From 79dff63f727db8a392aefb88df1e1c95146a7b0f Mon Sep 17 00:00:00 2001 From: Anwai Archit <52396323+anwai98@users.noreply.github.com> Date: Thu, 2 May 2024 17:41:35 +0200 Subject: [PATCH] Minor touch-up to finetuning directory (#577) Refactors the `finetuning` directory and moves old scripts under the `outdated` directory in the respective parent folders --- finetuning/evaluation/mitonet_baseline.py | 6 ++ finetuning/generalists/README.md | 26 ++++++ .../generalists/export_generalist_model.py | 24 ------ .../generalists/generate_model_comparison.py | 82 ------------------- .../{ => outdated}/compile_results.py | 0 .../{ => outdated}/create_tissuenet_data.py | 0 .../{ => outdated}/evaluate_generalist.py | 0 .../{ => outdated}/evaluate_generalist.sbatch | 0 .../evaluate_training_evolution.py | 0 .../evaluate_training_evolution.sbatch | 0 .../{ => outdated}/precompute_prompts.py | 0 finetuning/generalists/{ => outdated}/util.py | 0 .../generalists/precompute_prompts.sbatch | 10 --- finetuning/specialists/README.md | 7 +- .../outdated}/livecell/README.md | 10 +-- .../livecell/evaluation/evaluate_amg.py | 0 .../livecell/evaluation/evaluate_amg.sbatch | 0 .../evaluate_instance_segmentation.py | 0 .../evaluate_instance_segmentation.sbatch | 0 .../evaluation/iterative_prompting.py | 0 .../evaluation/iterative_prompting.sbatch | 0 .../livecell/evaluation/old/evaluation.py | 0 .../livecell/evaluation/old/evaluation.sbatch | 0 .../livecell/evaluation/old/inference.py | 0 .../livecell/evaluation/old/inference.sbatch | 0 .../evaluation/old/precompute_prompts.py | 0 .../evaluation/old/precompute_prompts.sbatch | 0 .../evaluation/precompute_embeddings.py | 0 .../evaluation/precompute_embeddings.sbatch | 0 .../livecell/evaluation/submit_evaluation.py | 0 .../evaluation/train_grid_search_eval.py | 0 .../outdated}/livecell/evaluation/util.py | 0 .../outdated}/livecell/experiments/README.md | 0 .../experiments/run_experiment_evaluation.py | 0 .../submit_experiment_finetuning.py | 0 .../joint_training/grid_search_train.py | 0 .../joint_training/joint_finetuning.py | 0 .../livecell/joint_training/results.md | 0 .../run_parameter_evaluation.py | 0 .../joint_training/unetr_inference.py | 0 .../evaluate_partially_finetuned.py | 0 .../evaluate_partially_finetuned.sbatch | 0 .../submit_partial_finetuning.py | 0 .../specialists/resource-efficient/README.md | 2 +- 44 files changed, 43 insertions(+), 124 deletions(-) create mode 100644 finetuning/generalists/README.md delete mode 100644 finetuning/generalists/export_generalist_model.py delete mode 100644 finetuning/generalists/generate_model_comparison.py rename finetuning/generalists/{ => outdated}/compile_results.py (100%) rename finetuning/generalists/{ => outdated}/create_tissuenet_data.py (100%) rename finetuning/generalists/{ => outdated}/evaluate_generalist.py (100%) rename finetuning/generalists/{ => outdated}/evaluate_generalist.sbatch (100%) rename finetuning/generalists/{ => outdated}/evaluate_training_evolution.py (100%) rename finetuning/generalists/{ => outdated}/evaluate_training_evolution.sbatch (100%) rename finetuning/generalists/{ => outdated}/precompute_prompts.py (100%) rename finetuning/generalists/{ => outdated}/util.py (100%) delete mode 100755 finetuning/generalists/precompute_prompts.sbatch rename finetuning/{ => specialists/outdated}/livecell/README.md (84%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/evaluate_amg.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/evaluate_amg.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/evaluate_instance_segmentation.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/evaluate_instance_segmentation.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/iterative_prompting.