def _plot_2D_component(factors, idx, axes_manager,
calibrate=True, ax=None,
comp_label=None, cmap=plt.cm.gray,
axes_decor='all'
):
shape = axes_manager._signal_shape_in_array
factors = to_numpy(factors[:, idx].reshape(shape))
if ax is None:
ax = plt.gca()
axes = axes_manager.signal_axes[::-1]
extent = None
if calibrate:
extent = (axes[1].low_value,
axes[1].high_value,
axes[0].high_value,
axes[0].low_value)
if comp_label:
plt.title(f'{idx}')
im = ax.imshow(factors, cmap=cmap, interpolation='nearest', extent=extent)
# Set axes decorations based on user input
set_axes_decor(ax, axes_decor)
div = make_axes_locatable(ax)
cax = div.append_axes("right", size="5%", pad=0.05)
plt.colorbar(im, cax=cax)
return ax
def _plot_loading(loadings, idx, axes_manager, ax=None,
comp_label=None, no_nans=True,
calibrate=True, cmap=plt.cm.gray,
same_window=False, axes_decor='all'):
loadings = to_numpy(loadings[idx])
if ax is None:
ax = plt.gca()
if no_nans:
loadings = np.nan_to_num(loadings)
axes = axes_manager.navigation_axes
if axes_manager.navigation_dimension == 2:
extent = None
# get calibration from a passed axes_manager
shape = axes_manager._navigation_shape_in_array
if calibrate:
extent = (axes[0].low_value,
axes[0].high_value,
axes[1].high_value,
axes[1].low_value)
im = ax.imshow(loadings.reshape(shape),
cmap=cmap, extent=extent,
interpolation='nearest')
if calibrate:
plt.xlabel(axes[0].units)
plt.ylabel(axes[1].units)
else:
plt.xlabel('pixels')
plt.ylabel('pixels')
if comp_label:
if same_window:
plt.title(f'{idx}')
else:
plt.title(f'{idx} #{idx}')
# Set axes decorations based on user input
set_axes_decor(ax, axes_decor)
div = make_axes_locatable(ax)
cax = div.append_axes("right", size="5%", pad=0.05)
plt.colorbar(im, cax=cax)
elif axes_manager.navigation_dimension == 1:
if calibrate:
x = axes[0].axis
else:
x = np.arange(axes[0].size)
ax.step(x, loadings, label=f'{idx}')
if comp_label and not same_window:
plt.title(f'{comp_label} #{idx}')
plt.ylabel('Score (a. u.)')
if calibrate:
if axes[0].units is not Undefined:
plt.xlabel(axes[0].units)
else:
plt.xlabel('depth')
else:
plt.xlabel('depth')
else:
raise ValueError('View not supported')
def _plot_1D_component(factors, idx, axes_manager, ax=None,
calibrate=True, comp_label=None,
same_window=False):
if ax is None:
ax = plt.gca()
axis = axes_manager.signal_axes[0]
if calibrate:
x = axis.axis
plt.xlabel(axis.units)
else:
x = np.arange(axis.size)
plt.xlabel('Channel index')
ax.plot(x, to_numpy(factors[:, idx]), label=f'{idx}')
if comp_label and not same_window:
plt.title(f'{comp_label}')
return ax
def test_to_numpy_error():
da_array = da.array([0, 1, 2])
with pytest.raises(LazyCupyConversion):
to_numpy(da_array)
def test_to_numpy():
cp_array = cp.array([0, 1, 2])
np_array = np.array([0, 1, 2])
np.testing.assert_allclose(to_numpy(cp_array), np_array)
np.testing.assert_allclose(to_numpy(np_array), np_array)