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Add probe propagation with initialization as a base feature to fancy_ptycho, and fix the test for orthogonalize_probes

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This commit is contained in:
Abe Levitan
2019-05-03 12:30:53 -04:00
parent 26de79ca92
commit 22899288fc
7 changed files with 70 additions and 26 deletions
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CDTools/tools/plotting.py
+10 -3
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@@ -81,6 +81,7 @@ def plot_1D(arr, fig = None, **kwargs):
ax = fig.add_subplot(111, **kwargs)
else:
plt.figure(fig.number)
plt.gcf().clear()
plt.scatter(np.arange(arr.shape[-1]), arr)
@@ -101,6 +102,7 @@ def plot_amplitude(im, fig = None, basis=None, units='um', **kwargs):
ax = fig.add_subplot(111, **kwargs)
else:
plt.figure(fig.number)
plt.gcf().clear()
if isinstance(im, t.Tensor):
absolute = cmath.cabs(im).detach().cpu().numpy()
@@ -145,6 +147,7 @@ def plot_phase(im, fig=None, basis=None, units='um', **kwargs):
ax = fig.add_subplot(111, **kwargs)
else:
plt.figure(fig.number)
plt.gcf().clear()
# If the user has matplotlib >=3.0, use the preferred colormap
if isinstance(im, t.Tensor):
@@ -198,6 +201,7 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
ax = fig.add_subplot(111, **kwargs)
else:
plt.figure(fig.number)
plt.gcf().clear()
if isinstance(im, t.Tensor):
im = cmath.torch_to_complex(im.detach().cpu())
@@ -226,16 +230,17 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
def plot_translations(translations, fig=None, units='um'):
def plot_translations(translations, fig=None, units='um', lines=True):
"""Plots a set of probe translations in a nicely formatted way
Args:
translations: An Nx2 or Nx3 set of translations in real space
fig : Optional, a figure to plot into
units : Default is um, units to report in (assuming input in m)
lines : Whether to plot the lines indicating the path
Returns:
None
"""
factor = get_units_factor(units)
@@ -245,13 +250,15 @@ def plot_translations(translations, fig=None, units='um'):
ax = fig.add_subplot(111)
else:
plt.figure(fig.number)
plt.gcf().clear()
if isinstance(translations, t.Tensor):
translations = translations.detach().cpu().numpy()
translations = translations * factor
plt.plot(translations[:,0], translations[:,1],'k.')
plt.plot(translations[:,0], translations[:,1],'b-', linewidth=0.5)
if lines:
plt.plot(translations[:,0], translations[:,1],'b-', linewidth=0.5)
plt.xlabel('X (' + units + ')')
plt.ylabel('Y (' + units + ')')