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/iterative_prompting.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/evaluation.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/evaluation.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/inference.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/inference.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/precompute_prompts.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/old/precompute_prompts.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/precompute_embeddings.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/precompute_embeddings.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/submit_evaluation.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/train_grid_search_eval.py (100%) rename finetuning/{ => specialists/outdated}/livecell/evaluation/util.py (100%) rename finetuning/{ => specialists/outdated}/livecell/experiments/README.md (100%) rename finetuning/{ => specialists/outdated}/livecell/experiments/run_experiment_evaluation.py (100%) rename finetuning/{ => specialists/outdated}/livecell/experiments/submit_experiment_finetuning.py (100%) rename finetuning/{ => specialists/outdated}/livecell/joint_training/grid_search_train.py (100%) rename finetuning/{ => specialists/outdated}/livecell/joint_training/joint_finetuning.py (100%) rename finetuning/{ => specialists/outdated}/livecell/joint_training/results.md (100%) rename finetuning/{ => specialists/outdated}/livecell/joint_training/run_parameter_evaluation.py (100%) rename finetuning/{ => specialists/outdated}/livecell/joint_training/unetr_inference.py (100%) rename finetuning/{ => specialists/outdated}/livecell/partial_finetuning/evaluate_partially_finetuned.py (100%) rename finetuning/{ => specialists/outdated}/livecell/partial_finetuning/evaluate_partially_finetuned.sbatch (100%) rename finetuning/{ => specialists/outdated}/livecell/partial_finetuning/submit_partial_finetuning.py (100%) diff --git a/finetuning/evaluation/mitonet_baseline.py b/finetuning/evaluation/mitonet_baseline.py index b80c681d..118a359b 100644 --- a/finetuning/evaluation/mitonet_baseline.py +++ b/finetuning/evaluation/mitonet_baseline.py @@ -1,3 +1,9 @@ +# NOTE: +# This script below the following: +# - stacks indivudual slice images into one volume for segmenting in empanada-napari +# - evaluates the segmentations with the mean segmentation accuracy metric + + import os from glob import glob diff --git a/finetuning/generalists/README.md b/finetuning/generalists/README.md new file mode 100644 index 00000000..a73fc775 --- /dev/null +++ b/finetuning/generalists/README.md @@ -0,0 +1,26 @@ +# Segment Anything Finetuning for Generalists Models + +Code for finetuning segment anything data on multiple microscopy datasets. + +## Finetuning Scripts + +- `training/`: The finetuning scripts for the two microscopy domains covered by `micro_sam`. + - Light Microscopy (LM) + - `light_microscopy/obtain_lm_datasets.py`: Scripts for getting the dataloader from multipe LM datasets. + - `light_microscopy/train_lm_generalist.py`: Finetuning on multiple LM datasets. + - Electron Microscopy (EM) + - `mito_nuc/obtain_mito_nuc_em_datasets.py`: Scripts for getting the dataloader from multiple EM datasets. + - `mito_nuc/train_mito_nuc_em_generalist.py`: Finetuning on multiple EM datasets for segmenting mitochondria and nuclei. + + +## Experimental Scripts +These scripts are a work-in-progress and often under active development. + +- `training/histopathology`: Finetuning Segment Anything on Histopathology datasets. +- `training/electron_microscopy/boundaries`: Finetuning Segment Anything on Electron Microscopy datasets for segmenting boundary-based dense structures. + +> For details on how to run the