Merge pull request #373 from FZJ-INM1-BDA/addTestForUnmatchedMapRegions

Test configured maps to get regions from parcellations

e2e/features/connectivity/test_connectivity.py

@@ -1,10 +1,12 @@
 import siibra
 import pytest
 from typing import List
-
+import sys
 from siibra.features.connectivity.regional_connectivity import RegionalConnectivity
 from e2e.util import check_duplicate
 
+pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="Fails due to memory limitation issues on Windows on Github actions. (Passes on local machines.)")
+
 features = [
     f
     for Cls in siibra.features.feature.Feature.SUBCLASSES[RegionalConnectivity]

e2e/volumes/test_mapshape.py

@@ -0,0 +1,60 @@
+import pytest
+import siibra
+from itertools import product
+
+
+# checks labelled/statistical returns volume size matches template
+# see https://github.com/FZJ-INM1-BDA/siibra-python/issues/302
+MNI152_ID = "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+COLIN_ID = "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+
+JBA_29_ID = (
+    "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290"
+)
+JBA_30_ID = (
+    "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-300"
+)
+
+HOC1_RIGHT = "Area hOc1 (V1, 17, CalcS) - right hemisphere"
+FP1_RIGHT = "Area Fp1 (FPole) - right hemisphere"
+
+STATISTIC_ENDPOINT = "statistical"
+LABELLED_ENDPOINT = "labelled"
+
+map_shape_args = product(
+    ((MNI152_ID, (193, 229, 193)),),
+    (JBA_29_ID,),
+    (STATISTIC_ENDPOINT, LABELLED_ENDPOINT),
+    (HOC1_RIGHT, FP1_RIGHT, None),
+)
+
+
+@pytest.mark.parametrize("space_shape,parc_id,map_endpoint,region_name", map_shape_args)
+def test_map_shape(space_shape, parc_id, map_endpoint, region_name):
+    if region_name is None and map_endpoint == STATISTIC_ENDPOINT:
+        assert True
+        return
+    space_id, expected_shape = space_shape
+
+    volume_data = None
+    if region_name is not None:
+        region = siibra.get_region(parc_id, region_name)
+        volume_data = region.fetch_regional_map(space_id, map_endpoint)
+    else:
+        labelled_map = siibra.get_map(parc_id, space_id, map_endpoint)
+        assert labelled_map is not None
+        volume_data = labelled_map.fetch()
+
+    assert volume_data
+    assert (
+        volume_data.get_fdata().shape == expected_shape
+    ), f"{volume_data.get_fdata().shape}, {expected_shape}, {region_name}, {map_endpoint}, {space_id}"
+
+
+def test_template_resampling():
+    mp = siibra.maps.COLIN27_JBA29_LABELLED
+    mp_img = mp.fetch()
+    template = mp.space.get_template().fetch()
+    assert mp_img.shape != template.shape
+    resamp_template = mp.get_resampled_template()
+    assert mp_img.shape == resamp_template.shape

e2e/volumes/test_parcellationmap.py

@@ -88,64 +88,18 @@ def test_merged_fragment_shape(siibramap: Map, format):
     assert vol_l.dataobj.shape == vol_r.dataobj.shape == vol_b.dataobj.shape
 
 
-def test_sparsemap_cache_uniqueness():
-    mp157 = siibra.get_map("julich 3.0", "colin 27", "statistical", spec="157")
-    mp175 = siibra.get_map("julich 3.0", "colin 27", "statistical", spec="175")
-    assert mp157.sparse_index.probs[0] != mp175.sparse_index.probs[0]
-
-
-# checks labelled/statistical returns volume size matches template
-# see https://github.com/FZJ-INM1-BDA/siibra-python/issues/302
-MNI152_ID = "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
-COLIN_ID = "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
-
-JBA_29_ID = (
-    "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290"
-)
-JBA_30_ID = (
-    "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-300"
-)
-
-HOC1_RIGHT = "Area hOc1 (V1, 17, CalcS) - right hemisphere"
-FP1_RIGHT = "Area Fp1 (FPole) - right hemisphere"
-
-STATISTIC_ENDPOINT = "statistical"
-LABELLED_ENDPOINT = "labelled"
-
-map_shape_args = product(
-    ((MNI152_ID, (193, 229, 193)),),
-    (JBA_29_ID,),
-    (STATISTIC_ENDPOINT, LABELLED_ENDPOINT),
-    (HOC1_RIGHT, FP1_RIGHT, None),
-)
-
-
-@pytest.mark.parametrize("space_shape,parc_id,map_endpoint,region_name", map_shape_args)
-def test_map_shape(space_shape, parc_id, map_endpoint, region_name):
-    if region_name is None and map_endpoint == STATISTIC_ENDPOINT:
-        assert True
-        return
-    space_id, expected_shape = space_shape
-
-    volume_data = None
-    if region_name is not None:
-        region = siibra.get_region(parc_id, region_name)
-        volume_data = region.fetch_regional_map(space_id, map_endpoint)
-    else:
-        labelled_map = siibra.get_map(parc_id, space_id, map_endpoint)
-        assert labelled_map is not None
-        volume_data = labelled_map.fetch()
-
-    assert volume_data
-    assert (
-        volume_data.get_fdata().shape == expected_shape
-    ), f"{volume_data.get_fdata().shape}, {expected_shape}, {region_name}, {map_endpoint}, {space_id}"
-
-
-def test_template_resampling():
-    mp = siibra.maps.COLIN27_JBA29_LABELLED
-    mp_img = mp.fetch()
-    template = mp.space.get_template().fetch()
-    assert mp_img.shape != template.shape
-    resamp_template = mp.get_resampled_template()
-    assert mp_img.shape == resamp_template.shape
+def test_region_1to1ness_in_parcellation():
+    failed = []
+    for m in Map.registry():
+        parc = m.parcellation
+        for region_name in m.regions:
+            try:
+                _ = parc.get_region(region_name)
+            except Exception:
+                failed.append(
+                    {
+                        "region name": region_name,
+                        "map": m.name
+                    }
+                )
+    assert len(failed) == 0, print("The regions in maps that can't be gotten in respective parcellations\n", failed)

e2e/volumes/test_sparsemap_cache_uniqueness.py

@@ -0,0 +1,7 @@
+import siibra
+
+
+def test_sparsemap_cache_uniqueness():
+    mp157 = siibra.get_map("julich 3.0", "colin 27", "statistical", spec="157")
+    mp175 = siibra.get_map("julich 3.0", "colin 27", "statistical", spec="175")
+    assert mp157.sparse_index.probs[0] != mp175.sparse_index.probs[0]

siibra/VERSION

@@ -1 +1 @@
-0.4a61
+0.4a62