def __init__(self, *args, **kwargs):
"""Identical to Slider.__init__, except for the "increment" kwarg.
"increment" specifies the step size that the slider will be discritized
to."""
self.inc = kwargs.pop('increment', 0.5)
self.discrete_val = round(kwargs['valinit'] / self.inc) * self.inc
Slider.__init__(self, *args, **kwargs)
def loadFile(self, filename):
self.filename = filename
sms_openSF(filename, self.sh)
sr = self.sh.iSamplingRate
print "maxbin before: ", self.maxFreq * (self.sizeSpec*2) / sr
self.maxBin = sms_power2(self.maxFreq * (self.sizeSpec*2) / sr)
self.peakParams.iSamplingRate = sr
self.maxFreq = self.maxBin * sr / (self.sizeSpec*2)
self.peakParams.fHighestFreq = self.maxFreq
print "maxbin after: ", self.maxBin
print "maxfreq after: ", self.maxFreq
self.specEnv = zeros(self.maxBin)
# set up time slider
nSeconds = self.sh.nSamples / float(sr)
axcolor = 'lightgoldenrodyellow'
self.axtime = axes([0.2, 0.15, 0.65, 0.03], axisbg=axcolor)
self.axorder = axes([0.2, 0.10, 0.65, 0.03], axisbg=axcolor)
self.axlambda = axes([0.2, 0.05, 0.65, 0.03], axisbg=axcolor)
self.stime = Slider(self.axtime, 'Time (seconds)', 0., nSeconds, valinit=0.05)
self.stime.on_changed(self.updateFrame)
self.sorder = Slider(self.axorder, 'Order (p)', 0., 100, valinit=20, valfmt='%d')
self.sorder.on_changed(self.updateOrder)
self.slambda = Slider(self.axlambda, 'lambda (power)', -10., -2, valinit=-5)
self.slambda.on_changed(self.updateLambda)
def plot_spin_lattice(spin_array, observables):
"""
Shows the spin_array for all temperature values.
"""
T_range = observables.T_range
fig = plt.figure(figsize=(4.5, 5))
ax = fig.add_subplot(111)
plt.subplots_adjust(bottom=0.12, top=1)
ax.set_title('$\\rm{\\bf Spin\,Lattice:}\;T= %.3f\,\\rm [K]$' % (T_range[-1]),
fontsize=14, loc=('center'))
im = ax.imshow(spin_array[:,:,-1], origin='lower', interpolation='none')
slider_ax = plt.axes([0.2, 0.06, 0.6, 0.03], axisbg='#7F0000')
spin_slider = Slider(slider_ax, '', 0, len(T_range)-1, len(T_range)-1,
valfmt ='%u', facecolor='#00007F')
def update(val):
i = int(val)
ax.set_title('$\\rm{\\bf Spin\,Lattice:}\;T= %.3f\,\\rm [K]$'
% (T_range[i]), fontsize=14, loc=('center'))
im.set_array(spin_array[:,:,i])
spin_slider.on_changed(update)
plt.annotate('Temperature Slider', xy=(0.32,0.025), xycoords='figure fraction', fontsize=12)
plt.show()
def showimages(img1, img2, pathtosave):
def press(event):
sys.stdout.flush()
if event.key == 'escape':
sys.exit(0)
elif event.key == ' ':
plt.savefig(os.path.join(pathtosave, 'overlay.pdf'), bbox_inches='tight')
print 'saved'
fig, ax = plt.subplots()
fig.canvas.mpl_connect('key_press_event', press)
plt.subplots_adjust(0.15, 0.1, 0.9, 0.98)
im = ax.imshow(img1)
axcolor = 'lightgoldenrodyellow'
BAR_HEIGHT = 0.03
axalpha = plt.axes([0.2, 0.2 * BAR_HEIGHT, 0.7, BAR_HEIGHT], axisbg = axcolor)
# axmax = plt.axes([0.2, BAR_HEIGHT + 0.4 * BAR_HEIGHT, 0.7, BAR_HEIGHT], axisbg = axcolor)
salpha = Slider(axalpha, 'Alpha', 0.0, 1.0, valinit = 1.0)
def update(event):
curralpha = salpha.val
ax.hold(False)
ax.imshow(img1, alpha = curralpha)
ax.hold(True)
ax.imshow(img2, alpha = 1 - curralpha)
plt.draw()
return curralpha
salpha.on_changed(update)
plt.show()
def plotter():
'''
This process is supposed to handle the graphs.
Not pretty at the moment... but then matplotlib never is.
'''
signal.signal(signal.SIGINT, signal.SIG_IGN) # Ignore keyboard interrupt signal, parent process will handle.
waterfall_size = 150 # This makes it about 75 seconds in theory. Drawing the graph sometimes takes a bit longer.
fig = plt.figure(figsize=(20,15))
plt.subplots_adjust(left = 0.1, bottom = 0.25)
ax = plt.subplot(1, 1, 1)
line_lcp, = ax.plot([], [], 'bo', lw=1)
line_rcp, = ax.plot([], [], 'ro', lw=1)
ax.set_xlim(0,400)
vav_data_lcp = collections.deque(maxlen = waterfall_size)
vav_data_rcp = collections.deque(maxlen = waterfall_size)
slider_ax = plt.axes([0.25, 0.1, 0.65, 0.03])
video_average_length_slider = Slider(slider_ax, 'VAv', 1, waterfall_size, valinit=video_average_length.value)
def update(val):
video_average_length.value = int(video_average_length_slider.val)
fig.canvas.draw_idle()
video_average_length_slider.on_changed(update)
def init():
x = np.zeros(data_width)
y = np.zeros(data_width)
line_lcp.set_data(x,y)
line_rcp.set_data(x,y)
return line,
def animate(*args):
if script_run.value != 1:
sys.exit()
x = np.arange(0, 400, 400.0 / 1024.0)
vav_data_lcp.appendleft(data_stream_1[:])
vav_data_rcp.appendleft(data_stream_2[:])
lcp = np.zeros(data_width)
rcp = np.zeros(data_width)
for i in range(video_average_length.value):
if i < len(vav_data):
lcp += np.array(vav_data_lcp[i])
rcp += np.array(vav_data_rcp[i])
lcp /= video_average_length.value
rcp /= video_average_length.value
graph_max = 0
if lcp.max() > rcp.max():
graph_max = lcp.max()
else:
graph_max = rcp.max()
ax.set_ylim(0,graph_max + 1)
line_lcp.set_data(x,lcp)
line_rcp.set_data(x.rcp)
return line,
# Set the animation off to a start...
anim = animation.FuncAnimation(fig, animate, init_func=init, blit=True, interval=500)
plt.show()
print 'plotter process finished.'
class SinSlider():
pi = 3.14159
def __init__(self, num):
self.init_plot(num)
self.init_slider(num)
def init_plot(self, num):
pylab.subplot(111)
pylab.subplots_adjust(bottom = 0.25)
pylab.axis([0.0, 2 * self.pi, -1.0, 1.0])
pylab.title("y = sin(num * x)")
pylab.xlabel("x")
pylab.ylabel("y")
x, y = self.calc_xy(num)
self.plot, = pylab.plot(x, y) # comma after 'self.plot'
def init_slider(self, num):
slider_axes = pylab.axes([0.1, 0.1, 0.8, 0.05]) # left, bottom, width, height
self.slider = Slider(slider_axes, 'num', 0.0, 4.0, valinit = num)
self.slider.on_changed(self.update)
def update(self, num):
_, new_y = self.calc_xy(num)
self.plot.set_ydata(new_y)
pylab.draw()
def calc_xy(self, num):
start = 0.0
stop = 2 * self.pi
step = 0.01
x = pylab.arange(start, stop, step)
y = pylab.sin(num * x)
return x, y
def preparePlot(shapeModeler):
global sliders, mainPlot, fig
fig, ax = plt.subplots();
whiteSpace = 0.15 + numParams*0.05;
plt.subplots_adjust( bottom=whiteSpace);
plt.axis('equal');
#plot of initial shape
params = np.zeros((numParams,1));
shape = shapeModeler.makeShape(params);
shape = ShapeModeler.normaliseShape(shape);
numPointsInShape = len(shape)/2;
x_shape = shape[0:numPointsInShape];
y_shape = shape[numPointsInShape:];
mainPlot, = plt.plot(x_shape, -y_shape);
plt.axis([-1, 1, -1, 1],autoscale_on=False, aspect='equal');
#add sliders to modify parameter values
parameterVariances = shapeModeler.getParameterVariances();
sliders = [0]*numParams;
for i in range(numParams):
slider = Slider(plt.axes([0.25, 0.1+0.05*(numParams-i-1), 0.65, 0.03], axisbg=axcolor),
'Parameter '+str(i+1), -5*parameterVariances[i], 5*parameterVariances[i], valinit=0);
slider.on_changed(update);
sliders[i] = slider;
resetax = plt.axes([0.8, 0.025, 0.1, 0.04])
button = Button(resetax, 'Reset', color=axcolor, hovercolor='0.975')
button.on_clicked(reset)
plt.show()
def mplot(func,x,**kwargs):
num_params = len(kwargs)
fig = plt.figure()
main_ax = fig.add_subplot(111)
fig.subplots_adjust(bottom=bottom_pad + (num_params+1)*per_slider)
param_vals = dict((param_name,(lo+hi)/2) for param_name, (lo,hi) in kwargs.items())
y = func(x,**param_vals)
l, = main_ax.plot(x,y)
def update(*args):
for param_name, slider in zip(param_vals,sliders):
param_vals[param_name] = slider.val
vals = func(x,**param_vals)
l.set_ydata(vals)
# using autoscale_view makes the axes shrink *and* grow
#main_ax.relim()
#main_ax.autoscale_view()
# setting ylim this way only lets the axes grow
ymin, ymax = main_ax.get_ylim()
main_ax.set_ylim(min(vals.min(),ymin),max(ymax,vals.max()))
fig.canvas.draw()
sliders = []
for idx, (param_name, (lo,hi)) in enumerate(kwargs.items()):
ax = fig.add_axes([0.25,bottom_pad+per_slider*idx,0.65,3/5*per_slider],axisbg=bgcolor)
slider = Slider(ax, param_name, lo, hi, valinit=param_vals[param_name])
slider.on_changed(update)
sliders.append(slider)
plt.axes(main_ax)
def from_partial(plot_func,**kwargs):
num_params = len(kwargs)
fig = plt.figure()
main_ax = fig.add_subplot(111)
fig.subplots_adjust(bottom=bottom_pad + (num_params+1)*per_slider)
param_vals = dict((param_name,(lo+hi)/2) for param_name, (lo,hi) in kwargs.items())
plot_func = partial(plot_func,main_ax)
plot_func(param_vals)
def update(*args):
for param_name, slider in zip(param_vals,sliders):
param_vals[param_name] = slider.val
main_ax.cla()
plot_func(param_vals)
# using autoscale_view makes the axes shrink *and* grow
main_ax.relim()
main_ax.autoscale_view()
fig.canvas.draw()
sliders = []
for idx, (param_name, (lo,hi)) in enumerate(kwargs.items()):
ax = fig.add_axes([0.25,bottom_pad+per_slider*idx,0.65,3/5*per_slider],axisbg=bgcolor)
slider = Slider(ax, param_name, lo, hi, valinit=param_vals[param_name])
slider.on_changed(update)
sliders.append(slider)
plt.axes(main_ax)
class ChangingPlot(object):
"""
Gives a pyplot object with a slider that shows the complex roots of
the truncated power series for the number of terms on the slider.
"""
def __init__(self,poly,NUMTERMS):
self.sols,self.NUMTERMS = solLists(poly,NUMTERMS)
self.windowBounds = minmax(self.sols)
self.inc = 1.0
self.fig, self.ax = plt.subplots()
self.sliderax = self.fig.add_axes([0.2, 0.02, 0.6, 0.03],
axisbg='yellow')
self.slider = Slider(self.sliderax, 'Value', 0, self.NUMTERMS-3, valinit=self.inc)
self.slider.on_changed(self.update)
self.slider.drawon = False
self.dot, = self.ax.plot(self.sols[0][0],self.sols[0][1], 'bo')
self.ax.axis(self.windowBounds)
def update(self, value):
value = int(value)
self.dot.set_data(self.sols[value][0],self.sols[value][1])
self.slider.valtext.set_text('{}'.format(value))
self.fig.canvas.draw()
def show(self):
plt.show()
def param_gui(letter_name, shapeModeler):
global sliders, mainPlot, fig, pca_params
fig, ax = plt.subplots()
whiteSpace = 0.15 + num_params*0.05
plt.subplots_adjust( bottom=whiteSpace)
plt.axis('equal')
#plot of initial shape
params = np.zeros((num_params,1))
shape = shapeModeler.makeShape(params)
shape = ShapeModeler.normaliseShape(shape)
numPointsInShape = len(shape)/2
x_shape = shape[0:numPointsInShape]
y_shape = shape[numPointsInShape:]
mainPlot, = plt.plot(x_shape, -y_shape)
plt.axis([-1, 1, -1, 1],autoscale_on=False, aspect='equal')
plt.title(letter_name)
#add sliders to modify parameter values
parameterVariances = shapeModeler.getParameterVariances()
sliders = [0]*num_params
for i in range(num_params):
slider = Slider(plt.axes([0.25, 0.1+0.05*(num_params-i-1), 0.65, 0.03], axisbg=axcolor),
'Parameter '+str(i+1), -5*parameterVariances[i], 5*parameterVariances[i], valinit=0)
slider.on_changed(partial(update, shapeModeler))
sliders[i] = slider
resetax = plt.axes([0.8, 0.025, 0.1, 0.04])
button = Button(resetax, 'Reset', color=axcolor, hovercolor='0.975')
button.on_clicked(reset)
plt.show()
return pca_params
class slider():
def __init__(self,res):
self.res=res
def slider_bar(self,res):
#setupthe slider
axcolor = 'lightgoldenrodyellow'
self.axtime = plt.axes([0.1, 0.05, 0.8, 0.03], axisbg=axcolor)
self.stime = Slider(self.axtime, 'Timestep', 0, len(res.resobj.fils.fid.dimensions['Time']), valinit=0)
def update(val,res):
t = self.stime.val
res.refresh_plot(t)
self.stime.on_changed(update(self,res))
def foward_button(self,res):
self.fwdax = plt.axes([0.1, 0.1, 0.1, 0.04])
self.fwdb = Button(self.fwdax, 'forward', color='lightgoldenrodyellow', hovercolor='0.975')
self.fwdb.on_clicked(slider.update(res.resobj.timestep-1,res))
def iplot_spectrum_ds(ds, init = True,
sigmarng = [0.05, 1.5], taurng = [0,4], **kwargs):
"""
Plots spectrum from TlacDatSet interactively using matplotlib.