scripts from above: `python _finetuning.py -h` + + +## Outdated Scripts +The scripts located at `outdated/` are not in working purpose with the latest version of `micro-sam`. diff --git a/finetuning/generalists/export_generalist_model.py b/finetuning/generalists/export_generalist_model.py deleted file mode 100644 index 11073364..00000000 --- a/finetuning/generalists/export_generalist_model.py +++ /dev/null @@ -1,24 +0,0 @@ -import os -from micro_sam.util import export_custom_sam_model -from evaluate_generalist import CHECKPOINTS, EXPERIMENT_ROOT - -OUT_ROOT = os.path.join(EXPERIMENT_ROOT, "exported") -os.makedirs(OUT_ROOT, exist_ok=True) - - -def export_generalist(model): - checkpoint_path = CHECKPOINTS[model] - model_type = model[:5] - save_path = os.path.join(OUT_ROOT, f"{model}.pth") - export_custom_sam_model(checkpoint_path, model_type, save_path) - - -def main(): - export_generalist("vit_b_em") - export_generalist("vit_h_em") - export_generalist("vit_b_lm") - export_generalist("vit_h_lm") - - -if __name__ == "__main__": - main() diff --git a/finetuning/generalists/generate_model_comparison.py b/finetuning/generalists/generate_model_comparison.py deleted file mode 100644 index f0ed3a9a..00000000 --- a/finetuning/generalists/generate_model_comparison.py +++ /dev/null @@ -1,82 +0,0 @@ -import os - -import imageio.v3 as imageio -import micro_sam.evaluation.model_comparison as comparison -import torch_em - -from util import get_data_paths, EM_DATASETS, LM_DATASETS - -OUTPUT_ROOT = "/scratch-grete/projects/nim00007/sam/experiments/model_comparison" - - -def _get_patch_shape(path): - im_shape = imageio.imread(path).shape[:2] - patch_shape = tuple(min(sh, 512) for sh in im_shape) - return patch_shape - - -def raw_trafo(raw): - raw = raw.transpose((2, 0, 1)) - print(raw.shape) - return raw - - -def get_loader(dataset): - image_paths, gt_paths = get_data_paths(dataset, split="test") - image_paths, gt_paths = image_paths[:100], gt_paths[:100] - - with_channels = dataset in ("hpa", "lizard") - - label_transform = torch_em.transform.label.connected_components - loader = torch_em.default_segmentation_loader( - image_paths, None, gt_paths, None, - batch_size=1, patch_shape=_get_patch_shape(image_paths[0]), - shuffle=True, n_samples=25, label_transform=label_transform, - with_channels=with_channels, is_seg_dataset=not with_channels - ) - return loader - - -def generate_comparison_for_dataset(dataset, model1, model2): - output_folder = os.path.join(OUTPUT_ROOT, dataset) - if os.path.exists(output_folder): - return output_folder - print("Generate model comparison data for", dataset) - loader = get_loader(dataset) - comparison.generate_data_for_model_comparison(loader, output_folder, model1, model2, n_samples=25) - return output_folder - - -def create_comparison_images(output_folder, dataset): - plot_folder = os.path.join(OUTPUT_ROOT, "images", dataset) - if os.path.exists(plot_folder): - return - comparison.model_comparison( - output_folder, n_images_per_sample=25, min_size=100, - plot_folder=plot_folder, outline_dilation=1 - ) - - -def generate_comparison_em(): - model1 = "vit_h" - model2 = "vit_h_em" - for dataset in EM_DATASETS: - folder = generate_comparison_for_dataset(dataset, model1, model2) - create_comparison_images(folder, dataset) - - -def generate_comparison_lm(): - model1 = "vit_h" - model2 = "vit_h_lm" - for dataset in LM_DATASETS: - folder = generate_comparison_for_dataset(dataset, model1, model2) - create_comparison_images(folder, dataset) - - -def main(): - generate_comparison_lm() - # generate_comparison_em() - - -if __name__ == "__main__": - main() diff --git a/finetuning/generalists/compile_results.py b/finetuning/generalists/outdated/compile_results.py similarity index 100% rename from