Merge pull request #115 from pycroscopy/main

-

.github/workflows/actions.yml

@@ -51,7 +51,6 @@ jobs:
     - name: Generate coverage report
       run: |
         pip install pytest pytest-cov pywget
-        pytest --cov=./ --cov-report=xml
         
         pip install -r extras_require.txt
         pytest --cov=./ --cov-report=xml

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

@@ -264,6 +264,18 @@ def get_image(self):
                                                                name='y', units='nm',
                                                                quantity='distance',
                                                                dimension_type='spatial'))
+
+            # for diffraction patterns
+            if '1/' in self.metadata['BinaryResult']['PixelUnitX']:
+                self.datasets[-1].set_dimension(0, sidpy.Dimension(np.arange(self.data_array.shape[0]) * (scale_x / 1e18),
+                                                                   name='u', units='1/nm',
+                                                                   quantity='reciprocal distance',
+                                                                   dimension_type='reciprocal'))
+                self.datasets[-1].set_dimension(1, sidpy.Dimension(np.arange(self.data_array.shape[1]) * (scale_y / 1e18),
+                                                                   name='v', units='1/nm',
+                                                                   quantity='reciprocal distance',
+                                                                   dimension_type='reciprocal'))
+
         else:
             # There is a problem with random access of data due to chunking in hdf5 files
             # Speed-up copied from hyperspy.ioplugins.EMDReader.FEIEMDReader

tests/readers/microscopy/spm/afm/test_gwy.py

@@ -0,0 +1,33 @@
+import pytest
+import sidpy
+import SciFiReaders as sr
+from pywget import wget
+import os
+try:
+    import gwyfile
+except ImportError:
+    import pip
+    pip.main(['install', 'gwyfile'])
+root_path = "https://github.com/pycroscopy/SciFiDatasets/blob/main/data/microscopy/spm/afm/"
+
+@pytest.fixture
+def gwy_file():
+    file_path = 'PTO_110_Virgin0001.gwy'
+    wget.download(root_path + "/PTO_110_Virgin0001.gwy?raw=true", out=file_path)
+    yield file_path
+    os.remove(file_path)
+
+def test_load_test_gwy_file(gwy_file):
+    data_translator = sr.GwyddionReader(gwy_file)
+    datasets = data_translator.read(verbose=False)
+    assert len(datasets) == 4, f"Length of dataset should be 2 but is instead {len(datasets)}"
+    channel_names = ['HeightRetrace', 'AmplitudeRetrace', 'DeflectionRetrace', 'PhaseRetrace']
+    channel_units = ['m', 'm', 'm', 'deg']
+    channel_labels = [['x (m)', 'y (m)'], ['x (m)', 'y (m)'], ['x (m)', 'y (m)'], ['x (m)', 'y (m)']]
+    for ind, dataset in enumerate(datasets):
+        assert isinstance(dataset, sidpy.sid.dataset.Dataset), f"Dataset No. {ind} not read in as sidpy dataset but was instead read in as {type(dataset)}"
+        assert dataset.shape[0] == 256, f"Dataset[{ind}] is of size 512 but was read in as {dataset.shape[0]}"
+        assert isinstance(dataset._axes[0], sidpy.sid.dimension.Dimension), "Dataset should have dimension type of sidpy Dimension, but is instead {}".format(type(dataset._axes))
+        assert dataset.quantity == channel_names[ind], "Dataset having inconsistent channel names"
+        assert dataset.units == channel_units[ind], "Dataset having inconsistent unit names"
+        assert dataset.labels == channel_labels[ind], "Dataset having inconsistent channel labels"