def spread_plot(args):
"""Draw the spreading as a function of time."""
# Get colours and line styles from default
colours = get_colours(args.colour, len(args.spreading))
labels, draw_legend = get_labels(args.label, len(args.spreading))
linestyles = {}
linestyles['line'] = get_linestyles(args.linestyle, len(args.spreading))
linestyles['fit'] = get_linestyles(args.fitstyle, len(args.spreading),
'dashed')
# Create linear fitting function
fitfunc = lambda p, t, r: r - p[0] - p[1] * t
pinit = [1.0, 1/7]
# Find shift array for synchronisation
shift_array = get_shift(args.spreading, sync=args.sync)
impact_shift = get_shift(args.spreading, sync='impact')
# Create dicts for lists of fit constants (r = amp * t**index)
amp = {}
index = {}
ampError = {}
indexError = {}
ampMean = []
ampMeanError = []
indexMean = []
indexMeanError = []
for i, spread_list in enumerate(args.spreading):
amp[i] = []
index[i] = []
ampError[i] = []
indexError[i] = []
spread, full_data = combine_spread(spread_list, shift=shift_array[i])
spread.times = np.array(spread.times) - spread.times[0]
for k, _file in enumerate(spread_list):
data = Spread().read(_file)
data.times = np.array(data.times) - impact_shift[i][k]
# Get radius and domain
radius = {'real': np.array(calc_radius(data))}
domain = {'real': np.array(data.times)}
# Cut times outside of range
for j, time in enumerate(domain['real']):
if time > args.tend:
radius['real'] = radius['real'][:j]
domain['real'] = domain['real'][:j]
# Add logged values
radius['log'] = np.log10(radius['real'][1:])
domain['log'] = np.log10(domain['real'][1:])
# Cut in log range
for j, logt in enumerate(domain['log']):
if logt > args.tendlog:
radius['log'] = radius['log'][:j]
domain['log'] = domain['log'][:j]
# Fit constants to data
out = optimize.leastsq(fitfunc, pinit,
args=(domain['log'], radius['log']), full_output=1)
pfinal = out[0]
covar = out[1]
# Add unlogged constants to lists
amp[i].append(10**pfinal[0])
index[i].append(pfinal[1])
ampError[i].append(np.sqrt(covar[1][1]) * amp[i][-1])
indexError[i].append(np.sqrt(covar[0][0]))
if args.draw == 'log' and args.nomean:
plot_line(
line=radius['log'],
domain=domain['log'],
color=colours[i],
linestyle=linestyles['line'][i]
)
if not args.nofit:
plot_line(
line=out[0][0] + out[0][1] * domain['log'],
domain=domain['log'],
color=colours[i], linestyle=linestyles['fit'][i]
)
if args.draw == 'real' and args.nomean:
plot_line(
line=radius['real'],
domain=domain['real'],
color=colours[i], linestyle=linestyles['line'][i]
)
if not args.nofit:
plot_line(
line=amp[i][-1] * (domain['real']**index[i][-1]),
domain=domain['real'],
color=colours[i], linestyle=linestyles['fit'][i]
)
ampMean.append(np.mean(amp[i]))
ampMeanError.append(np.std(amp[i]) / np.sqrt(len(amp[i]) - 1))
indexMean.append(np.mean(index[i]))
indexMeanError.append(np.std(index[i]) / np.sqrt(len(index[i]) - 1))
if not args.nomean:
if args.draw == 'log':
plot_line(
line=np.log10(calc_radius(spread)),
domain=np.log10(spread.times),
label=labels[i],
color=colours[i], linestyle=linestyles['line'][i]
)
if not args.nofit:
plot_line(
line=(np.log10(ampMean[i])
+ indexMean[i] * np.log10(spread.times)),
domain=np.log10(spread.times),
label='C=%.2f, n=%.2f'%(ampMean[i], indexMean[i]),
color=colours[i], linestyle=linestyles['fit'][i]
)
if args.draw == 'real':
plot_line(
line=calc_radius(spread),
domain=spread.times,
label=labels[i],
color=colours[i], linestyle=linestyles['line'][i]
)
if not args.nofit:
plot_line(
line=ampMean[i] * (domain['real']**indexMean[i]),
domain=domain['real'],
label='C=%.2f, n=%.2f'%(ampMean[i], indexMean[i]),
color=colours[i], linestyle=linestyles['fit'][i]
)
plt.title(args.title, fontsize='medium')
plt.axis('normal')
plt.legend()
# Default xlabel and xlims based on draw method
if args.draw == 'real':