finetuning/generalists/compile_results.py rename to finetuning/generalists/outdated/compile_results.py diff --git a/finetuning/generalists/create_tissuenet_data.py b/finetuning/generalists/outdated/create_tissuenet_data.py similarity index 100% rename from finetuning/generalists/create_tissuenet_data.py rename to finetuning/generalists/outdated/create_tissuenet_data.py diff --git a/finetuning/generalists/evaluate_generalist.py b/finetuning/generalists/outdated/evaluate_generalist.py similarity index 100% rename from finetuning/generalists/evaluate_generalist.py rename to finetuning/generalists/outdated/evaluate_generalist.py diff --git a/finetuning/generalists/evaluate_generalist.sbatch b/finetuning/generalists/outdated/evaluate_generalist.sbatch similarity index 100% rename from finetuning/generalists/evaluate_generalist.sbatch rename to finetuning/generalists/outdated/evaluate_generalist.sbatch diff --git a/finetuning/generalists/evaluate_training_evolution.py b/finetuning/generalists/outdated/evaluate_training_evolution.py similarity index 100% rename from finetuning/generalists/evaluate_training_evolution.py rename to finetuning/generalists/outdated/evaluate_training_evolution.py diff --git a/finetuning/generalists/evaluate_training_evolution.sbatch b/finetuning/generalists/outdated/evaluate_training_evolution.sbatch similarity index 100% rename from finetuning/generalists/evaluate_training_evolution.sbatch rename to finetuning/generalists/outdated/evaluate_training_evolution.sbatch diff --git a/finetuning/generalists/precompute_prompts.py b/finetuning/generalists/outdated/precompute_prompts.py similarity index 100% rename from finetuning/generalists/precompute_prompts.py rename to finetuning/generalists/outdated/precompute_prompts.py diff --git a/finetuning/generalists/util.py b/finetuning/generalists/outdated/util.py similarity index 100% rename from finetuning/generalists/util.py rename to finetuning/generalists/outdated/util.py diff --git a/finetuning/generalists/precompute_prompts.sbatch b/finetuning/generalists/precompute_prompts.sbatch deleted file mode 100755 index 2b04cc96..00000000 --- a/finetuning/generalists/precompute_prompts.sbatch +++ /dev/null @@ -1,10 +0,0 @@ -#! /bin/bash -#SBATCH -c 4 -#SBATCH --mem 48G -#SBATCH -t 2000 -#SBATCH -p grete:shared -#SBATCH -G A100:1 -#SBATCH -A nim00007 - -source activate sam -python precompute_prompts.py $@ diff --git a/finetuning/specialists/README.md b/finetuning/specialists/README.md index 3e33f5c8..5c61cebf 100644 --- a/finetuning/specialists/README.md +++ b/finetuning/specialists/README.md @@ -1,4 +1,4 @@ -# Segment Anything Finetuning for Specific Datasets +# Segment Anything Finetuning for Specialist Models Code for finetuning segment anything data on specific microscopy datasets. @@ -17,3 +17,8 @@ Code for finetuning segment anything data on specific microscopy datasets. > For details on how to run the scripts from above: `python _finetuning.py -h` - `resource_efficient_finetuning`: The experiments for finetuning a custom dataset on limited resources. + + +## Outdated Scripts +The scripts located at `outdated/` are not in working purpose with the latest version of `micro-sam`. +- It comprises of extensive experiments on "LIVECell" specialist, located at `outdated/livecell/`. \ No newline at end of file diff --git a/finetuning/livecell/README.md b/finetuning/specialists/outdated/livecell/README.md similarity index 84% rename from finetuning/livecell/README.md rename to finetuning/specialists/outdated/livecell/README.md index fceedcb7..10f526d3 100644 --- a/finetuning/livecell/README.md +++ b/finetuning/specialists/outdated/livecell/README.md @@ -1,16 +1,14 @@ -# Finetuning Segment Anything for LiveCELL +# Finetuning Segment Anything