Minor fixes

- Fix lower/upper behavior of fftplot
- Final tuning of Kerelsky_plus

pyGPA/imagetools.py

@@ -34,18 +34,19 @@ def fftplot(fftim, d=1, pcolormesh=True, contour=False, levels=None, **kwargs):
     Any other kwargs are forwarded to the call to
     `pcolormesh`"""
     x, y = [fftbounds(n, d) for n in fftim.shape]
+    origin = kwargs.pop('origin', 'upper')
     if 'ax' in kwargs:
         ax = kwargs.pop('ax')
     else:
         fig, ax = plt.subplots()
     if pcolormesh:
         X, Y = np.meshgrid(x, y, indexing='xy')
-        im = ax.pcolormesh(X, Y, fftim.T, **kwargs)
+        im = ax.pcolormesh(X, Y, fftim.T, origin=origin, **kwargs)
     else:
         extent = [x[0], x[-1], y[0], y[-1]]
-        im = ax.imshow(fftim.T, extent=extent, origin='lower', **kwargs)
+        im = ax.imshow(fftim.T, extent=extent, origin=origin, **kwargs)
         if contour:
-            ax.contour(fftim.T, colors='white', origin='lower',
+            ax.contour(fftim.T, colors='white',
                        extent=extent, alpha=0.3, levels=levels)
     ax.set_aspect('equal')
     return im

pyGPA/property_extract.py

@@ -680,7 +680,7 @@ def moire_diffs(args):
             print(res2)
         if res2.cost < res.cost:
             res = res2
-    if res.success and (res.cost <= 1e-10):
+    if res.success and (res.cost <= 0.1):
         params = res.x
     else:
         params = np.full(4, np.nan)

tests/test_phase_unwrap.py

@@ -13,13 +13,14 @@
 def test_equivalent_phase_unwrap_ref_phase_unwrap(kmax):
     N = 256
     xx, yy = np.meshgrid(np.arange(N), np.arange(N), indexing='ij')
-    psi0 = (yy+xx)/(4*np.sqrt(2))
+    psi0 = (yy+xx) / (4*np.sqrt(2))
     psi = pu._wrapToPi(psi0)
     weight = np.ones_like(psi)
     result_phase_unwrap_ref = pu.phase_unwrap_ref(
         psi=psi, weight=weight, kmax=kmax
     )
-    assert np.allclose(result_phase_unwrap_ref - result_phase_unwrap_ref.mean(), psi0-psi0.mean())
+    assert np.allclose(result_phase_unwrap_ref - result_phase_unwrap_ref.mean(), 
+                       psi0 - psi0.mean())
     result_phase_unwrap = pu.phase_unwrap(
         psi=psi, weight=weight, kmax=kmax
     )
@@ -33,7 +34,7 @@ def test_equivalent_phase_unwrap_ref_phase_unwrap(kmax):
 def test_equivalent_phase_unwrap_gaussian_weight():
     N = 256
     xx, yy = np.meshgrid(np.arange(N), np.arange(N), indexing='ij')
-    psi0 = (yy+xx)/(4*np.sqrt(2))
+    psi0 = (yy+xx) / (4*np.sqrt(2))
     psi = pu._wrapToPi(psi0)
     gaussian = np.exp(-((xx-N//2)**2+(yy-N//2)**2)/(0.3*N**2))
     result_phase_unwrap = pu.phase_unwrap(
@@ -50,7 +51,7 @@ def test_equivalent_phase_unwrap_gaussian_weight():
 def test_equivalent_phase_unwrap_ref_prediff_phase_unwrap_prediff(kmax):
     N = 256
     xx, yy = np.meshgrid(np.arange(N), np.arange(N), indexing='ij')
-    psi0 = (yy+xx)/(4*np.sqrt(2))
+    psi0 = (yy+xx) / (4*np.sqrt(2))
     psi = pu._wrapToPi(psi0)
     dx = np.diff(psi, axis=1)
     dy = np.diff(psi, axis=0)