Merge pull request #88 from pycroscopy/chunking

Update emd_reader.py

SciFiReaders/__version__.py

@@ -1,2 +1,2 @@
-version = '0.0.5'
-time = '2022-04-25 12:43:00'
+version = '0.0.6'
+time = '2022-12-16 12:43:00'

SciFiReaders/readers/microscopy/em/tem/emd_reader.py

@@ -211,7 +211,14 @@ def get_image(self):
                                                                quantity='distance',
                                                                dimension_type='spatial'))
         else:
-            self.data_array = np.moveaxis(self.data_array, source=[0, 1, 2], destination=[1, 2, 0])
+            # There is a problem with random access of data due to chunking in hdf5 files
+            # Speed-up copied from hyperspy.ioplugins.EMDReader.FEIEMDReader
+
+            data_array = np.empty(self.data_array.shape)
+            self.data_array.read_direct(data_array)
+            self.data_array = np.rollaxis(data_array, axis=2)
+            # np.moveaxis(data_array, source=[0, 1, 2], destination=[2, 0, 1])
+
             self.datasets.append(sidpy.Dataset.from_array(self.data_array))
             self.datasets[-1].data_type = 'image_stack'
             self.datasets[-1].set_dimension(0, sidpy.Dimension(np.arange(self.data_array.shape[0]),

setup.py

@@ -34,10 +34,10 @@
         'Natural Language :: English',
         'Operating System :: OS Independent',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: Implementation :: CPython',
         'Topic :: Scientific/Engineering :: Information Analysis'],
     keywords=['imaging', 'spectra', 'multidimensional', 'scientific'],