Fixed HSPY reader issue and tests for Hyperspy2.0

usnistgov · Apr 10, 2024 · b1804b7 · b1804b7
1 parent a8ffedb
commit b1804b7
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/tomotools/io.py b/tomotools/io.py
@@ -371,7 +371,7 @@ def load(filename, tilts=None):
     if type(filename) is str:
         ext = os.path.splitext(filename)[1]
         if ext.lower() in hspy_file_types:
-            stack = hspy.load(filename)
+            stack = hspy.load(filename, reader='HSPY')
             if stack.metadata.has_item("Tomography"):
                 tilts = stack.metadata.Tomography.tilts
         elif ext.lower() in dm_file_types:

diff --git a/tomotools/tests/test_io.py b/tomotools/tests/test_io.py
@@ -65,7 +65,8 @@ def test_load_mrc_with_rawtlt(self):
         filename = os.path.join(tomotools_path, "tests",
                                 "test_data", "HAADF.mrc")
         stack = tomotools.io.load(filename)
-        stack.original_metadata = {}
+        del stack.original_metadata.fei_header
+        del stack.original_metadata.std_header
         tilts = tomotools.io.get_mrc_tilts(stack, filename)
         assert type(tilts) is np.ndarray
         assert tilts.shape[0] == stack.data.shape[0]
@@ -74,7 +75,8 @@ def test_load_mrc_with_bad_rawtlt(self):
         filename = os.path.join(tomotools_path, "tests",
                                 "test_data", "HAADF.mrc")
         stack = tomotools.io.load(filename)
-        stack.original_metadata = {}
+        del stack.original_metadata.fei_header
+        del stack.original_metadata.std_header
         stack.data = np.append(stack.data, np.zeros([1, stack.data.shape[1], stack.data.shape[2]]), axis=0)
         with pytest.raises(ValueError):
             tomotools.io.get_mrc_tilts(stack, filename)
@@ -96,7 +98,7 @@ def test_convert_signal2d(self):
     def test_load_hspy_hdf5(self):
         filename = os.path.join(tomotools_path, "tests",
                                 "test_data", "HAADF_Aligned.hdf5")
-        stack_orig = hs.load(filename)
+        stack_orig = hs.load(filename, reader='HSPY')
         stack = tomotools.io.load(filename)
         with h5py.File(filename, 'r') as h5:
             h5_shape = h5['Experiments']['__unnamed__']['data'].shape