if args.ylabel == None:
args.ylabel = "Spread radius (nm)"
if args.xlabel == None:
args.xlabel = "Time (ps)"
if (args.tend and args.tendlog) < np.inf:
plt.xlim([None, min(args.tend, 10**args.tendlog)])
elif args.draw == 'log':
if args.ylabel == None:
args.ylabel = "log10 of radius (in nm)"
if args.xlabel == None:
args.xlabel = "log10 of time (in ps)"
if (args.tend and args.tendlog) < np.inf:
plt.xlim([None, min(args.tend, args.tendlog)])
plt.xlabel(args.xlabel, fontsize='medium')
plt.ylabel(args.ylabel, fontsize='medium')
if args.xlim:
plt.xlim(args.xlim)
# Print collected output
print("Fitting spread radius 'R' of input file sets to power law functions "
"of time 't' as 'R = C * (t ** n)' and taking means:")
for i, _ in enumerate(amp):
print()
# If nomean, print individual line values
if args.nomean:
for values in zip(amp[i], ampError[i], index[i], indexError[i]):
print("%f +/- %f" % (values[0], values[1]), end=', ')
print("%f +/- %f" % (values[2], values[3]))
# Print mean values
if args.nomean:
print(" -> ", end='')
print("C = %f +/- %f" % (ampMean[i], ampMeanError[i]))
if args.nomean:
print(" -> ", end='')
print("n = %f +/- %f" % (indexMean[i], indexMeanError[i]))
# Finish by saving and / or showing
if args.save:
plt.savefig(args.save)
if args.draw != 'off':
plt.show()
return None
draw_args.add_argument('--dpi', type=int, default=150, help="output graph dpi")
# Decorations
label_args = parser.add_argument_group('label options',
'pick labels for output figures')
label_args.add_argument('--xlabel', default='Time (ps)')
label_args.add_argument('--ylabel', default='Maximum shear (1/ps)')
label_args.add_argument('--title', default='Maximum found shear of system per time')
# Parse and control for action
args = parser.parse_args()
# Plot options
colours = get_colours(args.colour, 2)
linestyles = get_linestyles(args.linestyle, 2)
labels, draw_legend = get_labels(args.label, 2)
# Define system and add data maps
system = System()
system.files(base=args.datamap, start=args.begin, end=args.end)
# Collect shear data in list
frames = []
max_shear = []
floor = args.floor
ceil = floor + args.num_shear
if ceil <= floor:
parser.error('number of cell rows to calculate shear over (--number) must be positive')
rows = [floor, ceil]
def vel_plot(args):
"""Draw the spreading as a function of time."""
def plot_data(spread, times):
"""Plot either edges or radius of specified line."""
for _type in args.plot_type:
velocity = spread[_type]['val']
plot_line(
line=velocity,
domain=times,
color=colours[i], label=label,
linestyle=linestyles['line'][i]
)
return None
def calc_velocity(spread, plot_type, N, N_sample):
"""
Returns the velocity of the spreading curve, as a running average
over N frames.
"""
def get_velocity(spreading, times, N_sample):
velocity = []
for i, _ in enumerate(spreading):
i_min = max(0, i-N_sample)
i_max = min(i+N_sample, len(spreading)-1)
delta_x = spreading[i_max] - spreading[i_min]
delta_t = times[i_max] - times[i_min]
velocity.append(delta_x/delta_t)
return velocity
def calc_running_avg(velocity, full_times, N):
N0 = N
running_avg = {'val': [], 'std': []}
times = []
for i, _ in enumerate(velocity):
if args.include == 'equal':
N = min(i - max(0, i-N0), min(i+N0, len(velocity)-1)-i)
i_min = max(0, i-N)
i_max = min(i+N, len(velocity)-1)
if N == 0 or (args.include == 'limited' and i_max - i_min != 2*N):
continue
running_avg['val'].append(np.average(velocity[i_min:i_max+1]))
times.append(full_times[i])
return running_avg, times
running_avg = {}
for _type in plot_type:
velocity = get_velocity(spread.spread[_type]['val'], spread.times, N_sample)
running_avg[_type], times = calc_running_avg(velocity, spread.times, N)
return running_avg, times
def print_vel(velocity, times):
"""Output the mean spread velocity to standard output."""
