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Commit 058f5a20 authored by Unknown's avatar Unknown
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Swapped default colormap to new 'viridis'

parent ccec4dd1
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pycroscopy/viz/be_viz_utils.py
View file @ 058f5a20
......@@ -377,21 +377,21 @@ def jupyter_visualize_be_spectrograms(h5_main):
spatial_map = np.abs(np.reshape(h5_main[:, 0], pos_dims))
spectrogram = np.reshape(h5_main[0], (num_udvs_steps, -1))
fig, axes = plt.subplots(ncols=3, figsize=(12, 4))
# spatial_img = axes[0].imshow(np.abs(spatial_map), cmap=plt.cm.jet)
# spatial_img = axes[0].imshow(np.abs(spatial_map), cmap=plt.cm.viridis)
spatial_img = plot_map(axes[0], np.abs(spatial_map), origin='lower',
cmap=cmap_jet_white_center())
axes[0].set_xlabel('X')
axes[0].set_ylabel('Y')
main_vert_line = axes[0].axvline(x=int(0.5 * spatial_map.shape[1]), color='k')
main_hor_line = axes[0].axhline(y=int(0.5 * spatial_map.shape[0]), color='k')
amp_img = axes[1].imshow(np.abs(spectrogram), cmap=plt.cm.jet,
amp_img = axes[1].imshow(np.abs(spectrogram), cmap=plt.cm.viridis,
extent=[freqs_2d[0, 0], freqs_2d[-1, 0],
spectrogram.shape[0], 0],
interpolation='none')
axes[1].set_title('Amplitude')
axes[1].set_xlabel('Frequency (kHz)')
axes[1].set_ylabel('BE step')
phase_img = axes[2].imshow(np.angle(spectrogram), cmap=plt.cm.jet,
phase_img = axes[2].imshow(np.angle(spectrogram), cmap=plt.cm.viridis,
extent=[freqs_2d[0, 0], freqs_2d[-1, 0],
spectrogram.shape[0], 0],
interpolation='none')
......@@ -439,13 +439,13 @@ def jupyter_visualize_be_spectrograms(h5_main):
def plot_spectrogram(data, freq_vals):
fig, axes = plt.subplots(ncols=2, figsize=(9, 5), sharey=True)
im_handles = list()
im_handles.append(axes[0].imshow(np.abs(data), cmap=plt.cm.jet,
im_handles.append(axes[0].imshow(np.abs(data), cmap=plt.cm.viridis,
extent=[freqs_2d[0, 0], freqs_2d[-1, 0],
data.shape[0], 0],
interpolation='none'))
axes[0].set_title('Amplitude')
axes[0].set_ylabel('BE step')
im_handles.append(axes[1].imshow(np.angle(data), cmap=plt.cm.jet,
im_handles.append(axes[1].imshow(np.angle(data), cmap=plt.cm.viridis,
extent=[freqs_2d[0, 0], freqs_2d[-1, 0],
data.shape[0], 0],
interpolation='none'))
......
pycroscopy/viz/plot_utils.py
View file @ 058f5a20
......@@ -62,7 +62,7 @@ def cmap_jet_white_center():
Returns
-------
white_jet : matplotlib.colors.LinearSegmentedColormap object
color map object that can be used in place of plt.cm.jet
color map object that can be used in place of plt.cm.viridis
"""
# For red - central column is like brightness
# For blue - last column is like brightness
......@@ -170,7 +170,7 @@ def cmap_hot_desaturated():
return cmap_from_rgba('hot_desaturated', hot_desaturated, 255)
def discrete_cmap(num_bins, base_cmap=plt.cm.jet):
def discrete_cmap(num_bins, base_cmap=plt.cm.viridis):
"""
Create an N-bin discrete colormap from the specified input map
......@@ -226,7 +226,7 @@ def _add_loop_parameters(axes, switching_coef_vec):
return axes
def rainbow_plot(ax, ao_vec, ai_vec, num_steps=32, cmap=plt.cm.jet, **kwargs):
def rainbow_plot(ax, ao_vec, ai_vec, num_steps=32, cmap=plt.cm.viridis, **kwargs):
"""
Plots the input against the output waveform (typically loops).
