Skip to content

GitLab

Commit 94269222 authored by Somnath, Suhas's avatar Somnath, Suhas
Browse files

plot_map_stack now accepts a list of strings as titles for plots. 

plot_map_stack now has fewer rows and more columns wherever possible to suit common screen resolutions.
Using plot_map_stack instead of plotSHOMaps now. Latter function was redundant and therefore removed.
minor PEP8 cleaining
parent ae2365f5
Hide whitespace changes
Inline Side-by-side
pycroscopy/viz/plot_utils.py
View file @ 94269222
......@@ -188,7 +188,7 @@ def rainbowPlot(ax, ao_vec, ai_vec, num_steps=32, cmap=plt.cm.jet, **kwargs):
Colormap to be used
"""
pts_per_step = int(len(ai_vec) / num_steps)
for step in xrange(num_steps - 1):
for step in range(num_steps - 1):
ax.plot(ao_vec[step * pts_per_step:(step + 1) * pts_per_step],
ai_vec[step * pts_per_step:(step + 1) * pts_per_step],
color=cmap(255 * step / num_steps), **kwargs)
......@@ -231,7 +231,7 @@ def plot_line_family(ax, x_axis, line_family, line_names=None, label_prefix='Lin
warn('Line names of different length compared to provided dataset')
line_names = ['{} {} {}'.format(label_prefix, line_ind, label_suffix) for line_ind in range(num_lines)]
for line_ind in xrange(num_lines):
for line_ind in range(num_lines):
ax.plot(x_axis, line_family[line_ind],
label=line_names[line_ind],
color=cmap(int(255 * line_ind / (num_lines - 1))), **kwargs)
......@@ -251,19 +251,12 @@ def plot_map(axis, data, stdevs=2, show_colorbar=False, **kwargs):
Data to be plotted
stdevs : unsigned int (Optional. Default = 2)
Number of standard deviations to consider for plotting
show_colorbar : Boolean (Optional. Default = True)
Whether or not to show the color bar
Returns
-------
"""
data_mean = np.mean(data)
data_std = np.std(data)
# if show_colorbar:
# im = axis.pcolor(data,
# vmin=data_mean - stdevs * data_std, vmax=data_mean + stdevs * data_std, **kwargs)
# axis.figure.colorbar(pcol0, ax=axis)
# axis.axis('tight')
# else:
im = axis.imshow(data, interpolation='none',
vmin=data_mean - stdevs * data_std,
vmax=data_mean + stdevs * data_std,
......@@ -274,6 +267,7 @@ def plot_map(axis, data, stdevs=2, show_colorbar=False, **kwargs):
###############################################################################
def plotLoops(excit_wfm, h5_loops, h5_pos=None, central_resp_size=None,
evenly_spaced=True, plots_on_side=5, rainbow_plot=True,
x_label='', y_label='', subtitles='Eigenvector', title=None):
......@@ -355,41 +349,6 @@ def plotLoops(excit_wfm, h5_loops, h5_pos=None, central_resp_size=None,
return fig, axes
def plotSHOMaps(sho_maps, map_names, stdevs=2, title='', save_path=None):
"""
Plots the SHO quantity maps for a single UDVS step
Parameters
------------
sho_maps : List of 2D numpy arrays
Each SHO map is structured as [row, col]
map_names: List of strings
Titles for each of the SHO maps
stdevs : (Optional) Unsigned int
Number of standard deviations from the mean to be used to clip the color axis
title : (Optional) String
Title for the entire figure. Group name is most appropriate here
save_path : (Optional) String
Absolute path to write the figure to
Returns
----------
None
"""
fig, axes = plt.subplots(ncols=3, nrows=2, sharex=True, figsize=(15, 10))
for index, ax_hand, data_mat, qty_name in zip(range(len(map_names)), axes.flat, sho_maps, map_names):
plot_map(ax_hand, data_mat, stdevs=stdevs)
ax_hand.set_title(qty_name)
plt.setp([ax.get_xticklabels() for ax in axes[0, :]], visible=True)
axes[1, 2].axis('off')
plt.tight_layout()
if save_path:
fig.savefig(save_path, format='png', dpi=300)
def plotVSsnapshots(resp_mat, title='', stdevs=2, save_path=None):
"""
Plots the spatial distribution of the response at evenly spaced UDVS steps
......@@ -426,7 +385,7 @@ def plotVSsnapshots(resp_mat, title='', stdevs=2, save_path=None):