for LIVECell -TODO: explain the set-up - -These experiments are implemented for a slurm cluster with access to GPUs (and you ideally need access to A100s or H100s with 80GB of memory, if you only use ViT-b then using a GPU with 32 GB or 40 GB should suffice.) +These experiments are implemented for a slurm cluster with access to GPUs (and you ideally need access to A100s or H100s with 80GB of memory, if you only use ViT Base then using a GPU with 32 GB or 40 GB should suffice.) ## Training -TODO: add training code and explain how to run it +The relevant scripts are located in the top-level `finetuning` directory at: `finetuning/livecell_finetuning.py`. ## Evaluation -To run the evaluation experiments for the Segment Anything Models on LiveCELL follow these steps: +To run the evaluation experiments for the Segment Anything Models on LIVECell follow these steps: - Preparation: - Go to the `evaluation` directory. diff --git a/finetuning/livecell/evaluation/evaluate_amg.py b/finetuning/specialists/outdated/livecell/evaluation/evaluate_amg.py similarity index 100% rename from finetuning/livecell/evaluation/evaluate_amg.py rename to finetuning/specialists/outdated/livecell/evaluation/evaluate_amg.py diff --git a/finetuning/livecell/evaluation/evaluate_amg.sbatch b/finetuning/specialists/outdated/livecell/evaluation/evaluate_amg.sbatch similarity index 100% rename from finetuning/livecell/evaluation/evaluate_amg.sbatch rename to finetuning/specialists/outdated/livecell/evaluation/evaluate_amg.sbatch diff --git a/finetuning/livecell/evaluation/evaluate_instance_segmentation.py b/finetuning/specialists/outdated/livecell/evaluation/evaluate_instance_segmentation.py similarity index 100% rename from finetuning/livecell/evaluation/evaluate_instance_segmentation.py rename to finetuning/specialists/outdated/livecell/evaluation/evaluate_instance_segmentation.py diff --git a/finetuning/livecell/evaluation/evaluate_instance_segmentation.sbatch b/finetuning/specialists/outdated/livecell/evaluation/evaluate_instance_segmentation.sbatch similarity index 100% rename from finetuning/livecell/evaluation/evaluate_instance_segmentation.sbatch rename to finetuning/specialists/outdated/livecell/evaluation/evaluate_instance_segmentation.sbatch diff --git a/finetuning/livecell/evaluation/iterative_prompting.py 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from finetuning/livecell/partial_finetuning/evaluate_partially_finetuned.py rename to finetuning/specialists/outdated/livecell/partial_finetuning/evaluate_partially_finetuned.py diff --git a/finetuning/livecell/partial_finetuning/evaluate_partially_finetuned.sbatch b/finetuning/specialists/outdated/livecell/partial_finetuning/evaluate_partially_finetuned.sbatch similarity index 100% rename from finetuning/livecell/partial_finetuning/evaluate_partially_finetuned.sbatch rename to finetuning/specialists/outdated/livecell/partial_finetuning/evaluate_partially_finetuned.sbatch diff --git a/finetuning/livecell/partial_finetuning/submit_partial_finetuning.py b/finetuning/specialists/outdated/livecell/partial_finetuning/submit_partial_finetuning.py similarity index 100% rename from finetuning/livecell/partial_finetuning/submit_partial_finetuning.py rename to finetuning/specialists/outdated/livecell/partial_finetuning/submit_partial_finetuning.py diff --git a/finetuning/specialists/resource-efficient/README.md b/finetuning/specialists/resource-efficient/README.md index 7ec76889..ddb5a5a2 100644 --- a/finetuning/specialists/resource-efficient/README.md +++ b/finetuning/specialists/resource-efficient/README.md @@ -40,7 +40,7 @@ Fixed parameters: ### GPU Resources -(32G CPU memory, 8 CPU cores) +(32GB CPU memory, 8 CPU cores) 1. `gtx1080`: - `vit_t`: finetune all layers