all tests passing

src/cryo_challenge/_map_to_map/map_to_map_distance.py

@@ -47,11 +47,12 @@ def __init__(self, config):
         self.chunk_size_low_memory = self.config["analysis"]["low_memory"][
             "chunk_size_low_memory"
         ]
-        self.mask = (
-            mrcfile.open(self.config["data"]["mask"]["volume"])
-            .data.astype(bool)
-            .flatten()
-        )
+        if self.config["data"]["mask"]["do"]:
+            self.mask = (
+                mrcfile.open(self.config["data"]["mask"]["volume"])
+                .data.astype(bool)
+                .flatten()
+            )
 
     def get_distance(self, map1, map2):
         """Compute the distance between two maps."""
@@ -142,7 +143,8 @@ def get_distance(self, map1, map2, global_store_of_running_results):
                 raise NotImplementedError(
                     f"Normalization method {self.config['analysis']['normalize']['method']} not implemented."
                 )
-        map1 = map1[self.mask]
+        if self.config["data"]["mask"]["do"]:
+            map1 = map1[self.mask]
 
         return self.compute_cost(map1, map2)
 

tests/config_files/test_config_map_to_map_low_memory_subbatch_nomask_nonormalize.yaml

@@ -0,0 +1,31 @@
+data:
+  n_pix: 16
+  psize: 30.044
+  submission:
+    fname: tests/data/dataset_2_submissions/submission_1000.pt
+    volume_key: volumes
+    metadata_key: populations
+    label_key: id
+  ground_truth:
+    volumes: tests/data/Ground_truth/test_maps_gt_flat_10.npy
+    metadata: tests/data/Ground_truth/test_metadata_10.csv
+  mask:
+    do: false
+    volume: dummy-string
+analysis:
+  metrics:
+    - l2
+    - corr
+    - bioem
+    - fsc
+    - res
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  chunk_size_low_memory: 10
+  low_memory:
+    do: true
+    chunk_size_low_memory: 10
+  normalize:
+    do: false
+    method: dummy-string
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl

tests/test_map_to_map.py

@@ -7,9 +7,11 @@ def test_run_map2map_pipeline():
     for config_fname, config_fname_low_memory in zip(
         [
             "tests/config_files/test_config_map_to_map.yaml",
+            "tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml",
         ],
         [
             "tests/config_files/test_config_map_to_map_low_memory_subbatch.yaml",
+            "tests/config_files/test_config_map_to_map_low_memory_subbatch_nomask_nonormalize.yaml",
         ],
     ):
         args = OmegaConf.create({"config": config_fname})