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Make the colorized plot look nicer, with a more perceptually uniform mapping and a colorbar for accurate reading of phases

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allevitan
2026-03-21 17:35:14 +01:00
parent a4a38530d1
commit f04ac9f0ec
1 changed files with 27 additions and 16 deletions
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src/cdtools/tools/plotting/plotting.py
+27 -16
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@@ -31,7 +31,7 @@ __all__ = [
]
def colorize(z):
def colorize(z, use_cmocean=True):
""" Returns RGB values for a complex color plot given a complex array
This function returns a set of RGB values that can be used directly
in a call to imshow based on an input complex numpy array (not a
@@ -48,17 +48,26 @@ def colorize(z):
"""
amp = np.abs(z)
rmin = 0
rmax = np.max(amp)
amp = np.where(amp < rmin, rmin, amp)
amp = np.where(amp > rmax, rmax, amp)
ph = np.angle(z, deg=1) + 90
# HSV are values in range [0,1]
h = (ph % 360) / 360
s = 0.85 * np.ones_like(h)
v = (amp - rmin) / (rmax - rmin)
scaled_amp = amp / np.max(amp)
ph = np.angle(z, deg=1)
if not use_cmocean:
# HSV are values in range [0,1]
h = ((ph + 90) % 360) / 360
s = 0.85 * np.ones_like(h)
v = scaled_amp
return hsv_to_rgb(np.dstack((h,s,v)))
else:
base_rgb_values = []
for channel in range(3):
base_rgb_values.append(np.interp(ph%360,
np.linspace(0, 360, cm_data.shape [0]),
cm_data[:,channel]))
base_rgb_values = np.dstack(base_rgb_values)
rgb_values = base_rgb_values * scaled_amp[...,None]
return rgb_values
return hsv_to_rgb(np.dstack((h,s,v)))
def get_units_factor(units):
@@ -642,7 +651,9 @@ def plot_colorized(im, fig=None, basis=None, units='$\\mu$m', title=None, **kwar
"""
plot_func = lambda x: colorize(x)
return plot_image(im, plot_func=plot_func, fig=fig, basis=basis,
units=units, show_cbar=False, title=title, **kwargs)
cmap=cmocean_phase, vmin=-np.pi, vmax=np.pi,
cmap_label='Phase (rad)',
units=units, show_cbar=True, title=title, **kwargs)
def plot_translations(translations, fig=None, units='$\\mu$m', lines=True, invert_xaxis=True, clear_fig=True, label=None, color=None, marker='.', **kwargs):
@@ -1337,8 +1348,8 @@ cm_data = [[ 0.65830839, 0.46993917, 0.04941288],
[ 0.65121289, 0.47406244, 0.05044367],
[ 0.65830839, 0.46993917, 0.04941288]]
rgb = np.array(cm_data)
rgb_with_alpha = np.zeros((rgb.shape[0],4))
rgb_with_alpha[:,:3] = rgb
cm_data = np.array(cm_data)
rgb_with_alpha = np.zeros((cm_data.shape[0],4))
rgb_with_alpha[:,:3] = cm_data
rgb_with_alpha[:,3] = 1. #set alpha channel to 1
cmocean_phase = colors.ListedColormap(rgb_with_alpha, N=rgb.shape[0])
cmocean_phase = colors.ListedColormap(rgb_with_alpha, N=cm_data.shape[0])