def plot_histogram(self, bf, row, col, plot_sigma=True,
hold=False):
self.bf = bf
if self.bf is None:
raise Exception("Need to pass in a BinFile instance to plot object")
if not hasattr(self.bf, 'data_out'):
raise Exception("BinFile instance does not have any data.")
if not hold:
self.clear()
self.lines = []
try:
h = self.bf.data_out[row, col, :, :].real.flatten()
except:
print "Error in extracting histogram"
if hasattr(self.bf, 'pixel_label'):
label="Row%d, Col%d (Pix: %s)" % (self.bf.row_start+row, self.bf.col_start+col, self.bf.pixel_label.get((row, col), 'NC'))
else:
label="Row%d, Col%d" % (self.bf.row_start+row, self.bf.col_start+col)
self.hist(h, bins=20, label=label)
if MATPLOTLIBV1_0:
datacursor()
self.set_subplot_title("%s" % self.bf.basename)
if plot_sigma:
y1, y2 = self.get_ylims()
for x in (-8, 8):
self.plot([x, x], [y1, y2], 'r--', linewidth=2,
label="_nolegend_")
self.set_xlim(-64, 64)
self.set_legend(loc='best')
def Graph_Instant_boot():
print ('inside Graph_Instant_boot graph')
Plot1 = np.loadtxt('Output_VHFS_Instant_boot.txt')
Plot2 = np.loadtxt('Output_VHFS_Instant_boot_2.txt')
fig = plt.figure()
#pl.subplot(311)
pl.title('Instant_Boot: VHFS1 vs VHFS2')
pl.xlabel('Incrementals')
pl.ylabel('Time Taken in secs')
pl.xlim(-1,11)
x = Plot1[:,0]
y = Plot1[:,1]
y2 = Plot2[:,1]
#yerr = Plot1[:,4]
#xticks = Plot1[:,1]
#plt.xticks(xticks)
#plt.xscale('log')
#plt.yscale('log')
#plt.xticks(xticks)
#pl.errorbar(x,y,yerr,ecolor='b')
pl.plot(x,y, 'b', label = 'VHFS1', marker = 'o')
pl.plot(x,y2, 'y', label = 'VHFS2', marker = 'o')
pl.legend(loc = 'upper right', numpoints = 1)
datacursor(display='multiple', draggable=True)
#pl.show()
pl.savefig('Instant_boot_VHFS_vs_VHD.ps')
pl.savefig('Instant_boot_VHFS_vs_VHD.png')
pl.savefig('Instant_boot_VHFS_vs_VHD.pdf')
print ('endddd')
plt.close(fig)
def plot(self):
specs = pl.array( list(set([ l['spec'] for l in self.lines ])) )
specs.sort()
self.specs = specs
pl.figure()
pl.hold('on')
pl.grid('on')
pl.jet()
lines = []
lines_spec = list(pl.zeros(len(specs)))
for i in range(0,len(self.lines)):
ispc = pl.find( specs == self.lines[i]['spec'] )
self.colr = pl.cm.get_cmap()( float(ispc)/len(specs) )
wl = self.lines[i]['wave']
ri = float(self.lines[i]['rel_int'])
lines.append( pl.plot( [wl, wl], [0., ri if not isnan(ri) else 0.], '.-', color=self.colr )[0] )
lines_spec[ispc] = lines[-1]
datacursor(lines,formatter='x={x:8.3f}\ny={y:8.3f}'.format)
pl.rc('text',usetex=True)
pl.xlabel('$\lambda ~ [\AA]$')
pl.ylabel('relative intensity [arb]')
pl.title('Spectrum for '+self.spec+' from NIST ASD')
if len(specs) > 1:
pl.legend( lines_spec,specs )
pl.show()
def plot_k_walls(k_walls, plot_range=None,
plot_data_points=False,):
"""
Plot K-walls for debugging purpose.
"""
pyplot.figure()
pyplot.axes().set_aspect('equal')
for k_wall in k_walls:
xs = k_wall.get_xs()
ys = k_wall.get_ys()
pyplot.plot(xs, ys, '-', label=k_wall.identifier)
if(plot_data_points == True):
pyplot.plot(xs, ys, 'o', color='k', markersize=4)
if plot_range is None:
pyplot.autoscale(enable=True, axis='both', tight=None)
else:
[[x_min, x_max], [y_min, y_max]] = plot_range
pyplot.xlim(x_min, x_max)
pyplot.ylim(y_min, y_max)
mpldatacursor.datacursor(
formatter='{label}'.format,
hover=True,
)
pyplot.show()
def measure_iv(self):
self.get_vd_values()
self.textBrowser.append('Measuring I-V from ' + str(self.vd_start) +
'V to ' + str(self.vd_stop) + ' V')
vd_values = np.linspace(self.vd_start, self.vd_stop, num=self.vd_steps,
endpoint=True)
id_values = np.zeros_like(vd_values)
# self.measure_current()
for i, vd in np.ndenumerate(vd_values):
self.set_voltage_vd(vd)
id_values[i] = self.measure_current()
if self.stop_engaged:
print('stop')
self.stop_engaged = False
break
self.update_progress((i[0] + 1.0)/self.vd_steps)
self.set_voltage_vd(0)
self.textBrowser.append('Measurement completed')
data = pd.DataFrame({'Voltage': vd_values, 'Current': id_values})
data.set_index('Voltage', inplace=True)
self.data_iv = data
data.to_csv('measurement_iv.csv')
data.to_msgpack('measurement_iv.msgpack')
ax = data.plot()
datacursor(ax)
# datacursor(display='single', draggable=True)
winsound.Beep(750, 1000)
fig = ax.get_figure()
fig.savefig('measurement_iv.png')
plt.show()
def exploredata1d(data, slider='chans', stack='ants'):
""" Set up interactive 1d (line) plotting for vis data of dimension (ints, ants, chans). """
axdict = {'ints': 0, 'ants': 1, 'chans': 2}
assert slider in axdict.keys() and stack in axdict.keys(), 'slider or stack param not allowed'
slax = axdict[slider]
# need to account for axis shift after first 'take'
stax = axdict[stack] if axdict[stack] <= slax else axdict[stack] - 1
slmax = data.shape[axdict[slider]]
stmax = data.shape[axdict[stack]]
xaxis = [name for name in axdict.keys() if name != slider and name != stack][0]
fcndict = {'Real': np.real, 'Imag': np.imag, 'Amp': np.abs, 'Phase': np.angle}
@interact(sl=(0, slmax, 1), f=['Real', 'Imag', 'Amp', 'Phase'])
def plotautos(sl, f):
pl.figure(figsize=(15,8))
pl.clf()
pl.xlabel(xaxis)
pl.ylabel(f)
fcn = fcndict[f]
for st in range(stmax):
pl.plot(fcn(data.take(sl, axis=slax).take(st, axis=stax)), label='{0} {1}'.format(stack.rstrip('s'), st))
print('Plotting {0} vs. {1}.'.format(f, xaxis))
print('Slider for {0}. A line per {1}.'.format(slider, stack.rstrip('s')))
print('Click on a line to see {0} number'.format(stack.rstrip('s')))
datacursor(formatter='{label}'.format)
def main(icorr_mean_list):
suffix = rate2suffix(icorr_mean_list)
# load data
datapath = os.path.join(os.path.abspath('./'), 'data')
filename = 'popdata_'+suffix+'.npz'
datafile = os.path.join(datapath,filename)
if os.path.isfile(datafile) is False:
print 'no data available, execute Life_Cycle_Optimization.py with \
icorr_mean_list={} fist'.format(icorr_mean_list)
sys.exit(1)
else:
popdata = np.load(datafile)
allpop = popdata['allpop']
allfits = popdata['allfits']
front = popdata['front']
frontfits = popdata['frontfits']
pop = popdata['pop']
popfits = popdata['popfits']
plt.ion()
plt.close('all')
##plt.semilogx(np.array(frontfits)[:,0], np.array(frontfits)[:,1], 'bo', markeredgecolor='b')
#plt.semilogx(np.array(popfits)[:,0], np.array(popfits)[:,1], 'bo', markeredgecolor='b')
#for popfit in popfits:
for ind, popfit in zip(pop, popfits):
## journal version
#plt.semilogx(popfit[0], popfit[1], 'bo',markeredgecolor='b',
#label=u'flexure: {:d}, shear: {:d}, deck: {:d}'.format(ind[0], ind[1], ind[2]))
# conference version
plt.semilogx(popfit[0], popfit[1], 'bo',markeredgecolor='b',
label=u'({:d},{:d},{:d})'.format(ind[0], ind[1], ind[2]))
plt.ylim((-1,np.max(popfits)*1.1))
ax = plt.gca()
ax.ticklabel_format(axis='y', style='sci', scilimits=(-3,3))
plt.xlabel(u'Failure probability')
plt.ylabel(u'Strengthening cost (mm\\textsuperscript{3})')
## journal version
#annotate_text = u'P={x:.2e}, C={y:.2e}\n {{ {label} }}'
#datacursor(formatter=annotate_text.format,display='multiple', draggable=True,
#bbox=None, fontsize=9,
#arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
# conference version
annotate_text = u'{label}'
datacursor(formatter=annotate_text.format,display='multiple', draggable=True,
bbox=None, fontsize=9,
arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
pause = raw_input('press any key after annotation...')
