Merge pull request #360 from MICA-MNI/340-read_histology_profiletempl…

…ate=fslr32k-gives-error-in-h5_filegettemplate

340 read histology profiletemplate=fslr32k gives error in h5 filegettemplate

brainstat/context/histology.py

@@ -156,7 +156,10 @@ def read_histology_profile(
         )
 
     with h5py.File(histology_file, "r") as h5_file:
-        profiles = h5_file.get(template)[...]
+        if template == "fslr32k":
+            profiles = h5_file.get("fs_LR_64k")[...]
+        else:
+            profiles = h5_file.get(template)[...]
         if civet_template:
             fsaverage_surface = fetch_template_surface("fsaverage")
             civet_surface = fetch_template_surface(civet_template)
@@ -191,7 +194,10 @@ def download_histology_profiles(
 
     data_dir = Path(data_dir) if data_dir else data_directories["BIGBRAIN_DATA_DIR"]
     data_dir.mkdir(parents=True, exist_ok=True)
-    output_file = data_dir / ("histology_" + template + ".h5")
+    if template == "fslr32k":
+        output_file = data_dir / "histology_fslr32k.h5"
+    else:
+        output_file = data_dir / ("histology_" + template + ".h5")
 
     url = read_data_fetcher_json()["bigbrain_profiles"][template]["url"]
 

brainstat/tests/test_histology.py

@@ -1,9 +1,10 @@
 """Unit tests for the histology module."""
 import pytest
 import requests
+import numpy as np
 
 from brainstat._utils import read_data_fetcher_json
-
+from brainstat.context.histology import read_histology_profile
 parametrize = pytest.mark.parametrize
 json = read_data_fetcher_json()
 
@@ -19,3 +20,10 @@ def test_urls(template):
     """
     r = requests.head(json["bigbrain_profiles"][template]["url"])
     assert r.status_code == 200
+
+
+def test_histology_profiles_is_ndarray():
+    histology_profiles = read_histology_profile(template="fslr32k")
+
+    # Assert that histology_profiles is an ndarray
+    assert isinstance(histology_profiles, np.ndarray), "histology_profiles should be a NumPy ndarray"

brainstat/tests/test_mesh_edges.py

@@ -81,4 +81,4 @@ def test_nifti_input():
     edg = mesh_edges(nifti)
 
     assert edg.shape[1] == 2
-    assert np.amax(edg) <= nifti.get_data().sum() - 1
+    assert np.amax(edg) <= nifti.get_fdata().sum() - 1

brainstat/tests/test_terms.py

@@ -47,10 +47,10 @@ def test_fixed_overload():
     assert np.array_equal(fix_add_intercept.m, expected)
 
     # fix_sub = fix01 - fix12
-    # assert np.array_equal(fix_sub.m, random_data[:, 0][:, None])
+    # assert np.array_equal(fix_sub.m.to_numpy(), random_data[:, 0][:, None])
 
     # fix_mul = fix01 * fix2
-    # assert np.array_equal(fix_mul.m, random_data[:, :2] * random_data[:, 2][:, None])
+    # assert np.array_equal(fix_mul.m.to_numpy(), random_data[:, :2] * random_data[:, 2][:, None])
 
 
 def test_mixed_init():