From 14ca1b90f2a69c0a6a61e0cf33410dba51262d56 Mon Sep 17 00:00:00 2001 From: Ben Salmon Date: Wed, 21 Aug 2024 05:37:35 +0100 Subject: [PATCH] pretrained model --- 03_COSDD/bonus-solution-generation.ipynb | 6 +++--- 03_COSDD/solution.ipynb | 8 +++++--- setup.sh | 4 ++++ 3 files changed, 12 insertions(+), 6 deletions(-) diff --git a/03_COSDD/bonus-solution-generation.ipynb b/03_COSDD/bonus-solution-generation.ipynb index bd66a93..cd6d66c 100755 --- a/03_COSDD/bonus-solution-generation.ipynb +++ b/03_COSDD/bonus-solution-generation.ipynb @@ -61,7 +61,7 @@ "\n", "### Task 3.1.\n", "\n", - "Load the model trained in the first notebook by entering your `model_name`, or alternatively uncomment line 4 to load the pretrained model.\n", + "Load the model trained in the first notebook by entering your `model_name`, or alternatively, uncomment line 4 to load the pretrained model.\n", "" ] }, @@ -78,7 +78,7 @@ "model_name = ... # Insert a string here\n", "checkpoint_path = os.path.join(\"checkpoints\", model_name)\n", "\n", - "# checkpoint_path = TODO: Add pretrained\n", + "# checkpoint_path = \"checkpoints/mito-confocal-pretrained\"\n", "\n", "hub = Hub.load_from_checkpoint(os.path.join(checkpoint_path, \"final_model.ckpt\")).cuda()" ] @@ -96,7 +96,7 @@ "model_name = \"mito-confocal\" # Insert a string here\n", "checkpoint_path = os.path.join(\"checkpoints\", model_name)\n", "\n", - "# checkpoint_path = TODO: Add pretrained\n", + "# checkpoint_path = \"checkpoints/mito-confocal-pretrained\"\n", "\n", "hub = Hub.load_from_checkpoint(os.path.join(checkpoint_path, \"final_model.ckpt\")).cuda()" ] diff --git a/03_COSDD/solution.ipynb b/03_COSDD/solution.ipynb index a66d165..81a6035 100755 --- a/03_COSDD/solution.ipynb +++ b/03_COSDD/solution.ipynb @@ -612,6 +612,8 @@ "2. Enter `conda activate 05_image_restoration` to activate an environment with Tensorboard installed.\n", "3. Enter `tensorboard --logdir 05_image_restoration/03_COSDD/checkpoints`\n", "4. Finally, open a browser and enter localhost:6006 in the address bar.\n", + "\n", + "Once you're in tensorboard, you'll see the training logs of your model and the logs of a model that's been trained for 3.5 hours.\n", "" ] }, @@ -854,7 +856,7 @@ "\n", "Our model was only trained for 10 minutes. This is long enough to get some denoising results, but a model trained for longer would do better. In the cell below, load the trained model by recalling the value you gave for `model_name`. Then procede through the notebook to look at how well it performs. \n", "\n", - "Once you reach the end of the notebook, return to this cell to load a model that has been trained for 24 hours by uncommenting line 4, then run the notebook again to see how much difference the extra training time makes.\n", + "Once you reach the end of the notebook, return to this cell to load a model that has been trained for 3.5 hours by uncommenting line 4, then run the notebook again to see how much difference the extra training time makes. \n", "" ] }, @@ -867,7 +869,7 @@ "model_name = ... ### Insert a string here\n", "checkpoint_path = os.path.join(\"checkpoints\", model_name)\n", "\n", - "# checkpoint_path = TODO: Add pretrained checkpoint ### Once you reach the bottom of the notebook, return here and uncomment this line to see the pretrained model\n", + "# checkpoint_path = \"checkpoints/mito-confocal-pretrained\" ### Once you reach the bottom of the notebook, return here and uncomment this line to see the pretrained model\n", "\n", "hub = Hub.load_from_checkpoint(os.path.join(checkpoint_path, \"final_model.ckpt\"))\n", "\n", @@ -890,7 +892,7 @@ "model_name = \"mito-confocal\" ### Insert a string here\n", "checkpoint_path = os.path.join(\"checkpoints\", model_name)\n", "\n", - "# checkpoint_path = TODO: Add pretrained checkpoint ### Once you reach the bottom of the notebook, return here and uncomment this line to see the pretrained model\n", + "# checkpoint_path = \"checkpoints/mito-confocal-pretrained\" ### Once you reach the bottom of the notebook, return here and uncomment this line to see the pretrained model\n", "\n", "hub = Hub.load_from_checkpoint(os.path.join(checkpoint_path, \"final_model.ckpt\"))\n", "\n", diff --git a/setup.sh b/setup.sh index c5c56e4..04a6ab6 100755 --- a/setup.sh +++ b/setup.sh @@ -37,6 +37,10 @@ if [[ "$CONDA_DEFAULT_ENV" == "$ENV" ]]; then cd ER/ gdown 1Bho6Oymfxi7OV0tPb9wkINkVOCpTaL7M cd ../../ + mkdir 03_COSDD/checkpoints + cd 03_COSDD/checkpoints + gdown --folder 1_oUAxagFVin71xFASb9oLF6pz20HjqTr + cd ../../ fi