plt.semilogx(np.array(allfits)[:,0], np.array(allfits)[:,1], 'o', markerfacecolor='lightgrey',
markeredgecolor='lightgrey', alpha=0.8)
plt.semilogx(np.array(popfits)[:,0], np.array(popfits)[:,1], 'bo', markeredgecolor='b')
def implot_data(self, bf, data_type='amp',
vmin=None, vmax=None,
hold=False, title=None,
colorbar=True, sti=False, **kwargs):
self.bf = bf
if self.bf is None:
raise Exception("Need to pass in a BinFile instance to plot object")
self.check_alive()
if not hold:
self.clear()
if not hasattr(self.bf, 'cross_corr') and not hasattr(self.bf, 'sti_cc'):
raise Exception("BinFile does not have cross correlation data. get_cross_corr_data() first on binfile")
if sti:
if not hasattr(self.bf, 'sti_cc'):
raise Exception("BinFile does not have sti cross corr data. Run sti_cross_correlate first")
self.bf.cc = self.bf.sti_cc.mean(axis=3).mean(axis=2)
else:
self.bf.cc = self.bf.cross_corr.mean(axis=2)
if MATPLOTLIBV1_0:
interpolation = 'none'
else:
interpolation = 'nearest'
if data_type == 'amp':
self.image = self.imshow(10*numpy.log10(numpy.abs(self.bf.cc)),
cmap=cm.spectral, interpolation=interpolation,
vmin=vmin, vmax=vmax,
**kwargs)
else:
self.image = self.imshow(numpy.angle(self.bf.cc),
cmap=cm.spectral, interpolation=interpolation,
vmin=vmin, vmax=vmax,
**kwargs)
ax, kw = self.plotobj._get_current_axes()
if MATPLOTLIBV1_0:
datacursor(self.image, display='single',bbox=dict(fc='white'),
arrowprops=dict(arrowstyle='simple', fc='white', alpha=0.5),
formatter="x: {x:.0f}\ny: {y:.0f}\nz: {z:.2f}".format)
def format_coord(x, y):
if data_type == 'amp':
z = (10*numpy.log10(numpy.abs(self.bf.cc)))[x, y]
else:
z = (numpy.angle(self.bf.cc))[x, y]
return 'x=%.1f, y=%.1f, z=%.2f' % (x, y, z)
ax, kw = self.plotobj._get_current_axes()
ax.format_coord = format_coord
# self.set_subplot_title(title)
if title is None:
title = "%s" % self.bf.basename
self.set_subplot_title(title)
if colorbar:
self.colorbar()
def Graph_GFS_write():
print ('inside Graph_GFS graph')
Plot3 = np.loadtxt('Merge_write.txt')
Plot4 = np.loadtxt('Merge_read.txt')
fig = plt.figure()
pl.subplot(311)
pl.title('Write :: Chunk_and_Block Size vs Speed')
pl.xlabel('Chunk_and_Block Size in MB')
pl.ylabel('Speed in MBps')
#pl.xlim(0,10)
x = Plot3[:,1]
y = Plot3[:,3]
yerr = Plot3[:,4]
xticks = Plot3[:,1]
#plt.xticks(xticks)
plt.xscale('log')
#plt.yscale('log')
#plt.xticks(xticks)
pl.errorbar(x,y,yerr,ecolor='b')
#pl.plot(x,y, 'b-', marker ='o',)
datacursor(display='multiple', draggable=True)
#cursor = Dcursor.FollowDotCursor(ax, x, y)
#plt.show()
#pl.show()
pl.subplot(313)
pl.title('Read :: Chunk_and_Block Size vs Speed')
pl.xlabel('Chunk_and_Block Size in MB')
pl.ylabel('Speed in MBps')
#pl.xlim(0,10)
x = Plot4[:,1]
y = Plot4[:,3]
yerr = Plot4[:,4]
xticks = Plot4[:,1]
pl.xticks(xticks)
plt.xscale('log')
pl.errorbar(x,y,yerr,ecolor='b')
datacursor(display='multiple', draggable=True)
#pl.plot(x,y, 'b-', marker = 'o')
#pl.show()
#Dcursor2.DataCursor([write,read])
pl.show()
pl.savefig('GFS_Reading.ps')
pl.savefig('GFS_Reading.png')
pl.savefig('GFS_Reading.pdf')
print ('endddd')
plt.close(fig)
def omni_view(reds,vis,pol,int=10,chan=500,norm=False,cursor=True,save=None,colors=None,symbols=None, ex_ants=[]):
if not colors:
colors = ["#006BA4", "#FF7F0E", "#2CA02C", "#D61D28", "#9467BD", "#8C564B", "#E377C2", "#7F7F7F", "#BCBD22", "#17BECF"]
if not symbols:
symbols = ["o", "v", "^", "<", ">", "*"]
points = []
sym = []
col = []
bl = []
ngps = len(reds)
if save:
plt.clf()
plt.cla()
for i,gp in enumerate(reds):
c = colors[i%len(colors)]
s = symbols[i/len(colors)]
for r in gp:
if np.any([ant in r for ant in ex_ants]): continue
try:
points.append(vis[r][pol][int,chan])
bl.append(r)
except(KeyError):
points.append(np.conj(vis[r[::-1]][pol][int,chan]))
bl.append(r[::-1])
sym.append(s)
col.append(c)
points = np.array(points)
max_x=0
max_y=0
ax = plt.subplots(111)
for i,pt in enumerate(points):
if norm:
ax.scatter(pt.real/np.abs(pt), pt.imag/np.abs(pt), c=col[i], marker=sym[i], s=50, label='{}'.format(bl[i]))
else:
ax.scatter(pt.real, pt.imag, c=col[i], marker=sym[i], s=50, label='{}'.format(bl[i]))
if np.abs(pt.real) > max_x: max_x = np.abs(pt.real)
if np.abs(pt.imag) > max_y: max_y = np.abs(pt.imag)
if norm:
plt.xlim(-1,1)
plt.ylim(-1,1)
else:
plt.xlim(-max_x-.1*max_x,max_x+.1*max_x)
plt.ylim(-max_y-.1*max_y,max_y+.1*max_y)
plt.ylabel('imag(V)')
plt.xlabel('real(V)')
if cursor:
from mpldatacursor import datacursor
datacursor(formatter='{label}'.format)
if save:
plt.savefig(save)
return None
def lifetimefitting(icorr_mean_list, str_yr_list=[0., 0., 0.]):
from scipy import stats
from scipy.optimize import curve_fit
# load data
suffix = rate2suffix(icorr_mean_list)
filename = 'pfhistory_str_'
for ti in str_yr_list:
filename = filename + str(int(ti)) + '_'
datapath = os.path.join(os.path.abspath('./'), 'data')
filename = filename+suffix+'.npz'
datafile = os.path.join(datapath,filename)
if os.path.isfile(datafile) is False:
print 'no data available, execute Life_Cycle_History.py with \
icorr_mean_list={} and str_yr_list={} fist'.format(icorr_mean_list,
str_yr_list)
sys.exit(1)
else:
pfhistory = np.load(datafile)
time_array = pfhistory['time']
pf_sys = pfhistory['system']
# lifetime fitting
# candidate cdfs
def fitexpon(xdata, *params):
lbd = params[0]
return stats.expon.cdf(xdata, scale=1./lbd)
def fitweibull(xdata, *params):
k = params[0] # shape param k in Weibull wiki
lbd = params[1] # scale param lbd in Weibull wiki
return stats.weibull_min.cdf(xdata, k, scale=lbd)
def fitgamma(xdata, *params):
k=params[0]
theta = params[1]
return stats.gamma.cdf(xdata, k, scale=theta)
poptExpon, pcovExpon = curve_fit(fitexpon, time_array, pf_sys, p0=[1.], bounds=(0.,np.inf))
poptWbl, pcovWbl = curve_fit(fitweibull, time_array, pf_sys, p0=[1.,5.], bounds=([0.,0.],[np.inf, np.inf]))
poptGamma, pcovGamma = curve_fit(fitgamma, time_array, pf_sys, p0=[1.,1.], bounds=([0.,0.],[np.inf,np.inf]))
plt.ion()
plt.figure()
plt.semilogy(time_array, pf_sys, 'o', label='$T_f$ data')
plt.semilogy(time_array, fitexpon(time_array, poptExpon[0]), ls='--', label='Exponential')
plt.semilogy(time_array, fitweibull(time_array,poptWbl[0],poptWbl[1]), ls='-', label='Weibull')
plt.semilogy(time_array, fitgamma(time_array,poptGamma[0],poptGamma[1]), ls=':', label='Gamma')
plt.xlabel('Time (year)')
plt.ylabel('Failure probability')
#plt.legend(loc='lower right', fontsize=9)
datacursor(formatter='{label}'.format,display='multiple', draggable=True,
bbox=None, fontsize=9,
arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
def plot_avg_time_locked_data(timeLockedData, timeAxis, subplot=None, timeToPlot=None, remove_channels=None, picker=None, labels=False, figure_id=0, figure=None):
if timeToPlot==None:
if np.size(np.shape(timeLockedData)) > 1:
samplesToPlot = [0, np.shape(timeLockedData)[1]]
else:
samplesToPlot = [0, np.shape(timeLockedData)[0]]
else:
Freq = len(timeAxis)/(timeAxis[-1]-timeAxis[0])
startingTimeDif = timeToPlot[0] - timeAxis[0]
endingTimeDif = timeToPlot[1] - timeAxis[0]
if startingTimeDif < 0:
raise ArithmeticError("The starting time to plot must be after the starting time of the trial")
if endingTimeDif < 0:
raise ArithmeticError("The end time to plot must be after the starting time of the trial")
samplesToPlot = [startingTimeDif*Freq, endingTimeDif*Freq]
if figure is None:
fig = plt.figure(figure_id)
else:
fig = figure
if subplot is not None:
ax = fig.add_subplot(subplot)
else:
ax = fig.add_subplot(111)
if picker:
def on_pick(event):
event.artist.set_visible(not event.artist.get_visible())
print(ax.lines.index(event.artist))
fig.canvas.draw()
fig.canvas.callbacks.connect('pick_event', on_pick)
if remove_channels is not None:
timeLockedData[remove_channels, :] = float('nan')
if np.size(np.shape(timeLockedData)) > 1:
lines = ax.plot(timeAxis[samplesToPlot[0]:samplesToPlot[1]], np.transpose(timeLockedData[:, samplesToPlot[0]:samplesToPlot[1]]), picker=picker)
else:
lines = ax.plot(timeAxis[samplesToPlot[0]:samplesToPlot[1]], timeLockedData[samplesToPlot[0]:samplesToPlot[1]], picker=picker)
if labels:
datacursor(hover=True)
for i in np.arange(0,len(lines)):
lines[i].set_label(str(i))
fig.add_subplot(ax)
plt.show()
return ax
def plot_iv(data,range,res,symbol):
fig=plt.figure()
ax1 = fig.add_subplot(111)
ax2 = ax1.twiny()
act,=ax1.plot(data.DELTA,data.VOLATILITY,'r*',label='Actual Smile')
fit,=ax1.plot(range,res,'g',label='Fitted Smile')
ax1.set_xlabel('DELTA')
ax1.set_ylabel('VOLATILITY')
#ax2.plot(data.STRIKE_PR,data.VOLATILITY,'b*',label='Actual Smile')
ax2.set_xticks(data.DELTA)
ax2.set_xticklabels(data.STRIKE_PR,rotation=90,fontsize=12)
ax2.set_xlabel('STRIKE')
#plt.show()
datacursor()
plt.savefig("%s_VOL.jpg"%symbol)
def datacursor(self, widget, unit=None, labname='Label'):
''' Plot datacursors (useful when the number of lines gets confusing)
Parameters
----------
unit and labname:
to customize the info box'''
# Clean previous cursors (prevent overlaps with remaining cursors)
while len(self.cursors) > 0:
dc = self.cursors.pop()
dc.hide().disable()
if self.actionDatacursor.isChecked() and CURSOR_AVAIL:
def formatter(x=None, y=None, z=None, s=None, label=None, **kwargs):
ax = kwargs['event'].mouseevent.inaxes
output = []
output.append(u't: {0:0.3e} s'.format(x))
output.append(u'y: {0:0.3e} {1}'.format(y, unit))
for key, val in zip(['z', 's'], [z, s]):
if val is not None:
try:
output.append(
u'{key}: {val:0.3e}'.format(key=key, val=val))
except ValueError:
# X & Y will be strings at this point.
# For masked arrays, etc, "z" and s values may be a
# string
output.append(
u'{key}: {val}'.format(key=key, val=val))
# label may be None or an empty string (for an un-labeled AxesImage)...
# Un-labeled Line2D's will have labels that start with an
# underscore
if label and not label.startswith('_'):
output.append(u'{0}: {1}'.format(labname, label))
if kwargs.get(u'point_label', None) is not None:
output.append(
u'Point: ' + u', '.join(kwargs['point_label']))
return u'\n'.join(output)
for ax in widget.axes:
if not ax.cursorlines is None:
self.cursors.append(mpldatacursor.datacursor(
ax.cursorlines, hover=True, size=10, color='k',
bbox=dict(fc='white', alpha=0.9),
formatter=formatter))
return None
def front_deprecated(icorr_mean_list):
suffix = rate2suffix(icorr_mean_list)
# load data
datapath = os.path.join(os.path.abspath('./'), 'data')
filename = 'popdata_'+suffix+'.npz'
datafile = os.path.join(datapath,filename)
if os.path.isfile(datafile) is False:
print 'no data available, execute Life_Cycle_Optimization.py with \
icorr_mean_list={} fist'.format(icorr_mean_list)
sys.exit(1)
else:
popdata = np.load(datafile)
# all pop is the same as pop
allpop = popdata['allpop']
allfits = popdata['allfits']
front = popdata['front']
frontfits = popdata['frontfits']
pop = popdata['pop']
popfits = popdata['popfits']
plt.ion()
plt.figure()
##plt.semilogx(np.array(frontfits)[:,0], np.array(frontfits)[:,1], 'bo', markeredgecolor='b')
for ind, popfit in zip(front, frontfits):
plt.semilogx(popfit[0], popfit[1], 'bo',
label=u'flexure: {:d}, shear: {:d}, deck: {:d}'.format(ind[0], ind[1], ind[2]))
plt.ylim((-1,np.max(popfits)*1.01))
ax = plt.gca()
ax.ticklabel_format(axis='y', style='sci', scilimits=(-3,3))
plt.xlabel(u'Failure probability (log scale)', fontsize=12)
plt.ylabel(u'Strengthening cost (mm\\textsuperscript{3})', fontsize=12)
annotate_text = u'P={x:.2e}, C={y:.2e}\n {{ {label} }}'
datacursor(formatter=annotate_text.format,display='multiple', draggable=True,
bbox=None, fontsize=12,
arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
pause = raw_input('press any key after annotation...')
def u_plot(self, pvals, ufe):
"""
Plots U vs P for landau film.
Parameters
----------
pvals: 1d np array of polarization charge values
ufe: 1d np array of energy densities calculated at xVals.
