From 0f010dc3ab99bae7d06841ecbb8419da80723808 Mon Sep 17 00:00:00 2001
From: Ziwen Liu <ziwen.liu@czbiohub.org>
Date: Wed, 9 Oct 2024 15:00:53 -0700
Subject: [PATCH] fix import paths in example notebooks

---
 .../dlmbl_exercise/exercise.ipynb             | 36 +++++++++++++----
 .../dlmbl_exercise/solution.ipynb             | 40 +++++++++----------
 2 files changed, 48 insertions(+), 28 deletions(-)

diff --git a/examples/virtual_staining/dlmbl_exercise/exercise.ipynb b/examples/virtual_staining/dlmbl_exercise/exercise.ipynb
index 7e5fadff..2dcf49d8 100644
--- a/examples/virtual_staining/dlmbl_exercise/exercise.ipynb
+++ b/examples/virtual_staining/dlmbl_exercise/exercise.ipynb
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "68d4a6ef",
    "metadata": {
     "title": "Imports"
@@ -148,6 +148,7 @@
     "from natsort import natsorted\n",
     "from numpy.typing import ArrayLike\n",
     "from skimage import metrics  # for metrics.\n",
+    "\n",
     "# pytorch lightning wrapper for Tensorboard.\n",
     "from skimage.color import label2rgb\n",
     "from torch.utils.tensorboard import SummaryWriter  # for logging to tensorboard\n",
@@ -156,15 +157,22 @@
     "\n",
     "# HCSDataModule makes it easy to load data during training.\n",
     "from viscy.data.hcs import HCSDataModule\n",
-    "from viscy.evaluation.evaluation_metrics import mean_average_precision\n",
+    "from viscy.translation.evaluation_metrics import mean_average_precision\n",
+    "\n",
     "# Trainer class and UNet.\n",
     "from viscy.translation.engine import MixedLoss, VSUNet\n",
     "from viscy.translation.trainer import VSTrainer\n",
+    "\n",
     "# training augmentations\n",
-    "from viscy.transforms import (NormalizeSampled, RandAdjustContrastd,\n",
-    "                              RandAffined, RandGaussianNoised,\n",
-    "                              RandGaussianSmoothd, RandScaleIntensityd,\n",
-    "                              RandWeightedCropd)"
+    "from viscy.transforms import (\n",
+    "    NormalizeSampled,\n",
+    "    RandAdjustContrastd,\n",
+    "    RandAffined,\n",
+    "    RandGaussianNoised,\n",
+    "    RandGaussianSmoothd,\n",
+    "    RandScaleIntensityd,\n",
+    "    RandWeightedCropd,\n",
+    ")"
    ]
   },
   {
@@ -2352,8 +2360,22 @@
    "cell_metadata_filter": "all",
    "main_language": "python"
   },
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/examples/virtual_staining/dlmbl_exercise/solution.ipynb b/examples/virtual_staining/dlmbl_exercise/solution.ipynb
index c0c18c06..c3f853b6 100644
--- a/examples/virtual_staining/dlmbl_exercise/solution.ipynb
+++ b/examples/virtual_staining/dlmbl_exercise/solution.ipynb
@@ -122,21 +122,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "68d4a6ef",
    "metadata": {
     "title": "Imports"
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/hpc/mydata/eduardo.hirata/.conda/envs/06_image_translation/lib/python3.10/site-packages/viscy/light/engine.py:107: FutureWarning: `torch.cuda.amp.custom_fwd(args...)` is deprecated. Please use `torch.amp.custom_fwd(args..., device_type='cuda')` instead.\n",
-      "  @torch.cuda.amp.custom_fwd(cast_inputs=torch.float32)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "from glob import glob\n",
@@ -157,23 +148,30 @@
     "from natsort import natsorted\n",
     "from numpy.typing import ArrayLike\n",
     "from skimage import metrics  # for metrics.\n",
+    "\n",
     "# pytorch lightning wrapper for Tensorboard.\n",
-    "from skimage.color import label2rgb\n",
     "from torch.utils.tensorboard import SummaryWriter  # for logging to tensorboard\n",
     "from torchmetrics.functional import accuracy, dice, jaccard_index\n",
     "from tqdm import tqdm\n",
     "\n",
     "# HCSDataModule makes it easy to load data during training.\n",
     "from viscy.data.hcs import HCSDataModule\n",
-    "from viscy.evaluation.evaluation_metrics import mean_average_precision\n",
+    "\n",
+    "# training augmentations\n",
+    "from viscy.transforms import (\n",
+    "    NormalizeSampled,\n",
+    "    RandAdjustContrastd,\n",
+    "    RandAffined,\n",
+    "    RandGaussianNoised,\n",
+    "    RandGaussianSmoothd,\n",
+    "    RandScaleIntensityd,\n",
+    "    RandWeightedCropd,\n",
+    ")\n",
+    "\n",
     "# Trainer class and UNet.\n",
     "from viscy.translation.engine import MixedLoss, VSUNet\n",
-    "from viscy.translation.trainer import VSTrainer\n",
-    "# training augmentations\n",
-    "from viscy.transforms import (NormalizeSampled, RandAdjustContrastd,\n",
-    "                              RandAffined, RandGaussianNoised,\n",
-    "                              RandGaussianSmoothd, RandScaleIntensityd,\n",
-    "                              RandWeightedCropd)"
+    "from viscy.translation.evaluation_metrics import mean_average_precision\n",
+    "from viscy.translation.trainer import VSTrainer"
    ]
   },
   {
@@ -4541,7 +4539,7 @@
    "main_language": "python"
   },
   "kernelspec": {
-   "display_name": "06_image_translation",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -4555,7 +4553,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,