print("%9c Velocity of (nm / ps)" % ' ')
print("%9s " % "Time (ps)", end='')
for _key in velocity.keys():
print("%9s " % _key.capitalize(), end='')
print()
for i, time in enumerate(times[1:]):
print("%9g " % time, end='')
for _type in velocity.keys():
print("%9g " % velocity[_type]['val'][i+1], end='')
print()
return None
# Get colours, labels and line styles from default
colours = get_colours(args.colour, len(args.spreading))
labels, draw_legend = get_labels(args.label, len(args.spreading))
linestyles = {}
linestyles['line'] = get_linestyles(args.linestyle, len(args.spreading))
# Find shift array for synchronisation
shift_array = get_shift(args.spreading, sync=args.sync)
for i, spread_list in enumerate(args.spreading):
spread, data = combine_spread(spread_list, shift=shift_array[i])
# If --nomean, draw lines here
label = labels[i]
if args.nomean:
for spread_data in data:
vel, times = calc_velocity(spread_data, args.plot_type,
args.num_average, args.num_sample)
plot_data(vel, times)
label = '_nolegend_'
# Else draw the mean result
else:
vel, times = calc_velocity(spread, args.plot_type,
args.num_average, args.num_sample)
plot_data(vel, times)
plt.title(args.title, fontsize='medium')
plt.xlabel(args.xlabel, fontsize='medium')
plt.ylabel(args.ylabel, fontsize='medium')
if args.loglog:
plt.xscale('log')
plt.yscale('log')
plt.axis('normal')
plt.xlim([args.t0, args.tend])
if draw_legend:
plt.legend(loc=args.legend_loc)
# Finish by saving and / or showing
if args.save:
plt.savefig(
args.save, dpi=args.dpi,
transparent=args.transparent,
bbox_inches='tight'
)
if args.print:
if args.nomean:
vel = calc_velocity(spread, args.plot_type, args.num_average, args.num_sample)
print_vel(vel, spread.times)
if args.show:
plt.show()
return None
def sample_error_plot(args):
"""Draw the sample error for spread data."""
def plot(spreading, _type, shift, style):
def get_line(spread, _type):
if _type == 'left' or _type == 'right':
return spread.spread[_type]['std_error']
elif _type == 'radius':
_, radius = calc_radius(spread, error=True)
return radius
for i, spread_list in enumerate(spreading):
spread, _ = combine_spread(spread_list, shift=shift[0])
domain = spread.times
line = get_line(spread, _type)
plot_line(
line=line, domain=domain,
color=colours[i], label=labels[i],
linestyle=style[i],
hold=True
)
return None
colours = get_colours(args.colour, len(args.spreading))
labels, draw_legend = get_labels(args.label, len(args.spreading))
complabels, draw_comp = get_labels(args.complabel, len(args.spreading))
draw_legend = draw_legend or draw_comp
linestyles = {}
linestyles['line'] = get_linestyles(args.linestyle, len(args.spreading))
linestyles['compare'] = get_linestyles(args.compstyle, len(args.spreading),
'dotted')
for i, spread_list in enumerate(args.spreading):
if args.sync == 'com':
shift = get_shift([spread_list], sync='com')
comp_shift = get_shift([spread_list], sync='impact')
else:
shift = get_shift([spread_list], sync='impact')
comp_shift = get_shift([spread_list], sync='com')
if args.radius:
plot(args.spreading, 'radius', shift, linestyles['line'])
if args.compare:
plot(args.spreading, 'radius', comp_shift, linestyles['compare'])
else:
for _type in ('left', 'right'):
plot(args.spreading, _type, shift, linestyles['line'])
if args.compare:
plot(args.spreading, _type, comp_shift, linestyles['compare'])
plt.title(args.title)
plt.xlabel(args.xlabel)
plt.ylabel(args.ylabel)
plt.axis('normal')
plt.xlim([args.t0, args.tend])
if draw_legend:
plt.legend()
if args.save:
plt.savefig(args.save)
if args.show:
plt.show()
return None
def t_test_plot(args):
"""Perform a Welch's t-test on two sets of spread data, plot probability."""