Returns
-------
n/a
"""
fig1 = plt.figure()
fig1.set_facecolor("white")
plt.cla()
ax1 = fig1.add_subplot(111)
datacursor(ax1.plot(pvals * 1e6, ufe))
ax1.set_xlabel("Polarization Charge, P (uC/cm^2)")
ax1.set_ylabel("Energy, U")
def make_datacursor(mode, filename, my_plt, fig):
if mode == "mag":
datacursor(display='multiple',
tolerance=10,
formatter="Freq: {x:.3e} Hz \nAmp:{y:.1f} Db".format,
draggable=True)
else:
datacursor(display='multiple',
tolerance=10,
formatter="Freq: {x:.3e} Hz \nFase:{y:.1f} grados".format,
draggable=True)
my_plt.minorticks_on()
my_plt.grid(which='major', linestyle='-', linewidth=0.3, color='black')
my_plt.grid(which='minor', linestyle=':', linewidth=0.1, color='black')
my_plt.show()
input("Press Enter ")
fig.savefig(filename, dpi=300)
my_plt.cla()
my_plt.close()
def make_datacursor_zin(mode, filename, my_plt, fig, ax):
add_legend_zin(mode, ax, my_plt)
if mode == "mag":
datacursor(
display='multiple',
tolerance=10,
formatter="Freq: {x:.3e} Hz \nZin:{y:.1f} K $\Omega$".format,
draggable=True)
else:
datacursor(display='multiple',
tolerance=10,
formatter="Freq: {x:.3e} Hz \nFase:{y:.1f} grados".format,
draggable=True)
my_plt.show()
input("Press Enter ")
fig.savefig(filename, dpi=300)
my_plt.cla()
my_plt.close()
def plot_nist_lines_to_axis(self, axis, normalize_max=None, legend=True, measure='Aki', alpha=0.5): # measure='Aki'
if self._check_download_conditions():
self.get_lines()
logger.info("Plotting NIST lines to {0}".format(axis))
specs = np.array(list(set([l['spectrum'] for l in self.lines])))
specs.sort()
maxi = self._get_maximum_relative_intensity(measure)
lines = []
lines_spec = list(np.zeros(len(specs)))
for i in range(0,len(self.lines)):
wl = self.lines[i]['wave']
if wl > self.lower_wavelength and wl < self.upper_wavelength:
ispc, = np.nonzero(np.ravel(specs == self.lines[i]['spectrum']))
self.colr = plt.cm.get_cmap('tab20c_r')(float(ispc)/len(specs))
if normalize_max is None:
ri = float(self.lines[i][measure])
else:
ri = float(self.lines[i][measure]) / maxi * normalize_max
lines.append(axis.plot([wl, wl], [0., ri if not isnan(ri) else 1.e-6], '.-', lw=1., color=self.colr, alpha=alpha)[0])
assert len(ispc) == 1 # dont know if correct, but working
lines_spec[ispc[0]] = lines[-1]
# datacursor(lines)
logger.info("Plotting {0} lines of {1} in total for {2} from "
"{3:2.3e} to {4:2.3e} nm".format(len(lines), len(self.lines), self.spectrum, self.lower_wavelength,
self.upper_wavelength))
datacursor(lines, formatter='{x} nm'.format)
if legend:
if len(specs) > 1:
# axis.legend(handles=lines_spec, labels=specs, loc=0)
axis.legend(lines_spec, specs, loc=0)
def PlotFFT(self):
fig, axs = plt.subplots(nrows=1, ncols=2, figsize=(80, 60))
# signal plot
axs[0].plot(self.t, self.f)
axs[0].grid()
axs[0].set_xlabel('time (s)', fontsize=16)
axs[0].set_ylabel('Voltage', fontsize=16)
axs[0].set_title('Signal', fontweight='bold', fontsize=20)
# frequency
freqs, Ampts = self.Freq()
h = axs[1].plot(freqs, Ampts, 'r')
datacursor(h)
axs[1].grid()
axs[1].set_xlabel('frequency (Hz)', fontsize=16)
axs[1].set_ylabel('Voltage', fontsize=16)
axs[1].set_title('FFT', fontweight='bold', fontsize=20)
plt.show()
def drawChunkChangePlot(self):
x = range(0, len(self.changedChunksAll))
fig, ax = plt.subplots()
ax.plot(x, self.changedChunksBlock, label='changedChunksBlock')
ax.plot(x, self.changedChunksBlockEntity, label='changedChunksBlockEntity')
ax.plot(x, self.changedChunksEntity, label='changedChunksEntity')
ax.plot(x, self.changedChunksAll, label='changedChunksAll')
# ax.plot(self.serverWorldTimeTicks, self.changedEntities, label='# changed entities', linestyle="-", color='g')
# ax.plot(self.serverWorldTimeTicks, self.changedTileEntities, label='# changed tile entities', color='orange')
# ax.plot(self.serverWorldTimeTicks, self.changedBlocks, label='# changed blocks', color='red')
# ax.plot(self.serverWorldTimeTicks, self.changedSections, label='# changed sections', linestyle='-',
# color='blue')
# ax.plot(self.serverWorldTimeTicks, self.changedChunks, label='# changed chunks', color='black')
plt.legend()
ax.set(xlabel='Interval number (' + self.intervalLength + "s per Interval)", ylabel='Changed Chunks', title='Changed Chunks over time')
ax.grid()
datacursor()
plt.show()
def costkeeping(icorr_mean_list):
suffix = rate2suffix(icorr_mean_list)
# load data
datapath = os.path.join(os.path.abspath('./'), 'data')
filename = 'costkeeping_'+suffix+'.npz'
datafile = os.path.join(datapath,filename)
if os.path.isfile(datafile) is False:
print 'no data available, execute Life_Cycle_Optimization.py with \
icorr_mean_list={} fist'.format(icorr_mean_list)
sys.exit(1)
else:
costkeeping = np.load(datafile)
plt.ion()
plt.figure()
plt.plot(costkeeping['flexure'][0,:], costkeeping['flexure'][1,:], 'b-',
label='Flexure (girder)')
plt.plot(costkeeping['shear'][0,:], costkeeping['shear'][1,:], 'r--',
label='Shear (girder)')
plt.plot(costkeeping['deck'][0,:], costkeeping['deck'][1,:], 'g-.',
label='Deck')
service_life = np.max((np.max(costkeeping['flexure'][0,:]),
np.max(costkeeping['shear'][0,:]), np.max(costkeeping['deck'][0,:])))
max_cost = np.max((np.max(costkeeping['flexure'][1,:]),
np.max(costkeeping['shear'][1,:]), np.max(costkeeping['deck'][1,:])))
plt.xlim((-1,service_life+1))
plt.ylim((-1,max_cost*1.01))
plt.xlabel('Strengthening time (year)')
plt.ylabel('Volumn of FRP (mm\\textsuperscript{3})')
ax = plt.gca()
ax.ticklabel_format(axis='y', style='sci', scilimits=(-3,3))
datacursor(formatter='{label}'.format,display='multiple', draggable=True,
bbox=None, fontsize=9,
arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
pause = raw_input('press any key after annotation...')
def show_plot():
plt.ioff()
plt.rcParams['figure.figsize'] = [20, 15]
_fig, ax = plt.subplots()
x = [d[0] for d in n]
y = [d[1] for d in n]
ax.scatter(x, y, s=5)
mpldatacursor.datacursor(date_format="%x", bbox={
'boxstyle': 'round,pad=0.5',
'fc': 'lightblue',
'alpha': 0.95,
'edgecolor': 'black'
})
plt.ion()
plt.show()
def noMoreIntervals(self):
fig, ax = plt.subplots()
ax.plot(self.timepoints,
self.loaded_chunks,
label='#loaded chunks',
linestyle="-",
color='g')
ax.plot(self.timepoints,
self.tile_entities,
label='#tile entities',
color='orange')
ax.plot(self.timepoints, self.entities, label='#entities', color='red')
#ax.plot(self.timepoints, self.changed_entities, label='#changed entities', linestyle='--', color='red')
ax.plot(self.timepoints,
self.diff_times,
label='#time for statediff [ms]',
color='black')
ax2 = ax.twinx()
ax2.plot(self.timepoints,
self.online_players,
label='#online players',
color='b')
#ax2.plot(self.timepoints, self.changed_chunks, label='#changed chunks', linestyle='--', color='g')
#ax2.plot(self.timepoints, self.changed_tile_entities, label='#changed tile entities', linestyle='--', color='orange')
# fix legend
# lines, labels = ax.get_legend_handles_labels()
# lines2, labels2 = ax2.get_legend_handles_labels()
# ax.legend(lines + lines2, labels + labels2, loc=2)
ax.legend(loc=2) # upper left
ax2.legend(loc=1) # upper right
ax.set(xlabel='Time', title='Status information')
ax.grid()
datacursor()
plt.show()
def plot(sample, matrix):
""" Helper function that does the actual plotting.
Arguments:
sample: An element of self.samples
matrix: A string specifying which matrix to visualize. Must be 'ULM', 'SLM' of 'CM'
"""
mat_name = {
'CM': 'Correlation Matrix - ',
'ULM': 'Lead Matrix - ',
'SLM': 'Sorted Lead Matrix - '
}
mpl.figure()
try:
mpl.imshow(sample[matrix], interpolation=None)
except KeyError:
print('Error! Matrix not found. "mat" must be ULM, CM or SLM')
mpl.title(mat_name[matrix] + sample['Name'] + ':' +
sample['Session'] + '-' + sample['Run'] + '(' +
sample['Location'] + ')')
mpl.colorbar()
mpldatacursor.datacursor(bbox=dict(alpha=1, fc='w'),
formatter=label_point)
def plot_rl(self):
if self.cursor is not None: self.cursor.hide().disable()
matplotlib.rcdefaults()
self.figure.clf()
self.figure.subplots_adjust(left = 0.12, bottom = 0.12, right = 0.88, top = 0.98)
axes1 = self.figure.add_subplot(111)
axes1.cla()
axes1.xaxis.set_major_formatter(FuncFormatter(metric_prefix))
axes1.set_xlabel('Hz')
axes1.set_ylabel('Return loss, dB')
magnitude = np.absolute(self.gamma())
axes1.plot(self.xaxis, 20.0 * np.log10(magnitude), color = 'blue', label = 'Return loss')
self.cursor = datacursor(axes = self.figure.get_axes(), formatter = LabelFormatter(), display = 'multiple')
self.canvas.draw()
def get_opt_vol_data_hist(symbol):
db=MySQLdb.connect(config.host,config.user,config.password,'NSE')
points=pd.DataFrame()
fig=plt.figure()
for i in [0,1,5]:
date=pd.read_sql(last_date_query%i,db)
date=date.timestamp[0].__str__()
data=get_opt_vol_data(symbol, date)
(range,res,pol)=perform_spline_calc(data, xlow=0, xhigh=1, xsep=0.02)
if i==0:
points=data.DELTA
ax1 = fig.add_subplot(111)
ax2 = ax1.twiny()
act,=ax1.plot(data.DELTA,data.VOLATILITY,'r*',label='Actual Smile')
fit,=ax1.plot(range,res,'g',label='Fitted Smile')
ax1.set_xlabel('DELTA')
ax1.set_ylabel('VOLATILITY')
#ax2.plot(data.STRIKE_PR,data.VOLATILITY,'b*',label='Actual Smile')
ax2.set_xticks(data.DELTA)
ax2.set_xticklabels(data.STRIKE_PR,rotation=90,fontsize=12)
ax2.set_xlabel('STRIKE')
elif i==1:
ax1.plot(points,pol(points),'r',label='1 day ago')
else:
ax1.plot(points,pol(points),'b',label='7 days ago')
lgd=ax1.legend(loc='upper left',bbox_to_anchor=(1,1))
datacursor()
fig.savefig("%s_VOL.jpg"%symbol, bbox_extra_artists=(lgd,), bbox_inches='tight')
db.close()
def plot(self, dataframe, param, param2, color='red', label='no', ax=None):
df = self.select(dataframe, param)
df2 = self.select(dataframe, param2)
comb_df = df.join(df2)
if label == 'no':
comb_df.plot.scatter(x=param,
y=param2,
color=color,
title=param + ' Vs ' + param2)
datacursor(hover=True, point_labels=comb_df.index)
# getting the summary
print df.describe()
print df2.describe()
print comb_df
plt.show()
#return dataframe.plot()
else:
if ax == None:
return comb_df.plot.scatter(x=param,
y=param2,
color=color,
label=label)
else:
comb_df.plot.scatter(x=param,
y=param2,
color=color,
label=label,
ax=ax,
title=param + ' Vs ' + param2)
datacursor(hover=True, point_labels=comb_df.index)
# getting the summary
print df.describe()
print df2.describe()
print comb_df
plt.show()
def set_data_cursor(self):
if self.current_plot_idx is None:
return None
# Use a DataCursor to interactively display the label
# for artists of the current axes.
self.data_cursor = mpldatacursor.datacursor(
axes=self.plots[self.current_plot_idx],
formatter='{label}'.format,
tolerance=4,
# hover=True,
# display='single',
display='multiple',
draggable=True,
)
def make_datacursor_general(x1, u1, filename, my_plt, ax1):
datacursor(display='multiple',
tolerance=0,
formatter=(str(x1) + " (" + str(u1) +
"): {x:.3e} Hz \n").format,
draggable=True)
my_plt.gca().minorticks_on()
my_plt.gca().grid(which='major',
linestyle='-',
linewidth=0.3,
color='black')
my_plt.gca().grid(which='minor',
linestyle=':',
linewidth=0.1,
color='black')
# my_plt.show()
# input("Press Enter ")
my_plt.gcf().savefig(filename, dpi=300)
my_plt.cla()
my_plt.close()
def set_data_cursor(self):
if self.current_plot_idx is None:
return None
# Use a DataCursor to interactively display the label
# for artists of the current axes.
self.data_cursor = mpldatacursor.datacursor(
axes=self.plots[self.current_plot_idx],
formatter='{label}'.format,
tolerance=4,
hover=True,
#display='single',
#display='multiple',
#draggable=True,
)
def plot_swr(self):
if self.cursor is not None: self.cursor.hide().disable()
matplotlib.rcdefaults()
self.figure.clf()
self.figure.subplots_adjust(left = 0.12, bottom = 0.12, right = 0.88, top = 0.98)
axes1 = self.figure.add_subplot(111)
axes1.cla()
axes1.xaxis.set_major_formatter(FuncFormatter(metric_prefix))
axes1.yaxis.set_major_formatter(FuncFormatter(metric_prefix))
axes1.set_xlabel('Hz')
axes1.set_ylabel('SWR')
magnitude = np.absolute(self.gamma())
swr = np.maximum(1.0, np.minimum(100.0, (1.0 + magnitude) / np.maximum(1.0e-20, 1.0 - magnitude)))
axes1.plot(self.xaxis, swr, color = 'blue', label = 'SWR')
self.cursor = datacursor(axes = self.figure.get_axes(), formatter = LabelFormatter(), display = 'multiple')
self.canvas.draw()
def plot_smith(self):
if self.cursor is not None: self.cursor.hide().disable()
matplotlib.rcdefaults()
self.figure.clf()
self.figure.subplots_adjust(left = 0.0, bottom = 0.0, right = 1.0, top = 1.0)
axes1 = self.figure.add_subplot(111)
self.plot_smith_grid(axes1, 'blue')
gamma = self.gamma()
plot, = axes1.plot(gamma.real, gamma.imag, color = 'red')
axes1.axis('equal')
axes1.set_xlim(-1.12, 1.12)
axes1.set_ylim(-1.12, 1.12)
axes1.xaxis.set_visible(False)
axes1.yaxis.set_visible(False)
for loc, spine in axes1.spines.items():
spine.set_visible(False)
self.cursor = datacursor(plot, formatter = SmithFormatter(self.xaxis), display = 'multiple')
self.canvas.draw()
def createFigure(self):
# tkf= tk.Frame()
# self.mainFig= matplotlib.figure.Figure(figsize= (5,5),dpi=100)
self.mainFig = plt.figure()
a = self.mainFig.add_subplot(111)
line = a.plot([1, 2, 3, 4, 5, 6, 7, 8], [5, 6, 1, 3, 8, 9, 3, 5])
# plt.show( block= False )
root = tk.Tk()
root.iconbitmap('/home/chris/Desktop/download.jpg')
root.title("blah")
canvas = FigureCanvasTkAgg(self.mainFig, master=root)
canvas.show()
canvas.get_tk_widget().pack(side=tk.BOTTOM, fill=tk.BOTH, expand=True)
toolbar = NavigationToolbar2TkAgg(canvas, root)
toolbar.update()
canvas._tkcanvas.pack(side=tk.TOP, fill=tk.BOTH, expand=True)
dcObj = datacursor(line, snap=True)
print()
def plot_magphase(self, data):
if self.cursor is not None: self.cursor.hide().disable()
matplotlib.rcdefaults()
self.figure.clf()
self.figure.subplots_adjust(left = 0.12, bottom = 0.12, right = 0.88, top = 0.98)
axes1 = self.figure.add_subplot(111)
axes1.cla()
axes1.xaxis.set_major_formatter(FuncFormatter(metric_prefix))
axes1.yaxis.set_major_formatter(FuncFormatter(metric_prefix))
axes1.tick_params('y', color = 'blue', labelcolor = 'blue')
axes1.yaxis.label.set_color('blue')
axes1.plot(self.xaxis, np.absolute(data), color = 'blue', label = 'Magnitude')
axes2 = axes1.twinx()
axes2.spines['left'].set_color('blue')
axes2.spines['right'].set_color('red')
axes1.set_xlabel('Hz')
axes1.set_ylabel('Magnitude')
axes2.set_ylabel('Phase angle')
axes2.tick_params('y', color = 'red', labelcolor = 'red')
axes2.yaxis.label.set_color('red')
axes2.plot(self.xaxis, np.angle(data, deg = True), color = 'red', label = 'Phase angle')
self.cursor = datacursor(axes = self.figure.get_axes(), formatter = LabelFormatter(), display = 'multiple')
self.canvas.draw()
def plot_cluster_lines(estimator,
X,
fig=None,
ax=None,
sample_colors=None,
sample_labels=None,
cluster_labels=None,
colormap=plt.cm.get_cmap('rainbow'),
xlabel=None,
ylabel=None,
title=None):
"""Implementation of the plotting of the results of the
:func:`Fuzzy K-Means <fda.clustering.fuzzy_kmeans>` method.
A kind of Parallel Coordinates plot is generated in this function with the
membership values obtained from the algorithm. A line is plotted for each
sample with the values for each cluster. See `Clustering Example
<../auto_examples/plot_clustering.html>`_.
Args:
estimator (BaseEstimator object): estimator used to calculate the
clusters.
X (FDataGrd object): contains the samples which are grouped
into different clusters.
fig (figure object, optional): figure over which the graph is
plotted in case ax is not specified. If None and ax is also None,
the figure is initialized.
ax (axis object, optional): axis over where the graph is plotted.
If None, see param fig.
sample_colors (list of colors, optional): contains in order the colors of each
sample of the fdatagrid.
sample_labels (list of str, optional): contains in order the labels
of each sample of the fdatagrid.
cluster_labels (list of str, optional): contains in order the names of each
cluster the samples of the fdatagrid are classified into.
colormap(colormap, optional): colormap from which the colors of the plot are taken.
xlabel (str): Label for the x-axis. Defaults to "Sample".
ylabel (str): Label for the y-axis. Defaults to "Membership grade".
title (str, optional): Title for the figure where the clustering results are ploted.
Defaults to "Membership grades of the samples to each cluster".
Returns:
(tuple): tuple containing:
fig (figure object): figure object in which the graphs are plotted in case ax is None.
ax (axes object): axes in which the graphs are plotted.
"""
fdatagrid = X
_check_if_estimator(estimator)
if not isinstance(estimator, FuzzyKMeans):
raise ValueError("The estimator must be a FuzzyKMeans object.")
try:
estimator._check_is_fitted()
estimator._check_test_data(X)
except NotFittedError:
estimator.fit(X)
fig, ax = _fig_and_ax_checks(fig, ax)
_plot_clustering_checks(estimator, fdatagrid, sample_colors, sample_labels,
None, cluster_labels, None, None)
xlabel, ylabel, title = _set_labels(xlabel, ylabel, title, "Cluster")
if sample_colors is None:
cluster_colors = colormap(
np.arange(estimator.n_clusters) / (estimator.n_clusters - 1))
labels_by_cluster = np.argmax(estimator.labels_, axis=1)
sample_colors = cluster_colors[labels_by_cluster]
if sample_labels is None:
sample_labels = [
'$SAMPLE: {}$'.format(i) for i in range(fdatagrid.nsamples)
]
if cluster_labels is None:
cluster_labels = [
'${}$'.format(i) for i in range(estimator.n_clusters)
]
ax.get_xaxis().set_major_locator(MaxNLocator(integer=True))
for i in range(fdatagrid.nsamples):
ax.plot(np.arange(estimator.n_clusters),
estimator.labels_[i],
label=sample_labels[i],
color=sample_colors[i])
ax.set_xticks(np.arange(estimator.n_clusters))
ax.set_xticklabels(cluster_labels)
ax.set_xlabel(xlabel)
ax.set_ylabel(ylabel)
datacursor(formatter='{label}'.format)
fig.suptitle(title)
return fig, ax
def plot(fn,
inprefix='model_full', inpath=os.curdir,
outprefix='model_ibc', outpath=os.curdir,
ext='.su', isSU=True, endian='Little',
clip=1e3, aspect='auto', cmap='seismic',
interpolation='bicubic', title=None,
colorbar=True, style='shot_gather',
extent=[0, 1, 1, 0],
figsize=(10, 8)):
""" Create a plot """
if isinstance(fn, basestring):
data = SEGYFile('/'.join([inpath, fn + ext]), isSU=isSU, endian=endian)
data = data[:]
elif isinstance(fn, np.ndarray):
data = fn
else:
raise TypeError('LOL!')
fig = plt.figure(figsize=figsize, facecolor='w', edgecolor='k')
gs = gridspec.GridSpec(1, 1)
ax = fig.add_subplot(gs[0, 0])
# ax.spines['right'].set_color('none')
# ax.spines['top'].set_color('none')
# Remove the ugly ticks
plt.tick_params(
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off', # ticks along the top edge are off
right='off' # ticks along the top edge are off
)
# Set style-specific attributes
if style == 'shot_gather':
clipmin = -clip
clipmax = +clip
ax.xaxis.set_label_text('Horizontal location [m]')
ax.yaxis.set_label_text('Time [s]')
if title is None:
ax.set_title('Shot gather')
else:
ax.set_title(title)
cb_label = 'Amplitude'
elif style == 'slice':
clipmin = -clip
clipmax = +clip
ax.xaxis.set_label_text('Horizontal location [m]')
ax.yaxis.set_label_text('Depth [m]')
if title is None:
ax.set_title('Slice')
else:
ax.set_title(title)
cb_label = 'Amplitude'
elif style == 'sub_volume_boundary':
clipmin = -clip
clipmax = +clip
ax.xaxis.set_label_text('Horizontal location [m]')
ax.yaxis.set_label_text('Time [s]')
if title is None:
ax.set_title('Volume boundary')
else:
ax.set_title(title)
cb_label = 'Amplitude'
elif style == 'velocity':
clipmin = data.min()
clipmax = data.max()
#ax.xaxis.set_label_text('Horizontal location [m]')
ax.xaxis.set_label_text('Inline [m]')
#ax.yaxis.set_label_text('Crossline [m]')
ax.yaxis.set_label_text('Depth [m]')
if title is None:
ax.set_title('Velocity')
else:
ax.set_title(title)
cb_label = 'Amplitude [m/s]'
elif style == 'density':
clipmin = data.min()
clipmax = data.max()
ax.xaxis.set_label_text('Horizontal location [m]')
ax.yaxis.set_label_text('Depth [m]')
if title is None:
ax.set_title('Density')
else:
ax.set_title(title)
cb_label = 'Amplitude [kg/m^3]'
# plt.xticks(np.linspace(2e3,4e3,3))
# Plot options
plotopts = {
'vmin': clipmin,
'vmax': clipmax,
'aspect': aspect,
'cmap': cmap,
'interpolation': interpolation,
'extent': extent
}
# Create image
im = ax.imshow(data.T, picker=True, **plotopts)
# Colorbar
if colorbar:
cbax = plt.colorbar(im, orientation='vertical', shrink=0.9)
cbax.set_ticks(range(int(clipmin+1), int(clipmax+1), int((clipmax-clipmin)/5)))
cbax.set_label(cb_label)
datacursor(display='single')
fig.canvas.mpl_connect('pick_event', onclick)
#fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
return ax
def __init__(self, config, global_max_min):
self.config = config
print(config)
_, _, _, self.raw_data, self.glo_max_score, self.glo_min_score = assemble_data(
config['data'])
Xs, npz_files, npz_dims, _, _, _ = assemble_data(
config['data'],
ext='.' + config['method']['name'] + '.' + config['data']['key'] +
'.',
dict_key=config['data']['key'])
print(self.glo_max_score, self.glo_min_score)
print(npz_dims, npz_files)
self.fig = plt.figure(config['data']['key'].upper(), figsize=(14, 7))
self.ax = self.fig.add_subplot(111)
plt.subplots_adjust(left=0.5, right=0.9)
self.fig.canvas.mpl_connect('pick_event', self.onpick)
checkb_labels = []
idx = 0
list_of_artists = []
labels_cursor = {}
for data, file in zip(Xs, npz_files):
print(data.shape)
algo = file.split('/')[-3]
rollout = int(file.split('/')[-1].split('_')[0][-1])
scores = self.raw_data[algo][str(rollout)]['score']
if global_max_min:
global_limit = (self.glo_max_score, self.glo_min_score)
else:
global_limit = None
hex_list = color_list(idx % len(COLORS),
scores,
global_limit=global_limit)
artist = self.ax.scatter(data[:, 0],
data[:, 1],
c=hex_list,
visible=False)
list_of_artists.append(artist)
labels_cursor[artist] = []
for i in range(data.shape[0]):
labels_cursor[artist].append(algo.upper() + " r" +
str(rollout) + " s" + str(i) +
": " + str(scores[i]))
#artist.set_visible(True)
#artist.set_picker(5)
artist2data[artist] = (algo, rollout)
label = algo.upper() + " rollout#" + str(rollout)
label2artist[label] = artist
checkb_labels.append(label)
idx += 1
formatter = lambda **kwargs: ', '.join(kwargs['point_label'])
self.dc = datacursor(list_of_artists,
hover=True,
formatter=formatter,
point_labels=labels_cursor)
checkb_ax = self.fig.add_axes([0.1, 0.1, 0.4, 0.8])
checkb_ax.axis('off')
self.checkb = CheckButtons(checkb_ax, checkb_labels,
[False] * len(checkb_labels))
self.checkb.on_clicked(checkb_click)
def imview(img,
title=None,
copy=True,
fltscl=False,
intrp='nearest',
norm=None,
cbar=False,
cmap=None,
fgsz=None,
fgnm=None,
fig=None,
ax=None):
"""
Display an image. Pixel values are displayed when the pointer is over
valid image data. If a figure object is specified then the image is
drawn in that figure, and ``fig.show()`` is not called. The figure is
closed on key entry 'q'.
Parameters
----------
img : array_like, shape (Nr, Nc) or (Nr, Nc, 3) or (Nr, Nc, 4)
Image to display
title : string, optional (default None)
Figure title
copy : boolean, optional (default True)
If True, create a copy of input `img` as a reference for displayed
pixel values, ensuring that displayed values do not change when the
array changes in the calling scope. Set this flag to False if the
overhead of an additional copy of the input image is not acceptable.
fltscl : boolean, optional (default False)
If True, rescale and shift floating point arrays to [0,1]
intrp : string, optional (default 'nearest')
Specify type of interpolation used to display image (see
``interpolation`` parameter of :meth:`matplotlib.axes.Axes.imshow`)
norm : :class:`matplotlib.colors.Normalize` object, optional (default None)
Specify the :class:`matplotlib.colors.Normalize` instance used to
scale pixel values for input to the colour map
cbar : boolean, optional (default False)
Flag indicating whether to display colorbar
cmap : :class:`matplotlib.colors.Colormap`, optional (default None)
Colour map for image. If none specifed, defaults to cm.Greys_r
for monochrome image
fgsz : tuple (width,height), optional (default None)
Specify figure dimensions in inches
fgnm : integer, optional (default None)
Figure number of figure
fig : :class:`matplotlib.figure.Figure` object, optional (default None)
Draw in specified figure instead of creating one
ax : :class:`matplotlib.axes.Axes` object, optional (default None)
Plot in specified axes instead of current axes of figure
Returns
-------
fig : :class:`matplotlib.figure.Figure` object
Figure object for this figure
ax : :class:`matplotlib.axes.Axes` object
Axes object for this plot
"""
if img.ndim > 2 and img.shape[2] != 3:
raise ValueError('Argument img must be an Nr x Nc array or an '
'Nr x Nc x 3 array')
figp = fig
if fig is None:
fig = plt.figure(num=fgnm, figsize=fgsz)
fig.clf()
ax = fig.gca()
elif ax is None:
ax = fig.gca()
# Deal with removal of 'box-forced' adjustable in Matplotlib 2.2.0
mplv = matplotlib.__version__.split('.')
if int(mplv[0]) > 2 or (int(mplv[0]) == 2 and int(mplv[1]) >= 2):
try:
ax.set_adjustable('box')
except Exception:
ax.set_adjustable('datalim')
else:
ax.set_adjustable('box-forced')
imgd = img.copy()
if copy:
# Keep a separate copy of the input image so that the original
# pixel values can be display rather than the scaled pixel
# values that are actually plotted.
img = img.copy()
if cmap is None and img.ndim == 2:
cmap = cm.Greys_r
if np.issubdtype(img.dtype, np.floating):
if fltscl:
imgd -= imgd.min()
imgd /= imgd.max()
if img.ndim > 2:
imgd = np.clip(imgd, 0.0, 1.0)
elif img.dtype == np.uint16:
imgd = np.float16(imgd) / np.iinfo(np.uint16).max
elif img.dtype == np.int16:
imgd = np.float16(imgd) - imgd.min()
imgd /= imgd.max()
if norm is None:
im = ax.imshow(imgd,
cmap=cmap,
interpolation=intrp,
vmin=imgd.min(),
vmax=imgd.max())
else:
im = ax.imshow(imgd, cmap=cmap, interpolation=intrp, norm=norm)
ax.set_yticklabels([])
ax.set_xticklabels([])
if title is not None:
ax.set_title(title)
if cbar or cbar is None:
orient = 'vertical' if img.shape[0] >= img.shape[1] else 'horizontal'
pos = 'right' if orient == 'vertical' else 'bottom'
divider = make_axes_locatable(ax)
cax = divider.append_axes(pos, size="5%", pad=0.2)
if cbar is None:
# See http://chris35wills.github.io/matplotlib_axis
if hasattr(cax, 'set_facecolor'):
cax.set_facecolor('none')
else:
cax.set_axis_bgcolor('none')
for axis in ['top', 'bottom', 'left', 'right']:
cax.spines[axis].set_linewidth(0)
cax.set_xticks([])
cax.set_yticks([])
else:
plt.colorbar(im, ax=ax, cax=cax, orientation=orient)
def format_coord(x, y):
nr, nc = imgd.shape[0:2]
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col < nc and row >= 0 and row < nr:
z = img[row, col]
if imgd.ndim == 2:
return 'x=%6.2f, y=%6.2f, z=%.2f' % (x, y, z)
else:
return 'x=%6.2f, y=%6.2f, z=(%.2f,%.2f,%.2f)' % \
sum(((x,), (y,), tuple(z)), ())
else:
return 'x=%.2f, y=%.2f' % (x, y)
ax.format_coord = format_coord
if fig.canvas.toolbar is not None:
# See https://stackoverflow.com/a/47086132
def mouse_move(self, event):
if event.inaxes and event.inaxes.get_navigate():
s = event.inaxes.format_coord(event.xdata, event.ydata)
self.set_message(s)
def mouse_move_patch(arg):
return mouse_move(fig.canvas.toolbar, arg)
fig.canvas.toolbar._idDrag = fig.canvas.mpl_connect(
'motion_notify_event', mouse_move_patch)
attach_keypress(fig)
attach_zoom(ax)
if have_mpldc:
mpldc.datacursor(display='single')
if figp is None:
fig.show()
return fig, ax
def contour(z,
x=None,
y=None,
v=5,
xlog=False,
ylog=False,
xlbl=None,
ylbl=None,
title=None,
cfmt=None,
cfntsz=10,
lfntsz=None,
alpha=1.0,
cmap=None,
vmin=None,
vmax=None,
fgsz=None,
fgnm=None,
fig=None,
ax=None):
"""
Contour plot of a 2D surface. If a figure object is specified then the
plot is drawn in that figure, and ``fig.show()`` is not called. The
figure is closed on key entry 'q'.
Parameters
----------
z : array_like
2d array of data to plot
x : array_like, optional (default None)
Values for x-axis of the plot
y : array_like, optional (default None)
Values for y-axis of the plot
v : int or sequence of floats, optional (default 5)
An int specifies the number of contours to plot, and a sequence
specifies the specific contour levels to plot.
xlog : boolean, optional (default False)
Set x-axis to log scale
ylog : boolean, optional (default False)
Set y-axis to log scale
xlbl : string, optional (default None)
Label for x-axis
ylbl : string, optional (default None)
Label for y-axis
title : string, optional (default None)
Figure title
cfmt : string, optional (default None)
Format string for contour labels.
cfntsz : int or None, optional (default 10)
Contour label font size. No contour labels are displayed if
set to 0 or None.
lfntsz : int, optional (default None)
Axis label font size. The default font size is used if set to None.
alpha : float, optional (default 1.0)
Underlying image display alpha value
cmap : :class:`matplotlib.colors.Colormap`, optional (default None)
Colour map for surface. If none specifed, defaults to cm.YlOrRd
vmin, vmax : float, optional (default None)
Set upper and lower bounds for the colour map (see the corresponding
parameters of :meth:`matplotlib.axes.Axes.imshow`)
fgsz : tuple (width,height), optional (default None)
Specify figure dimensions in inches
fgnm : integer, optional (default None)
Figure number of figure
fig : :class:`matplotlib.figure.Figure` object, optional (default None)
Draw in specified figure instead of creating one
ax : :class:`matplotlib.axes.Axes` object, optional (default None)
Plot in specified axes instead of current axes of figure
Returns
-------
fig : :class:`matplotlib.figure.Figure` object
Figure object for this figure
ax : :class:`matplotlib.axes.Axes` object
Axes object for this plot
"""
figp = fig
if fig is None:
fig = plt.figure(num=fgnm, figsize=fgsz)
fig.clf()
ax = fig.gca()
elif ax is None:
ax = fig.gca()
if xlog:
ax.set_xscale('log')
if ylog:
ax.set_yscale('log')
if cmap is None:
cmap = cm.YlOrRd
if x is None:
x = np.arange(z.shape[1])
else:
x = np.array(x)
if y is None:
y = np.arange(z.shape[0])
else:
y = np.array(y)
xg, yg = np.meshgrid(x, y)
cntr = ax.contour(xg, yg, z, v, colors='black')
kwargs = {}
if cfntsz is not None and cfntsz > 0:
kwargs['fontsize'] = cfntsz
if cfmt is not None:
kwargs['fmt'] = cfmt
if kwargs:
plt.clabel(cntr, inline=True, **kwargs)
pc = ax.pcolormesh(xg,
yg,
z,
cmap=cmap,
vmin=vmin,
vmax=vmax,
alpha=alpha,
shading='gouraud',
clim=(vmin, vmax))
if xlog:
ax.fmt_xdata = lambda x: "{: .2e}".format(x)
else:
ax.fmt_xdata = lambda x: "{: .2f}".format(x)
if ylog:
ax.fmt_ydata = lambda x: "{: .2e}".format(x)
else:
ax.fmt_ydata = lambda x: "{: .2f}".format(x)
if title is not None:
ax.set_title(title)
if xlbl is not None:
ax.set_xlabel(xlbl, fontsize=lfntsz)
if ylbl is not None:
ax.set_ylabel(ylbl, fontsize=lfntsz)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.2)
plt.colorbar(pc, ax=ax, cax=cax)
attach_keypress(fig)
attach_zoom(ax)
if have_mpldc:
mpldc.datacursor()
if figp is None:
fig.show()
return fig, ax
def plot(y,
x=None,
ptyp='plot',
xlbl=None,
ylbl=None,
title=None,
lgnd=None,
lglc=None,
**kwargs):
"""
Plot points or lines in 2D. If a figure object is specified then the
plot is drawn in that figure, and ``fig.show()`` is not called. The
figure is closed on key entry 'q'.
Parameters
----------
y : array_like
1d or 2d array of data to plot. If a 2d array, each column is
plotted as a separate curve.
x : array_like, optional (default None)
Values for x-axis of the plot
ptyp : string, optional (default 'plot')
Plot type specification (options are 'plot', 'semilogx',
'semilogy', and 'loglog')
xlbl : string, optional (default None)
Label for x-axis
ylbl : string, optional (default None)
Label for y-axis
title : string, optional (default None)
Figure title
lgnd : list of strings, optional (default None)
List of legend string
lglc : string, optional (default None)
Legend location string
**kwargs : :class:`matplotlib.lines.Line2D` properties or figure \
properties, optional
Keyword arguments specifying :class:`matplotlib.lines.Line2D`
properties, e.g. ``lw=2.0`` sets a line width of 2, or properties
of the figure and axes. If not specified, the defaults for line
width (``lw``) and marker size (``ms``) are 1.5 and 6.0
respectively. The valid figure and axes keyword arguments are
listed below:
.. |mplfg| replace:: :class:`matplotlib.figure.Figure` object
.. |mplax| replace:: :class:`matplotlib.axes.Axes` object
.. rst-class:: kwargs
===== ==================== ======================================
kwarg Accepts Description
===== ==================== ======================================
fgsz tuple (width,height) Specify figure dimensions in inches
fgnm integer Figure number of figure
fig |mplfg| Draw in specified figure instead of
creating one
ax |mplax| Plot in specified axes instead of
current axes of figure
===== ==================== ======================================
Returns
-------
fig : :class:`matplotlib.figure.Figure` object
Figure object for this figure
ax : :class:`matplotlib.axes.Axes` object
Axes object for this plot
"""
# Extract kwargs entries that are not related to line properties
fgsz = kwargs.pop('fgsz', None)
fgnm = kwargs.pop('fgnm', None)
fig = kwargs.pop('fig', None)
ax = kwargs.pop('ax', None)
figp = fig
if fig is None:
fig = plt.figure(num=fgnm, figsize=fgsz)
fig.clf()
ax = fig.gca()
elif ax is None:
ax = fig.gca()
# Set defaults for line width and marker size
if 'lw' not in kwargs and 'linewidth' not in kwargs:
kwargs['lw'] = 1.5
if 'ms' not in kwargs and 'markersize' not in kwargs:
kwargs['ms'] = 6.0
if ptyp not in ('plot', 'semilogx', 'semilogy', 'loglog'):
raise ValueError("Invalid plot type '%s'" % ptyp)
pltmth = getattr(ax, ptyp)
if x is None:
pltln = pltmth(y, **kwargs)
else:
pltln = pltmth(x, y, **kwargs)
ax.fmt_xdata = lambda x: "{: .2f}".format(x)
ax.fmt_ydata = lambda x: "{: .2f}".format(x)
if title is not None:
ax.set_title(title)
if xlbl is not None:
ax.set_xlabel(xlbl)
if ylbl is not None:
ax.set_ylabel(ylbl)
if lgnd is not None:
ax.legend(lgnd, loc=lglc)
attach_keypress(fig)
attach_zoom(ax)
if have_mpldc:
mpldc.datacursor(pltln)
if figp is None:
fig.show()
return fig, ax
"""
An example of how to customize the keyboard shortcuts.
By default mpldatacursor will use "t" to toggle interactivity and "d" to
hide/delete annotation boxes.
"""
import matplotlib.pyplot as plt
from mpldatacursor import datacursor
fig, ax = plt.subplots()
ax.plot(range(10), 'bo-')
ax.set_title('Press "e" to enable/disable the datacursor\n'
'Press "h" to hide any annotation boxes')
dc = datacursor(keybindings=dict(hide='h', toggle='e'))
plt.show()
import numpy as np import matplotlib.pyplot as plt import mpldatacursor x, y, z = np.random.random((3, 10)) fig, ax = plt.subplots() ax.scatter(x, y, c=z, s=100 * np.random.random(10)) mpldatacursor.datacursor() plt.show()
def _plot_clusters(estimator, fdatagrid, fig, ax, nrows, ncols, labels,
sample_labels, cluster_colors, cluster_labels,
center_colors, center_labels, colormap):
"""Implementation of the plot of the FDataGrid samples by clusters.
Args:
estimator (BaseEstimator object): estimator used to calculate the
clusters.
fdatagrid (FDataGrd object): contains the samples which are grouped
into different clusters.
fig (figure object): figure over which the graphs are plotted in
case ax is not specified. If None and ax is also None, the figure
is initialized.
ax (list of axis objects): axis over where the graphs are plotted.
If None, see param fig.
nrows(int): designates the number of rows of the figure to plot the
different dimensions of the image. Only specified if fig and
ax are None.
ncols(int): designates the number of columns of the figure to plot
the different dimensions of the image. Only specified if fig
and ax are None.
labels (numpy.ndarray, int: (nsamples, ndim_image)): 2-dimensional
matrix where each row contains the number of cluster cluster
that observation belongs to.
sample_labels (list of str): contains in order the labels of each sample
of the fdatagrid.
cluster_colors (list of colors): contains in order the colors of each
cluster the samples of the fdatagrid are classified into.
cluster_labels (list of str): contains in order the names of each
cluster the samples of the fdatagrid are classified into.
center_colors (list of colors): contains in order the colors of each
centroid of the clusters the samples of the fdatagrid are classified into.
center_labels list of colors): contains in order the labels of each
centroid of the clusters the samples of the fdatagrid are classified into.
colormap(colormap): colormap from which the colors of the plot are taken.
Returns:
(tuple): tuple containing:
fig (figure object): figure object in which the graphs are plotted in case ax is None.
ax (axes object): axes in which the graphs are plotted.
"""
fig, ax = fdatagrid.generic_plotting_checks(fig, ax, nrows, ncols)
_plot_clustering_checks(estimator, fdatagrid, None, sample_labels,
cluster_colors, cluster_labels, center_colors,
center_labels)
if sample_labels is None:
sample_labels = [
'$SAMPLE: {}$'.format(i) for i in range(fdatagrid.nsamples)
]
if cluster_colors is None:
cluster_colors = colormap(
np.arange(estimator.n_clusters) / (estimator.n_clusters - 1))
if cluster_labels is None:
cluster_labels = [
'$CLUSTER: {}$'.format(i) for i in range(estimator.n_clusters)
]
if center_colors is None:
center_colors = ["black"] * estimator.n_clusters
if center_labels is None:
center_labels = [
'$CENTER: {}$'.format(i) for i in range(estimator.n_clusters)
]
colors_by_cluster = cluster_colors[labels]
patches = []
for i in range(estimator.n_clusters):
patches.append(
mpatches.Patch(color=cluster_colors[i], label=cluster_labels[i]))
for j in range(fdatagrid.ndim_image):
for i in range(fdatagrid.nsamples):
ax[j].plot(fdatagrid.sample_points[0],
fdatagrid.data_matrix[i, :, j],
c=colors_by_cluster[i],
label=sample_labels[i])
for i in range(estimator.n_clusters):
ax[j].plot(fdatagrid.sample_points[0],
estimator.cluster_centers_.data_matrix[i, :, j],
c=center_colors[i],
label=center_labels[i])
ax[j].legend(handles=patches)
datacursor(formatter='{label}'.format)
fdatagrid.set_labels(fig, ax)
return fig, ax
def get_coverage(self):
if not self.wcs:
QMessageBox.information(self.iface.mainWindow(), "Error", "Set configuration on \"Configuration\" tab")
return
wcs_params = {}
rangesubset = self.dlg.bandsInput.text()
col_min, col_max = self.dlg.colMin.text(), self.dlg.colMax.text()
row_min, row_max = self.dlg.rowMin.text(), self.dlg.rowMax.text()
if rangesubset:
wcs_params['rangesubset'] = rangesubset
print("OI")
# self.wcs.get_coverage(coverage_id=self.dlg.comboCoverage.currentText(), rangesubset=rangesubset)
print("FORA OI")
start_date = self.dlg.startDateInput.text() or self.start_date
end_date = self.dlg.endDateInput.text() or self.end_date
wcs_params['subset'] = [
"col_id(%s,%s)" % (str(col_min), str(col_max)),
"row_id(%s,%s)" % (str(row_min), str(row_max)),
"time_id(%s,%s)" % (str(start_date), str(end_date))]
print("PARAMS SUBSET")
self.wcs.get_coverage(coverage_id=self.dlg.comboCoverage.currentText(), **wcs_params)
print("GETADO")
self.dlg.dataOutput.setText("")
self.dlg.dataOutput.append(self.wcs.values)
data_strings = ""
elements = self.wcs.values.split(',')
bands_values = [e.lstrip().split(' ') for e in elements]
bands_it = len(elements[0].split(' '))
# plot (use with subplot)
# figure = plt.figure()
begin_date = parser.parse(start_date)
final_date = parser.parse(end_date)
dates = []
period = int(self.wcs.period)
while begin_date <= final_date:
dates.append(begin_date)
begin_date += timedelta(days=period)
import matplotlib.dates as mdates
print(dates)
for i in xrange(bands_it):
array = []
for element in bands_values:
array.append(int(element[i]))
data_strings += element[i].lstrip()
fact, remainder = divmod(len(array), len(dates))
if not remainder:
dts = sorted(dates * fact)
plt.gca().xaxis.set_major_formatter(mdates.DateFormatter('%m/%d/%Y'))
# plt.gca().xaxis.set_major_locator(mdates.DayLocator())
plt.plot(dts, array)
plt.gcf().autofmt_xdate()
else:
plt.plot(array, marker='o')
# Uncomment next lines to enable one graph per band
# ax = figure.add_subplot(bands_it, 1, i)
# ax.set_title('b1')
# plt.plot(array)
datacursor(hover=True)
self.dlg.dataOutput.setText(data_strings)
plt.show()
def bode_joaco(datos,mode,spice_filename ,output_filename):
master_spice_data = read_file_spice("input/spice_data/" + spice_filename)
# freq_arr = np.asarray(spice_data["f"])
# abs_arr = np.asarray(spice_data["abs"])
# pha_arr = np.asarray(spice_data["pha"])
#
# freq_arr.shape = (len(freq_arr),1)
# abs_arr.shape = (len(abs_arr), 1)
# pha_arr.shape = (len(pha_arr), 1)
# mat_aux = np.column_stack((freq_arr, abs_arr,pha_arr))
# mat_aux.sort(axis=0)
#
# spice_data_aux = dict()
# spice_data_aux["f"] = []
# spice_data_aux["abs"] = []
# spice_data_aux["pha"] = []
# for i in range (len(freq_arr)):
# spice_data_aux["f"].append(freq_arr[i])
# for i in range(len(abs_arr)):
# spice_data_aux["abs"].append(abs_arr[i])
# for i in range(len(pha_arr)):
# spice_data_aux["pha"].append(pha_arr[i])
#
# spice_data=spice_data_aux
for j in range(len(master_spice_data)):
spice_data=master_spice_data[j]
# for i in range(len(spice_data["pha"])):
# if spice_data["f"][i] < 9 :
# spice_data["pha"][i] = spice_data["pha"][i]+360
# spice_data["pha"][i] -= 360
if mode == "mag":
ax1.semilogx(spice_data["f"], spice_data["abs"], "magenta", linewidth=0.1, alpha=0.9)
else:
ax1.semilogx(spice_data["f"], spice_data["pha"], "magenta", linewidth=2.5, alpha=0.9)
### Real
if mode == "mag":
ax1.set_title('Diagrama de Bode (Módulo)')
ax1.semilogx(datos["f"], datos["abs"], "cyan", linewidth=1, alpha=1)
ax1.set_xlabel('Frecuencia (Hz)', fontsize=10)
ax1.set_ylabel('|H(s)|db', fontsize=10)
#ax1.semilogx(f, mag,"darkblue",linewidth=1, alpha=1)
else:
ax1.set_title('Diagrama de Bode (Fase)')
ax1.semilogx(datos["f"], datos["pha"], "cyan", linewidth=1, alpha=1)
ax1.set_xlabel('Frecuencia (Hz)', fontsize=10)
ax1.set_ylabel('Fase (grados)', fontsize=10)
#ax1.semilogx(f, phase, "darkblue",linewidth=1, alpha=1)
blue_patch = mpatches.Patch(color='magenta', label='Simulación')
green_patch = mpatches.Patch(color='cyan', label='Práctica')
#red_patch = mpatches.Patch(color='darkblue', label='Teórico')
#plt.legend(handles=[green_patch, blue_patch, red_patch])
plt.legend(handles=[green_patch, blue_patch])
ax1.minorticks_on()
ax1.grid(which='major', linestyle='-', linewidth=0.3, color='black')
ax1.grid(which='minor', linestyle=':', linewidth=0.1, color='black')
# datacursor(display='multiple',formatter="Frec: {x:.3e} Hz \nAmp:{y:.1f}dB".format, draggable=True)
datacursor(display='multiple', tolerance=10, formatter="Frec: {x:.3e} Hz \nAmp:{y:.1f} dB".format,draggable=True)
plt.show()
input("Press Enter ")
fig.savefig("output/dataset1/" + output_filename, dpi=300)
plt.cla()
plt.close()
def show_tradeoff(self):
"""Plot the tradeoff between coverage and density.
Generates a plot of the tradeoff between coverage and density for the
peeling/pasting trajectories. Color is used to denote the number of
restricted dimensions.
Returns
-------
the Matplotlib figure
"""
fig = plt.figure()
ax = fig.add_subplot(111, aspect='equal')
# setup the color map for coloring the number of restricted dimensions
cmap = mpl.cm.YlGnBu_r #@UndefinedVariable
boundaries = np.arange(-0.5,
max(self.peeling_trajectory['res dim']) + 1.5,
step=1)
ncolors = cmap.N
norm = mpl.colors.BoundaryNorm(boundaries, ncolors)
# plot the tradeoff
p = ax.scatter(self.peeling_trajectory['coverage'],
self.peeling_trajectory['density'],
c=self.peeling_trajectory['res dim'],
norm=norm,
cmap=cmap,
picker=True)
ax.set_ylabel('Density')
ax.set_xlabel('Coverage')
ax.set_ylim(0, 1.2)
ax.set_xlim(0, 1.2)
ticklocs = np.arange(0,
max(self.peeling_trajectory['res dim']) + 1,
step=1)
cb = fig.colorbar(p, spacing='uniform', ticks=ticklocs, drawedges=True)
cb.set_label("# of Restricted Dimensions")
# enable mouse interaction
def handle_click(event):
if hasattr(event, "ind"):
i = event.ind[0]
self.select(i)
self.show_details().show()
def formatter(**kwargs):
i = kwargs.get("ind")[0]
data = self.peeling_trajectory.ix[i]
return (
("Box %d\n" + "Coverage: %2.1f%%\n" + "Density: %2.1f%%\n" +
"Mass: %2.1f%%\n" + "Res Dim: %d") %
(i, 100 * data["coverage"], 100 * data["density"],
100 * data["mass"], data["res dim"]))
mpldatacursor.datacursor(formatter=formatter, hover=True)
fig.canvas.mpl_connect('pick_event', handle_click)
# enable tooltips on IPython Notebook
if mpld3:
css = """
table {
border-collapse: collapse;
}
th {
background-color: rgba(255,255,255,0.95);
}
td {
background-color: rgba(255,255,255,0.95);
}
table, th, td {
font-family:Tahoma, Tahoma, sans-serif;
font-size: 16px;
border: 1px solid black;
text-align: right;
}
"""
labels = []
columns_to_include = ['coverage', 'density', 'mass', 'res dim']
frmt = lambda x: '{:.2f}'.format(x)
for i in range(len(self.peeling_trajectory['coverage'])):
label = self.peeling_trajectory.ix[[i], columns_to_include]
label.columns = ["Coverage", "Density", "Mass", "Res. Dim."]
label = label.T
label.columns = ["Box {0}".format(i)]
labels.append(str(label.to_html(float_format=frmt)))
tooltip = mpld3.plugins.PointHTMLTooltip(p,
labels,
voffset=10,
hoffset=10,
css=css)
mpld3.plugins.connect(fig, tooltip)
return fig
def plot_coxeter_projection(
sage_data_str, root_system=None, n_of_v_0=None, weight_index=None,
is_interactive=True, image_format=None,
):
import matplotlib
if is_interactive:
matplotlib.use('TkAgg')
else:
matplotlib.use('Agg')
import mpldatacursor
import matplotlib.pyplot as pyplot
if not is_interactive:
pyplot.clf()
# Unpack data from the sage script.
data = eval(sage_data_str)
weyl_orbit_strs = data["weyl_orbit_strs"]
W_critical = data["W_critical"]
root_strs = data["root_strs"]
simple_soliton_table = data["simple_soliton_table"]
v_c = data["coxeter_vector"]
weyl_orbit = [eval(v_str) for v_str in weyl_orbit_strs]
roots = [eval(r_str) for r_str in root_strs]
title = root_system + "_" + str(n_of_v_0)
max_n_digits = ceil(log10(len(weyl_orbit)))
# Plot a figure of the projection of the soliton polytope.
figure_size = 6 * max_n_digits
figure = pyplot.figure(
title, facecolor='w',
figsize=(figure_size, figure_size),
)
pyplot.axis('off')
pyplot.axes().set_aspect('equal')
mpldatacursor_artists = []
# Plot critical points.
W_marker_size = 25
W_font_size = 18.0 / max_n_digits
W_point_labels = ["$v_{{{}}} = {}$".format(i, v_i)
for i, v_i in enumerate(weyl_orbit)]
grouped_W_c = group_degenerate_W_c(W_critical)
for W, indices in grouped_W_c:
mplobjs = pyplot.plot(
W.real, W.imag,
'o',
markersize=W_marker_size,
markeredgewidth=1.5,
markerfacecolor='w',
color='k',
label=', '.join(W_point_labels[i] for i in indices),
)
pyplot.text(
W.real, W.imag,
','.join(str(i + 1) for i in indices),
fontsize=W_font_size/len(indices),
verticalalignment='center',
horizontalalignment='center',
)
if is_interactive:
mpldatacursor_artists.append(mplobjs[0])
# Plot solitons connecting critical points.
soliton_colormap = matplotlib.cm.ScalarMappable(
norm=matplotlib.colors.Normalize(vmin=0, vmax=len(roots)),
cmap=matplotlib.cm.get_cmap('jet'),
)
soliton_colors = [soliton_colormap.to_rgba(i)
for i in range(len(roots))]
random.shuffle(soliton_colors)
if (weight_index is None
or weight_index > len(weyl_orbit)
or weight_index < 1):
i_list = range(len(weyl_orbit))
else:
i_list = [weight_index-1]
for i in i_list:
W_i = W_critical[i]
for j in range(len(weyl_orbit)):
soliton_data = simple_soliton_table[i][j]
if soliton_data is None:
continue
else:
soliton, sign = soliton_data
W_j = W_critical[j]
if sign == -1:
sign_str = '-'
else:
sign_str = ''
root = tuple([sign*r_k for r_k in roots[soliton]])
label = "${}\\alpha_{{{}}} = {}$".format(
sign_str, soliton, root
)
offset = .05 / max_n_digits
x = W_i.real
y = W_i.imag
dx = W_j.real - x
dy = W_j.imag - y
r = sqrt(dx**2 + dy**2)
mplobjs = pyplot.arrow(
x + (offset * dx)/r,
y + (offset * dy)/r,
(1 - 2*offset/r)*dx,
(1 - 2*offset/r)*dy,
length_includes_head=True,
label=label, color=soliton_colors[soliton],
)
mpldatacursor_artists.append(mplobjs)
mpldatacursor.datacursor(
artists=mpldatacursor_artists,
formatter="{label}".format,
display="multiple",
draggable=True,
)
pyplot.margins(.05)
if is_interactive is True:
matplotlib.rcParams["savefig.directory"] = "./"
# Display the plot.
pyplot.show()
else:
# Return the plot to web frontend.
img = BytesIO()
pyplot.savefig(img, format=image_format)
img.seek(0)
return img
def remoteGene(gene):
global Transcript_Annotations_File
global ExonRegion_File
global Selected_Gene
global Prt_Trans_File
global Prt_Regions_File
global Prt_Boundaries_File
global Etc_File
import unique
Selected_Gene = gene
ExonRegion_File = unique.filepath("ExonViewFiles/Hs_Ensembl_exon.txt")
Transcript_Annotations_File = unique.filepath(
"ExonViewFiles/Hs_Ensembl_transcript-annotations.txt")
Prt_Trans_File = unique.filepath(
"ExonViewFiles/Hs_Ensembl_Protein__65_37.txt")
Prt_Regions_File = unique.filepath(
"ExonViewFiles/Hs_ProteinFeatures_build_65_37.txt")
Prt_Boundaries_File = unique.filepath(
"ExonViewFiles/Hs_ProteinCoordinates_build_65_37.tab")
Etc_File = unique.filepath(
"ExonViewFiles/Hs_RNASeq_K562_SRSF2_P95mut_vs_K562_SRSF2_WT.ExpCutoff-5.0_average-splicing-index-ProcessedSpliceData.txt"
)
#"ENSG00000005801"
#"ENSG00000110514"
total_val = ProteinCentricIsoformView(Selected_Gene)
junctions = total_val[0]
p_boundaries = total_val[1]
p_domains = total_val[2]
transcript_db = total_val[3]
exon_db = total_val[4]
splice_db = total_val[5]
#for i in exon_db["ENST00000349238"]:
# print(i[2].EnsemblRegion())
domain_color_list = []
for i in p_domains:
ploy = p_domains[i]
for a in ploy:
domain_color_list.append(a[1])
domain_color_list = list(set(domain_color_list))
domain_color_key = {}
c_color1 = [0.8, 0.6, 0.1]
c_color2 = [0.1, 0.6, 0.8]
c_color3 = [0.6, 0.1, 0.8]
c_color4 = [0.95, 0.6, 0.3]
c_color5 = [0.3, 0.6, 0.95]
c_color6 = [0.6, 0.3, 0.95]
FLAG = 1
for item in domain_color_list:
if (FLAG == 1):
domain_color_key[item] = c_color1
FLAG = FLAG + 1
continue
if (FLAG == 2):
domain_color_key[item] = c_color2
FLAG = FLAG + 1
continue
if (FLAG == 3):
domain_color_key[item] = c_color3
FLAG = FLAG + 1
continue
if (FLAG == 4):
domain_color_key[item] = c_color4
FLAG = FLAG + 1
continue
if (FLAG == 5):
domain_color_key[item] = c_color5
FLAG = FLAG + 1
continue
if (FLAG == 6):
domain_color_key[item] = c_color6
FLAG = 1
continue
for i in domain_color_key:
print(i, domain_color_key[i], "\n")
Y = 50
Transcript_to_Y = {}
for transcript in transcript_db:
Transcript_to_Y[transcript] = Y
Y = Y + 200
import traceback
ylim = Y + 200
currentAxis = plt.gca()
ax = plt.axes()
X_Pos_List = []
for transcript in transcript_db:
try:
Junc_List = junctions[transcript]
y_pos = Transcript_to_Y[transcript]
Gene_List = exon_db[transcript]
color_flag = 1
for entry in Gene_List:
G_start = entry[0][0]
G_end = entry[0][1]
Exon_Object = entry[2]
try:
LabelClass = splice_db[Exon_Object.EnsemblRegion()]
ExonName = Exon_Object.EnsemblExon()
RegCall = LabelClass.RegCall()
SplicingIndex = LabelClass.SplicingIndex()
PVal = LabelClass.PVal()
Midas = LabelClass.Midas()
Label = "\n" + "Exon: " + str(
ExonName) + "\n" + "RegCall: " + str(
RegCall) + "\n" + "Splicing Index: " + str(
SplicingIndex) + "\n" + "P-Value: " + str(
PVal) + "\n" + "Midas Value: " + str(Midas)
if (RegCall == "UC"):
color_choice = "Grey"
else:
S_Int = float(SplicingIndex)
if (S_Int > 0):
color_choice = (0.7, 0.7, 0.99)
if (S_Int < 0):
color_choice = (0.8, 0.4, 0.4)
except:
#print(traceback.format_exc());sys.exit()
Label = ""
color_choice = "Grey"
#print("Start", G_start, "end", G_end, "Region", entry[2].EnsemblRegion())
if ((color_flag % 2) == 0):
currentAxis.add_patch(
Rectangle((G_start, y_pos), (G_end - G_start),
50,
color=color_choice,
label=(entry[2].EnsemblRegion() + Label)))
if ((color_flag % 2) != 0):
currentAxis.add_patch(
Rectangle((G_start, y_pos), (G_end - G_start),
50,
color=color_choice,
label=(entry[2].EnsemblRegion() + Label)))
color_flag = color_flag + 1
for entry in Junc_List:
try:
LabelClass = splice_db[entry[2]]
RegCall = LabelClass.RegCall()
SplicingIndex = LabelClass.SplicingIndex()
PVal = LabelClass.PVal()
Midas = LabelClass.Midas()
Label = "\n" + "RegCall: " + str(
RegCall) + "\n" + "Splicing Index: " + str(
SplicingIndex) + "\n" + "P-Value: " + str(
PVal) + "\n" + "Midas Value: " + str(Midas)
if (float(SplicingIndex) > 0):
color_junc = "blue"
if (float(SplicingIndex) < 0):
color_junc = "red"
if (RegCall == "UC"):
color_junc = "grey"
except:
Label = ""
color_junc = "grey"
currentAxis.add_patch(
Rectangle((entry[0], y_pos), (entry[1] - entry[0]),
50,
color="White",
label=(str(entry[2]) + Label)))
ax.arrow(entry[0], (y_pos + 50),
8,
40,
label=(str(entry[2]) + Label),
color=color_junc)
ax.arrow((entry[0] + 8), (y_pos + 90),
11,
-40,
label=(str(entry[2]) + Label),
color=color_junc)
P_Bound_List = p_boundaries[transcript]
P_Domain_List = p_domains[transcript]
E_Start = P_Bound_List[-2]
E_End = P_Bound_List[-1]
P_Start = P_Bound_List[1]
P_End = P_Bound_List[2]
#print("Boundaries: ", P_Start, P_End)
X_Pos_List.append(int(E_End))
#currentAxis.add_patch(Rectangle((E_Start, y_pos), E_End, 50, color = "Blue"))
try:
currentAxis.add_patch(
Rectangle((P_Start, (y_pos + 120)), (P_End - P_Start),
10,
label=("Protein: " + str(P_Bound_List[0]))))
except:
pass
for entry in P_Domain_List:
#print("Domain", entry)
color_domain_choice = domain_color_key[entry[1]]
currentAxis.add_patch(
Rectangle((entry[2], y_pos + 100), (entry[3] - entry[2]),
50,
color=color_domain_choice,
label=("Protein: " + str(entry[0]) + "\n" +
"Domain: " + str(entry[1]))))
except:
continue
plt.ylim([0.0, ylim])
try:
max_x = max(X_Pos_List)
except:
max_x = 5000
try:
plt.xlim([0.0, max_x])
except:
plt.xlim([0.0, 3000])
datacursor(hover=True,
formatter='{label}'.format,
bbox=dict(fc='yellow', alpha=1),
arrowprops=None)
plt.show()
color='red')
ax.plot(timepoints,
diff_times,
label='#time for statediff [ms]',
color='black')
ax2 = ax.twinx()
ax2.plot(timepoints, online_players, label='#online players', color='b')
ax2.plot(timepoints,
changed_chunks,
label='#changed chunks',
linestyle='--',
color='g')
ax2.plot(timepoints,
changed_tile_entities,
label='#changed tile entities',
linestyle='--',
color='orange')
# fix legend
#lines, labels = ax.get_legend_handles_labels()
#lines2, labels2 = ax2.get_legend_handles_labels()
#ax.legend(lines + lines2, labels + labels2, loc=2)
ax.legend(loc=2) # upper left
ax2.legend(loc=1) # upper right
ax.set(xlabel='Time', title='Status information')
ax.grid()
datacursor()
plt.show()
"""
A bar plot where each bar's height and name will be displayed above the top of
the bar when it is moused over. This serves as an example of overriding the
x,y position of the "popup" annotation using the `props_override` option.