The color of the curve changes as a function of time using the jet colorscheme
......@@ -254,11 +254,11 @@ def rainbow_plot(ax, ao_vec, ai_vec, num_steps=32, cmap=plt.cm.jet, **kwargs):
ai_vec[(num_steps - 1) * pts_per_step:],
color=cmap(255 * num_steps / num_steps), **kwargs)
"""
CS3=plt.contourf([[0,0],[0,0]], range(0,310),cmap=plt.cm.jet)
CS3=plt.contourf([[0,0],[0,0]], range(0,310),cmap=plt.cm.viridis)
fig.colorbar(CS3)"""
def plot_line_family(axis, x_axis, line_family, line_names=None, label_prefix='Line', label_suffix='', cmap=plt.cm.jet,
def plot_line_family(axis, x_axis, line_family, line_names=None, label_prefix='Line', label_suffix='', cmap=plt.cm.viridis,
**kwargs):
"""
Plots a family of lines with a sequence of colors
......@@ -760,7 +760,7 @@ def plot_cluster_h5_group(h5_group, y_spec_label, centroids_together=True):
###############################################################################
def plot_cluster_results_together(label_mat, mean_response, spec_val=None, cmap=plt.cm.jet,
def plot_cluster_results_together(label_mat, mean_response, spec_val=None, cmap=plt.cm.viridis,
spec_label='Spectroscopic Value', resp_label='Response',
pos_labels=('X', 'Y'), pos_ticks=None):
"""
......@@ -860,9 +860,9 @@ def plot_cluster_results_together(label_mat, mean_response, spec_val=None, cmap=
"""divider = make_axes_locatable(ax_map)
cax = divider.append_axes("right", size="5%", pad=0.05) # space for colorbar
fig.colorbar(im, cax=cax, ticks=np.arange(num_clusters),
cmap=discrete_cmap(num_clusters, base_cmap=plt.cm.jet))
cmap=discrete_cmap(num_clusters, base_cmap=plt.cm.viridis))
ax_map.axis('tight')"""
pcol0 = ax_map.pcolor(label_mat, cmap=discrete_cmap(num_clusters, base_cmap=plt.cm.jet))
pcol0 = ax_map.pcolor(label_mat, cmap=discrete_cmap(num_clusters, base_cmap=plt.cm.viridis))
fig.colorbar(pcol0, ax=ax_map, ticks=np.arange(num_clusters))
ax_map.axis('tight')
ax_map.set_aspect('auto')
......@@ -933,7 +933,7 @@ def plot_cluster_results_separate(label_mat, cluster_centroids, max_centroids=4,
# First plot the labels map:
pcol0 = fax1.pcolor(label_mat, cmap=discrete_cmap(cluster_centroids.shape[0],
base_cmap=plt.cm.jet))
base_cmap=plt.cm.viridis))
fig501.colorbar(pcol0, ax=fax1, ticks=np.arange(cluster_centroids.shape[0]))
fax1.axis('tight')
fax1.set_aspect('auto')
......@@ -950,7 +950,7 @@ def plot_cluster_results_separate(label_mat, cluster_centroids, max_centroids=4,
for ax, index in zip(axes_handles[1: max_centroids + 1], np.arange(max_centroids)):
if cluster_centroids.ndim == 2:
ax.plot(spec_val, cluster_centroids[index, :],
color=plt.cm.jet(int(255 * index / (cluster_centroids.shape[0] - 1))))
color=plt.cm.viridis(int(255 * index / (cluster_centroids.shape[0] - 1))))
ax.set_xlabel(x_label)
ax.set_ylabel(y_label)
elif cluster_centroids.ndim == 3:
......@@ -1110,7 +1110,7 @@ def plot_2d_spectrogram(mean_spectrogram, freq, title, cmap=None, figure_path=No
title : String
Plot group name
cmap : matplotlib.colors.LinearSegmentedColormap object
color map. Default = plt.cm.jet
color map. Default = plt.cm.viridis
figure_path : String / Unicode
Absolute path of the file to write the figure to
......@@ -1129,7 +1129,7 @@ def plot_2d_spectrogram(mean_spectrogram, freq, title, cmap=None, figure_path=No
"""cmap = kwargs.get('cmap')
kwargs.pop('cmap')"""
if cmap is None: # unpack from kwargs instead
col_map = plt.cm.jet # overriding default
col_map = plt.cm.viridis # overriding default
freq *= 1E-3 # to kHz
fig, ax = plt.subplots(nrows=2, ncols=1, sharex=True)
......
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