Merge pull request #268 from ContactEngineering/22_sur_reader_height_scale_factor

BUG: SUR reader reported wrong `height_scale_factor` in channel info

Author: pastewka

.github/workflows/flake8.yml

@@ -15,21 +15,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
 
     - name: Set up python3 ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         sudo apt-get update -qy
-        sudo apt-get install -y python3-dev python3-pip libfftw3-dev libopenblas-dev
+        sudo apt-get install -y python3-dev python3-pip libfftw3-dev libopenblas-dev meson
 
     - name: Build extension module
       run: |
-        python3 -m pip install --no-binary numpy ".[test]"
+        python3 -m pip install ".[test]"
 
     - name: Flake8 via pytest
       run: |

.github/workflows/test-code-functionality.yml

@@ -29,7 +29,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up python3 ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

SurfaceTopography/ChangeLog.md

@@ -1,9 +1,10 @@
 Change log for SurfaceTopography
-=============================
+================================
 
-v1.2.6 (not yet released)
--------------------------
+v1.2.6 (29Dec22)
+----------------
 
+- BUG: SUR reader reported wrong `height_scale_factor` in channel info  
 - BUILD: Yet another fix for version discovery when installing from source 
   package
 

SurfaceTopography/Generation.py

@@ -263,13 +263,13 @@ def fourier_synthesis(nb_grid_pts, physical_sizes,
 
     # Create in-memory or memory-mapped arrays as storage buffers
     if rfn is None:
-        rarr = np.empty(nb_grid_pts, dtype=np.float64)
+        rarr = np.empty(nb_grid_pts, dtype=float)
     else:
-        rarr = np.memmap(rfn, np.float64, 'w+', shape=nb_grid_pts)
+        rarr = np.memmap(rfn, float, 'w+', shape=nb_grid_pts)
     if kfn is None:
-        karr = np.empty(kshape, dtype=np.complex128)
+        karr = np.empty(kshape, dtype=complex)
     else:
-        karr = np.memmap(kfn, np.complex128, 'w+', shape=kshape)
+        karr = np.memmap(kfn, complex, 'w+', shape=kshape)
 
     qy = 2 * np.pi * np.arange(kny) / sy
     for x in range(nx):

SurfaceTopography/IO/SUR.py

@@ -179,6 +179,7 @@ def channels(self):
                             dim=2,
                             nb_grid_pts=self._nb_grid_pts,
                             physical_sizes=self._physical_sizes,
+                            height_scale_factor=float(self._header['height_scale_factor']),
                             uniform=True,
                             unit=self._unit)]
 

SurfaceTopography/Nonuniform/PowerSpectrum.py

@@ -191,7 +191,7 @@ def power_spectrum(self, reliable=True, algorithm='fft', wavevectors=None, nb_in
         L = x[-1] - x[0]
         if wavevectors is None:
             wavevectors = 2 * np.pi * np.arange(int(L / np.diff(x).min())) / L
-        y_q = np.zeros_like(wavevectors, dtype=np.complex128)
+        y_q = np.zeros_like(wavevectors, dtype=complex)
         for x1, x2, y1, y2 in zip(x[:-1], x[1:], y[:-1], y[1:]):
             dx = x2 - x1
             if dx > 0:

SurfaceTopography/Uniform/Filtering.py

@@ -199,11 +199,11 @@ def heights(self):
             nx, ny = self.parent_topography.nb_grid_pts
             sx, sy = self.parent_topography.physical_sizes
 
-            qx = np.arange(0, nx, dtype=np.float64).reshape(-1, 1)
+            qx = np.arange(0, nx, dtype=float).reshape(-1, 1)
             qx = np.where(qx <= nx // 2, qx / sx,  (qx - nx) / sx)
             qx *= 2 * np.pi
 
-            qy = np.arange(0, ny // 2 + 1, dtype=np.float64).reshape(1, -1)
+            qy = np.arange(0, ny // 2 + 1, dtype=float).reshape(1, -1)
             qy *= 2 * np.pi / sy
 
             if self.is_filter_isotropic:

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["meson>=0.46.0", "meson-python>=0.11.0", "ninja", "numpy"]
+requires = ["meson>=0.46.0", "meson-python>=0.11.0", "ninja", "numpy<1.24.0"]
 build-backend = "mesonpy"
 
 [project]
@@ -19,7 +19,7 @@ dynamic = [ "version" ]
 dependencies = [
     "defusedxml",
     "h5py",
-    "igor",
+    "igor",  # FIXME! Igor no longer works with numpy 1.24.0 or later
     "matplotlib>=1.0.0",
     "muFFT>=0.24.0",
     "NuMPI>=0.3.1",
@@ -31,7 +31,7 @@ dependencies = [
     "requests",
     "scipy",
     "tiffile",
-    "numpy"
+    "numpy<1.24.0"
 ]
 
 [project.optional-dependencies]

test/IO/test_io.py

@@ -98,6 +98,7 @@ def _convert_filelist(filelist):
                                                  'example.vk3',
                                                  'example.vk4',
                                                  'example.vk6',
+                                                 'example.sur',
                                                  'mitutoyo_mock.xlsx',
                                                  'mitutoyo_nonuniform_mock.xlsx',
                                                  'example_ps.tiff',
@@ -339,7 +340,7 @@ def test_nb_grid_pts_and_physical_sizes_are_tuples_or_none(fn):
 
 @pytest.mark.parametrize('fn', text_example_file_list + text_example_without_size_file_list + binary_example_file_list +
                          binary_without_stream_support_example_file_list)
-def test_reader_topography_same(fn):
+def test_channel_info_and_topography_have_same_metadata(fn):
     """
     Tests that properties like physical sizes, units and nb_grid_pts are
     the same in the ChannelInfo and the loaded topography.
@@ -366,8 +367,10 @@ def test_reader_topography_same(fn):
         if channel.physical_sizes is not None:
             assert channel.physical_sizes == topography.physical_sizes
 
-        if channel.height_scale_factor is not None and hasattr(topography, 'scale_factor'):
-            assert channel.height_scale_factor == topography.scale_factor
+        if channel.height_scale_factor is not None:
+            assert channel.height_scale_factor == topography.height_scale_factor
+        else:
+            assert not hasattr(topography, 'height_scale_factor')
 
         if channel.is_periodic is not None:
             assert isinstance(channel.is_periodic, (bool, np.bool_))

test/IO/test_nc.py

@@ -39,6 +39,9 @@
 from .test_io import binary_example_file_list, explicit_physical_sizes
 
 
+@pytest.mark.skipif(
+    MPI.COMM_WORLD.Get_size() > 1,
+    reason="FIXME! This tests often stalls (randomly) on multiple MPI processes; disabling for now")
 def test_save_and_load(maxcomm):
     nb_grid_pts = (128, 128)
     size = (3, 3)