Merge pull request #366 from ContactEngineering/24_April_fixes

BUG: Assorted fixes for April

SurfaceTopography/ChangeLog.md

@@ -1,6 +1,13 @@
 Change log for SurfaceTopography
 ================================
 
+v1.13.13 (16Apr24)
+------------------
+
+- BUG: Fixed reader for MetroPro v3 files, close #364
+- BUG: Wrong data layout in SUR files
+- TST: scipy.signal.triang -> scipy.signal.windows.triang, closes #365
+
 v1.13.12 (21Mar24)
 ------------------
 

SurfaceTopography/IO/MetroPro.py

@@ -33,11 +33,12 @@
 
 import numpy as np
 
+from ..Exceptions import (CorruptFile, FileFormatMismatch,
+                          MetadataAlreadyFixedByFile)
+from ..UniformLineScanAndTopography import Topography
 from .binary import decode
 from .common import OpenFromAny
-from .Reader import ReaderBase, ChannelInfo
-from ..Exceptions import CorruptFile, FileFormatMismatch, MetadataAlreadyFixedByFile
-from ..UniformLineScanAndTopography import Topography
+from .Reader import ChannelInfo, ReaderBase
 
 
 class MetroProReader(ReaderBase):
@@ -256,10 +257,10 @@ class MetroProReader(ReaderBase):
         ('asphere_att8', '>f'),
         ('asphere_aperture_pct', '>f'),
         ('asphere_optimized_r0', '>f'),
-        ('iff_state', 'gint16_le'),
+        ('iff_state', '<i'),
         ('iff_idr_filename', '42s'),
         ('iff_ise_filename', '42s'),
-        (None, '2s'),
+        (None, '2b'),
         ('asphere_eqn_r0', '>f'),
         ('asphere_eqn_k', '>f'),
         ('asphere_eqn_coef', '>21f'),
@@ -289,7 +290,7 @@ class MetroProReader(ReaderBase):
         ('field_stop_name', '12s'),
         ('apert_stop_name', '12s'),
         ('illum_filt_name', '12s'),
-        (None, '2606b')
+        (None, '2608b')
     ]
 
     # Reads in the positions of all the data and metadata
@@ -318,7 +319,6 @@ def __init__(self, file_path):
             else:
                 if self._header['header_size'] != self._HEADER_SIZE3:
                     raise CorruptFile('Reported header size does not match expected header size.')
-                # TODO: We have no example file to actually test this code
                 header, size3 = decode(f, self._header_structure3, return_size=True)
                 assert size + size3 == self._HEADER_SIZE3
                 self._header.update(header)

SurfaceTopography/IO/SUR.py

@@ -31,10 +31,11 @@
 
 import numpy as np
 
-from .binary import BinaryArray, BinaryStructure, Convert, Validate
-from .Reader import DeclarativeReaderBase, ChannelInfo, CompoundLayout
-from ..Exceptions import CorruptFile, FileFormatMismatch, UnsupportedFormatFeature
+from ..Exceptions import (CorruptFile, FileFormatMismatch,
+                          UnsupportedFormatFeature)
 from ..Support.UnitConversion import get_unit_conversion_factor
+from .binary import BinaryArray, BinaryStructure, Convert, Validate
+from .Reader import ChannelInfo, CompoundLayout, DeclarativeReaderBase
 
 
 class SURReader(DeclarativeReaderBase):
@@ -115,8 +116,9 @@ class SURReader(DeclarativeReaderBase):
         ], name='header'),
         BinaryArray(
             'data',
-            lambda context: (context.header.nb_grid_pts_x, context.header.nb_grid_pts_y),
-            lambda context: np.dtype('<i2') if context.header.itemsize == 16 else np.dtype('<i4')
+            lambda context: (context.header.nb_grid_pts_y, context.header.nb_grid_pts_x),
+            lambda context: np.dtype('<i2') if context.header.itemsize == 16 else np.dtype('<i4'),
+            conversion_fun=lambda arr: arr.T
         )
     ])
 

test/IO/test_sur.py

@@ -26,7 +26,6 @@
 
 import numpy as np
 import pytest
-
 from NuMPI import MPI
 
 from SurfaceTopography import read_topography
@@ -88,3 +87,51 @@ def test_sur3_metadata(file_format_examples):
     assert t.unit == 'm'
 
     np.testing.assert_allclose(t.rms_height_from_area(), 0.0019200491394179297, rtol=1e-6)
+
+
+def test_sur4_metadata(file_format_examples, plot=False):
+    file_path = os.path.join(file_format_examples, 'sur-4.sur')
+
+    r = SURReader(file_path)
+    t = r.topography()
+
+    if plot:
+        import matplotlib.pyplot as plt
+        t.plot()
+        plt.show()
+
+    nx, ny = t.nb_grid_pts
+    assert nx == 1232
+    assert ny == 1028
+
+    sx, sy = t.physical_sizes
+    np.testing.assert_allclose(sx, 0.3400320075452328, rtol=1e-6)
+    np.testing.assert_allclose(sy, 0.2837280062958598, rtol=1e-6)
+
+    assert t.unit == 'mm'
+
+    np.testing.assert_allclose(t.rms_height_from_area(), 0.1269314744701442, rtol=1e-6)
+
+
+def test_sur5_metadata(file_format_examples, plot=False):
+    file_path = os.path.join(file_format_examples, 'sur-5.sur')
+
+    r = SURReader(file_path)
+    t = r.topography()
+
+    if plot:
+        import matplotlib.pyplot as plt
+        t.plot()
+        plt.show()
+
+    nx, ny = t.nb_grid_pts
+    assert nx == 2560
+    assert ny == 2560
+
+    sx, sy = t.physical_sizes
+    np.testing.assert_allclose(sx, 0.631917268037796, rtol=1e-6)
+    np.testing.assert_allclose(sy, 0.631917268037796, rtol=1e-6)
+
+    assert t.unit == 'mm'
+
+    np.testing.assert_allclose(t.rms_height_from_area(), 0.007327675492217414, rtol=1e-6)

test/test_bearing_area.py

@@ -37,7 +37,7 @@ def test_bearing_area_nonuniform(plot=False):
     hm = 0.1
     X = np.arange(n)  # n+1 because we need the endpoint
     # sinsurf = np.sin(2 * np.pi * X / L) * hm
-    trisurf = hm * scipy.signal.triang(n)
+    trisurf = hm * scipy.signal.windows.triang(n)
 
     t = NonuniformLineScan(X, trisurf)