wget from osf, test. full data

.github/workflows/testing.yml

@@ -27,6 +27,12 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
           pip install pytest
+      - name: Get test data
+        run: |
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O data/gt_maps_flat_float16.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/metadata.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
           pytest tests/

tests/config_files/test_config_distribution_to_distribution.yaml

@@ -0,0 +1,12 @@
+input_fname: results/test_map_to_map_distance_matrix_submission_0.pkl
+metrics:
+  - l2
+gt_metadata_fname: data/metadata.csv
+n_replicates: 3
+n_pool_microstate: 2
+replicate_fraction: 0.9
+cvxpy_solver: ECOS
+optimal_q_kl:
+  n_iter: 100000
+  break_atol: 0.0001
+output_fname: results/test_distribution_to_distribution_submission_0.pkl

tests/config_files/test_config_map_to_map.yaml

@@ -0,0 +1,23 @@
+data:
+  n_pix: 224
+  psize: 2.146 
+  submission:
+    fname: tests/data/dataset_2_submissions/submission_0.pt
+    volume_key: volumes
+    metadata_key: populations
+    label_key: id
+  ground_truth:
+    volumes: data/gt_maps_flat_float16.pt 
+    metadata: data/metadata.csv 
+  mask: 
+    do: true
+    volume: data/mask_dilated_wide_224x224.mrc
+analysis:
+  metrics:
+    - l2
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: true
+    method: median_zscore
+output: tests/test_map_to_map_distance_matrix_submission_0.pkl