diff --git a/03_COSDD/exercise.ipynb b/03_COSDD/exercise.ipynb index ba95cdc..b1dc8d5 100644 --- a/03_COSDD/exercise.ipynb +++ b/03_COSDD/exercise.ipynb @@ -30,7 +30,6 @@ "outputs": [], "source": [ "import os\n", - "import logging\n", "\n", "import torch\n", "import tifffile\n", @@ -307,8 +306,8 @@ "metadata": {}, "outputs": [], "source": [ - "real_batch_size = 16\n", - "n_grad_batches = 1\n", + "real_batch_size = 4\n", + "n_grad_batches = 4\n", "print(f\"Effective batch size: {real_batch_size * n_grad_batches}\")\n", "crop_size = (256, 256)\n", "train_split = 0.9\n", @@ -408,9 +407,9 @@ "outputs": [], "source": [ "dimensions = ... ### Insert a value here\n", - "s_code_channels = 16\n", + "s_code_channels = 32\n", "\n", - "n_layers = 4\n", + "n_layers = 6\n", "z_dims = [s_code_channels // 2] * n_layers\n", "downsampling = [1] * n_layers\n", "lvae = LadderVAE(\n", @@ -428,8 +427,8 @@ " s_code_channels=s_code_channels,\n", " kernel_size=5,\n", " noise_direction=... ### Insert a value here\n", - " n_filters=16,\n", - " n_layers=3,\n", + " n_filters=32,\n", + " n_layers=4,\n", " n_gaussians=4,\n", " dimensions=dimensions,\n", ")\n", @@ -462,7 +461,7 @@ " data_mean=low_snr.mean(),\n", " data_std=low_snr.std(),\n", " n_grad_batches=n_grad_batches,\n", - " checkpointed=False,\n", + " checkpointed=True,\n", ")" ] }, @@ -579,7 +578,6 @@ " max_time=max_time, # Remove this time limit to train the model fully\n", " log_every_n_steps=len(train_set) // (n_grad_batches * real_batch_size),\n", " callbacks=[EarlyStopping(patience=patience, monitor=\"val/elbo\")],\n", - " precision=\"bf16-mixed\",\n", ")" ] }, @@ -613,22 +611,12 @@ "# Exercise 2. Inference with COSDD" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "logger = logging.getLogger('pytorch_lightning')\n", - "logger.setLevel(logging.WARNING)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2.1. Load test data\n", - "The images that we want to denoise are loaded here. These are the same that we used for training, but we'll only load 2 to speed up inference." + "The images that we want to denoise are loaded here. These are the same that we used for training, but we'll only load 10 to speed up inference." ] }, { @@ -638,7 +626,7 @@ "outputs": [], "source": [ "lowsnr_path = \"./../data/mito-confocal-lowsnr.tif\"\n", - "n_test_images = 2\n", + "n_test_images = 10\n", "# load the data\n", "test_set = tifffile.imread(lowsnr_path)\n", "test_set = test_set[:n_test_images, np.newaxis]\n", @@ -724,7 +712,6 @@ " enable_progress_bar=False,\n", " enable_checkpointing=False,\n", " logger=False,\n", - " precision=\"bf16-mixed\",\n", ")" ] }, @@ -747,7 +734,6 @@ " enable_progress_bar=False,\n", " enable_checkpointing=False,\n", " logger=False,\n", - " precision=\"bf16-mixed\",\n", ")" ] }, diff --git a/04_DenoiSplit/exercise.ipynb b/04_DenoiSplit/exercise.ipynb index e269f84..b84a78f 100644 --- a/04_DenoiSplit/exercise.ipynb +++ b/04_DenoiSplit/exercise.ipynb @@ -796,7 +796,7 @@ }, { "cell_type": "markdown", - "id": "ccb2694d", + "id": "337b207c", "metadata": {}, "source": [ "