tests for proprocess and svd

.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
+

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

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

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/

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

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"
+    }
+}

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 
+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

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)

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)

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",