Merge pull request #287 from ericpre/fix_sum_EDS_detectors_emd_velox

EMD Velox: fix reading EDS stream detector lazily with `sum_EDS_detectors=True`

rsciio/emd/_emd_velox.py

@@ -950,7 +950,6 @@ def stream_to_sparse_array(self, stream_data):
         """
         # Here we load the stream data into memory, which is fine is the
         # arrays are small. We could load them lazily when lazy.
-        stream_data = self.stream_group["Data"][:].T[0]
         sparse_array = stream_readers.stream_to_sparse_COO_array(
             stream_data=stream_data,
             spatial_shape=self.reader.spatial_shape,
@@ -967,8 +966,8 @@ def stream_to_array(self, stream_data, spectrum_image=None):
 
         Parameters
         ----------
-        stream_data: array
-        spectrum_image: array or None
+        stream_data : numpy.ndarray
+        spectrum_image : numpy.ndarray or None
             If array, the data from the stream are added to the array.
             Otherwise it creates a new array and returns it.
 

rsciio/tests/test_emd_velox.py

@@ -405,6 +405,27 @@ def test_fei_si_4detectors(self, lazy, sum_EDS_detectors):
         assert len(signal) == length
         # TODO: add parsing azimuth_angle
 
+    @pytest.mark.parametrize("lazy", (False, True))
+    @pytest.mark.parametrize("sum_frames", (False, True))
+    def test_fei_si_4detectors_compare(self, lazy, sum_frames):
+        fname = self.fei_files_path / "fei_SI_EDS-HAADF-4detectors_2frames.emd"
+        kwargs = dict(lazy=lazy, sum_frames=sum_frames)
+        s_sum_EDS = hs.load(fname, sum_EDS_detectors=True, **kwargs)[-1]
+        s = hs.load(fname, sum_EDS_detectors=False, **kwargs)[-4:]
+        if lazy:
+            s_sum_EDS.compute()
+            for s_ in s:
+                s_.compute()
+
+        s2 = hs.stack(s, new_axis_name="detector").sum("detector")
+
+        np.testing.assert_allclose(s[-1].data.sum(), 865236)
+        np.testing.assert_allclose(s[-2].data.sum(), 913682)
+        np.testing.assert_allclose(s[-3].data.sum(), 867647)
+        np.testing.assert_allclose(s[-4].data.sum(), 916174)
+        np.testing.assert_allclose(s2.data.sum(), 3562739)
+        np.testing.assert_allclose(s2.data, s_sum_EDS.data)
+
     def test_fei_emd_ceta_camera(self):
         signal = hs.load(self.fei_files_path / "1532 Camera Ceta.emd")
         np.testing.assert_allclose(signal.data, np.zeros((64, 64)))

rsciio/utils/fei_stream_readers.py

@@ -363,13 +363,13 @@ def stream_to_array(
                 dtype=dtype,
             )
 
-            _fill_array_with_stream(
-                spectrum_image=spectrum_image,
-                stream=stream,
-                first_frame=first_frame,
-                last_frame=last_frame,
-                rebin_energy=rebin_energy,
-            )
+        _fill_array_with_stream(
+            spectrum_image=spectrum_image,
+            stream=stream,
+            first_frame=first_frame,
+            last_frame=last_frame,
+            rebin_energy=rebin_energy,
+        )
     else:
         if spectrum_image is None:
             spectrum_image = np.zeros(

upcoming_changes/287.bugfix.rst

@@ -0,0 +1,4 @@
+:ref:`EMD Velox <emd_fei-format>` fixes for reading files containing multiple EDS streams:
+
+- fix reading multiple EDS streams lazily with ``sum_EDS_detectors=True``,
+- fix reading separate EDS stream and individual frames when using ``sum_EDS_detectors=False`` and ``sum_frames=False``.