def plot(spreading, _type, shift_array):
def get_line(spread, _type):
if _type == 'left' or _type == 'right':
return spread.spread[_type]['val']
elif _type == 'radius':
return calc_radius(spread)
data = {}
n = 0
for i, spread_list in enumerate(spreading):
for j, _file in enumerate(spread_list):
spread = Spread().read(_file)
line = get_line(spread, _type)
times = np.array(spread.times) - shift_array[i][j]
data[n] = Series(data=line, index=times)
n += 1
# Create DataFrame for all values and drop nan
df = DataFrame(data).dropna()
domain = df.index
n = 0
data = [[], []]
for i, spread_list in enumerate(spreading):
for j, _ in enumerate(spread_list):
data[i].append(df[n].tolist())
n += 1
t, p = stats.ttest_ind(data[0], data[1], equal_var=False)
plot_line(line=p, domain=domain, label=label[0], color=colour[0],
linestyle=linestyle['line'][0], hold=True)
return None
# Two sets of data must be given
if len(args.spreading) != 2:
parser.error("exactly two sets of spread data must be supplied with -f "
"(%d given)" % len(args.spreading))
# Get colours, labels and line styles from default
colour = get_colours(args.colour, len(args.spreading))
label, draw_legend = get_labels(args.label, len(args.spreading))
linestyle = {}
linestyle['line'] = get_linestyles(args.linestyle, 2)
# Find shift array for synchronisation
shift_array = get_shift(args.spreading, sync=args.sync)
if args.radius:
plot(args.spreading, 'radius', shift_array)
else:
plot(args.spreading, 'left', shift_array)
plot(args.spreading, 'right', shift_array)
plt.axis('normal')
plt.title(args.title)
plt.xlabel(args.xlabel)
plt.ylabel(args.ylabel)
plt.xlim([args.t0, args.tend])
if draw_legend:
plt.legend()
# Finish by saving and / or showing
if args.save:
plt.savefig(args.save)
if args.show:
plt.show()
return None
def com_plot(args):
"""Draw the center of mass height as a function of time."""
# Get colours, labels and line styles from default
colours = get_colours(args.colour, len(args.spreading))
labels, draw_legend = get_labels(args.label, len(args.spreading))
linestyles = {}
linestyles['line'] = get_linestyles(args.linestyle, len(args.spreading))
linestyles['error'] = get_linestyles(args.errorstyle, len(args.spreading),
'dashed')
# Find shift array for synchronisation
shift_array = get_shift(args.spreading, sync=args.sync)
for i, spread_list in enumerate(args.spreading):
spread, data = combine_spread(spread_list, shift=shift_array[i])
# Check if error bars need to be included
error = args.error and len(spread_list) > 1
# Create graph
if args.nomean:
label = labels[i]
for spread_data in data:
domain = spread_data.times
line = spread_data.dist
plot_line(line=line, domain=domain, color=colours[i],
label=label, linestyle=linestyles['line'][i])
label = '_nolegend_'
else:
domain = spread.times
line = spread.dist
plot_line(line=line, domain=domain, color=colours[i],
label=labels[i], linestyle=linestyles['line'][i])
if error:
domain = spread.times
line = list(np.array(spread.dist)
+ np.array(spread.spread['dist']['std_error'])
* args.sigma)
plot_line(line=line, domain=domain, color=colours[i],
linestyle=linestyles['error'][i])
line = list(np.array(spread.dist)
- np.array(spread.spread['dist']['std_error'])
* args.sigma)
plot_line(line=line, domain=domain, color=colours[i],
linestyle=linestyles['error'][i])
plt.title(args.title)
plt.xlabel(args.xlabel)
plt.ylabel(args.ylabel)
plt.axis('normal')
plt.xlim([args.t0, args.tend])
if draw_legend:
plt.legend()
# Finish by saving and / or showing
if args.save:
plt.savefig(args.save)
if args.show:
plt.show()
return None
def spread_plot(args):
"""Draw the spreading of sets of droplets as a function of time."""
def add_xvgdata(spread, xvg_set):
"""
Adds data for current line to list of data to output in
.xvg format.
"""
add = {}
line = []
for _type in plot_type:
add['legend'] = labels[i]
add['line'] = spread.spread[_type]['val'][0:]
add['time'] = np.array(spread.times[0:])
line.append(add.copy())
xvg_set.append(line)
return None
def save_xvgdata(xvg_data):
"""
Saves spreading lines to .xvg files of input filenames.
"""
def print_xvgfile(line, fnin):
fnout = fnin.rsplit('.', 1)[0] + '.xvg'
backup_file(fnout)
with open(fnout, 'w') as _file:
_file.write(
"@ title \"%s\"\n"
"@ xaxis label \"%s\"\n"
"@ yaxis label \"%s\"\n"
"@TYPE xy\n"
% (args.title, args.xlabel, args.ylabel)
)
# Output legend information
_file.write(
"@ legend on\n"
"@ legend box on\n"
"@ legend loctype view\n"
"@ legend 0.78 0.8\n"
"@ legend length 2\n"
"@s0 legend \"%s\"\n\n"
% line[0]['legend']
)
for i in range(len(line[0]['time'])):
time = line[0]['time'][i]
_file.write("%f " % time)
for j in range(len(line)):
value = line[j]['line'][i]
_file.write("%f " % value)
_file.write("\n")
return None
def backup_file(fn):
"""If a file 'fn' exists, move to backup location."""