NOT FINISHED >> see tlac_web instead
Keyword Arguments:
ds -- TlacDatSet instance to plot
init --- If true (default) plot will be initialized first
sigmarng -- Range for intrinsic spectrum width. Measured in
units of the actual sigma_i (default [0,1.5])
taurng -- Range for dust optical depth tau_d (default [0, 4])
**kwargs -- Will be passes to `tlac_analysis.plot_spectrum`
"""
if(not isinstance(ds, TlacDatSet)):
raise ValueError("ds has to be a TlacDatSet instance")
dat = ds['Lya','x']
sigmar = ds.header['emission', 'frequency_param' ]
if(init):
plot_init()
plt.gcf().subplots_adjust(top = 0.95, bottom = 0.05)
plot_spectrum(dat, np.ones(len(dat)), **kwargs)
fig = plt.gcf()
ax = fig.axes[0]
line = ax.lines[-1]
nbins = len(line.get_xdata())
bm = fig.subplotpars.bottom
fig.subplots_adjust(bottom = bm + 0.04)
axsigma = plt.axes([0.2, bm - 0.03, 0.65, 0.03])
ssigma = Slider(axsigma, r"$\sigma_i$", sigmarng[0] * sigmar,
sigmarng[1] * sigmar, valinit=sigmar)
def update(val):
sigma = ssigma.val
w = tlac_weights(ds, sigma, 0)
x,y = plot_spectrum(dat, w, plot = False, **kwargs)
line.set_xdata(x)
line.set_ydata(y)
ymax = ax.get_ylim()[1]
if(np.max(y) > 1.1 * ymax):
ax.set_ylim(ymax = 1.5 * ymax)
elif(np.max(y) < 0.5 * ymax):
ax.set_ylim(ymax = 0.5 * ymax)
fig.canvas.draw_idle()
ssigma.on_changed(update)
# change current axis back
plt.sca(ax)
plt.show()
# have to return ref to slider. otherwise unresponsive!
return fig, ax, ssigma
def __init__(self, image, low, high):
self.image_name = image
self.low = low
self.high = high
self.filter = None
self.output = None
self.filter_type = None
self.padRows = None
self.padCols = None
original_input = cv2.imread(image,0)
rows, cols = original_input.shape
if(rows < cols):
original_input = cv2.transpose(original_input)
self.transposed = True
else:
self.transposed = False
rows, cols = original_input.shape
optimalRows = cv2.getOptimalDFTSize(rows)
optimalCols = cv2.getOptimalDFTSize(cols)
self.padRows = optimalRows - rows
self.padCols = optimalCols - cols
self.input = np.zeros((optimalRows,optimalCols))
self.input[:rows,:cols] = original_input
self.dftshift = get_dft_shift(self.input)
plt.subplots_adjust(left=0, bottom=0.05, right=1, top=1, wspace=0, hspace=0)
plt.subplot(131)
plt.axis('off')
plt.title('original image')
plt.imshow(self.input, cmap = 'gray',interpolation='nearest')
self.axslow = plt.axes([0.05, 0.01, 0.5, 0.02])
self.slow = Slider(self.axslow, 'low', 0.01, 1, valinit=self.low)
self.slow.on_changed(self.updateLow)
self.axhigh = plt.axes([0.05, 0.03, 0.5, 0.02])
self.shigh = Slider(self.axhigh, 'high', 0.01, 1, valinit=self.high)
self.shigh.on_changed(self.updateHigh)
self.slow.slidermax=self.shigh
self.shigh.slidermin=self.slow
self.axfilter = plt.axes([0.62, 0.01, 0.15, 0.04])
self.rfilter = RadioButtons(self.axfilter, ('Gaussian Filter', 'Ideal Filter'))
self.rfilter.on_clicked(self.updateFilterType)
self.filter_type = self.rfilter.value_selected
self.axprocess = plt.axes([0.8, 0.01, 0.08, 0.04])
self.bprocess = Button(self.axprocess, 'Process')
self.bprocess.on_clicked(self.process)
self.axsave = plt.axes([0.88, 0.01, 0.08, 0.04])
self.bsave = Button(self.axsave, 'Save')
self.bsave.on_clicked(self.save)
def plotInteractive( data ):
ax = plt.subplot(111)
plt.subplots_adjust(bottom=0.25)
t = sorted(data.keys())
pl = plt.scatter([0],[0],s=10,linewidths=(0,0,0))
plt.axis([0, 2, 0, 2])
axTime = plt.axes([0.25, 0.1, 0.65, 0.03])
sTime = Slider(axTime, 'Time', min(t), max(t), valinit=min(t))
def updateTime(val):
t0 = sTime.val
dt = abs(np.array(t)-t0)
t_in = t[dt.argmin()]
px = getpx(data,t_in)
pv = getpv(data,t_in)
pl.set_offsets(px)
pl.set_array(pv)
plt.draw()
updateTime(min(t))
sTime.on_changed(updateTime)
plt.show(block=False)
def vis(gt,f,est=False,title=False):
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider #, Button, RadioButtons
from matplotlib.patches import Ellipse
fig = plt.figure()
if title :
fig.suptitle(title, fontsize=14, fontweight='bold')
ax = plt.subplot(111, aspect='equal')
fig.subplots_adjust(left=0.25, bottom=0.25)
ax.clear()
axcolor = 'lightgoldenrodyellow'
ax2 = fig.add_axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor)
def update(val):
val=int(val)
ax.clear()
loc=find_locs(f[val])
if est is not False:
p=np.random.permutation(est[val].max()+1)
p2=np.random.permutation(gt[val].max()+1)
calc_distance_vis(loc,f[val],p[est[val]],3500,ax)
ax.scatter(f[val][:,1],f[val][:,2], c=p2[gt[val]],vmin=0, vmax=gt[val].max(),s=100)
update(0)
slider = Slider(ax2, 'Frame', 0, gt.shape[0] - 1,
valinit=0, valfmt='%i')
slider.on_changed(update)
plt.show()
def _create_controls(self):
self._freq_ax = plt.axes([0.2, 0.19, 0.2, 0.03])
self._freq_slider = Slider(self._freq_ax,
'Frequency',
0,
self.samplerate / 2.0,
valinit = self.frequency)
self._freq_slider.on_changed(self.set_signal_frequency)
self._ampl_ax = plt.axes([0.2, 0.1, 0.2, 0.03])
self._ampl_slider = Slider(self._ampl_ax,
'Amplitude',
-100,
0,
valinit = dcv.lin2db(self.amplitude))
self._ampl_slider.on_changed(self.set_signal_amplitude)
self._signaltype_ax = plt.axes([0.5, 0.05, 0.15, 0.20])
self._signaltype_radio = RadioButtons(self._signaltype_ax,
('Sine', 'Square', 'Sawtooth',
'Triangle', 'Noise', 'Constant'))
self._signaltype_radio.on_clicked(self.set_signal_type)
self._windowtype_ax = plt.axes([0.7, 0.05, 0.15, 0.20])
self._windowtype_radio = RadioButtons(self._windowtype_ax,
('Flat', 'Hanning', 'Hamming', 'Blackman'))
self._windowtype_radio.on_clicked(self.set_window_type)
class ChangingPlot(object):
def __init__(self):
data = np.genfromtxt('AR.csv', dtype=None, delimiter=',', skip_header=1)
[aa,bb]=data.shape
self.bb=int(bb)
self.freq=data[:,0]
self.AR_sim=data[:,1]
# change this for the stepsize
self.inc = 1.0
self.fig, self.ax = plt.subplots()
self.sliderax = self.fig.add_axes([0.2, 0.02, 0.6, 0.03], axisbg='yellow')
self.slider = Slider(self.sliderax, 'Value', 0, self.bb, valinit=self.inc)
self.slider.on_changed(self.update)
self.slider.drawon = False
self.dot, = self.ax.plot(self.freq, self.AR_sim)
self.ax.axhline(y=3,linestyle='-.',color='b',linewidth=0.5)
def update(self, value):
value = int(value / self.inc) * self.inc
data = np.genfromtxt('AR.csv', dtype=None, delimiter=',', skip_header=1)
[aa,bb]=data.shape
self.freq=data[:,0]
self.AR_sim=data[:,[value]]
self.dot.set_data([self.freq,self.AR_sim])
self.slider.valtext.set_text('{}'.format(value))
self.fig.canvas.draw()
def show(self):
plt.show()
def getBubbleChart(d): def generateX(): return np.repeat(np.arange(len(d.index.values)),len(d.index.values)) def generateY(): return np.tile(np.arange(len(d.index.values)),len(d.index.values)) fig, ax = plt.subplots() plt.subplots_adjust(left=0.25, bottom=0.25) l = plt.scatter(generateX(),generateY(),s=d*50) basic_sizes = l._sizes plt.xticks(np.arange(0, len(d), 1.0),d.index.values,ha='right', rotation=45) plt.yticks(np.arange(0, len(d), 1.0),d.index.values) plt.grid() axcolor = 'lightgoldenrodyellow' axsize = plt.axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor) ssize = Slider(axsize, 'Size', 1, 20, valinit=50) def update(val): new_coef = ssize.val/50 new_sizes = [x * new_coef for x in basic_sizes] l._sizes = new_sizes fig.canvas.draw_idle() ssize.on_changed(update) plt.show()
def plot_fits(self, X, X_pred, plot_preds = True):
self.plot_preds = plot_preds
import matplotlib
self.colors = ['r', 'g', 'b']
more_colors = matplotlib.colors.cnames.keys()
shuffle(more_colors)
# print self.colors
# print more_colors
self.colors.extend(more_colors)
self.trial_groups = self.split_trial_groups()
self.X = X
self.X_pred = X_pred
# set-up the plot window
self.fig, self.ax = plt.subplots(figsize=(12,8))
plt.subplots_adjust(bottom=0.25)
# make sliders
axcolor = 'lightgoldenrodyellow'
self.axtrial = plt.axes([0.25, 0.05, 0.65, 0.03], axisbg=axcolor)
self.axspot = plt.axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor)
self.axclass = plt.axes([0.25, 0.15, 0.65, 0.03], axisbg=axcolor)
# need to update to find the number of classes, trial_groups
self.strial = Slider(self.axtrial, 'Trial', 0, self.n_trial_groups, valinit=0)
self.sspot = Slider(self.axspot, 'Spot', 1, len(self.column_headers), valinit=1)
self.sclass = Slider(self.axclass, 'Class', 0, len(self.groups), valinit=0)
self.strial.on_changed(self.update_fits)
self.sspot.on_changed(self.update_fits)
self.sclass.on_changed(self.update_fits)
self.plot_fit(spot=1, group=0, trial=0, averages=self.averages)
plt.show()
def __init__(self, *args, **kwargs):
"""Identical to Slider.__init__, except for the "increment" kwarg.
"increment" specifies the step size that the slider will be discritized
to."""
self.inc = kwargs.pop("increment", 1.0)
Slider.__init__(self, *args, **kwargs)
self.dval = int(self.val + 0.5)
def cal_threshold(image, tr):
'''
shows the before and after for thresholding, where the threshold can be set
by a slider
'''
assert image.ndim ==2, 'This is not a single-channel image! Use single-channel images'
im = image.astype('uint8')
#create the axes for the slider
axcolor = 'teal'
ax1 = plt.axes([.15,.2,.65,.03],axisbg=axcolor)
#create the slider
s1 = Slider(ax1, 'Threshold', 0, 255, valinit=tr)
#actual thresholding: compare each pixel in the image to the threshold
trim = im > tr
plt.subplot(221),plt.imshow(im),plt.title('Original')
plt.subplot(222),plt.imshow(trim),plt.title('After thresholding')
def update(val):
vtr = s1.val
trim = im > vtr
plt.subplot(222),plt.imshow(trim),plt.title('After thresholding')
s1.on_changed(update)
plt.show()
#trim is a binary image - convert it to full colorscale by multiplying with
#255
return trim*255, s1.val
def cube_show_slider(cube, axis=2, **kwargs):
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider, Button, RadioButtons
# check dim
if not cube.ndim == 3:
raise ValueError("cube should be an ndarray with ndim == 3")
# generate figure
fig = plt.figure()
ax = plt.subplot(111)
fig.subplots_adjust(left=0.25, bottom=0.25)
# select first image
s = [slice(0, 1) if i == axis else slice(None) for i in xrange(3)]
im = cube[s].squeeze()
# display image
l = ax.imshow(im, **kwargs)
axcolor = 'lightgoldenrodyellow'
ax = fig.add_axes([0.25, 0.1, 0.65, 0.03], axisbg=axcolor)
slider = Slider(ax, 'Axis %i index' % axis, 0, cube.shape[axis] - 1,
valinit=0, valfmt='%i')
def update(val):
ind = int(slider.val)
s = [slice(ind, ind + 1) if i == axis else slice(None) for i in xrange(3)]
im = cube[s].squeeze()
l.set_data(im, **kwargs)
fig.canvas.draw()
slider.on_changed(update)
plt.show()
def create_sliders(self): for i, name in enumerate(self.names): dim = self.def_dim + i * self.del_dim axes = self.f.add_axes(dim, axisbg = self.axcolor) slider = Slider(axes, name, 0, 10, valinit=1) slider.on_changed(self.update) self.cont_of_slid[name] = (axes, slider)
def initUI(self):
self.fig, self.ax = plt.subplots()
self.fig.canvas.set_window_title('Numerik DGL 2 - Schattenprojektion')
self.fig.suptitle('Vorwaertsproblem')
plt.subplots_adjust(bottom=0.3)
plt.axis([0, 200, -100, 100])
plt.axis('equal')
axColor = 'lightgoldenrodyellow'
# Slider - Phi
axPhi = plt.axes([0.18, 0.2, 0.65, 0.03], axisbg=axColor)
self.sliderPhi = Slider(axPhi, 'Phi', 0, 360, valinit=self.phi, valfmt='%1d')
self.sliderPhi.on_changed(self.onUpdate)
# Slider - Delta Phi
axDeltaPhi = plt.axes([0.18, 0.15, 0.65, 0.03], axisbg=axColor)
self.sliderDeltaPhi = Slider(axDeltaPhi, 'Delta Phi', 5, 360, valinit=self.delta_phi, valfmt='%1d')
self.sliderDeltaPhi.on_changed(self.onUpdate)
# Slider - Psi
axPsi = plt.axes([0.18, 0.1, 0.65, 0.03], axisbg=axColor)
self.sliderPsi = Slider(axPsi, 'Psi', 0, 180, valinit=self.psi, valfmt='%1d')
self.sliderPsi.on_changed(self.onUpdate)
# Button - Previous
axPrev = plt.axes([0.18, 0.03, 0.1, 0.05])
self.buttonPrev = Button(axPrev, 'Previous')
self.buttonPrev.on_clicked(self.onPrevious)
# Button - Next
axNext = plt.axes([0.29, 0.03, 0.1, 0.05])
self.buttonNext = Button(axNext, 'Next')
self.buttonNext.on_clicked(self.onNext)
# Button - Reset
axReset = plt.axes([0.73, 0.03, 0.1, 0.05])
self.buttonReset = Button(axReset, 'Reset')
self.buttonReset.on_clicked(self.onReset)
self.onDraw()
class Explorer(object):
"""A simple interactive slicer that "pans" a series of 2D slices along a
given axis of a 3D volume. Additional kwargs are passed to "imshow"."""
def __init__(self, data, axis=2, **kwargs):
self.data = data
self.axis = axis
self.start, self.stop = 0, data.shape[self.axis] - 1
kwargs['cmap'] = kwargs.get('cmap', 'gray_r')
self.fig, self.ax = plt.subplots()
self.im = self.ax.imshow(self[self.start], **kwargs)
self.ax.axis('off')
self.sliderax = self.fig.add_axes([0.2, 0.02, 0.6, 0.03])
self.slider = Slider(self.sliderax, 'Z-slice', self.start, self.stop,
valinit=self.start, valfmt='%i')
self.slider.on_changed(self.update)
def __getitem__(self, i):
slices = self.data.ndim * [slice(None)]
slices[self.axis] = i
return self.data[slices].swapaxes(0, 1)
def update(self, val):
dat = self[int(val)]
self.im.set(data=dat, clim=[dat.min(), dat.max()])
self.fig.canvas.draw()
def show(self):
plt.show()
def init():
""" Set up the initial conditions """
# Sets up initial dimensions
M.figure(figsize=(8,8))
density=N.loadtxt(os.path.join(sys.path[0], './densmesh.txt'))
# Real Fourier transform of "density"
density_k = N.fft.rfftn(density*1e3) # 1e3 to enhance contrast
global psi
psi = zeldovich(density_k)
# Zel'dovich displacement field
global scale
global slider_scale
scale = 1.0
slider_scale = 50.0
axcolor = 'lightgoldenrodyellow'
axScale = plt.axes([0.15, 0.1, 0.7, 0.03], axisbg=axcolor)
slider_scale = Slider(axScale, 'Scale', 0.0, 50.0, 1.0)
slider_scale.on_changed(update)
# Attempting to removed axes from the graph
plt.axes([0.15, 0.15, 0.7, 0.7])
plt.xticks([])
plt.yticks([])
return density_k, psi
def run(self):
for varname,range in self.ranges.iteritems():
if range is None:
raise ValueError("no range specified for slider %s." % varname)
def update(val):
d = dict([(k, self.sliders[k].val) for k in self.sliders.keys()])
# pull members into current scope -> no self. in cutstring
vars = self.vars
weights = self.weights
basemask = self.basemask
# evaluate cutstring and combine with basemask
mask = basemask & eval(self.cutstring % d)
self.updatefunc(self, vars, weights, mask)
self.sliderfig = p.figure(figsize=(3,len(self.ranges)*.4))
self.sliders = dict()
space = .05
height = (1. - (len(self.ranges)+2)*space) / float(len(self.ranges))
for i,(varname,range) in enumerate(self.ranges.iteritems()):
ax = p.axes([0.25, 1-float(i+1)*(space+height), 0.5, height])
slider = Slider(ax, varname, range[0],range[1], valinit=(range[1]-range[0])/2.)
