From 6def1bf6e6a20a4c3f50652002f23eb5f53fc1c2 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Tue, 10 Sep 2024 21:15:21 -0400
Subject: [PATCH]  tests for masking and normalization

---
 ..._to_map_low_memory_nomask_nonormalize.yaml | 27 +++++++++
 ..._config_map_to_map_nomask_nonormalize.yaml | 27 +++++++++
 tests/test_map_to_map.py                      | 56 ++++++++++---------
 3 files changed, 85 insertions(+), 25 deletions(-)
 create mode 100644 tests/config_files/test_config_map_to_map_low_memory_nomask_nonormalize.yaml
 create mode 100644 tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml

diff --git a/tests/config_files/test_config_map_to_map_low_memory_nomask_nonormalize.yaml b/tests/config_files/test_config_map_to_map_low_memory_nomask_nonormalize.yaml
new file mode 100644
index 0000000..13a1cf4
--- /dev/null
+++ b/tests/config_files/test_config_map_to_map_low_memory_nomask_nonormalize.yaml
@@ -0,0 +1,27 @@
+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: tests/data/Ground_truth/test_mask_dilated_wide.mrc
+analysis:
+  metrics:
+    - l2_low_memory
+    - corr_low_memory
+    - bioem_low_memory
+    - fsc_low_memory
+    - res_low_memory
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: false
+    method: median_zscore
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
diff --git a/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml b/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml
new file mode 100644
index 0000000..7856db4
--- /dev/null
+++ b/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml
@@ -0,0 +1,27 @@
+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.pt
+    metadata: tests/data/Ground_truth/test_metadata_10.csv
+  mask:
+    do: false
+    volume: tests/data/Ground_truth/test_mask_dilated_wide.mrc
+analysis:
+  metrics:
+    - l2
+    - corr
+    - bioem
+    - fsc
+    - res
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: false
+    method: median_zscore
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index ed91815..957a9b1 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -4,31 +4,37 @@
 
 
 def test_run_map2map_pipeline():
-    args = OmegaConf.create(
-        {"config": "tests/config_files/test_config_map_to_map.yaml"}
-    )
-    results_dict = run_map2map_pipeline.main(args)
+    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.yaml",
+        ],
+        [
+            "tests/config_files/test_config_map_to_map_low_memory.yaml",
+            "tests/config_files/test_config_map_to_map_low_memory.yaml",
+        ],
+    ):
+        args = OmegaConf.create({"config": config_fname})
+        results_dict = run_map2map_pipeline.main(args)
 
-    args_low_memory = OmegaConf.create(
-        {"config": "tests/config_files/test_config_map_to_map_low_memory.yaml"}
-    )
-    results_dict_low_memory = run_map2map_pipeline.main(args_low_memory)
-    for metric in ["fsc", "corr", "l2", "bioem"]:
-        if metric == "fsc":
+        args_low_memory = OmegaConf.create({"config": config_fname_low_memory})
+        results_dict_low_memory = run_map2map_pipeline.main(args_low_memory)
+        for metric in ["fsc", "corr", "l2", "bioem"]:
+            if metric == "fsc":
+                np.allclose(
+                    results_dict[metric]["computed_assets"]["fsc_matrix"],
+                    results_dict_low_memory[metric + "_low_memory"]["computed_assets"][
+                        "fsc_matrix"
+                    ],
+                )
+            elif metric == "res":
+                np.allclose(
+                    results_dict[metric]["computed_assets"]["fraction_nyquist"],
+                    results_dict_low_memory[metric + "_low_memory"]["computed_assets"][
+                        "fraction_nyquist"
+                    ],
+                )
             np.allclose(
-                results_dict[metric]["computed_assets"]["fsc_matrix"],
-                results_dict_low_memory[metric + "_low_memory"]["computed_assets"][
-                    "fsc_matrix"
-                ],
+                results_dict[metric]["cost_matrix"].values,
+                results_dict_low_memory[metric + "_low_memory"]["cost_matrix"].values,
             )
-        elif metric == "res":
-            np.allclose(
-                results_dict[metric]["computed_assets"]["fraction_nyquist"],
-                results_dict_low_memory[metric + "_low_memory"]["computed_assets"][
-                    "fraction_nyquist"
-                ],
-            )
-        np.allclose(
-            results_dict[metric]["cost_matrix"].values,
-            results_dict_low_memory[metric + "_low_memory"]["cost_matrix"].values,
-        )