Example works now

Signed-off-by: Eric Kerfoot <[email protected]>

Author: ericspod

generation/3d_ddpm/3d_ddpm_tutorial.ipynb

@@ -56,7 +56,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "cdea37d5",
    "metadata": {},
    "outputs": [
@@ -120,7 +120,7 @@
     "    LoadImaged,\n",
     "    Resized,\n",
     "    ScaleIntensityd,\n",
-    "    ScaleIntensityRangePercentilesd\n",
+    "    ScaleIntensityRangePercentilesd,\n",
     ")\n",
     "from monai.utils import set_determinism\n",
     "from monai.inferers import DiffusionInferer\n",
@@ -159,7 +159,7 @@
     }
    ],
    "source": [
-    "directory = os.path.abspath(\"./data\")  # os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]
@@ -223,7 +223,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "ddd61e60",
    "metadata": {
     "lines_to_next_cell": 2
@@ -247,7 +247,7 @@
     "    task=\"Task01_BrainTumour\",\n",
     "    transform=data_transform,\n",
     "    section=\"training\",\n",
-    "    download=False,  #True,\n",
+    "    download=True,\n",
     "    num_workers=num_workers,\n",
     ")\n",
     "\n",
@@ -260,7 +260,7 @@
     "    task=\"Task01_BrainTumour\",\n",
     "    transform=data_transform,\n",
     "    section=\"validation\",\n",
-    "    download=False,  #True,\n",
+    "    download=True,\n",
     "    num_workers=num_workers,\n",
     ")\n",
     "\n",
@@ -393,14 +393,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "id": "6c1de5ad",
    "metadata": {},
    "outputs": [],
    "source": [
     "num_train_timesteps = 1000\n",
     "scheduler = DDPMScheduler(\n",
-    "    num_train_timesteps=num_train_timesteps #, schedule=\"scaled_linear_beta\", beta_start=0.0005, beta_end=0.0195, clip_sample=False\n",
+    "    num_train_timesteps=num_train_timesteps  # , schedule=\"scaled_linear_beta\", beta_start=0.0005, beta_end=0.0195, clip_sample=False\n",
     ")"
    ]
   },
@@ -468,7 +468,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "id": "bd10b595",
    "metadata": {
     "lines_to_next_cell": 0
@@ -653,7 +653,7 @@
     "    if (epoch + 1) % val_interval == 0:\n",
     "        model.eval()\n",
     "\n",
-    "        torch.save(model.state_dict(),f\"model_{epoch:04}.pth\")\n",
+    "        torch.save(model.state_dict(), f\"model_{epoch:04}.pth\")\n",
     "\n",
     "        val_epoch_loss = 0\n",
     "        for step, batch in enumerate(val_loader):\n",