slider.on_changed(update)
self.sliders[varname] = slider
self.initfunc(self,self.vars,self.weights,self.basemask)
def interpolation(threshold, X_Smooth1, Smooth_Y_Coordinates):
Smooth_X_npy = np.asarray(X_Coordinates)
Smooth_Y_npy = np.asarray(Smooth_Y_Coordinates)
f = interp1d(Smooth_X_npy, Smooth_Y_npy, kind = "cubic" )
temp = f(X_Coordinates)
plt.close('all')
fig, ax = plt.subplots(5)
fig.suptitle("Neutron Imaging Curve Smoothing", fontsize="x-large")
ax[0] = plt.subplot2grid((6,7), (0,0), rowspan=2, colspan=3)
ax[0].plot(X_Coordinates, Y_Coordinates)
ax[0].set_title('Original Plot')
ax[1] = plt.subplot2grid((6,7), (3,0), rowspan=2, colspan=3)
ax[1].plot(X_Coordinates, beta_list, 'r.-')
ax[1].axhline(y=threshold, linewidth=1, color='k')
ax[1].set_title('Peak Plot', )
ax[2] = plt.subplot2grid((6,7), (0,4), rowspan=2, colspan=3)
ax[2].plot(X_Coordinates, Smooth_Y_Coordinates)
ax[2].set_title('Smoothed graph')
ax[3] = plt.subplot2grid((6,7), (3,4), rowspan=2, colspan=3)
ax[3].plot(X_Coordinates, f(X_Coordinates))
ax[3].set_title('Interpolated')
ax[4] = plt.subplot2grid((6,7), (5,0), colspan=7)
ax[4].set_position([0.25, 0.1, 0.65, 0.03])
thres = Slider(ax[4], 'Threshold', 0.000, 0.005, valinit = threshold, valfmt='%1.5f')
workbook = xlwt.Workbook(encoding='ascii')
sheet = workbook.add_sheet("Sheet")
sheet.write(0, 0, "(Raw-OB)/OB")
sheet.write(0, 1, "wavelength (angs)")
for i in range(len(X_Coordinates)):
sheet.write(i+1, 0, X_Coordinates[i])
sheet.write(i+1, 1, temp[i])
workbook.save(outputfile)
def update(val):
threshold = thres.val
print ("Threshold value: "), threshold
smoothing_Plot(total_Span, threshold)
fig.canvas.draw_idle()
thres.on_changed(update)
plt.show()
fig2, ax2 = plt.subplots(2)
ax2[0] = plt.subplot2grid((7,2), (0,0), rowspan=3, colspan=2)
ax2[0].plot(X_Coordinates, Y_Coordinates)
ax2[0].set_title('Original Plot')
for i in X_Smooth1:
plt.axvline(x = i, linewidth=1, color='k')
ax2[1] = plt.subplot2grid((7,2), (4,0), rowspan=3, colspan=2)
ax2[1].plot(X_Coordinates, f(X_Coordinates))
ax2[1].set_title('Interpolated')
for i in X_Smooth1:
plt.axvline(x = i, linewidth=1, color='k')
plt.show()
def __init__(self, image, dragging=True, **kwargs):
# init PointBrowser
super(FindCenters,self).__init__(image,[[None,None]],**kwargs);
self.axis.set_title('FitHexagonCenters: %s' % self.imginfo['desc']);
self.fig.subplots_adjust(bottom=0.2); # space for sliders
# add slider for neighborhood size
self.nbhd_size = 5; # neighborhood size
axNbhd = self.fig.add_axes([0.2, 0.05, 0.1, 0.04]);
self.sNbhd = Slider(axNbhd,'neighbors ',2,20,valinit=self.nbhd_size,\
valfmt=' (%d)',dragging=dragging);
self.sNbhd.on_changed(self.ChangeNeighborhood);
# add slider for number of points
self.num_points = 1e6; # number of local maxima to find
axNum = self.fig.add_axes([0.45, 0.05, 0.3, 0.04]);
self.sNum = Slider(axNum, 'points ',0,100,valinit=self.num_points,\
valfmt=' (%d)',dragging=dragging);
self.sNum.on_changed(self.ChangeMaxPoints);
# add buttons
axRefine = self.fig.add_axes([0.85, 0.7, 0.1, 0.04]);
self.bRefine = Button(axRefine,'Refine');
self.bRefine.on_clicked(self.RefineCenters);
# initial calculation of local maximas
self.ChangeNeighborhood(self.nbhd_size);
ax.set_title(filename + "; total frames: " + str(num_frames))
ax2 = fig.add_subplot(111)
ax2.autoscale(True)
ax3 = fig.add_subplot(111)
ax3.autoscale(True)
# plot first data set
frame = 0
ln, = ax.plot(xdata[frame:frame_size], ydata[frame:frame_size])
ln2, = ax2.plot(xdata[frame:frame_size], samples2[frame:frame_size])
ln3, = ax3.plot(xdata[frame:frame_size], samples3[frame:frame_size], 'ro')
axframe = plt.axes([0.25, 0.1, 0.65, 0.03])
sframe = Slider(axframe, 'Frame', 0, num_frames, valinit=0, valfmt='%d')
def update(val):
frame = numpy.floor(sframe.val)
start, end = int(frame * frame_size), int((frame + 1) * frame_size)
#print to_string(samples2[start:end])
print "FRAME", start, end
ln.set_xdata(xdata[start:end])
ln.set_ydata(ydata[start:end])
ln2.set_xdata(xdata[start:end])
ln2.set_ydata(samples2[start:end])
ln3.set_xdata(xdata[start:end])
ln3.set_ydata(samples3[start:end])
ax.relim()
ax.autoscale_view()
class Renderer:
def __init__(self, file_name, hide, n, interval=100, hide_widgets=False):
self.root = tkinter.Tk()
if not file_name:
file_name = askopenfilename(initialdir="output", title="Select param", filetypes=[
("param files", "*.param")])
self.file_name = file_name
X = pickle.load(open(file_name, 'rb'))
self.plotter = Plotter(X, hide, n)
self.interval = interval
self.hide_widgets = hide_widgets
def render(self):
print(f'drawing with {self.plotter.n} circles')
self.fig = Figure(figsize=(13, 13), dpi=100)
self.ax = self.fig.subplots()
self.root.wm_title(f"Render - {base_name(args.file_name, True)}")
canvas = FigureCanvasTkAgg(self.fig, master=self.root)
canvas.draw()
canvas.get_tk_widget().pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
if not self.hide_widgets:
rax = self.fig.add_axes([0.05, 0.0, 0.1, 0.1])
rax.axis('off')
self.check = CheckButtons(rax, ('hide',), (self.plotter.hide,))
self.check.on_clicked(lambda _: self.plotter.toggle_hide())
nax = self.fig.add_axes([0.2, 0.07, 0.7, 0.02])
self.nslider = Slider(nax, 'n', 2, self.plotter.frames,
valinit=self.plotter.n, valstep=1)
self.nslider.on_changed(self._update_n)
fpsax = self.fig.add_axes([0.2, 0.03, 0.7, 0.02])
self.fpsslider = Slider(fpsax, 'fps', 1, 50,
valinit=10, valstep=1)
self.fpsslider.on_changed(self._update_fps)
self._init_animation()
if args.save:
self.save(args.out)
else:
tkinter.mainloop()
def _init_animation(self):
self.animation = FuncAnimation(self.fig,
self.plotter.render_frame,
frames=range(self.plotter.frames),
interval=self.interval,
repeat_delay=1000,
init_func=partial(
self.plotter.init_frame, self.ax),
repeat=True)
def _update_fps(self, fps):
self.animation.event_source.stop()
self.interval = int(1000 / fps)
self._init_animation()
def _update_n(self, n):
self.animation.event_source.stop()
self.plotter = Plotter(self.plotter.X, self.plotter.hide, int(n))
self._init_animation()
def save(self, out_fname):
if not out_fname:
out_fname = f'output/{base_name(self.file_name)}.mp4'
print(f'saving to {out_fname}')
self.animation.save(
out_fname, writer=FFMpegWriter(fps=10, bitrate=1000))
#fig_manager = plot.get_current_fig_manager()
#if hasattr(fig_manager, 'window'):
# fig_manager.window.showMaximized()
#creation de l' "Axes" et ajustement de sa position
ax = fig.add_subplot(111)
ax2 = ax.twinx()
fig.subplots_adjust(left=0.1,right=0.6, bottom=0.25)
# création des Sliders
V_slider_ax = fig.add_axes([0.7, 0.25, 0.03, 0.65])
V_slider = VertSlider(V_slider_ax, "V0/E", -0.8, 2, valinit=0)
w_slider_ax = fig.add_axes([0.1, 0.1, 0.5, 0.03])
w_slider = Slider(w_slider_ax, 'width', 0.1, 5.0, valinit=w)
zoom_slider_ax = fig.add_axes([0.1, 0.05, 0.5, 0.03])
zoom_slider = Slider(zoom_slider_ax, 'zoom', 0.1, 2.0, valinit=zoom)
prec_slider_ax = fig.add_axes([0.8, 0.25, 0.03, 0.65])
prec_slider = VertSlider(prec_slider_ax, "precision", 1, 500, valinit=precision)
#configuration des events handlers
V_slider.on_changed(sliders_on_changed)
w_slider.on_changed(sliders_on_changed)
zoom_slider.on_changed(sliders_on_changed)
prec_slider.on_changed(sliders_on_changed)
# création du Bouton reset
reset_button_ax = fig.add_axes([0.7, 0.1, 0.1, 0.04])
reset_button = Button(reset_button_ax, 'Reset', color = axisColor, hovercolor='0.975')
class VideoViewer(object):
"""
A matplotlib-based video viewer.
Parameters
----------
video : list-like, iterator
A list of a tuple of 2D arrays or a generator of a tuple of 2D arrays.
If an iterator is provided, you must set 'n' as well.
n: int
Length of the video. When this is set it displays only first 'n' frames of the video.
id : int, optional
For multi-frame data specifies camera index.
title : str, optional
Plot title.
"""
def __init__(self, video, n=None, id=0, title=""):
if n is None:
try:
n = len(video)
except TypeError:
raise Exception("You must specify nframes!")
self.id = id
self.index = 0
self.video = video
self.fig, self.ax = plt.subplots()
self.ax.set_title(title)
plt.subplots_adjust(bottom=0.25)
frame = next(iter(video)) #take first frame
frame = self._prepare_image(frame)
self.img = self.ax.imshow(frame)
self.axframe = plt.axes([0.25, 0.1, 0.65, 0.03])
self.sframe = Slider(self.axframe,
'Frame',
0,
n - 1,
valinit=0,
valstep=1,
valfmt='%i')
def update(val):
i = int(self.sframe.val)
try:
frame = self.video[i] #assume list-like object
self.index = i
except TypeError:
#assume generator
frame = None
if i > self.index:
for frame in self.video:
self.index += 1
if self.index >= i:
break
if frame is not None:
frame = self._prepare_image(frame)
self.img.set_data(frame)
self.fig.canvas.draw_idle()
self.sframe.on_changed(update)
def _prepare_image(self, im):
if isinstance(im, tuple) or isinstance(im, list):
return im[self.id]
else:
return im
def show(self):
"""Shows video."""
plt.show()
fig, ax = plt.subplots()
plt.subplots_adjust(left=0.25, bottom=0.25)
t = np.arange(0.0, 1.0, 0.001)
a0 = 5
f0 = 3
delta_f = 5.0
s = a0 * np.sin(2 * np.pi * f0 * t)
l, = plt.plot(t, s, lw=2)
plt.axis([0, 1, -10, 10])
axcolor = 'lightgoldenrodyellow'
axfreq = plt.axes([0.25, 0.1, 0.65, 0.03], facecolor=axcolor)
axamp = plt.axes([0.25, 0.15, 0.65, 0.03], facecolor=axcolor)
sfreq = Slider(axfreq, 'Freq', 0.1, 30.0, valinit=f0, valstep=delta_f)
samp = Slider(axamp, 'Amp', 0.1, 10.0, valinit=a0)
def update(val):
amp = samp.val
freq = sfreq.val
l.set_ydata(amp*np.sin(2*np.pi*freq*t))
fig.canvas.draw_idle()
sfreq.on_changed(update)
samp.on_changed(update)
resetax = plt.axes([0.8, 0.025, 0.1, 0.04])
button = Button(resetax, 'Reset', color=axcolor, hovercolor='0.975')
ax.xaxis.set_ticks_position('bottom')
xMiddleLine = ax.axvline(xInitial, color="orange")
# Text boxes
# Function
axbox = plt.axes([0.125, 0.05, 0.8, 0.0400]) #left bottom width height
text_box = TextBox(axbox, 'Function', initial=initial_function)
# X Lower
axbox2 = plt.axes([0.180, 0.13, 0.2, 0.0400])
xMiddleBox = TextBox(axbox2, 'Initial X guess', initial=str(xInitial))
# Slider
# Iteration count
axbox4 = plt.axes([0.125, 0.21, 0.3, 0.0400])
iterSlider = Slider(axbox4,
'Iteration',
0,
10,
valinit=initial_iteration - 1,
valstep=1)
# Update iteration
def updateIteration(val):
# Get values from the slider
iteration = iterSlider.val
# Remove existing xMiddle
ax.lines[-1].remove()
# Get updated xMiddle
xMiddle = newRaph(float(xMiddleBox.text), iteration)
# Set the xMiddle
xMiddleLine = ax.axvline((xMiddle), color="Orange")
plt.draw()
class DoS():
"""
Definition of the density of state class
"""
def __init__(self,
bandarrays=None,
energies=None,
evals=None,
units='eV',
label='1',
sigma=0.2,
npts=2500,
fermi_level=None,
norm=1.0,
sdos=None,
e_min=None,
e_max=None):
"""
Extract a quantity which is associated to the DoS, that can be plotted
"""
import numpy as np
self.ens = []
self.labels = []
self.ef = None
# self.norms=[]
self.npts = npts
if e_min is not None:
self.e_min = e_min
else:
self.e_min = 1.e100
if e_max is not None:
self.e_max = e_max
else:
self.e_max = -1.e100
if bandarrays is not None:
self.append_from_bandarray(bandarrays, label)
if evals is not None:
self.append_from_dict(evals, label)
if energies is not None:
self.append(
np.array([energies]),
label=label,
units=units,
norm=(np.array([norm]) if isinstance(norm, float) else norm))
self.sigma = sigma
self.fermi_level(fermi_level, units=units)
if sdos is not None:
self._embed_sdos(sdos)
def _embed_sdos(self, sdos):
self.sdos = []
for i, xdos in enumerate(sdos):
self.sdos.append({'coord': xdos['coord']})
jdos = 0
for subspin in xdos['dos']:
if len(subspin[0]) == 0:
continue
d = {'doslist': subspin}
try:
self.ens[jdos]['sdos'].append(d)
except KeyError:
self.ens[jdos]['sdos'] = [d]
jdos += 1
def append_from_bandarray(self, bandarrays, label):
"""
Add a new band array to the previous DoS. Important for kpoints DOS
"""
import numpy as np
for jspin in range(2):
kptlists, lbl = _bandarray_to_data(jspin, bandarrays)
self.append(np.array(kptlists[0]),
label=label + lbl,
units='AU',
norm=np.array(kptlists[1]))
def append_from_dict(self, evals, label):
import numpy as np
"Get the energies from the different flavours given by the dict"
evs = [[], []]
ef = None
for ev in evals:
occ = self.get_ev(ev, ['e_occ', 'e_occupied'])
if occ:
ef = max(occ)
vrt = self.get_ev(ev, ['e_vrt', 'e_virt'])
eigen = False
if occ:
eigen = occ
if vrt:
eigen = vrt
if not eigen:
eigen = self.get_ev(ev)
if not occ and not vrt and eigen:
ef = max(eigen)
if not eigen:
continue
for i, e in enumerate(eigen):
if e:
evs[i].append(e)
for i, energs in enumerate(evs):
if len(energs) == 0:
continue
self.append(np.array(energs),
label=label,
units='AU',
norm=1.0 - 2.0 * i)
if ef:
self.fermi_level(ef, units='AU')
def get_ev(self, ev, keys=None):
"Get the correct list of the energies for this eigenvalue"
res = False
if keys is None:
ener = ev.get('e')
spin = ev.get('s')
if ener and spin == 1:
res = [ener]
elif ener and spin == -1:
res = [None, ener]
else:
for k in keys:
if k in ev:
res = ev[k]
if not isinstance(res, list):
res = [res]
break
return res
def append(self, energies, label=None, units='eV', norm=1.0):
if not isinstance(norm, float) and len(norm) == 0:
return
dos = self.conversion_factor(units) * energies
self.ens.append({'dos': DiracSuperposition(dos, wgts=norm)})
lbl = label if label is not None else str(len(self.labels) + 1)
self.labels.append(lbl)
# self.norms.append(norm)
self.range = self._set_range()
def conversion_factor(self, units):
if units == 'AU':
fac = AU_eV
elif units == 'eV':
fac = 1.0
else:
raise ValueError('Unrecognized units (' + units + ')')
return fac
def fermi_level(self, fermi_level, units='eV'):
if fermi_level is not None:
self.ef = fermi_level * self.conversion_factor(units)
def _set_range(self, npts=None, e_min=None, e_max=None):
import numpy as np
if npts is None:
npts = self.npts
if e_min is None:
e_min = self.e_min
if e_max is None:
e_max = self.e_max
for dos in self.ens:
mn, mx = dos['dos'].xlim
e_min = min(e_min, mn)
e_max = max(e_max, mx)
return np.arange(e_min, e_max, (e_max - e_min) / npts)
def curve(self, dos, norm, sigma=None):
import numpy as np
if sigma is None:
sigma = self.sigma
nrm = np.sqrt(2.0 * np.pi) * sigma / norm
dos_g = []
for e_i in self.range:
if len(dos.shape) == 2:
nkpt = dos.shape[0]
value = 0.0
for ikpt in range(nkpt):
value += np.sum(
np.exp(-(e_i - dos[ikpt, :])**2 / (2.0 * sigma**2)) /
nrm[ikpt])
else:
value = np.sum(
np.exp(-(e_i - dos[:])**2 / (2.0 * sigma**2)) / nrm)
# Append data corresponding to each energy grid
dos_g.append(value)
return np.array(dos_g)
def dump(self, sigma=None):
"For Gnuplot"
if sigma is None:
sigma = self.sigma
# data=[self.curve(dos,norm=self.norms[i],sigma=sigma)
# for i,dos in enumerate(self.ens)]
data = [
dos['dos'].curve(self.range, sigma=sigma)[1] for dos in self.ens
]
for i, e in enumerate(self.range):
safe_print(e, ' '.join(map(str, [d[i] for d in data])))
def plot(self,
sigma=None,
legend=True,
xlmin=None,
xlmax=None,
ylmin=None,
ylmax=None,
width=6.4,
height=4.8):
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider # , Button, RadioButtons
if sigma is None:
sigma = self.sigma
self.fig, self.ax1 = plt.subplots(figsize=(width, height))
self.plotl = []
for i, dos in enumerate(self.ens):
# self.plotl.append(self.ax1.plot(self.range,self.curve(dos,norm=self.norms[i],sigma=sigma),label=self.labels[i]))
self.plotl.append(
self.ax1.plot(*dos['dos'].curve(self.range, sigma=sigma),
label=self.labels[i]))
if xlmax is not None:
plt.xlim(xmax=xlmax)
if xlmin is not None:
plt.xlim(xmin=xlmin)
if ylmax is not None:
plt.ylim(ymax=ylmax)
if ylmin is not None:
plt.ylim(ymin=ylmin)
plt.xlabel('Energy [eV]', fontsize=18)
plt.ylabel('DoS', fontsize=18)
if self.ef is not None:
plt.axvline(self.ef, color='k', linestyle='--')
# self.ax1.annotate('Fermi level', xy=(self.ef,2),
# xytext=(self.ef, 10),
# arrowprops=dict(facecolor='white', shrink=0.05),
# )
if len(self.labels) > 1 and legend:
plt.legend(loc='best')
axcolor = 'lightgoldenrodyellow'
try:
axsigma = plt.axes([0.2, 0.93, 0.65, 0.03], facecolor=axcolor)
except AttributeError:
axsigma = plt.axes([0.2, 0.93, 0.65, 0.03], axisbg=axcolor)
self.ssig = Slider(axsigma, 'Smearing', 0.0, 0.4, valinit=sigma)
self.ssig.on_changed(self.update)
if hasattr(self, 'sdos') and self.sdos:
self._set_sdos_selector()
self._set_sdos()
plt.show()
def _set_sdos_selector(self):
import matplotlib.pyplot as plt
from matplotlib.widgets import RadioButtons
self.sdos_selector = RadioButtons(plt.axes(
[0.93, 0.05, 0.04, 0.11], axisbg='lightgoldenrodyellow'),
('x', 'y', 'z'),
active=1)
self.isdos = 1
self.sdos_selector.on_clicked(self._update_sdos)
def _set_sdos(self):
import numpy
xs = self.sdos[self.isdos]['coord']
self._set_sdos_sliders(numpy.min(xs), numpy.max(xs))
self._update_sdos(0.0) # fake value as it is unused
def _sdos_curve(self, sdos, vmin, vmax):
import numpy
xs = self.sdos[self.isdos]['coord']
imin = numpy.argmin(numpy.abs(xs - vmin))
imax = numpy.argmin(numpy.abs(xs - vmax))
doslist = sdos[self.isdos]['doslist']
# norms=self.sdos[self.isdos]['norms'][ispin]
tocurve = [0.0 for i in doslist[imin]]
for d in doslist[imin:imax + 1]:
tocurve = [t + dd for t, dd in zip(tocurve, d)]
# tocurve=numpy.sum([ d[ispin] for d in doslist[imin:imax+1]],axis=0)
return tocurve
# float(len(xs))/float(imax+1-imin)*tocurve,norms
def _update_sdos(self, val):
isdos = self.isdos
if val == 'x':
isdos = 0
elif val == 'y':
isdos = 1
elif val == 'z':
isdos = 2
if isdos != self.isdos:
self.isdos = isdos
self._set_sdos()
vmin, vmax = (s.val for s in self.ssdos)
if vmax < vmin:
self.ssdos[1].set_val(vmin)
vmax = vmin
if vmin > vmax:
self.ssdos[0].set_val(vmax)
vmin = vmax
# now plot the sdos curve associated to the given value
sig = self.ssig.val
curves = []
for dos in self.ens:
if 'sdos' not in dos:
continue
renorms = self._sdos_curve(dos['sdos'], vmin, vmax)
curve = dos['dos'].curve(self.range, sigma=sig, wgts=renorms)
curves.append(curve)
if hasattr(self, '_sdos_plots'):
for pl, curve in zip(self._sdos_plots, curves):
pl[0].set_ydata(curve[1])
else:
self._sdos_plots = []
for c in curves:
self._sdos_plots.append(self.ax1.plot(*c, label='sdos'))
self.ax1.relim()
self.ax1.autoscale_view()
self.fig.canvas.draw_idle()
def _set_sdos_sliders(self, cmin, cmax):
import matplotlib.pyplot as plt
from futile.Figures import VertSlider
if hasattr(self, 'ssdos'):
self.ssdos[0].ax.clear()
self.ssdos[0].__init__(self.ssdos[0].ax,
'SDos',
cmin,
cmax,
valinit=cmin)
self.ssdos[1].ax.clear()
self.ssdos[1].__init__(self.ssdos[1].ax,
'',
cmin,
cmax,
valinit=cmax)
else:
axcolor = 'red'
axmin = plt.axes([0.93, 0.2, 0.02, 0.65], axisbg=axcolor)
axmax = plt.axes([0.95, 0.2, 0.02, 0.65], axisbg=axcolor)
self.ssdos = [
VertSlider(axmin, 'SDos', cmin, cmax, valinit=cmin),
VertSlider(axmax, '', cmin, cmax, valinit=cmax)
]
self.ssdos[0].valtext.set_ha('right')
self.ssdos[1].valtext.set_ha('left')
self.ssdos[0].on_changed(self._update_sdos)
self.ssdos[1].on_changed(self._update_sdos)
def update(self, val):
sig = self.ssig.val
for i, dos in enumerate(self.ens):
self.plotl[i][0].set_ydata(dos['dos'].curve(self.range,
sigma=sig)[1])
# self.plotl[i][0].set_ydata(self.curve(dos,norm=self.norms[i],sigma=sig))
self.ax1.relim()
self.ax1.autoscale_view()
self.fig.canvas.draw_idle()
def GUI(self): # ,makefigs=True):
print('I am here')
mpl.rcParams['toolbar'] = 'None'
self.Nphf = self.Npix / 2
self.robfac = 0.0
self.figSPEC = pl.figure(figsize=(20, 16))
# self.gs1 = self.figSPEC.add_gridspec(nrows=4, ncols=3, left=0.05, right=0.48,
# wspace=0.05)
if self.tks is None:
self.canvas = self.figSPEC.canvas
else:
self.canvas = FigureCanvasTkAgg(self.figSPEC, master=self.tks)
self.canvas.show()
menubar = Tk.Menu(self.tks)
menubar.add_command(label="Help", command=self._getHelp)
menubar.add_command(label="Quit", command=self.quit)
self.tks.config(menu=menubar)
self.canvas.get_tk_widget().pack(side=Tk.TOP,
fill=Tk.BOTH,
expand=1)
self.specPlot = self.figSPEC.add_subplot(221)
self.freqPlot = self.figSPEC.add_subplot(222)
self.timePlot = self.figSPEC.add_subplot(223)
# self.eventprofilePlot = self.figSPEC.add_subplot(224)
self.specPlot.set_position([0.1, 0.45, 0.45, 0.45])
self.freqPlot.set_position([0.58, 0.45, 0.125, 0.45])
self.timePlot.set_position([0.1, 0.28, 0.45, 0.15])
# self.dirtyPlot = self.figUV.add_subplot(236,aspect='equal')
#self.spherePlot = pl.axes([0.53,0.82,0.12,0.12],projection='3d',aspect='equal')
u = np.linspace(0, 2 * np.pi, 100)
v = np.linspace(0, np.pi, 100)
x = 10 * np.outer(np.cos(u), np.sin(v))
y = 10 * np.outer(np.sin(u), np.sin(v))
z = 10 * np.outer(np.ones(np.size(u)), np.cos(v))
#self.spherePlotPlot = self.spherePlot.plot_surface(x, y, z, rstride=4, cstride=4, color=(0.8,0.8,1.0))
#self.spherePlot._axis3don = False
#self.spherePlot.patch.set_alpha(0.8)
#beta = np.zeros(100)
#self.arrayPath = [np.zeros(self.nH), np.zeros(self.nH), np.zeros(self.nH)]
#self.sphereArray = self.spherePlot.plot([],[],[],'y',linewidth=3)
#self.spherePlot.set_xlim3d((-6,6))
#self.spherePlot.set_ylim3d((-6,6))
#self.spherePlot.set_zlim3d((-6,6))
#self.spherePlot.patch.set_alpha(0.8)
#self.spherePlot.elev = 45.
self.canvas.mpl_connect('button_press_event', self.on_press)
#self.figSPEC.subplots_adjust(left=0.01,right=0.99,top=0.95,bottom=0.071,hspace=0.15)
#self.canvas.mpl_connect('mouse_event', self.mouse_move)
#self.canvas.mpl_connect('motion_notify_event', self._onAntennaDrag)
#self.canvas.mpl_connect('button_release_event',self._onRelease)
#self.canvas.mpl_connect('button_press_event',self._onPress)
#self.canvas.mpl_connect('key_press_event', self._onKeyPress)
self.pickAnt = False
self.fmtH = r'$\phi = $ %3.1f$^\circ$ $\delta = $ %3.1f$^\circ$' "\n" r'H = %3.1fh / %3.1fh'
self.fmtBas = r'Bas %i $-$ %i at H = %4.2fh'
self.fmtVis = r'Amp: %.1e Jy. Phase: %5.1f deg.'
self.fmtA = 'N = %i'
self.fmtA2 = ' Picked Ant. #%i'
self.fmtA3 = '\n%6.1fm | %6.1fm'
self.wax = {}
self.widget = {}
self.wax['freq'] = pl.axes([0.075, 0.15, 0.1, 0.04])
self.wax['freq_min'] = pl.axes([0.4, 0.15, 0.1, 0.04])
self.wax['freq_max'] = pl.axes([0.6, 0.15, 0.1, 0.04])
self.wax['smooth'] = pl.axes([0.045, 0.25, 0.1, 0.04])
self.wax['open'] = pl.axes([0.002, 0.90, 0.075, 0.04])
self.wax['plot'] = pl.axes([0.003, 0.8, 0.075, 0.04])
self.wax['reduce'] = pl.axes([0.07, 0.1, 0.25, 0.04])
self.widget['freq'] = Slider(self.wax['freq'],
r'frequency',
self.st_freq,
self.stp_freq,
valinit=80.0)
self.widget['freq_min'] = Slider(self.wax['freq_min'],
r'frequency_min',
self.st_freq,
self.stp_freq,
valinit=45.0)
self.widget['freq_max'] = Slider(self.wax['freq_max'],
r'frequency_max',
self.st_freq,
self.stp_freq,
valinit=155.0)
self.widget['smooth'] = Slider(self.wax['smooth'],
r'smooth',
valmin=1,
valmax=101,
valinit=51.0)
self.widget['open'] = Button(self.wax['open'], r' Open File')
self.widget['plot'] = Button(self.wax['plot'], r' plot')
self.widget['reduce'] = Button(self.wax['reduce'], r'Reduce data')
self.widget['freq'].on_changed(self.onFreq)
self.widget['freq_min'].on_changed(self.onFreq_min_axis_change)
self.widget['freq_max'].on_changed(self.onFreq_max_axis_change)
self.widget['smooth'].on_changed(self.onSmooth)
# self.widget['loadfile'].on_clicked(self.loadFile)
self.widget['open'].on_clicked(self.loadFile)
self.widget['plot'].on_clicked(self.onPlot)
self._prepareSpec_data()
self.canvas.draw()
def draw(os,
rays=None,
hold_on=False,
do_not_draw_surfaces=[],
do_not_draw_raybundles=[],
interactive=False,
show_box=True,
label=None,
linewidth=1.0,
export_type="pdf",
export=None,
**kwargs):
"""
Convenience function for drawing optical system and list of raybundles
Use figsize=(..,..) to control aspect ratio for export.
:param os - OpticalSystem
:param rb - list of raybundles
"""
if export is not None:
interactive = False
if label is None:
label = str(uuid.uuid4())
axis_color = "lightgoldenrodyellow"
dpi = kwargs.pop("dpi", None)
figsize = kwargs.pop("figsize", None)
fig = plt.figure(1, dpi=dpi, figsize=figsize)
if not show_box:
ax = plt.Axes(fig, [0., 0., 1., 1.], label=label)
ax.set_axis_off()
fig.add_axes(ax)
else:
ax = fig.add_subplot(1, 1, 1, label=label)
if interactive:
fig.subplots_adjust(left=0.25, bottom=0.25)
xz_angle_slider_size = [0.25, 0.15, 0.65, 0.03]
up_angle_slider_size = [0.25, 0.10, 0.65, 0.03]
if StrictVersion(matplotlib.__version__) < StrictVersion("2.0.0"):
xz_angle_slider_ax = fig.add_axes(xz_angle_slider_size,
axisbg=axis_color)
up_angle_slider_ax = fig.add_axes(up_angle_slider_size,
axisbg=axis_color)
else:
xz_angle_slider_ax = fig.add_axes(xz_angle_slider_size,
facecolor=axis_color)
up_angle_slider_ax = fig.add_axes(up_angle_slider_size,
facecolor=axis_color)
xz_angle_slider = Slider(xz_angle_slider_ax,
"XZ angle",
0.0,
360.0,
valinit=0.0,
valfmt="%0.0f")
up_angle_slider = Slider(up_angle_slider_ax,
"UP angle",
0.0,
360.0,
valinit=0.0,
valfmt="%0.0f")
ax.axis("equal")
if StrictVersion(matplotlib.__version__) < StrictVersion("2.0.0"):
ax.set_axis_bgcolor("white")
else:
ax.set_facecolor("white")
def draw_rays(ax, rays, do_not_draw_raybundles=[], **kwargs):
if rays is not None:
if isinstance(rays, list):
for rpl in rays:
ray_color = tuple(np.random.random(3))
if isinstance(rpl, list):
for rp in rpl:
ray_color = tuple(np.random.random(3))
rp.draw2d(
ax,
color=ray_color,
do_not_draw_raybundles=do_not_draw_raybundles,
**kwargs)
elif isinstance(rpl, tuple):
(rl, ray_color) = rpl
if isinstance(rl, list):
# draw(s, [([rp1, ..], color1), (....)])
for r in rl:
r.draw2d(ax, color=ray_color, **kwargs)
else:
# draw(s, [(rp1, color1), (....)])
rl.draw2d(ax, color=ray_color, **kwargs)
else:
rpl.draw2d(
ax,
color=ray_color,
do_not_draw_raybundles=do_not_draw_raybundles,
**kwargs)
elif isinstance(rays, RayPath):
# draw(s, raypath)
ray_color = tuple(np.random.random(3))
rays.draw2d(ax,
color=ray_color,
do_not_draw_raybundles=do_not_draw_raybundles,
**kwargs)
elif isinstance(rays, RayBundle):
# draw(s, raybundle)
ray_color = tuple(np.random.random(3))
rays.draw2d(ax, color=ray_color, **kwargs)
elif isinstance(rays, tuple):
(rl, ray_color) = rays
if isinstance(rl, list):
# draw(s, ([raypath1, ...], color))
for r in rl:
r.draw2d(ax, color=ray_color, **kwargs)
else:
# draw(s, (raypath, color))
rl.draw2d(ax,
color=ray_color,
do_not_draw_raybundles=do_not_draw_raybundles,
**kwargs)
def sliders_on_changed(val):
ax.clear()
round_val_xz = np.round(xz_angle_slider.val)
round_val_up = np.round(up_angle_slider.val)
phi = round_val_xz * degree
theta = round_val_up * degree
# new_ex = np.array([np.cos(phi),
# 0,
# np.sin(phi)])
# new_up = np.array([-np.sin(theta),
# np.cos(theta),
# 0.])
new_ex = np.array([
np.cos(phi) * np.cos(theta),
np.sin(theta),
np.sin(phi) * np.cos(theta)
])
new_up = np.array([
-np.cos(phi) * np.sin(theta),
np.cos(theta), -np.sin(phi) * np.sin(theta)
])
inyzplane = np.abs(round_val_xz) < numerical_tolerance\
and np.abs(round_val_up) < numerical_tolerance
os.draw2d(ax,
color="grey",
inyzplane=inyzplane,
plane_normal=new_ex,
up=new_up,
**kwargs)
draw_rays(ax, rays, plane_normal=new_ex, up=new_up, **kwargs)
if interactive:
xz_angle_slider.on_changed(sliders_on_changed)
up_angle_slider.on_changed(sliders_on_changed)
draw_rays(ax,
rays,
linewidth=linewidth,
do_not_draw_raybundles=do_not_draw_raybundles,
**kwargs)
os.draw2d(ax,
color="grey",
linewidth=linewidth,
do_not_draw_surfaces=do_not_draw_surfaces,
**kwargs)
if export is not None:
# ax.autoscale(enable=True, axis='both', tight=True)
fig.savefig(export,
format=export_type,
bbox_inches='tight',
pad_inches=0)
if not hold_on:
plt.show()
def _add_teach_panel(self, robot):
fig = self.fig
# Add text to the plots
def text_trans(text): # pragma: no cover
T = robot.fkine()
t = np.round(T.t, 3)
r = np.round(T.rpy(), 3)
text[0].set_text("x: {0}".format(t[0]))
text[1].set_text("y: {0}".format(t[1]))
text[2].set_text("yaw: {0}".format(r[2]))
# Update the self state in mpl and the text
def update(val, text, robot): # pragma: no cover
for i in range(robot.n):
robot.q[i] = self.sjoint[i].val * np.pi/180
text_trans(text)
# Step the environment
self.step(0)
fig.subplots_adjust(left=0.38)
text = []
x1 = 0.04
x2 = 0.22
yh = 0.04
ym = 0.5 - (robot.n * yh) / 2 + 0.17/2
self.axjoint = []
self.sjoint = []
qlim = np.copy(robot.qlim) * 180/np.pi
if np.all(qlim == 0): # pragma nocover
qlim[0, :] = -180
qlim[1, :] = 180
# Set the pose text
T = robot.fkine()
t = np.round(T.t, 3)
r = np.round(T.rpy(), 3)
fig.text(
0.02, 1 - ym + 0.25, "End-effector Pose",
fontsize=9, weight="bold", color="#4f4f4f")
text.append(fig.text(
0.03, 1 - ym + 0.20, "x: {0}".format(t[0]),
fontsize=9, color="#2b2b2b"))
text.append(fig.text(
0.03, 1 - ym + 0.16, "y: {0}".format(t[1]),
fontsize=9, color="#2b2b2b"))
text.append(fig.text(
0.15, 1 - ym + 0.20, "yaw: {0}".format(r[0]),
fontsize=9, color="#2b2b2b"))
fig.text(
0.02, 1 - ym + 0.06, "Joint angles",
fontsize=9, weight="bold", color="#4f4f4f")
for i in range(robot.n):
ymin = (1 - ym) - i * yh
self.axjoint.append(
fig.add_axes([x1, ymin, x2, 0.03], facecolor='#dbdbdb'))
self.sjoint.append(
Slider(
self.axjoint[i], 'q' + str(i),
qlim[0, i], qlim[1, i], robot.q[i] * 180/np.pi))
self.sjoint[i].on_changed(lambda x: update(x, text, robot))
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(8, 6))
fig.subplots_adjust(bottom=0.25)
ax.set_xlabel('Time', fontsize=14)
ax.set_ylabel('', fontsize=14)
ax.set_title('Michaelis Menten', fontsize=14)
l1, l2, l3, l4 = ax.plot(time, res)
l1.set_label('$dS$')
l2.set_label('$dE$')
l3.set_label('$dES$')
l4.set_label('$dP$')
ax.margins(x=0)
axcolor = 'lightgoldenrodyellow'
axkf = plt.axes([.25, .02, .65, .03], facecolor=axcolor)
axkb = plt.axes([.25, .07, .65, .03], facecolor=axcolor)
axki = plt.axes([.25, .12, .65, .03], facecolor=axcolor)
skf = Slider(axkf, r'$k_f$', 0., 10., valinit=kf, valstep=.1)
skb = Slider(axkb, r'$k_b$', 0., 10., valinit=kb, valstep=.1)
ski = Slider(axki, r'Kirr', 0., 10., valinit=Kirr, valstep=.1)
skf.on_changed(update)
skb.on_changed(update)
ski.on_changed(update)
ax.legend(loc='best', fontsize=14)
plt.show()
g1.set_xlabel("temps (s)")
ls,=g1.plot(t,resolution(0,1)[1],"r-",label="Amplitude du système")
lf,=g1.plot(t,sin(w_forcage*t),"g-",label="Force excitatrice")
legend()
show()
'''
ajuster la pulsation de l'excitateur par ui avec un curseur
'''
subplots_adjust(bottom=0.3)#réduit g1 pour laisser palce au slider
rect=f.add_axes([0.1,0.12,0.8,0.03])#emplacement du curseur
slider=Slider(rect,r"$\frac{\omega_{forçage}}{\omega _0}$",0.01,2,1)#paramètres du curseur
slider.label.set_size(30)
rect2=f.add_axes([0.1,0.05,0.8,0.03])#emplacement du curseur
slider2=Slider(rect2,r"$\Gamma$",0.01,2,1)#paramètres du curseur
slider2.label.set_size(30)
def maj(_):#met à jour l1 avec les valeurs du curseur
global w_forcage
global gamma
w_forcage=slider.val
gamma=slider2.val
ls.set_ydata(resolution(0,1)[1])
lf.set_ydata(sin(w_forcage*t))
slider.on_changed(maj)
slider2.on_changed(maj)
class NormalizedWormPlottable(animation.TimedAnimation):
"""
A class that renders matplotlib plots of worm measurement and
feature data.
This follows the [animated subplots example]
(http://matplotlib.org/1.3.0/examples/animation/subplots.html)
in inheriting from TimedAnimation rather than
using PyLab-shell-type calls to construct the animation.
"""
def __init__(self,
normalized_worm,
motion_mode=None,
interactive=False,
interpolate_nan_frames=False):
"""
Initialize the animation of the worm's attributes.
Parameters
---------------------------------------
normalized_worm: NormalizedWorm
the NormalizedWorm object to be plotted.
motion_mode: 1-dimensional numpy array (optional)
The motion mode of the worm over time. Must have
length = normalized_worm.num_frames
interactive: boolean (optional)
if interactive is set to False, then:
suppress the drawing of the figure, until an explicit plt.show()
is called. this allows NormalizedWormPlottable to be instantiated
without just automatically being displayed. Instead, the user
must call NormalizedWormPlottable.show() to have plt.show() be
called.
interpolate_nan_frames: interpolate the flickering nan frames
Note: this is currently not implemented
Notes
---------------------------------------
To initialize the animation, we must do six things:
1. set up the data to be used from the normalized_worm
2. create the figure
3. create subplots in the figure, assigning them Axis handles
4. create Artist objects for all objects in the subplots
5. assign the Artist objects to the correct Axis handle
6. call the base class __init__
"""
# A NormalizedWormPlottable instance can be instantiated to be
# interactive, or by default it is set to NOT interactive, which
# means that NormalizedWormPlottable.show() must be called to get
# it to display.
plt.interactive(interactive)
self._paused = False
# 1. set up the data to be used
self.nw = normalized_worm
self.motion_mode = motion_mode
self.motion_mode_options = {-1: 'backward', 0: 'paused', 1: 'forward'}
self.motion_mode_colours = {
-1: 'b', # blue
0: 'r', # red
1: 'g'
} # green
# 2. create the figure
fig = plt.figure(figsize=(5, 5))
# We have blit=True, so the animation only redraws the elements that
# have changed. This means that if the window is resized, everything
# other than the plot area will be black. To fix this, here we have
# matplotlib explicitly redraw everything if a resizing event occurs.
# DEBUG: this actually doesn't appear to work.
def refresh_plot(event):
print("refresh_plot called")
# We must reset this or else repetitive expanding and contracting
# of the window will cause the view to zoom in on the subplots
self.set_axes_extents()
fig.canvas.draw()
self.refresh_connection_id = fig.canvas.mpl_connect(
'resize_event', refresh_plot)
fig.suptitle('C. elegans attributes', fontsize=20)
# 3. Add the subplots
self.ax1 = plt.subplot2grid((3, 3), (0, 0), rowspan=2, colspan=2)
self.ax1.set_title('Position')
self.ax1.plot(self.nw.skeleton[0, 0, :], self.nw.skeleton[0, 1, :])
self.ax1.set_xlabel('x')
self.ax1.set_ylabel('y')
#ax1.set_aspect(aspect='equal', adjustable='datalim')
# ax1.set_autoscale_on()
self.annotation1a = \
self.ax1.annotate("(motion mode data not available)",
xy=(-10, 10), xycoords='axes points',
horizontalalignment='right',
verticalalignment='top',
fontsize=10)
self.annotation1b = \
self.ax1.annotate("bottom right (points)",
xy=(-10, 10), xycoords='axes points',
horizontalalignment='right',
verticalalignment='bottom',
fontsize=10)
# WIDGETS
# [left,botton,width,height] as a proportion of
# figure width and height
frame_slider_axes = fig.add_axes([0.2, 0.02, 0.33, 0.02],
axisbg='lightgoldenrodyellow')
self.frame_slider = Slider(frame_slider_axes,
label='Frame#',
valmin=1,
valmax=self.nw.num_frames,
valinit=1,
valfmt=u'%d')
def frame_slider_update(val):
print("Slider value: %d" % round(val, 0))
self.frame_seq = self.new_frame_seq(int(round(val, 0)))
fig.canvas.draw()
self.frame_slider.on_changed(frame_slider_update)
button_axes = fig.add_axes([0.8, 0.025, 0.1, 0.04])
#ax4 = plt.subplot2grid((3, 3), (2, 2))
button = Button(button_axes,
'Pause',
color='lightgoldenrodyellow',
hovercolor='0.975')
def pause(event):
if not self._paused:
self._stop()
else:
self.event_source = fig.canvas.new_timer()
self.event_source.interval = self._interval
self._start()
# Toggle the paused state
self._paused = 1 - self._paused
button.on_clicked(pause)
self.ax2 = plt.subplot2grid((3, 3), (0, 2))
self.ax2.set_title('Morphology')
self.ax2.set_aspect(aspect='equal', adjustable='datalim')
self.annotation2 = self.ax2.annotate(
"Worm head",
xy=(0, 0),
xycoords='data',
xytext=(10, 10),
textcoords='data',
arrowprops=dict(arrowstyle="fancy", connectionstyle="arc3,rad=.2"))
self.ax3 = plt.subplot2grid((3, 3), (1, 2))
self.ax3.set_title('Orientation-free')
# DON'T USE set_xbound, it changes dynmically
self.ax3.set_aspect(aspect='equal', adjustable='datalim')
# Length and Area over time
self.ax4a = plt.subplot2grid((3, 3), (2, 0), rowspan=1, colspan=2)
self.ax4a.plot(self.nw.length, 'o-')
self.ax4a.set_title('Length and Area over time')
self.ax4a.set_ylabel('Microns')
self.ax4b = self.ax4a.twinx()
self.ax4b.plot(self.nw.area, 'xr-')
self.ax4b.set_ylabel('Microns ^ 2')
# Widths and Angles
self.ax5a = plt.subplot2grid((3, 3), (2, 2))
self.ax5a.set_title('Widths and Angles')
self.ax5a.set_xlabel('Skeleton point')
self.widths = Line2D([], [])
self.ax5a.set_ylabel('Microns')
self.ax5b = self.ax5a.twinx()
self.angles = Line2D([], [])
self.ax5b.set_ylabel('Degrees')
# 4. create Artist objects
self.time_marker = Line2D([], [])
self.line1W = Line2D([], [],
color='green',
linestyle='point marker',
marker='o',
markersize=5)
self.line1W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.line1C = Line2D([], [],
color='yellow',
linestyle='point marker',
marker='o',
markersize=5)
self.patch1E = Ellipse(xy=(0, 0),
width=1000,
height=500,
angle=0,
alpha=0.3)
self.line2W = Line2D([], [], color='black', marker='o', markersize=5)
self.line2W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.line2C = Line2D([], [], color='blue')
self.line2C2 = Line2D([], [], color='orange')
self.line3W = Line2D([], [], color='black', marker='o', markersize=5)
self.line3W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.artists_with_data = [
self.line1W, self.line1W_head, self.line1C, self.line2W,
self.line2W_head, self.line2C, self.line2C2, self.line3W,
self.line3W_head, self.widths, self.angles, self.time_marker
]
# This list is a superset of self.artists_with_data
self.artists_to_be_drawn = ([
self.patch1E, self.annotation1a, self.annotation1b,
self.annotation2
] + self.artists_with_data)
self.set_axes_extents()
# 5. assign Artist objects to the relevant subplot
self.ax1.add_line(self.line1W)
self.ax1.add_line(self.line1W_head)
self.ax1.add_line(self.line1C)
self.ax1.add_artist(self.patch1E)
self.ax2.add_line(self.line2W)
self.ax2.add_line(self.line2W_head)
self.ax2.add_line(self.line2C)
self.ax2.add_line(self.line2C2)
self.ax3.add_line(self.line3W)
self.ax3.add_line(self.line3W_head)
self.ax4a.add_line(self.time_marker)
self.ax5a.add_line(self.widths)
self.ax5b.add_line(self.angles)
# So labels don't overlap:
#plt.tight_layout()
# 6. call the base class __init__
# TimedAnimation draws a new frame every *interval* milliseconds.
# so this is how we convert from FPS to interval:
interval = 1000 / self.nw.video_info.fps
return animation.TimedAnimation.__init__(self,
fig,
interval=interval,
blit=True)
def set_axes_extents(self):
# DON'T USE set_xbound; it changes dynamically
self.ax1.set_xlim(self.nw.position_limits(0))
self.ax1.set_ylim(self.nw.position_limits(1))
self.ax2.set_xlim((-500, 500))
self.ax2.set_ylim((-500, 500))
self.ax3.set_xlim((-800, 800))
self.ax3.set_ylim((-500, 500))
self.ax4a.set_xlim((0, self.nw.num_frames))
self.ax5a.set_xlim((0, 49))
self.ax5a.set_ylim((0, np.nanmax(self.nw.widths)))
self.ax5b.set_ylim(
(np.nanmin(self.nw.angles), np.nanmax(self.nw.angles)))
def set_frame_data(self, frame_index):
self._current_frame = frame_index
i = frame_index
if self._paused:
return
self.line1W.set_data(self.nw.skeleton[:, 0, i], self.nw.skeleton[:, 1,
i])
self.line1W_head.set_data(self.nw.skeleton[0, 0, i],
self.nw.skeleton[0, 1, i])
self.line1C.set_data(self.nw.ventral_contour[:, 0, i],
self.nw.ventral_contour[:, 1, i])
self.patch1E.center = (self.nw.centre[:, i]) # skeleton centre
self.patch1E.angle = self.nw.angle[i] # orientation
# Set the values of our annotation text in the main subplot:
if self.motion_mode is not None:
if np.isnan(self.motion_mode[i]):
self.patch1E.set_facecolor('w')
self.annotation1a.set_text("Motion mode: {}".format('NaN'))
else:
# Set the colour of the ellipse surrounding the worm to a
# colour corresponding to the current motion mode of the worm
self.patch1E.set_facecolor(
self.motion_mode_colours[self.motion_mode[i]])
# Annotate the current motion mode of the worm in text
self.annotation1a.set_text("Motion mode: {}".format(
self.motion_mode_options[self.motion_mode[i]]))
self.annotation1b.set_text("Frame {} of {}".format(i, self.num_frames))
self.line2W.set_data(self.nw.centred_skeleton[:, 0, i],
self.nw.centred_skeleton[:, 1, i])
self.line2W_head.set_data(self.nw.centred_skeleton[0, 0, i],
self.nw.centred_skeleton[0, 1, i])
self.line2C.set_data(self.nw.centred_skeleton[:, 0, i] + \
(self.nw.ventral_contour[:, 0, i] - self.nw.skeleton[:, 0, i]),
self.nw.centred_skeleton[:, 1, i] + \
(self.nw.ventral_contour[:, 1, i] - self.nw.skeleton[:, 1, i]))
self.line2C2.set_data(
self.nw.centred_skeleton[:, 0, i] +
(self.nw.dorsal_contour[:, 0, i] - self.nw.skeleton[:, 0, i]),
self.nw.centred_skeleton[:, 1, i] +
(self.nw.dorsal_contour[:, 1, i] - self.nw.skeleton[:, 1, i]))
self.annotation2.xy = (self.nw.centred_skeleton[0, 0, i],
self.nw.centred_skeleton[0, 1, i])
self.line3W.set_data(self.nw.orientation_free_skeleton[:, 0, i],
self.nw.orientation_free_skeleton[:, 1, i])
self.line3W_head.set_data(self.nw.orientation_free_skeleton[0, 0, i],
self.nw.orientation_free_skeleton[0, 1, i])
self.widths.set_data(np.arange(49), self.nw.widths[:, i])
self.angles.set_data(np.arange(49), self.nw.angles[:, i])
# Draw a vertical line to mark the passage of time
self.time_marker.set_data([i, i], [0, 10000])
@property
def num_frames(self):
"""
Return the total number of frames in the animation
"""
return self.nw.num_frames
def show(self):
"""
Draw the figure in a window on the screen
"""
plt.show()
def _draw_frame(self, frame_index):
"""
Called sequentially for each frame of the animation. Thus
we must set our plot to look like it should for the given frame.
Parameters
---------------------------------------
frame_index: int
An integer between 0 and the number of frames, giving
the current frame.
"""
# Make the canvas elements visible now
# (We made them invisible in _init_draw() so that the first
# frame of the animation wouldn't remain stuck on the canvas)
for l in self.artists_to_be_drawn:
l.set_visible(True)
self.set_frame_data(frame_index)
self._drawn_artists = self.artists_to_be_drawn
def new_frame_seq(self, start_frame=0):
"""
Returns an iterator that iterates over the frames
in the animation
Parameters
---------------
start_frame: int
Start the sequence at this frame then loop back around
to start_frame-1.
"""
s = start_frame
n = self.num_frames
return iter(np.mod(np.arange(s, s + n), n))
def _init_draw(self):
"""
Called when first drawing the animation.
It is an abstract method in Animation, to be implemented here for
the first time.
"""
for l in self.artists_with_data:
l.set_data([], [])
# Keep the drawing elements invisible for the first frame to avoid
# the first frame remaining on the canvas
for l in self.artists_to_be_drawn:
l.set_visible(False)
def save(self,
filename,
file_title='C. elegans movement video',
file_comment='C. elegans movement video from Schafer lab'):
"""
Save the animation as an mp4.
Parameters
---------------------------------------
filename: string
The name of the file to be saved as an mp4.
file_title: string (optional)
A title to be embedded in the file's saved metadata.
file_comment: string (optional)
A comment to be embedded in the file's saved metadata.
Notes
---------------------------------------
Requires ffmpeg or mencoder to be installed. To install ffmpeg
on Windows, see:
http://www.wikihow.com/Install-FFmpeg-on-Windows
The code specifies extra_args=['-vcodec', 'libx264'], to ensure
that the x264 codec is used, so that the video can be embedded
in html5. You may need to adjust this for your system. For more
information, see:
http://matplotlib.sourceforge.net/api/animation_api.html
"""
fps = self.nw.video_info.fps
FFMpegWriter = animation.writers['ffmpeg']
metadata = dict(title=file_title,
artist='matplotlib',
comment=file_comment)
writer = FFMpegWriter(fps=fps, metadata=metadata)
animation.TimedAnimation.save(self,
filename,
writer=writer,
fps=fps,
extra_args=['-vcodec', 'libx264'])
# plotting code snippet taken from
# https://stackoverflow.com/questions/31001713/plotting-the-data-with-scrollable-x-time-horizontal-axis-on-linux
fig, ax = plt.subplots(figsize=(12, 5))
plt.subplots_adjust(bottom=0.25, left=0.1)
t = np.arange(0.0, length / 10, 0.1)
l1, = plt.plot(t, xs, color='blue', label="xs")
l2, = plt.plot(t, ys, color='green', label="ys")
l3, = plt.plot(t, zs, color='red', label="zs")
plt.legend(loc="lower left")
plt.xlabel("Time (sec)")
plt.ylabel("Acceleration (cm/s^2)")
plt.grid()
plt.axis([0, 5, -3000, 3000])
axcolor = 'lightgoldenrodyellow'
axpos = plt.axes([0.2, 0.1, 0.65, 0.03], facecolor=axcolor)
spos = Slider(axpos, 'Second', 0.1, float((length / 10) - 5))
def update(val):
pos = spos.val
ax.axis([pos, pos + 5, -3000, 3000])
fig.canvas.draw_idle()
spos.on_changed(update)
plt.show()
l.append(0)
v.append(0)
l[k] = ax.plot(omega/(2*np.pi), var_plot, '-') #, label='Mismatch phase = {}°'.format(phase_mm[k] * 180 / np.pi)
# plt.legend()
v[k] = ax.plot(omega/(2*np.pi), var_plot_vac, '--', color='black', linewidth=1)
if sliders:
axcolor = 'lightgoldenrodyellow'
axangle = plt.axes([0.25, 0.1, 0.65, 0.03], facecolor=axcolor)
axdetuning = plt.axes([0.25, 0.15, 0.65, 0.03], facecolor=axcolor)
axtransmission = plt.axes([0.25, 0.2, 0.65, 0.03], facecolor=axcolor)
axfreqmin = plt.axes([0.25, 0.25, 0.1, 0.05], facecolor=axcolor)
axfreqmax = plt.axes([0.6, 0.25, 0.1, 0.05], facecolor=axcolor)
sangle = Slider(axangle, 'Homodyne angle (°)', 0, 180, valinit=angle_init, valstep=angle_step)
sdetuning = Slider(axdetuning, 'Detuning (MHz)', detuning_min, detuning_max, valinit=detuning_init, valstep=detuning_step)
stransmission = Slider(axtransmission, 'Input mirror transmission', transmission_min, transmission_max, valinit=transmission_init, valstep=transmission_step)
sfreqmin = TextBox(axfreqmin, 'Min frequency (MHz)', initial=str(freq_min * 1e-6), color='.95', hovercolor='1')
sfreqmax = TextBox(axfreqmax, 'Max frequency (MHz)', initial=str(freq_max * 1e-6), color='.95', hovercolor='1')
def update(val):
angle = np.pi * sangle.val /180
detuning = 2 * np.pi * sdetuning.val * 1e6
transmission = stransmission.val
omega_min = 2 * np.pi * float(sfreqmin.text) * 1e6 #s-1
omega_max = 2 * np.pi * float(sfreqmax.text) * 1e6 #s-1 <- range of sideband frequencies observed
# nb_freq = 1000 # <- freq resolution
omega = np.linspace(omega_min, omega_max, nb_freq)
for k in range(len(phase_mm)):
var_plot = np.zeros(nb_freq)
def __init__(self,
normalized_worm,
motion_mode=None,
interactive=False,
interpolate_nan_frames=False):
"""
Initialize the animation of the worm's attributes.
Parameters
---------------------------------------
normalized_worm: NormalizedWorm
the NormalizedWorm object to be plotted.
motion_mode: 1-dimensional numpy array (optional)
The motion mode of the worm over time. Must have
length = normalized_worm.num_frames
interactive: boolean (optional)
if interactive is set to False, then:
suppress the drawing of the figure, until an explicit plt.show()
is called. this allows NormalizedWormPlottable to be instantiated
without just automatically being displayed. Instead, the user
must call NormalizedWormPlottable.show() to have plt.show() be
called.
interpolate_nan_frames: interpolate the flickering nan frames
Note: this is currently not implemented
Notes
---------------------------------------
To initialize the animation, we must do six things:
1. set up the data to be used from the normalized_worm
2. create the figure
3. create subplots in the figure, assigning them Axis handles
4. create Artist objects for all objects in the subplots
5. assign the Artist objects to the correct Axis handle
6. call the base class __init__
"""
# A NormalizedWormPlottable instance can be instantiated to be
# interactive, or by default it is set to NOT interactive, which
# means that NormalizedWormPlottable.show() must be called to get
# it to display.
plt.interactive(interactive)
self._paused = False
# 1. set up the data to be used
self.nw = normalized_worm
self.motion_mode = motion_mode
self.motion_mode_options = {-1: 'backward', 0: 'paused', 1: 'forward'}
self.motion_mode_colours = {
-1: 'b', # blue
0: 'r', # red
1: 'g'
} # green
# 2. create the figure
fig = plt.figure(figsize=(5, 5))
# We have blit=True, so the animation only redraws the elements that
# have changed. This means that if the window is resized, everything
# other than the plot area will be black. To fix this, here we have
# matplotlib explicitly redraw everything if a resizing event occurs.
# DEBUG: this actually doesn't appear to work.
def refresh_plot(event):
print("refresh_plot called")
# We must reset this or else repetitive expanding and contracting
# of the window will cause the view to zoom in on the subplots
self.set_axes_extents()
fig.canvas.draw()
self.refresh_connection_id = fig.canvas.mpl_connect(
'resize_event', refresh_plot)
fig.suptitle('C. elegans attributes', fontsize=20)
# 3. Add the subplots
self.ax1 = plt.subplot2grid((3, 3), (0, 0), rowspan=2, colspan=2)
self.ax1.set_title('Position')
self.ax1.plot(self.nw.skeleton[0, 0, :], self.nw.skeleton[0, 1, :])
self.ax1.set_xlabel('x')
self.ax1.set_ylabel('y')
#ax1.set_aspect(aspect='equal', adjustable='datalim')
# ax1.set_autoscale_on()
self.annotation1a = \
self.ax1.annotate("(motion mode data not available)",
xy=(-10, 10), xycoords='axes points',
horizontalalignment='right',
verticalalignment='top',
fontsize=10)
self.annotation1b = \
self.ax1.annotate("bottom right (points)",
xy=(-10, 10), xycoords='axes points',
horizontalalignment='right',
verticalalignment='bottom',
fontsize=10)
# WIDGETS
# [left,botton,width,height] as a proportion of
# figure width and height
frame_slider_axes = fig.add_axes([0.2, 0.02, 0.33, 0.02],
axisbg='lightgoldenrodyellow')
self.frame_slider = Slider(frame_slider_axes,
label='Frame#',
valmin=1,
valmax=self.nw.num_frames,
valinit=1,
valfmt=u'%d')
def frame_slider_update(val):
print("Slider value: %d" % round(val, 0))
self.frame_seq = self.new_frame_seq(int(round(val, 0)))
fig.canvas.draw()
self.frame_slider.on_changed(frame_slider_update)
button_axes = fig.add_axes([0.8, 0.025, 0.1, 0.04])
#ax4 = plt.subplot2grid((3, 3), (2, 2))
button = Button(button_axes,
'Pause',
color='lightgoldenrodyellow',
hovercolor='0.975')
def pause(event):
if not self._paused:
self._stop()
else:
self.event_source = fig.canvas.new_timer()
self.event_source.interval = self._interval
self._start()
# Toggle the paused state
self._paused = 1 - self._paused
button.on_clicked(pause)
self.ax2 = plt.subplot2grid((3, 3), (0, 2))
self.ax2.set_title('Morphology')
self.ax2.set_aspect(aspect='equal', adjustable='datalim')
self.annotation2 = self.ax2.annotate(
"Worm head",
xy=(0, 0),
xycoords='data',
xytext=(10, 10),
textcoords='data',
arrowprops=dict(arrowstyle="fancy", connectionstyle="arc3,rad=.2"))
self.ax3 = plt.subplot2grid((3, 3), (1, 2))
self.ax3.set_title('Orientation-free')
# DON'T USE set_xbound, it changes dynmically
self.ax3.set_aspect(aspect='equal', adjustable='datalim')
# Length and Area over time
self.ax4a = plt.subplot2grid((3, 3), (2, 0), rowspan=1, colspan=2)
self.ax4a.plot(self.nw.length, 'o-')
self.ax4a.set_title('Length and Area over time')
self.ax4a.set_ylabel('Microns')
self.ax4b = self.ax4a.twinx()
self.ax4b.plot(self.nw.area, 'xr-')
self.ax4b.set_ylabel('Microns ^ 2')
# Widths and Angles
self.ax5a = plt.subplot2grid((3, 3), (2, 2))
self.ax5a.set_title('Widths and Angles')
self.ax5a.set_xlabel('Skeleton point')
self.widths = Line2D([], [])
self.ax5a.set_ylabel('Microns')
self.ax5b = self.ax5a.twinx()
self.angles = Line2D([], [])
self.ax5b.set_ylabel('Degrees')
# 4. create Artist objects
self.time_marker = Line2D([], [])
self.line1W = Line2D([], [],
color='green',
linestyle='point marker',
marker='o',
markersize=5)
self.line1W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.line1C = Line2D([], [],
color='yellow',
linestyle='point marker',
marker='o',
markersize=5)
self.patch1E = Ellipse(xy=(0, 0),
width=1000,
height=500,
angle=0,
alpha=0.3)
self.line2W = Line2D([], [], color='black', marker='o', markersize=5)
self.line2W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.line2C = Line2D([], [], color='blue')
self.line2C2 = Line2D([], [], color='orange')
self.line3W = Line2D([], [], color='black', marker='o', markersize=5)
self.line3W_head = Line2D([], [],
color='red',
linestyle='point marker',
marker='o',
markersize=7)
self.artists_with_data = [
self.line1W, self.line1W_head, self.line1C, self.line2W,
self.line2W_head, self.line2C, self.line2C2, self.line3W,
self.line3W_head, self.widths, self.angles, self.time_marker
]
# This list is a superset of self.artists_with_data
self.artists_to_be_drawn = ([
self.patch1E, self.annotation1a, self.annotation1b,
self.annotation2
] + self.artists_with_data)
self.set_axes_extents()
# 5. assign Artist objects to the relevant subplot
self.ax1.add_line(self.line1W)
self.ax1.add_line(self.line1W_head)
self.ax1.add_line(self.line1C)
self.ax1.add_artist(self.patch1E)
self.ax2.add_line(self.line2W)
self.ax2.add_line(self.line2W_head)
self.ax2.add_line(self.line2C)
self.ax2.add_line(self.line2C2)
self.ax3.add_line(self.line3W)
self.ax3.add_line(self.line3W_head)
self.ax4a.add_line(self.time_marker)
self.ax5a.add_line(self.widths)
self.ax5b.add_line(self.angles)
# So labels don't overlap:
#plt.tight_layout()
# 6. call the base class __init__
# TimedAnimation draws a new frame every *interval* milliseconds.
# so this is how we convert from FPS to interval:
interval = 1000 / self.nw.video_info.fps
return animation.TimedAnimation.__init__(self,
fig,
interval=interval,
blit=True)
ax1.set_ylim(-0.1, 1)
ax.set_xlabel('Time')
ax.set_ylabel('Synaptic Paramter')
axcolor = 'lightgoldenrodyellow'
axsInject = plt.axes([0.6, 0.7, 0.35, 0.04], facecolor=axcolor)
axsg_AM_E = plt.axes([0.6, 0.65, 0.35, 0.04], facecolor=axcolor)
axsg_AM_I = plt.axes([0.6, 0.6, 0.35, 0.04], facecolor=axcolor)
axsg_GABA_E = plt.axes([0.6, 0.55, 0.35, 0.04], facecolor=axcolor)
axsg_GABA_I = plt.axes([0.6, 0.50, 0.35, 0.04], facecolor=axcolor)
axstau_G = plt.axes([0.6, 0.45, 0.35, 0.04], facecolor=axcolor)
axstau_A = plt.axes([0.6, 0.40, 0.35, 0.04], facecolor=axcolor)
axh = plt.axes([-1, -1, 1, 1])
# Make sliders that control parameters
sInj = Slider(axsInject, r'Current', 0, 2, valinit=0.14, color='maroon')
sg_AM_E = Slider(axsg_AM_E,
r'AM E',
0,
10.0,
valinit=1.8,
color='midnightblue')
sg_AM_I = Slider(axsg_AM_I,
r'AM I',
0.0,
10.0,
valinit=1,
color='midnightblue')
sg_GABA_E = Slider(axsg_GABA_E,
r'GABA E',
0.0,
# Add the first image
ax.imshow(img)
ax.set_xticks([])
ax.set_yticks([])
ax.set_title("Original Image")
# add the first image again (since initially there should be no filtering)
ax2.imshow(img)
ax2.set_xticks([])
ax2.set_yticks([])
ax2.set_title("Blurred Image")
# Add a slider for our blurring Kernel
# Define an axes area and draw a slider in it
kernel_slider_ax = fig.add_axes([0.25, 0.15, 0.65, 0.03])
kernel_slider = Slider(kernel_slider_ax, 'Kernel Size', 1, 10)
# When the slider changes, we replace the original image (ax2 version) with the blurred image
def sliders_on_changed(val):
# Have to cast the slider value as an int to properly calculate the kernel
ax2.imshow(blurred_image((int)(kernel_slider.val)))
fig.canvas.draw_idle()
kernel_slider.on_changed(sliders_on_changed)
# Add a button for resetting the parameters
reset_button_ax = fig.add_axes([0.8, 0.025, 0.1, 0.04])
reset_button = Button(reset_button_ax, 'Reset', hovercolor='0.975')
def main(argv=None):
if argv is None:
argv = sys.argv
if len(argv) != 2:
print("usage: %s SIMNAME" % os.path.basename(sys.argv[0]))
return 2
# process arguments
simname = argv[1]
tslice = 0
# read elapsed hour/datetime key file
dts, hrs = pltutils.timekeys(simname)
nts = len(dts)
datetimes = []
for dt in dts:
datetimes.append(datetime.strftime(dt, "%Y-%m-%d %H:%M:%S"))
# read data files
# cair
z, acair = pltutils.get1Dvar(simname, "met", "cair")
cair = acair[:, tslice]
# h2o
z, ah2o = pltutils.get1Dvar(simname, "met", "h2o")
h2o = ah2o[:, tslice]
# kv
z, akv = pltutils.get1Dvar(simname, "met", "kv")
kv = akv[:, tslice]
# pmb
z, apmb = pltutils.get1Dvar(simname, "met", "pmb")
pmb = apmb[:, tslice]
# ppfd
z, appfd = pltutils.get1Dvar(simname, "met", "ppfd")
ppfd = appfd[:, tslice]
# qh
z, aqh = pltutils.get1Dvar(simname, "met", "qh")
qh = aqh[:, tslice]
# rh
z, arh = pltutils.get1Dvar(simname, "met", "rh")
rh = arh[:, tslice]
# tk
z, atk = pltutils.get1Dvar(simname, "met", "tk")
tk = atk[:, tslice]
# ubar
z, aubar = pltutils.get1Dvar(simname, "met", "ubar")
ubar = aubar[:, tslice]
# create the plots
fig = plt.figure(figsize=(12, 12))
# air density (molec/cm3)
ax1 = fig.add_subplot(2, 4, 1)
pcair, = ax1.plot(cair,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="c$_{air}$")
pltutils.setstdfmts(ax1, tlmaj, tlmin, tlbsize, tlbpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.85, 0.05))
# plt.xlim(xmax=1.0, xmin=0.0)
plt.ylim(ymax=43.0, ymin=0.0)
# water density (molecules/cm3)
ax2 = fig.add_subplot(2, 4, 2)
ph2o, = ax2.plot(h2o,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="H$_2$O")
pltutils.setstdfmts(ax2, tlmaj, tlmin, tlbsize, tlbpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.55, 0.05))
# plt.xlim(xmax=1200.0, xmin=-100.0)
plt.ylim(ymax=43.0, ymin=0.0)
# eddy diffusivity (cm2/s)
ax3 = fig.add_subplot(2, 4, 3)
pkv, = ax3.plot(kv,
z,
color=colors[4],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="K$_{v}$")
pltutils.setstdfmts(ax3, tlmaj, tlmin, tlbsize, tlbpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.95, 0.05))
plt.ylim(ymax=43.0, ymin=0.0)
# air pressure (mb)
ax4 = fig.add_subplot(2, 4, 4)
ppmb, = ax4.plot(pmb,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="p$_{air}$")
pltutils.setstdfmts(ax4, tlmaj, tlmin, tlbsize, tlbpad)
# plt.xlabel("$\mu$mol m$^{-2}$ s$^{-1}$", fontsize=xfsize, labelpad=xtpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.95, 0.05))
# plt.xlim(xmax=20., xmin=-1.)
plt.ylim(ymax=43.0, ymin=0.0)
# ppfd
ax5 = fig.add_subplot(2, 4, 5)
pppfd, = ax5.plot(ppfd,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="PPFD")
pltutils.setstdfmts(ax5, tlmaj, tlmin, tlbsize, tlbpad)
# plt.xlabel("W/m$^2$", fontsize=xfsize, labelpad=xtpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.65, 0.05))
# plt.xlim(xmax=1200.0, xmin=-100.0)
plt.ylim(ymax=43.0, ymin=0.0)
# qh
ax6 = fig.add_subplot(2, 4, 6)
pqh, = ax6.plot(qh,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="q$_h$")
pltutils.setstdfmts(ax6, tlmaj, tlmin, tlbsize, tlbpad)
# plt.xlabel("W/m$^2$", fontsize=xfsize, labelpad=xtpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.65, 0.05))
# plt.xlim(xmax=1200.0, xmin=-100.0)
plt.ylim(ymax=43.0, ymin=0.0)
# rh
ax7 = fig.add_subplot(2, 4, 7)
prh, = ax7.plot(rh,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="RH")
pltutils.setstdfmts(ax7, tlmaj, tlmin, tlbsize, tlbpad)
# plt.xlabel("W/m$^2$", fontsize=xfsize, labelpad=xtpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.65, 0.05))
# plt.xlim(xmax=500.0, xmin=-20.0)
plt.ylim(ymax=43.0, ymin=0.0)
# ubar
ax8 = fig.add_subplot(2, 4, 8)
pubar, = ax8.plot(ubar,
z,
color=colors[3],
linestyle="-",
marker="None",
linewidth=lnwdth,
label="u$_{mean}$")
# xmin, xmax = ax8.get_xlim()
# plt.xticks(np.arange(xmin, xmax+1, 1000.))
pltutils.setstdfmts(ax8, tlmaj, tlmin, tlbsize, tlbpad)
# plt.xlabel("s m$^{-1}$", fontsize=xfsize, labelpad=xtpad)
plt.legend(loc=4, fontsize=lfsize, bbox_to_anchor=(0.95, 0.05))
# plt.xlim(xmax=2000., xmin=-100.)
plt.ylim(ymax=43.0, ymin=0.0)
psupttle = plt.suptitle(simname + " - " + datetimes[tslice],
fontsize=tfsize,
y=tyloc)
# make room for the slider
plt.subplots_adjust(bottom=0.15)
# make a slider to control the time slice
slidercolor = "cyan"
axtime = plt.axes([0.25, 0.03, 0.55, 0.02], facecolor=slidercolor)
time_slider = Slider(ax=axtime,
label="Time",
valmin=0,
valmax=nts - 1,
valstep=1,
valinit=0)
# update function for the slider
def update(val):
tslice = int(time_slider.val)
psupttle.set_text(simname + " - " + datetimes[tslice])
xmax = np.amax(acair[:, tslice])
xmin = np.amin(acair[:, tslice])
pcair.set_xdata(acair[:, tslice])
ax1.set_xlim(xmax=xmax * 1.1, xmin=xmin * 0.95)
xmax = np.amax(ah2o[:, tslice])
xmin = np.amin(ah2o[:, tslice])
ph2o.set_xdata(ah2o[:, tslice])
ax2.set_xlim(xmax=xmax * 1.1, xmin=xmin * 0.95)
xmax = np.amax(akv[:, tslice])
pkv.set_xdata(akv[:, tslice])
ax3.set_xlim(xmax=xmax * 1.1, xmin=-20.0)
xmax = np.amax(apmb[:, tslice])
xmin = np.amin(apmb[:, tslice])
ppmb.set_xdata(apmb[:, tslice])
ax4.set_xlim(xmax=xmax * 1.1, xmin=xmin * 0.95)
xmax = np.amax(appfd[:, tslice])
xmin = np.amin(appfd[:, tslice])
pppfd.set_xdata(appfd[:, tslice])
ax5.set_xlim(xmax=2500., xmin=-20.0)
xmax = np.amax(aqh[:, tslice])
xmin = np.amin(aqh[:, tslice])
pqh.set_xdata(aqh[:, tslice])
ax6.set_xlim(xmax=xmax * 1.1, xmin=xmin * 0.95)
xmax = np.amax(arh[:, tslice])
xmin = np.amin(arh[:, tslice])
prh.set_xdata(arh[:, tslice])
ax7.set_xlim(xmax=100., xmin=0.0)
xmax = np.amax(aubar[:, tslice])
xmin = np.amin(aubar[:, tslice])
pubar.set_xdata(aubar[:, tslice])
ax8.set_xlim(xmax=xmax * 1.1, xmin=0.0)
fig.canvas.draw_idle()
# register the update function with the slider
time_slider.on_changed(update)
# allow slider to be moved by "left" and "right" arrow keys
def onarrow(event):
if event.key == "left":
if (time_slider.val == 0):
val = 0
else:
val = time_slider.val - 1
time_slider.set_val(val)
elif event.key == "right":
if (time_slider.val == (nts - 1)):
val = nts - 1
else:
val = time_slider.val + 1
time_slider.set_val(val)
else:
pass
# bind key event to the arrow key handler
kid = fig.canvas.mpl_connect("key_press_event", onarrow)
plt.show()
return 0
def __init__(self, name):
self.name = name
self.data = None
self.xspace = None
self.fit = None
self.peak = {}
self.bounds = {
'Background': [-np.inf, np.inf],
}
self.current_peak = None
self.background = 0
self.fig = plt.figure("Curvefit", figsize=(8, 8))
self.mainAx = self.fig.add_axes([0.1, 0.3, 0.7, 0.6])
#self.mainAx.plot(data[0], data[1], ".")
##button axes#####
self.buttonAx = {}
self.button = {}
self.buttonState = {
'Add': False,
'Gauss': False,
'Lorentz': False,
}
self.buttonAx['Add'] = plt.axes([0.83, 0.82, 0.1, 0.075])
self.button['Add'] = Button(self.buttonAx['Add'], 'Add', color='grey')
self.button['Add'].on_clicked(self.add_clicked)
self.buttonAx['Gauss'] = plt.axes([0.83, 0.72, 0.1, 0.075])
self.button['Gauss'] = Button(self.buttonAx['Gauss'],
'Gauss',
color='grey')
self.button['Gauss'].on_clicked(self.gauss_clicked)
self.buttonAx['Lorentz'] = plt.axes([0.83, 0.62, 0.1, 0.075])
self.button['Lorentz'] = Button(self.buttonAx['Lorentz'],
'Lorentz',
color='grey')
self.button['Lorentz'].on_clicked(self.lorentz_clicked)
###
# self.buttonAx['AmpBound'] = plt.axes([0.65, 0.2, 0.065, 0.03])
# self.button['AmpBound'] = Button(self.buttonAx['AmpBound'] ,'Bound', color='grey')
#
# self.buttonAx['MeanBound'] = plt.axes([0.65, 0.15, 0.065, 0.03])
# self.button['MeanBound'] = Button(self.buttonAx['MeanBound'] ,'Bound', color='grey')
# self.buttonAx['StdBound+'] = plt.axes([0.65, 0.10, 0.04, 0.03])
# self.button['StdBound+'] = Button(self.buttonAx['StdBound+'] ,'+', color='grey')
# self.button['StdBound+'].on_clicked(self.std_up_bound_clicked)
# self.buttonAx['StdBound-'] = plt.axes([0.60, 0.10, 0.04, 0.03])
# self.button['StdBound-'] = Button(self.buttonAx['StdBound-'] ,'-', color='grey')
# self.button['StdBound-'].on_clicked(self.std_low_bound_clicked)
# self.buttonAx['BgBound+'] = plt.axes([0.65, 0.05, 0.04, 0.03])
# self.button['BgBound+'] = Button(self.buttonAx['BgBound+'], '+', color ='grey')
# self.button['BgBound+'].on_clicked(self.bg_up_bound_clicked)
# self.buttonAx['BgBound-'] = plt.axes([0.60, 0.05, 0.04, 0.03])
# self.button['BgBound-'] = Button(self.buttonAx['BgBound-'], '-', color ='grey')
# self.button['BgBound-'].on_clicked(self.bg_low_bound_clicked)
# ###
#
self.buttonAx['Peak-'] = plt.axes([0.83, 0.5, 0.035, 0.03])
self.button['Peak-'] = Button(self.buttonAx['Peak-'],
'<',
color='grey')
self.button['Peak-'].on_clicked(self.toggle_peaks_left)
self.peak_number_ax = plt.axes([0.85, 0.54, 0.06, 0.03])
self.peak_number_ax.set_axis_off()
self.buttonAx['Peak+'] = plt.axes([0.895, 0.5, 0.035, 0.03])
self.button['Peak+'] = Button(self.buttonAx['Peak+'],
'>',
color='grey')
self.button['Peak+'].on_clicked(self.toggle_peaks_right)
self.buttonAx['Save'] = plt.axes([0.83, 0.32, 0.1, 0.075])
self.button['Save'] = Button(self.buttonAx['Save'],
"Save",
color='grey')
self.button['Save'].on_clicked(self.save_fit)
##sliders#####
self.sliderAx = {}
self.slider = {}
self.sliderVals = {'Amp': 0.5, 'Mean': 0.5, 'Std': 0.5}
self.sliderAx['Amp'] = plt.axes([0.15, 0.2, 0.25, 0.03])
self.slider['Amp'] = Slider(self.sliderAx['Amp'],
"Amp",
0,
1,
valinit=0.5,
color='grey')
self.slider['Amp'].on_changed(self.amp_slider_changed)
self.sliderAx['Mean'] = plt.axes([0.15, 0.15, 0.25, 0.03])
self.slider['Mean'] = Slider(self.sliderAx['Mean'],
"Mean",
0,
1,
valinit=0.5,
color='grey')
self.sliderAx['Std'] = plt.axes([0.15, 0.10, 0.25, 0.03])
self.slider['Std'] = Slider(self.sliderAx['Std'],
"Std",
0,
4,
valinit=2,
color='grey')
self.slider['Std'].on_changed(self.std_slider_changed)
self.sliderAx['Bg'] = plt.axes([0.15, 0.05, 0.25, 0.03])
self.slider['Bg'] = Slider(self.sliderAx['Bg'],
"Bg",
0,
1,
valinit=0.5,
color='grey')
self.slider['Bg'].on_changed(self.bg_slider_changed)
#TEXT BOX
self.textboxAx = {}
self.textbox = {}
self.textboxAx['Bg'] = plt.axes([0.5, 0.05, 0.06, 0.03])
self.textbox['Bg'] = TextBox(self.textboxAx['Bg'], "", "0")
self.textbox['Bg'].on_submit(self.bg_submit)
self.textboxAx['Std'] = plt.axes([0.5, 0.10, 0.06, 0.03])
self.textbox['Std'] = TextBox(self.textboxAx['Std'], "", "0")
self.textbox['Std'].on_submit(self.std_submit)
self.textboxAx['Mean'] = plt.axes([0.5, 0.15, 0.06, 0.03])
self.textbox['Mean'] = TextBox(self.textboxAx['Mean'], "", "0")
self.textbox['Mean'].on_submit(self.mean_submit)
self.textboxAx['Amp'] = plt.axes([0.5, 0.2, 0.06, 0.03])
self.textbox['Amp'] = TextBox(self.textboxAx['Amp'], "", "0")
self.textbox['Amp'].on_submit(self.amp_submit)
self.clickid = self.fig.canvas.mpl_connect('button_press_event',
self.mainAx_click)
####
self.datapoints = None
plt.draw # redraw the plot
#button_declaration
axButton = plt.axes([0.92, 0.6, 0.06, 0.06]) #xloc,yloc,width,heights
btn = Button(axButton, ' ADD ')
#button on click callback function
btn.on_clicked(setValue)
#Sliders declaration
axSlider1 = plt.axes([0.1, 0.20, 0.55, 0.02]) #xloc,yloc,width,height
slider1 = Slider(ax=axSlider1,
label='Tox',
valmin=1 * 10**(-9),
valmax=5 * 10**(-9),
valinit=tox,
valfmt='tox is ' + '%1.11f' + ' in m',
color="green")
axSlider2 = plt.axes([0.1, 0.15, 0.55, 0.02]) #xloc,yloc,width,height
slider2 = Slider(axSlider2,
'NA',
valmin=1,
valmax=20,
valinit=NA / (10**23),
valfmt='NA is ' + '%1.2f' + ' in 10**23 m^-3')
axSlider3 = plt.axes([0.1, 0.10, 0.55, 0.02]) #xloc,yloc,width,height
slider3 = Slider(axSlider3,
'Phi_m',
edges = camimg
edges = cv2.Canny(edges, 50, 100)
fig, ax = plt.subplots()
plt.subplots_adjust(bottom=0.25)
plt.subplot(1, 2, 1), plt.imshow(camimg, cmap='gray')
plt.title('Original'), plt.xticks([]), plt.yticks([])
plt.subplot(1, 2, 2)
edge_plot = plt.imshow(edges, cmap='gray')
plt.title('Edges'), plt.xticks([]), plt.yticks([])
axcolor = 'lightgoldenrodyellow'
axupper = plt.axes([0.15, 0.15, 0.7, 0.03], axisbg=axcolor)
upper = Slider(axupper, 'Upper', 0, 255, valinit=100)
axlower = plt.axes([0.15, 0.1, 0.7, 0.03], axisbg=axcolor)
lower = Slider(axlower, 'Lower', 0, 255, valinit=50)
def update(val):
global edges
edges = camimg
edges = cv2.Canny(edges, lower.val, upper.val)
"""
contours = measure.find_contours(edges, 0.5)
contours.sort(key=lambda x: -len(x))
final = []
for cont in contours[:ncont]:
vcirc_tot = np.sqrt(vcirc_bulge**2 + vcirc_disk**2 + vcirc_halo**2)
plot4_disk, = ax4.plot(mymdar.r, vcirc_disk, label='disk')
plot4_halo, = ax4.plot(mymdar.r, vcirc_halo, label='halo')
plot4_bulge, = ax4.plot(mymdar.r, vcirc_bulge, label='bulge')
plot4_tot, = ax4.plot(mymdar.r, vcirc_tot, label='total')
ax4.set_xlim(0, 40)
ax4.set_ylim(0, 300)
#a.plot_galaxy(ax=ax3)
#mymdar.plot_vcirc(ax=ax4)
#ax4.legend(loc='upper left', ncol=2, frameon=False)
s_Mgal = Slider(ax_Mgal, 'Mbar', 3, 15.0, valinit=np.log10(Mgal))
s_Rh = Slider(ax_Rh, 'R50', 0.01, 15.0, valinit=Rh)
s_m200 = Slider(ax_m200, 'M200', 10, 14, valinit=np.log10(M200))
s_fmbulge = Slider(ax_fmbulge, 'Bul_frac', 0.01, 1.0, valinit=f_mbulge)
s_fabulge = Slider(ax_fabulge, 'Bul_size', 0.01, 3.0, valinit=f_abulge)
data_behroozi = np.loadtxt('m200-mstr.txt')
ax1.plot(np.log10(data_behroozi[:, 0]),
np.log10(data_behroozi[:, 1] * data_behroozi[:, 0]),
ls='--')
galaxy_mstr_mhalo, = ax1.plot(np.log10(mymdar.M200), np.log10(mymdar.Mgal),
'o')
mass_concentration = np.loadtxt('mass_concentration.txt')
get_concentration = interp1d(
print 'flip map left and right'
if inps.flip_ud:
ax_v.invert_yaxis()
print 'flip map up and down'
# Colorbar
cbar = fig_v.colorbar(img, orientation='vertical')
cbar.set_label('Displacement [%s]' % inps.disp_unit)
# Axes 2 - Time Slider
ax_time = fig_v.add_axes([0.125, 0.1, 0.6, 0.07],
axisbg='lightgoldenrodyellow',
yticks=[])
tslider = Slider(ax_time,
'Years',
tims[0],
tims[-1],
valinit=tims[inps.epoch_num])
tslider.ax.bar(tims,
np.ones(len(tims)),
facecolor='black',
width=0.01,
ecolor=None)
tslider.ax.set_xticks(
np.round(np.linspace(tims[0], tims[-1], num=5) * 100) / 100)
def time_slider_update(val):
'''Update Displacement Map using Slider'''
global fig_v, ax_v, img, mask, inps, tims
timein = tslider.val
idx_nearest = np.argmin(np.abs(np.array(tims) - timein))
ax1.set_xlim(0, 1)
ax1.set_ylim(0, 100)
axcolor = 'lightgoldenrodyellow'
axs_I = plt.axes([0.7, 0.85, 0.2, 0.03], axisbg=axcolor)
axs_A = plt.axes([0.7, 0.5, 0.2, 0.03], axisbg=axcolor)
axs_R = plt.axes([0.7, 0.6, 0.2, 0.03], axisbg=axcolor)
axs_C = plt.axes([0.7, 0.55, 0.2, 0.03], axisbg=axcolor)
axs_vl = plt.axes([0.7, 0.65, 0.2, 0.03], axisbg=axcolor)
axs_vth = plt.axes([0.7, 0.8, 0.2, 0.03], axisbg=axcolor)
axs_vres = plt.axes([0.7, 0.75, 0.2, 0.03], axisbg=axcolor)
axs_tref = plt.axes([0.7, 0.7, 0.2, 0.03], axisbg=axcolor)
# Make sliders that control parameters
s_I = Slider(axs_I, r'$I \, [nA]$', 0, 1.0, valinit=0.5, color='maroon')
s_A = Slider(axs_A,
r'$A \, [mm^2\!]$',
0.01,
0.2,
valinit=0.05,
color='midnightblue')
s_R = Slider(axs_R,
r'$r \, [M\Omega\ mm^2\!]$',
0.1,
10.0,
valinit=2,
color='midnightblue')
s_C = Slider(axs_C,
r'$c \, [nF/mm^2\!]$',
1.,
def ishow(self):
"""
interactive show of trajectories
Examples
--------
.. plot::
:include-source:
>>> from pylayers.mobility.trajectory import *
>>> T=Trajectories()
>>> T.loadh5()
>>> T.ishow()
"""
fig, ax = plt.subplots()
fig.subplots_adjust(bottom=0.2, left=0.3)
t = np.arange(0, len(self[0].index), self[0].ts)
L = Layout(self.Lfilename)
fig, ax = L.showG('s', fig=fig, ax=ax)
valinit = 0
lines = []
labels = []
colors = "bgrcmykw"
for iT, T in enumerate(self):
if T.typ == 'ag':
lines.extend(
ax.plot(T['x'][0:valinit],
T['y'][0:valinit],
'o',
color=colors[iT],
visible=True))
labels.append(T.name + ':' + T.ID)
else:
lines.extend(
ax.plot(T['x'][0],
T['y'][0],
'^',
ms=12,
color=colors[iT],
visible=True))
labels.append(T.name + ':' + T.ID)
t = self[0].time()
# init boolean value for visible in checkbutton
blabels = [True] * len(labels)
########
# slider
########
slider_ax = plt.axes([0.1, 0.1, 0.8, 0.02])
slider = Slider(slider_ax,
"time",
self[0].tmin,
self[0].tmax,
valinit=valinit,
color='#AAAAAA')
def update(val):
if val >= 1:
pval = np.where(val > t)[0]
ax.set_title(str(
self[0].index[pval[-1]].time())[:11].ljust(12),
loc='left')
for iT, T in enumerate(self):
if T.typ == 'ag':
lines[iT].set_xdata(T['x'][pval])
lines[iT].set_ydata(T['y'][pval])
fig.canvas.draw()
slider.on_changed(update)
########
# choose
########
rax = plt.axes([0.02, 0.5, 0.3, 0.2], aspect='equal')
# check (ax.object, name of the object , bool value for the obsject)
check = CheckButtons(rax, labels, tuple(blabels))
def func(label):
i = labels.index(label)
lines[i].set_visible(not lines[i].get_visible())
fig.canvas.draw()
check.on_clicked(func)
fig.canvas.draw()
plt.show(fig)
"""cuantas veces presentamos el estimulo y cuantas veces el sujeto responde al estimulo"""
ensayos = 60
estimulo = numpy.linspace(0, ensayos, ensayos)
valor_ud = numpy.zeros(len(estimulo)) #len dice longitud
"""parametros de la ley de weber"""
k = 1
c = [k] * ensayos #constante de Weber repitela cuantas veces ensayos haya
S0 = 10 #umbral debajo del cual el estimulo es percibido
"""plots"""
fig, ax = plt.subplots(2)
plt.subplots_adjust(left=0.15, bottom=0.25)
ax_k = plt.axes([0.15, 0.1, 0.65, 0.03], axisbg='lightgoldenrodyellow')
slider_k = Slider(ax_k, 'k', .5, 1.5, valinit=k)
for i in range(len(estimulo)):
if estimulo[i] <= S0:
valor_ud[i] = 0
else:
valor_ud[i] = S0 + k * estimulo[i - S0]
def update(var):
k = slider_k.val
c = [k] * ensayos
for i in range(len(estimulo)):
if estimulo[i] <= S0:
valor_ud[i] = 0
else:
##########################################################################################################
fig, ax = plt.subplots()
plt.subplots_adjust(left=0.25, bottom=0.25)
f0 = 1
delta_f = 1
g = nx.random_k_out_graph(n=f0, k=2, alpha=0.5)
axcolor = 'lightgray'
axfreq = plt.axes([0.25, 0.06, 0.65, 0.03], facecolor=axcolor)
sfreq = Slider(axfreq,
'noise',
1,
20,
valinit=f0,
valstep=delta_f,
valfmt='%0.0f')
active_nodes = []
non_active_nodes = []
for i in range(number_of_clusters):
Net.nodes[control_nodes[i]] = 1
for i in range(len(Net.nodes)):
if Net.nodes[i] == 1:
active_nodes.append(i)
else:
non_active_nodes.append(i)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for i in range(xlin.shape[0]):
ax.plot(xlin[i], ylin[i], zlin[i])
s = np.zeros(v.shape[0])
c = np.zeros(v.shape[0])
val = 1
s = np.absolute(v[:, val - 1])
s = s * 300
c = np.where(v[:, val - 1] > 0, 0, 1)
Stateplot = ax.scatter(xyz[:, 0], xyz[:, 1], xyz[:, 2], zdir='z', s=s)
Stateplot.set_cmap("bwr")
plt.subplots_adjust(bottom=0.25)
axcolor = 'lightgoldenrodyellow'
axfreq = plt.axes([0.25, 0.1, 0.65, 0.03], facecolor=axcolor)
state = Slider(axfreq, 'State', 1, v.shape[0], valinit=1, valstep=1)
def update(val):
val = state.val
val = int(val)
s = np.absolute(v[:, val - 1])
s = s * 300
print(s)
c = np.where(v[:, val - 1] > 0, 0, 1)
print(c)
Stateplot._sizes = s
Stateplot.set_array(c)
fig.canvas.draw_idle()
def main():
fig, ax = plt.subplots()
plt.subplots_adjust(left=0.12, bottom=0.4,top=0.8)
phasesample = np.linspace(0,1,101)
l, = ax.plot(phasesample,phasesample, lw=2)
ax.set_ylabel("rel. flux (%)")
ax.set_xlabel("phase")
ax.set_ylim(-10,10)
ax.margins(x=0)
topax = ax.twiny()
topax.set_xticks([0,0.25,0.5,0.75,1])
topax.set_xticklabels(['farthest','toward','nearest','away','farthest'])
axcolor = 'lightgoldenrodyellow'
axteff = plt.axes([0.25, 0.05, 0.6, 0.03], facecolor=axcolor)
axlogg = plt.axes([0.25, 0.1, 0.6, 0.03], facecolor=axcolor)
axporb = plt.axes([0.25, 0.15, 0.6, 0.03], facecolor=axcolor)
axk = plt.axes([0.25, 0.2, 0.6, 0.03], facecolor=axcolor)
axinc = plt.axes([0.25, 0.25, 0.6, 0.03], facecolor=axcolor)
steff = Slider(axteff, 'Teff (K)', 8300, 30000, valinit=10000, valfmt=u'%1.0f') #valstep=50,
slogg = Slider(axlogg, 'log(g) (cgs)', 4, 7.4, valinit=5.5, valfmt=u'%1.1f') #valstep = 0.1,
sporb = Slider(axporb, 'P_orb (hours)', 0.25, 24, valinit=2 ) #valstep = 0.05
sk = Slider(axk, 'K (km/s)', 20, 620, valinit=200, valfmt=u'%1.0f') #valstep = 10,
sinc = Slider(axinc, 'inc (deg)', 1, 90, valinit=45, valfmt=u'%1.0f') #valstep = 1,
def update(val):
df = calc(teff=steff.val,logg=slogg.val,porb=sporb.val,k=sk.val,inc=sinc.val)
l.set_ydata(-df["EV (%)"][0]*np.cos(phasesample*4*np.pi) +
df["DB (%)"][0]*np.sin(phasesample*2*np.pi))
for i in range(len(df.values[0])):
mpl_table._cells[(1, i)]._text.set_text('%.4f' % df.values[0][i])
fig.canvas.draw_idle()
df = calc(teff=steff.val,logg=slogg.val,porb=sporb.val,k=sk.val,inc=sinc.val)
axvals = plt.axes([0.12, 0.88, 0.78, 0.1], facecolor=axcolor)
font_size=8
bbox=[0, 0, 1, 1]
axvals.axis('off')
mpl_table = axvals.table(cellText = [['%.4f' % j for j in i] for i in df.values],
bbox=bbox, colLabels=df.columns)
mpl_table.auto_set_font_size(False)
mpl_table.set_fontsize(font_size)
update(1)
steff.on_changed(update)
slogg.on_changed(update)
sporb.on_changed(update)
sk.on_changed(update)
sinc.on_changed(update)
plt.show()