else:
axes_lin = axes
for count, posn in enumerate(xrange(0,num_udvs, delta_pos)):
for count, posn in enumerate(range(0,num_udvs, delta_pos)):
snapshot = np.squeeze(resp_mat[:,:,posn])
amp_mean = np.mean(snapshot)
......@@ -481,7 +440,7 @@ def plotSpectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='St
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title(title)
for index in xrange(num_comps):
for index in range(num_comps):
cur_map = np.transpose(eigenvectors[index, :, :])
ax = axes201.flat[index]
mean = np.mean(cur_map)
......@@ -528,7 +487,7 @@ def plotBEspectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title(title)
for index in xrange(num_comps):
for index in range(num_comps):
cur_map = np.transpose(eigenvectors[index, :, :])
axes = [axes201.flat[index], axes201.flat[index + num_comps]]
funcs = [np.abs, np.angle]
......@@ -580,7 +539,7 @@ def plotBEeigenvectors(eigenvectors, num_comps=4, xlabel=''):
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title("Eigenvectors")
for index in xrange(num_comps):
for index in range(num_comps):
cur_map = eigenvectors[index, :]
# axes = [axes201.flat[index], axes201.flat[index+num_comps], axes201.flat[index+2*num_comps], axes201.flat[index+3*num_comps]]
axes = [axes201.flat[index], axes201.flat[index + num_comps]]
......@@ -622,7 +581,7 @@ def plotBELoops(xaxis, xlabel, amp_mat, phase_mat, num_comps, title=None):
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title(title)
for index in xrange(num_comps):
for index in range(num_comps):
axes = [axes201.flat[index], axes201.flat[index + num_comps]]
resp_vecs = [amp_mat[index, :], phase_mat[index, :]]
resp_titles = ['Amplitude', 'Phase']
......@@ -666,45 +625,6 @@ def plotScree(S, title='Scree'):
# ###############################################################################
#
# def plot_map_stack(map_stack, num_comps=4, stdevs=2, show_colorbar=False,
# title='Component', heading='Map Stack', **kwargs):
# """
# Plots the provided stack of maps
#
# Parameters:
# -------------
# map_stack : 3D real numpy array
# structured as [rows, cols, component]
# num_comps : int
# Number of components to plot
# stdevs : int
# Number of standard deviations to consider for plotting
# colormap : string or object from matplotlib.colors (Optional. Default = jet or rainbow)
# Colormap for the plots
# show_colorbar : Boolean (Optional. Default = True)
# Whether or not to show the color bar
#
# Returns:
# ---------
# fig, axes
# """
# fig_h, fig_w = (4, 4 + show_colorbar * 1.00)
# p_rows = int(np.ceil(np.sqrt(num_comps)))
# p_cols = int(np.floor(num_comps / p_rows))
# if p_rows*p_cols < num_comps:
# p_cols += 1
# fig202, axes202 = plt.subplots(p_cols, p_rows, figsize=(p_cols * fig_w, p_rows * fig_h))
# fig202.subplots_adjust(hspace=0.4, wspace=0.4)
# fig202.canvas.set_window_title(heading)
# fig202.suptitle(heading, fontsize=16)
#
# for index in xrange(num_comps):
# plot_map(axes202.flat[index], map_stack[:, :, index], stdevs=stdevs, show_colorbar=show_colorbar, **kwargs)
# axes202.flat[index].set_title('{} {}'.format(title, index))
# fig202.tight_layout()
#
# return fig202, axes202
def plot_map_stack(map_stack, num_comps=4, stdevs=2, color_bar_mode=None,
......@@ -716,23 +636,36 @@ def plot_map_stack(map_stack, num_comps=4, stdevs=2, color_bar_mode=None,
-------------
map_stack : 3D real numpy array
structured as [rows, cols, component]
num_comps : int
num_comps : unsigned int
Number of components to plot
stdevs : int
Number of standard deviations to consider for plotting
colormap : string or object from matplotlib.colors (Optional. Default = jet or rainbow)
Colormap for the plots
color_bar_mode : String, Optional
Options are None, single or each.
