_example_usage/usage_all.ipynb b/0_example_usage/usage_all.ipynb
diff --git a/0_example_usage/usage_circle-crop.ipynb b/0_example_usage/usage_circle-crop.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/0_example_usage/usage_fovea-od_inference.ipynb b/0_example_usage/usage_fovea-od_inference.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -79,16 +79,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2025-01-29 12:12:55--  https://upload.wikimedia.org/wikipedia/commons/3/37/Fundus_photograph_of_normal_right_eye.jpg\n",
+      "--2025-01-31 14:58:16--  https://upload.wikimedia.org/wikipedia/commons/3/37/Fundus_photograph_of_normal_right_eye.jpg\n",
       "Resolving upload.wikimedia.org (upload.wikimedia.org)... 185.15.59.240, 2a02:ec80:300:ed1a::2:b\n",
       "Connecting to upload.wikimedia.org (upload.wikimedia.org)|185.15.59.240|:443... connected.\n",
       "HTTP request sent, awaiting response... 200 OK\n",
       "Length: 253968 (248K) [image/jpeg]\n",
       "Saving to: 'imgs/fundus.jpg'\n",
       "\n",
-      "imgs/fundus.jpg     100%[===================>] 248.02K  --.-KB/s    in 0.07s   \n",
+      "imgs/fundus.jpg     100%[===================>] 248.02K  --.-KB/s    in 0.08s   \n",
       "\n",
-      "2025-01-29 12:12:56 (3.47 MB/s) - 'imgs/fundus.jpg' saved [253968/253968]\n",
+      "2025-01-31 14:58:17 (3.12 MB/s) - 'imgs/fundus.jpg' saved [253968/253968]\n",
       "\n"
      ]
     }

diff --git a/0_example_usage/usage_quality.ipynb b/0_example_usage/usage_quality.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -30,16 +30,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2025-01-29 12:13:26--  https://upload.wikimedia.org/wikipedia/commons/3/37/Fundus_photograph_of_normal_right_eye.jpg\n",
+      "--2025-01-31 14:58:19--  https://upload.wikimedia.org/wikipedia/commons/3/37/Fundus_photograph_of_normal_right_eye.jpg\n",
       "Resolving upload.wikimedia.org (upload.wikimedia.org)... 185.15.59.240, 2a02:ec80:300:ed1a::2:b\n",
       "Connecting to upload.wikimedia.org (upload.wikimedia.org)|185.15.59.240|:443... connected.\n",
       "HTTP request sent, awaiting response... 200 OK\n",
       "Length: 253968 (248K) [image/jpeg]\n",
       "Saving to: 'fundus.jpg'\n",
       "\n",
-      "fundus.jpg          100%[===================>] 248.02K  --.-KB/s    in 0.07s   \n",
+      "fundus.jpg          100%[===================>] 248.02K  --.-KB/s    in 0.08s   \n",
       "\n",
-      "2025-01-29 12:13:26 (3.43 MB/s) - 'fundus.jpg' saved [253968/253968]\n",
+      "2025-01-31 14:58:19 (3.13 MB/s) - 'fundus.jpg' saved [253968/253968]\n",
       "\n"
      ]
     }
@@ -84,7 +84,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x7f40ab393670>"
+       "<matplotlib.image.AxesImage at 0x7fc6bfdf8400>"
       ]
      },
      "execution_count": 4,

diff --git a/0_example_usage/usage_registration.ipynb b/0_example_usage/usage_registration.ipynb
diff --git a/0_example_usage/usage_vessel-segmentation.ipynb b/0_example_usage/usage_vessel-segmentation.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,16 +66,7 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/gpfs01/berens/user/jgervelmeyer/fundus_image_toolbox/fundus_image_toolbox/vessel_segmentation/segmentation/utils/notebook_utils.py:18: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.\n",
-      "  checkpoint= torch.load(predictor_path, map_location=device)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "ensemble = fit.load_segmentation_ensemble(device=device)"
    ]
@@ -142,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [