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Using $\mu instead of um for micrometers

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This commit is contained in:
David Rower
2019-12-11 16:19:45 -05:00
parent 3cf44cff9f
commit 384ced5b00
1 changed files with 34 additions and 34 deletions
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CDTools/tools/plotting.py
+34 -34
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@@ -32,7 +32,7 @@ def colorize(z):
A complex-valued array
Returns
-------
rgb : list(array)
rgb : list(array)
A list of arrays for the R,G, and B channels of an image
"""
@@ -57,13 +57,13 @@ def get_units_factor(units):
----------
units : str
The abbreviation for the unit type
Returns
-------
factor : float
The factor meters / (unit)
"""
u = units.lower()
if u=='m':
factor=1
@@ -71,7 +71,7 @@ def get_units_factor(units):
factor=1e2
if u=='mm':
factor=1e3
if u=='um':
if u=='um' or u=="$\mu$m":
factor=1e6
if u=='nm':
factor=1e9
@@ -81,16 +81,16 @@ def get_units_factor(units):
factor=1e12
return factor
def plot_amplitude(im, fig = None, basis=None, units='um', cmap='viridis', **kwargs):
def plot_amplitude(im, fig = None, basis=None, units='$\mu$m', cmap='viridis', **kwargs):
"""Plots the amplitude of a complex array with dimensions NxM
If a figure is given explicitly, it will clear that existing figure and
plot over it. Otherwise, it will generate a new figure.
If a basis is explicitly passed, the image will be plotted in real-space
coordinates
Parameters
----------
im : array
@@ -129,11 +129,11 @@ def plot_amplitude(im, fig = None, basis=None, units='um', cmap='viridis', **kwa
basis = basis.detach().cpu().numpy()
basis_norm = np.linalg.norm(basis, axis = 0)
basis_norm = basis_norm * get_units_factor(units)
extent = [0, absolute.shape[-1]*basis_norm[1], 0, absolute.shape[-2]*basis_norm[0]]
else:
extent=None
plt.imshow(absolute, cmap = cmap, extent = extent)
cbar = plt.colorbar()
cbar.set_label('Amplitude (a.u.)')
@@ -144,11 +144,11 @@ def plot_amplitude(im, fig = None, basis=None, units='um', cmap='viridis', **kwa
else:
plt.xlabel('j (pixels)')
plt.ylabel('i (pixels)')
return fig
def plot_phase(im, fig=None, basis=None, units='um', cmap='auto', **kwargs):
def plot_phase(im, fig=None, basis=None, units='$\mu$m', cmap='auto', **kwargs):
""" Plots the phase of a complex array with dimensions NxMx2
If a figure is given explicitly, it will clear that existing figure and
@@ -156,7 +156,7 @@ def plot_phase(im, fig=None, basis=None, units='um', cmap='auto', **kwargs):
If a basis is explicitly passed, the image will be plotted in real-space
coordinates
Parameters
----------
im : array
@@ -194,12 +194,12 @@ def plot_phase(im, fig=None, basis=None, units='um', cmap='auto', **kwargs):
basis = basis.detach().cpu().numpy()
basis_norm = np.linalg.norm(basis, axis = 0)
basis_norm = basis_norm * get_units_factor(units)
extent = [0, phase.shape[-1]*basis_norm[1], 0, phase.shape[-2]*basis_norm[0]]
else:
extent=None
# If the user has matplotlib >=3.0, use the preferred colormap
if cmap == 'auto':
try:
@@ -208,21 +208,21 @@ def plot_phase(im, fig=None, basis=None, units='um', cmap='auto', **kwargs):
plt.imshow(phase, cmap = 'hsv', extent=extent)
else:
plt.imshow(phase)#, cmap = cmap, extent=extent)
cbar = plt.colorbar()
cbar.set_label('Phase (rad)')
if basis is not None:
plt.xlabel('X (' + units + ')')
plt.ylabel('Y (' + units + ')')
else:
plt.xlabel('j (pixels)')
plt.ylabel('i (pixels)')
return fig
def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
def plot_colorized(im, fig=None, basis=None, units='$\mu$m', **kwargs):
""" Plots the colorized version of a complex array with dimensions NxM
The darkness corresponds to the intensity of the image, and the color
@@ -233,7 +233,7 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
If a basis is explicitly passed, the image will be plotted in real-space
coordinates
Parameters
----------
im : array
@@ -258,7 +258,7 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
else:
plt.figure(fig.number)
plt.gcf().clear()
if isinstance(im, t.Tensor):
im = cmath.torch_to_complex(im.detach().cpu())
@@ -267,7 +267,7 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
basis = basis.detach().cpu().numpy()
basis_norm = np.linalg.norm(basis, axis = 0)
basis_norm = basis_norm * get_units_factor(units)
extent = [0, im.shape[-1]*basis_norm[1], 0, im.shape[-2]*basis_norm[0]]
else:
extent=None
@@ -281,14 +281,14 @@ def plot_colorized(im, fig=None, basis=None, units='um', **kwargs):
else:
plt.xlabel('j (pixels)')
plt.ylabel('i (pixels)')
return fig
def plot_translations(translations, fig=None, units='um', lines=True, **kwargs):
def plot_translations(translations, fig=None, units='$\mu$m', lines=True, **kwargs):
"""Plots a set of probe translations in a nicely formatted way
Parameters
----------
translations : array
@@ -308,9 +308,9 @@ def plot_translations(translations, fig=None, units='um', lines=True, **kwargs):
used_fig : matplotlib.figure.Figure
The figure object that was actually plotted to.
"""
factor = get_units_factor(units)
if fig is None:
fig = plt.figure()
ax = fig.add_subplot(111, **kwargs)
@@ -320,7 +320,7 @@ def plot_translations(translations, fig=None, units='um', lines=True, **kwargs):
if isinstance(translations, t.Tensor):
translations = translations.detach().cpu().numpy()
translations = translations * factor
plt.plot(translations[:,0], translations[:,1],'k.')
if lines:
@@ -330,10 +330,10 @@ def plot_translations(translations, fig=None, units='um', lines=True, **kwargs):
return fig
def plot_nanomap(translations, values, fig=None, units='um', convention='probe'):
def plot_nanomap(translations, values, fig=None, units='$\mu$m', convention='probe'):
"""Plots a set of nanomap data in a flexible way
Parameters
----------
translations : array
@@ -374,12 +374,12 @@ def plot_nanomap(translations, values, fig=None, units='um', convention='probe')
if convention.lower() != 'probe':
trans = trans * -1
s = bbox.width * bbox.height / trans.shape[0] * 72**2 #72 is points per inch
s /= 4 # A rough value to make the size work out
plt.scatter(factor * trans[:,0],factor * trans[:,1],s=s,c=values)
plt.gca().set_facecolor('k')
plt.xlabel('Translation x (' + units + ')')
plt.ylabel('Translation y (' + units + ')')