Merge pull request #2838 from nem1234/jeol_pts_scale

io_plugins/jeol.py : Get scale information from pts file itself.
hyperspy · Oct 22, 2021 · d7be376 · d7be376
2 parents 19dab6e + 3eab7b3
commit d7be376
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Showing 2 changed files with 27 additions and 14 deletions.
diff --git a/hyperspy/io_plugins/jeol.py b/hyperspy/io_plugins/jeol.py
@@ -121,9 +121,10 @@ def read_img(filename, scale=None, **kwargs):
             yscale = scale[3] / height
             units = "µm"
         else:
-            xscale = 1
-            yscale = 1
-            units = "px"
+            scale = header_long["Instrument"]["ScanSize"] / header_long["Instrument"]["Mag"] * 1.0E3
+            xscale = scale / width
+            yscale = scale / height
+            units = "µm"
 
         axes = [
             {
@@ -247,9 +248,10 @@ def check_multiple(factor, number, string):
             yscale = scale[3] / height
             units = "µm"
         else:
-            xscale = 1
-            yscale = 1
-            units = "px"
+            scale = header["PTTD Param"]["Params"]["PARAMPAGE0_SEM"]["ScanSize"] / meas_data_header["MeasCond"]["Mag"] * 1.0E3
+            xscale = scale / width
+            yscale = scale / height
+            units = "µm"
 
         ch_mod = meas_data_header["Meas Cond"]["Tpl"]
         ch_res = meas_data_header["Doc"]["CoefA"]

diff --git a/hyperspy/tests/io/test_jeol.py b/hyperspy/tests/io/test_jeol.py
@@ -72,6 +72,17 @@ def test_load_project():
     np.testing.assert_allclose(s[-1].axes_manager[2].scale, 0.00999866)
     assert s[-1].axes_manager[2].name == 'Energy'
 
+    # check scale (image)
+    filename = TESTS_FILE_PATH / 'Sample' / '00_View000' / test_files[1]
+    s1 = hs.load(filename)
+    np.testing.assert_allclose(s[0].axes_manager[0].scale, s1.axes_manager[0].scale)
+    assert s[0].axes_manager[0].units == s1.axes_manager[0].units
+    # check scale (pts)
+    filename = TESTS_FILE_PATH / 'Sample' / '00_View000' / test_files[7]
+    s2 = hs.load(filename)
+    np.testing.assert_allclose(s[6].axes_manager[0].scale, s2.axes_manager[0].scale)
+    assert s[6].axes_manager[0].units == s2.axes_manager[0].units
+
 
 def test_load_image():
     # test load work area haadf image
@@ -81,11 +92,11 @@ def test_load_image():
     assert s.data.dtype == np.uint8
     assert s.data.shape == (512, 512)
     assert s.axes_manager.signal_dimension == 2
-    assert s.axes_manager[0].units == 'px'
-    assert s.axes_manager[0].scale == 1
+    assert s.axes_manager[0].units == 'µm'
+    np.testing.assert_allclose(s.axes_manager[0].scale, 0.00869140587747097)
     assert s.axes_manager[0].name == 'x'
-    assert s.axes_manager[1].units == 'px'
-    assert s.axes_manager[1].scale == 1
+    assert s.axes_manager[1].units == 'µm'
+    np.testing.assert_allclose(s.axes_manager[1].scale, 0.00869140587747097)
     assert s.axes_manager[1].name == 'y'
 
 
@@ -98,11 +109,11 @@ def test_load_datacube(SI_dtype):
     assert s.data.shape == (512, 512, 4096)
     assert s.axes_manager.signal_dimension == 1
     assert s.axes_manager.navigation_dimension == 2
-    assert s.axes_manager[0].units == 'px'
-    assert s.axes_manager[0].scale == 1
+    assert s.axes_manager[0].units == 'µm'
+    np.testing.assert_allclose(s.axes_manager[0].scale, 0.00869140587747097)
     assert s.axes_manager[0].name == 'x'
-    assert s.axes_manager[1].units == 'px'
-    assert s.axes_manager[1].scale == 1
+    assert s.axes_manager[1].units == 'µm'
+    np.testing.assert_allclose(s.axes_manager[1].scale, 0.00869140587747097)
     assert s.axes_manager[1].name == 'y'
     assert s.axes_manager[2].units == 'keV'
     np.testing.assert_allclose(s.axes_manager[2].offset, -0.000789965-0.00999866*96)