fnmv = fn
n = 0
while (os.path.isfile(fnmv)):
n += 1
try:
_path, _file = fn.rsplit('/', 1)
_path += '/'
except ValueError:
_path = ''
_file = fn
fnmv = _path + '#' + _file.rsplit('.', 1)[0] + '.xvg.%d#' % n
if (n > 0):
print("File '%s' backed up to '%s'" % (fn, fnmv))
shutil.move(fn, fnmv)
return None
for i, xvg_set in enumerate(xvg_data):
# Print either all lines to separate files with extension switch
if args.nomean:
for j, line in enumerate(xvg_set):
# Replace last extension with .xvg
fnin = args.spreading[i][j]
print_xvgfile(line, fnin)
# Or print combined lines to files with base filename as first file
else:
line = xvg_set[0]
fnin = args.spreading[i][0]
print_xvgfile(line, fnin)
return None
def plot_data(spread, times):
"""Plot either edges or radius of specified line."""
for _type in plot_type:
plot_line(
line=spread[_type]['val'][0:],
domain=np.array(times[0:]),
color=colours[i], label=label,
linestyle=linestyles['line'][i],
linewidth=2
)
return None
def plot_error(spread):
"""Plot the error of either the edges or radius of a line."""
def draw_error_line(spread):
mean = np.array(get_line(spread, _type, error=False))
std = np.array(get_line(spread, _type, error=True))
# If not standard deviation desired, calculate std error
if args.std:
error = std
else:
error = (std / np.sqrt(spread.spread['num']))*args.sigma
plot_line(
line=(mean + error),
domain=spread.times,
color=colours[i],
linestyle=linestyles['error'][i]
)
plot_line(
line=(mean - error),
domain=spread.times,
color=colours[i],
linestyle=linestyles['error'][i]
)
return None
for _type in plot_type:
draw_error_line(spread)
return None
def get_line(spread, _type, error=False):
"""Return a desired line to plot."""
_value = 'val'
if error:
_value = 'std'
return spread.spread[_type][_value]
def get_scaling(input_time, input_radius,
num_factors, default=1.0):
"""Get scaling factors for time and radii of all lines."""
scaling = {}
input_factors = {'time': input_time, 'radius': input_radius}
for key in ['time', 'radius']:
scaling[key] = []
for i in range(0, num_factors):
if i < len(input_factors[key]):
scaling[key].append(input_factors[key][i])
else:
scaling[key].append(default)
return scaling
def apply_scaling(spread, all_data, scaling, num):
"""Apply time and radius scaling onto all spread data."""
spread.scale_data(scaling['time'][num], scaling['radius'][num])
for i, _ in enumerate(all_data):
all_data[i].scale_data(scaling['time'][num], scaling['radius'][num])
return None
# Get colours, labels and line styles from default
colours = get_colours(args.colour, len(args.spreading))
labels, draw_legend = get_labels(args.label, len(args.spreading))
linestyles = {}
linestyles['line'] = get_linestyles(args.linestyle, len(args.spreading))
linestyles['error'] = get_linestyles(args.errorstyle, len(args.spreading),
'dashed')
# Find scaling factors for lines
scaling = get_scaling(args.time_scaling, args.radius,
len(args.spreading))
# Find shift array for synchronisation
shift_array = get_shift(args.spreading, sync=args.sync,
radius_array=scaling['radius'], radius_fraction=args.sync_radius_fraction)
# Initiate xvg data
xvgdata = []
for i, spread_list in enumerate(args.spreading):
spread, data = combine_spread(spread_list, shift=shift_array[i])
apply_scaling(spread, data, scaling, i)
# Either draw all or a combined line; set which set here
xvg_set = []
if args.nomean:
spread_array = data
else:
spread_array = [spread]
label = labels[i]
for spread_data in spread_array:
plot_data(spread_data.spread, spread_data.times)
label = '_nolegend_'
if args.xvg:
add_xvgdata(spread_data, xvg_set)
# If error for line is desired, calculate and plot
if args.error:
plot_error(spread)
# Add set of xvg data to array
if args.xvg:
xvgdata.append(xvg_set)
plt.title(args.title, fontsize='medium')
plt.xlabel(args.xlabel, fontsize='medium')
plt.ylabel(args.ylabel, fontsize='medium')
if args.loglog:
plt.xscale('log')
plt.yscale('log')
plt.axis('normal')
plt.xlim([args.t0, args.tend])
if draw_legend:
plt.legend(loc=args.legend_loc)
# Finish by saving and / or showing
if args.save:
plt.savefig(
args.save,
dpi=args.dpi,
transparent=args.transparent,
bbox_inches='tight'
)
if args.xvg:
save_xvgdata(xvgdata)
if args.show:
plt.show()
return None