Default None
Options are None, single or each. Default None
title : String or list of strings
The titles for each of the plots.
If a single string is provided, the plot titles become ['title 01', title 02', ...].
if a list of strings (equal to the number of components) are provided, these are used instead.
Returns:
---------
fig, axes
"""
if isinstance(title, list):
if len(title) > num_comps:
# remove additional titles
title = title[:num_comps]
elif len(title) < num_comps:
# add titles
title = title + ['Component' + ' ' + str(x) for x in range(len(title), num_comps)]
else:
if not isinstance(title, str):
title = 'Component'
title = [title + ' ' + str(x) for x in range(num_comps)]
fig_h, fig_w = (4, 4)
p_rows = int(np.ceil(np.sqrt(num_comps)))
p_cols = int(np.floor(num_comps / p_rows))
p_rows = int(np.floor(np.sqrt(num_comps)))
p_cols = int(np.ceil(num_comps / p_rows))
if p_rows*p_cols < num_comps:
p_cols += 1
fig202 = plt.figure(figsize=(p_cols * fig_w, p_rows * fig_h))
......@@ -746,12 +679,12 @@ def plot_map_stack(map_stack, num_comps=4, stdevs=2, color_bar_mode=None,
fig202.canvas.set_window_title(heading)
fig202.suptitle(heading, fontsize=16)
for index in range(num_comps):
for index, subtitle in enumerate(title):
im = plot_map(axes202[index],
map_stack[:, :, index],
stdevs=stdevs,
show_colorbar=False, **kwargs)
axes202[index].set_title('{} {}'.format(title, index))
axes202[index].set_title(subtitle)
if color_bar_mode is 'each':
axes202.cbar_axes[index].colorbar(im)
......@@ -1075,10 +1008,10 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
d_sort = sort_mode
centroid_mat = np.zeros([num_cluster, num_comp])
for k1 in xrange(num_cluster):
for k1 in range(num_cluster):
[i_x, i_y] = np.where(label_mat == k1)
u_stack = np.zeros([len(i_x), num_comp])
for k2 in xrange(len(i_x)):
for k2 in range(len(i_x)):
u_stack[k2, :] = np.abs(e_vals[i_x[k2], i_y[k2], :num_comp])
centroid_mat[k1, :] = np.mean(u_stack, 0)
......@@ -1302,7 +1235,7 @@ def plotSHOLoops(dc_vec, resp_mat, x_label='', y_label='', title=None, save_path
else:
axes_lin = axes
for count, posn in enumerate(xrange(0, num_pos, delta_pos)):
for count, posn in enumerate(range(0, num_pos, delta_pos)):
axes_lin[count].plot(dc_vec, np.squeeze(resp_mat[posn, :]))
axes_lin[count].set_title('Pixel #' + str(posn))
axes_lin[count].set_xlabel(x_label)
......@@ -1466,9 +1399,12 @@ def visualizeSHOResults(h5_main, save_plots=True, show_plots=True):
rsqr_mat = rsqr_mat.reshape(num_rows, num_cols)
if save_plots:
plt_path = os.path.join(folder_path, basename + '_' + grp_name + 'Maps.png')
plotSHOMaps([amp_mat, freq_mat, q_mat, phase_mat, rsqr_mat],
['Amplitude (mV)', 'Frequency (kHz)', 'Quality Factor',
'Phase (deg)', 'R^2 Criterion'], title=grp_name, save_path=plt_path)
fig_ms, ax_ms = plot_map_stack(np.dstack((amp_mat, freq_mat, q_mat, phase_mat, rsqr_mat)),
num_comps=5, color_bar_mode='each', heading=grp_name,
title=['Amplitude (mV)', 'Frequency (kHz)', 'Quality Factor', 'Phase (deg)',
'R^2 Criterion'], cmap=cmap_jet_white_center())
fig_ms.savefig(plt_path, format='png', dpi=300)
if show_plots:
plt.show()
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment