diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 45538ae..829a237 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -55,5 +55,8 @@ jobs: - name: Test with pytest run: | + pytest tests/test_preprocessing.py + pytest tests/test_svd.py pytest tests/test_map_to_map.py pytest tests/test_distribution_to_distribution.py + diff --git a/tests/config_files/test_config_distribution_to_distribution.yaml b/tests/config_files/test_config_distribution_to_distribution.yaml index 9359e58..a1f03af 100644 --- a/tests/config_files/test_config_distribution_to_distribution.yaml +++ b/tests/config_files/test_config_distribution_to_distribution.yaml @@ -1,7 +1,7 @@ input_fname: tests/results/test_map_to_map_distance_matrix_submission_0.pkl metrics: - l2 -gt_metadata_fname: tests/data/test_metadata_10.csv +gt_metadata_fname: tests/data/Ground_truth/test_metadata_10.csv n_replicates: 3 n_pool_microstate: 2 replicate_fraction: 0.9 diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml index eed5fb0..85d663d 100644 --- a/tests/config_files/test_config_map_to_map.yaml +++ b/tests/config_files/test_config_map_to_map.yaml @@ -7,11 +7,11 @@ data: metadata_key: populations label_key: id ground_truth: - volumes: tests/data/test_maps_gt_flat_10.pt - metadata: tests/data/test_metadata_10.csv + volumes: tests/data/Ground_truth/test_maps_gt_flat_10.pt + metadata: tests/data/Ground_truth/test_metadata_10.csv mask: do: true - volume: data/mask_dilated_wide_224x224.mrc + volume: data/Ground_truth/mask_dilated_wide_224x224.mrc analysis: metrics: - l2 diff --git a/tests/config_files/test_config_preproc.yaml b/tests/config_files/test_config_preproc.yaml new file mode 100644 index 0000000..0a27d7e --- /dev/null +++ b/tests/config_files/test_config_preproc.yaml @@ -0,0 +1,8 @@ +submission_config_file: tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json +seed_flavor_assignment: 0 +thresh_percentile: 93.0 +BOT_box_size: 32 +BOT_loss: wemd +BOT_iter: 200 +BOT_refine: True +output_path: tests/results/preproccessed_submission_x/ diff --git a/tests/config_files/test_config_svd.yaml b/tests/config_files/test_config_svd.yaml new file mode 100644 index 0000000..c392525 --- /dev/null +++ b/tests/config_files/test_config_svd.yaml @@ -0,0 +1,14 @@ +path_to_volumes: tests/data/dataset_2_submissions/ +box_size_ds: 32 +submission_list: [0] +experiment_mode: "all_vs_ref" # options are "all_vs_all", "all_vs_ref" +# optional unless experiment_mode is "all_vs_ref" +path_to_reference: tests/data/Ground_truth/test_maps_gt_flat_10.pt +dtype: "float32" # options are "float32", "float64" +output_options: + # path will be created if it does not exist + output_path: tests/results/svd + # whether or not to save the processed volumes (downsampled, normalized, etc.) + save_volumes: True + # whether or not to save the SVD matrices (U, S, V) + save_svd_matrices: True diff --git a/tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json b/tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json new file mode 100644 index 0000000..87184aa --- /dev/null +++ b/tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json @@ -0,0 +1,16 @@ +{ + "gt": { + "name": "gt", + "path": "tests/data/unprocessed_dataset_2_submissions/submission_x", + "box_size": 224, + "pixel_size": 2.146, + "ref_align_fname": "1.mrc" + }, + "0": { + "name": "raw_submission_in_testdata", + "align": 1, + "box_size": 244, + "pixel_size": 2.146, + "path": "tests/data/unprocessed_dataset_2_submissions/submission_x" + } +} \ No newline at end of file diff --git a/tests/scripts/fetch_test_data.sh b/tests/scripts/fetch_test_data.sh index 740d895..5b58f23 100644 --- a/tests/scripts/fetch_test_data.sh +++ b/tests/scripts/fetch_test_data.sh @@ -1,5 +1,12 @@ -mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results -wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt -wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/test_maps_gt_flat_10.pt -wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/test_metadata_10.csv -wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc \ No newline at end of file +mkdir -p tests/data/dataset_2_submissions data/dataset_2_submissions tests/results tests/data/unprocessed_dataset_2_submissions/submission_x tests/data/Ground_truth/ data/Ground_truth +wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt +ADIR=$(pwd) +ln -s $ADIR/tests/data/dataset_2_submissions/test_submission_0_n8.pt $ADIR/tests/data/dataset_2_submissions/submission_0.pt # symlink for svd which needs submission_0.pt for filename +wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/Ground_truth/test_maps_gt_flat_10.pt +wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/test_metadata_10.csv?download=true -O tests/data/Ground_truth/test_metadata_10.csv +wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/1.mrc?download=true -O tests/data/Ground_truth/1.mrc +wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/Ground_truth/mask_dilated_wide_224x224.mrc +for FILE in 1.mrc 2.mrc 3.mrc 4.mrc populations.txt +do + wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/unprocessed_dataset_2_submissions/submission_x/${FILE}?download=true -O tests/data/unprocessed_dataset_2_submissions/submission_x/${FILE} +done diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py new file mode 100644 index 0000000..cbf54e4 --- /dev/null +++ b/tests/test_preprocessing.py @@ -0,0 +1,7 @@ +from omegaconf import OmegaConf +from cryo_challenge._commands import run_preprocessing + + +def test_run_preprocessing(): + args = OmegaConf.create({'config': 'tests/config_files/test_config_preproc.yaml'}) + run_preprocessing.main(args) \ No newline at end of file diff --git a/tests/test_svd.py b/tests/test_svd.py new file mode 100644 index 0000000..568370e --- /dev/null +++ b/tests/test_svd.py @@ -0,0 +1,7 @@ +from omegaconf import OmegaConf +from cryo_challenge._commands import run_svd + + +def test_run_preprocessing(): + args = OmegaConf.create({'config': 'tests/config_files/test_config_svd.yaml'}) + run_svd.main(args) \ No newline at end of file diff --git a/tutorials/2_tutorial_svd.ipynb b/tutorials/2_tutorial_svd.ipynb index e0f33ac..b41bfba 100644 --- a/tutorials/2_tutorial_svd.ipynb +++ b/tutorials/2_tutorial_svd.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -12,7 +12,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -40,9 +40,24 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "c199472d76994ca7b2639a2709536f6d", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "FileChooser(path='/mnt/home/gwoollard', filename='', title='', show_hidden=False, select_desc='Select', change…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "# Select path to SVD config file\n", "# An example of this file is available in the path ../config_files/config_svd.yaml\n",