"""
import string
import matplotlib.pyplot as plt
from mpldatacursor import datacursor
fig, ax = plt.subplots()
ax.bar(range(9), range(1, 10), align='center')
labels = string.ascii_uppercase[:9]
ax.set(xticks=range(9), xticklabels=labels, title='Hover over a bar')
# By default, the "popup" annotation will appear at the mouse's position.
# Instead, you might want it to appear centered at the top of the rectangle in
# the bar plot. By changing the x and y values using the "props_override"
# option, we can customize where the "popup" appears.
def override(**kwargs):
kwargs['x'] = kwargs['left'] + 0.5 * kwargs['width']
kwargs['y'] = kwargs['bottom'] + kwargs['height']
kwargs['label'] = labels[int(kwargs['x'])]
return kwargs
datacursor(hover=True, xytext=(0, 20), props_override=override,
formatter='{label}: {height}'.format)
plt.show()
def show_plot():
plt.ioff()
degree = 1
register_matplotlib_converters()
plt.rcParams['figure.figsize'] = [20, 15]
years_fmt = mdates.DateFormatter('%Y-%m-%d')
fig, ax = plt.subplots()
dataset = data2
dates = [y['upload_date'] for y in dataset]
y_a = np.array([x['view_count'] for x in dataset])
x_a = np.array([dd.timestamp() / 10000 for dd in dates])
z, resid = np.polyfit(x_a, y_a, degree, full=True)[:2]
#y_a_fit = np.polyval(z, x_a)
#y_a_adj = y_a - y_a_fit
p = np.poly1d(z)
scats = []
for v in dataset:
y = v['view_count']
x = v['upload_date']
sc = ax.scatter(x,
y,
s=20,
label='{} | {} | {:,}'.format(v['title'],
x.strftime('%Y-%m-%d'),
y))
scats.append(sc)
ax.plot(dates, p(x_a), 'r--')
ax.xaxis.set_major_formatter(years_fmt)
ax.format_xdata = mdates.DateFormatter('%Y-%m-%d %H')
fig.autofmt_xdate()
plt.title('y = {0:.4f}(x) {2} {1:+.4f} RSq: {3}'.format(
round(z[0], 4), round(z[-1], 4), ' '.join([
'{:+.4f}(x^{})'.format(round(fc, 4), ii + 2)
for ii, fc in enumerate(z[1:-1])
]), round(1 - (resid / (y_a.size * y_a.var()))[0], 4)))
plt.xlabel('date')
plt.ylabel('views')
plt.subplots_adjust(top=.94, bottom=.12, right=.98, left=.04)
#plt.show()
mpldatacursor.datacursor(scats,
formatter='{label}'.format,
keep_inside=True,
hover=True,
bbox={
'boxstyle': 'round,pad=0.5',
'fc': 'lightblue',
'alpha': 0.95,
'edgecolor': 'black'
})
plt.ion()
"\\usepackage{siunitx}", # load additional packages
]
}
mpl.rcParams.update(pgf_with_custom_preamble)
import matplotlib.pyplot as plt
from mpldatacursor import datacursor
plt.ion()
plt.close('all')
if __name__ == '__main__':
costkeeping = np.load('costkeeping_bbb.npz')
plt.figure()
plt.plot(costkeeping['flexure'][0,:], costkeeping['flexure'][1,:], 'bo',
label='flexure cost')
plt.plot(costkeeping['shear'][0,:], costkeeping['shear'][1,:], 'r^',
label='shear cost')
plt.plot(costkeeping['deck'][0,:], costkeeping['deck'][1,:], 'gv',
label='deck cost')
plt.xlim((-1,101))
plt.ylim((-1,8e7))
plt.xlabel('strengthening time (year)', fontsize=12)
plt.ylabel('cost (mm\\textsuperscript{3})', fontsize=12)
ax = plt.gca()
ax.ticklabel_format(axis='y', style='sci', scilimits=(-3,3))
datacursor(formatter='{label}'.format,display='multiple', draggable=True,
bbox=None, fontsize=12,
arrowprops=dict(arrowstyle='-|>', connectionstyle='arc3', facecolor='k'))
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
import mpldatacursor
import sys
sys.path.append(
r'c:\users\johnn\appdata\local\programs\python\python37-32\lib\site-packages'
)
class Formatter(object):
def __init__(self, im):
self.im = im
def __call__(self, x, y):
z = self.im.get_array()[int(y), int(x)]
return 'x={:.01f}, y={:.01f}, z={:.01f}'.format(x, y, z)
data = np.random.random((10, 10))
fig, ax = plt.subplots()
im = ax.imshow(data, interpolation='none')
ax.format_coord = Formatter(im)
plt.show()
mpldatacursor.datacursor(hover=True, bbox=dict(alpha=1, fc='w'))
plt.show()
def perfect_1d_plot(dirlist,attribs,xattr="psi",normname="norms.namelist",speciesname="species",psiN_to_psiname="psiAHat.h5",global_term_multiplier_name="globalTermMultiplier.h5",cm=cm.rainbow,lg=True,markers=None,linestyles=None,xlims=None,same_plot=False,outputname="default",ylabels=None,label_all=False,global_ylabel="",sort_species=True,first=["D","He"],last=["e"],generic_labels=True,label_dict={"D":"i","He":"z","N":"z","e":"e"},vlines=None,hlines=None,share_scale=[],interactive=False):
#dirlist: list of simulation directories
#attribs: list of fields to plot from simulation
#speciesname: species filename in the simuldir
#normname: norm filename in the simuldir
#lg: controls whether to interpret nearby simulations as being paired
if type(attribs) is not list:
attribs=[attribs]
if ylabels is not None:
if type(ylabels) is not list:
ylabels=[ylabels]*len(attribs)
else:
if len(ylabels) != len(attribs):
print "p_1d_plot: error: ylabels not the same size as attribs"
exit(1)
else:
ylabels=['']*len(attribs)
normlist=[x + "/" + normname for x in dirlist]
specieslist=[x + "/" + speciesname for x in dirlist]
psiN_to_psiList=[x + "/" + psiN_to_psiname for x in dirlist]
global_term_multiplierList=[x + "/" + global_term_multiplier_name for x in dirlist]
simulList=perfect_simulations_from_dirs(dirlist,normlist,specieslist,psiN_to_psiList,global_term_multiplierList)
if markers == None:
markers=['']*len(simulList)
#some logic to differentiate between species independent
#and species quantities further down will fail if there are simulations
#one species (which you really shouldn't do due to quasi-neutrality!!)
num_species_array=numpy.array([len(simul.species) for simul in simulList])
one_species_list=numpy.where(num_species_array<=1)
if len(num_species_array[one_species_list])>0:
print "p_1d_plot: warning: there are simulations with one (or) less species! Logic to determine whether attribute is a species property will not work."
if generic_labels:
for simul in simulList:
simul.species_list=generic_species_labels(simul.species_list,label_dict)
first=generic_species_labels(first,label_dict)
last=generic_species_labels(last,label_dict)
species_set=set([])
for simul in simulList:
species_set = species_set | set(simul.species)
#print gridspec
i=-1
psp_lists=[] #list of lists of perfect subplot object
gridspec_list=[]
colors=cm(numpy.linspace(0,1,len(simulList)))
#assign colors to simulations
all_linecolors=[]
color_index=0
local=[simul.local for simul in simulList]
noddpsi=[simul.no_ddpsi for simul in simulList]
if lg:
colors=cm(numpy.linspace(0,1,len(simulList)-sum(local)-sum(noddpsi)))
if sum(local)>0:
#if we have local simulations, increment color after them
for loc in local:
all_linecolors.append(colors[color_index])
if loc == True:
color_index=color_index+1
elif sum(noddpsi)>0:
#otherwise, increment color after noddpsi simulation
for nd in noddpsi:
all_linecolors.append(colors[color_index])
if nd == True:
color_index=color_index+1
else:
#else, always increment
all_linecolors=cm(numpy.linspace(0,1,len(simulList)))
else:
# force always increment behavior
all_linecolors=cm(numpy.linspace(0,1,len(simulList)))
if linestyles == None:
linestyles=[] #linestyles generated from local or global
for n,l in zip(noddpsi,local):
# local overrides noddpsi in code as well
if l:
linestyles=linestyles+["dashed"]
elif n:
linestyles=linestyles+["dashdot"]
else:
linestyles=linestyles+["solid"]
for i_a,attrib in enumerate(attribs):
psp_list=[]
#check whether attribute is species dependent
#it will be assumed to be if the lenght along the 1 axis
#is equal to the number of species in a simulation for all simulations
#at least as long as there is more than one species in the simulation.
attrib_sp_dep = is_attribute_species_dependent(simulList,attrib)
#we will assign data to the following attribute related groups
attrib_groupname=attrib
if attrib_sp_dep:
species_attrib_groupname="species_dependent"
else:
species_attrib_groupname="species_independent"
if same_plot:
if i_a == len(attribs)-1:
perhaps_last=True
else:
perhaps_last=False
else:
perhaps_last=True
if sort_species:
species_set=sort_species_list(list(species_set),first,last)
if attrib_sp_dep:
for i_sp,s in enumerate(species_set):
i=i+1
#data is taken for a given species for all simulations
#index of species in simulation given by index to index
index=[[ind for ind,spec in enumerate(simul.species) if spec==s] for simul in simulList]
if all(len(ind)<=1 for ind in index):
data=[getattr(simul,attrib)[:,index[i_si][0]] for i_si,simul in enumerate(simulList) if s in simul.species]
else:
print "p_1d_plot: warning: more than one of the same species in the simulation. Will add contributions."
data=[numpy.sum(getattr(simul,attrib)[:,index[i_si]],axis=1) for i_si,simul in enumerate(simulList) if s in simul.species]
if xattr=="theta":
x_scale=1/numpy.pi
else:
x_scale=1
if xattr != None:
x=[getattr(simul,xattr)*x_scale for simul in simulList if s in simul.species]
else:
# If xattrib is None, we plot against the index of the data
# This probably will not work if we are not plotting against
# the first index of data
x=[numpy.array(range(len(getattr(simul,attrib)))) for simul in simulList if s in simul.species]
if xlims == None:
# min to max among all the simulations
xlims = [numpy.min(x),numpy.max(x)]
linecolors=[all_linecolors[i_si] for i_si,simul in enumerate(simulList) if s in simul.species]
coordinates=(i,0)
if perhaps_last and (i_sp == len(species_set) - 1):
last_groupname="last"
gridspec_list.append([i+1,1])
else:
last_groupname="not_last"
psp_list.append(perfect_subplot(data,x,subplot_coordinates=coordinates,groups=[s,attrib_groupname,species_attrib_groupname,last_groupname],linestyles=linestyles,colors=linecolors,markers=markers)) #yaxis_label=ylabels[i_a]
else:
i=i+1
if perhaps_last:
last_groupname="last"
gridspec_list.append([i+1,1])
else:
last_groupname="not_last"
#species independent plot
data=[getattr(simul,attrib) for simul in simulList]
x=[getattr(simul,xattr) for simul in simulList]
linecolors=all_linecolors
coordinates=(i,0)
psp_list.append(perfect_subplot(data,x,subplot_coordinates=coordinates,groups=[attrib_groupname,species_attrib_groupname,last_groupname],linestyles=linestyles,colors=linecolors,markers=markers)) #yaxis_label=ylabels[i_a]
psp_lists.append(psp_list)
if not same_plot:
i=-1
#merge the psp_lists if everything is supposed to go in the same plot
if same_plot:
final_psp_lists=[]
for psp_list in psp_lists:
final_psp_lists = final_psp_lists + psp_list
psp_lists=[final_psp_lists]
for i_li,psp_list in enumerate(psp_lists):
for psp in psp_list:
print psp.groups
psp.xlims=xlims
psp.data=psp.data_inrange()
psp.x=psp.x_inrange()
if same_plot:
attrib_groups=[perfect_subplot_group(psp_list,groups=[a]) for a in attribs]
for ylabel,attrib_group in zip(ylabels,attrib_groups):
if label_all:
attrib_group.setattrs("yaxis_label",ylabel)
else:
attrib_group.set_middle_ylabel(ylabel)
else:
attrib_groups=[perfect_subplot_group(psp_list,groups=[a]) for a in [attribs[i_li]]]
for ylabel,attrib_group in zip([ylabels[i_li]],attrib_groups):
if label_all:
attrib_group.setattrs("yaxis_label",ylabel)
else:
attrib_group.set_middle_ylabel(ylabel)
if len(share_scale)>0:
share_scale_group=perfect_subplot_group(psp_list,groups=share_scale,logic="or")
share_scale_group.setattrs("ylims",[share_scale_group.get_min("data",margin=0.1),share_scale_group.get_max("data",margin=0.1)])
species_groups=[perfect_subplot_group(psp_list,groups=[s]) for s in species_set]
species_indep_groups=perfect_subplot_group(psp_list,groups=["species_independent"])
local_group = perfect_subplot_group(psp_list,groups=["local"])
global_group = perfect_subplot_group(psp_list,groups=["global"])
last_group = perfect_subplot_group(psp_list,groups=["last"])
all_group=perfect_subplot_group(psp_list,groups='',get_all=True)
for species_group,s in zip(species_groups,species_set):
species_group.setattrs("title",s)
for attrib_group in attrib_groups:
this_species_groups=[perfect_subplot_group(attrib_group.p_subplot_list,groups=[s]) for s in species_set]
for this_species_group in this_species_groups:
if len(this_species_group.p_subplot_list)>0:
this_species_group.setattrs("ylims",[this_species_group.get_min("data",margin=0.1),this_species_group.get_max("data",margin=0.1)])
#print [this_species_group.get_min("data",margin=0.1),this_species_group.get_max("data",margin=0.1)]
this_species_indep_group=perfect_subplot_group(attrib_group.p_subplot_list,groups=["species_independent"])
if len(this_species_indep_group.p_subplot_list)>0:
this_species_indep_group.setattrs("ylims",[this_species_indep_group.get_min("data",margin=0.1),this_species_indep_group.get_max("data",margin=0.1)])
this_share_scale_group=perfect_subplot_group(attrib_group.p_subplot_list,groups=share_scale,logic="or")
if len(this_share_scale_group.p_subplot_list)>0:
this_share_scale_group.setattrs("ylims",[this_share_scale_group.get_min("data",margin=0.1),this_share_scale_group.get_max("data",margin=0.1)])
all_group.setattrs("show_yaxis_ticklabel",True)
all_group.setattrs("vlines",vlines)
all_group.setattrs("hlines",hlines)
last_group.setattrs("show_xaxis_ticklabel",True)
#print gridspec_list[i_li]
if xattr=="psi":
global_xlabel=r"$\psi_N$"
elif xattr=="theta":
global_xlabel=r"$\theta/\pi$"
elif xattr=="sqrtpsi":
global_xlabel=r"$\sqrt{\psi_N}$"
elif xattr=="psiOverOrbitWidth":
global_xlabel=r"$\sqrt{\psi_N}$"
elif xattr=="actual_psi":
global_xlabel=r"$\hat{\psi}$"
elif xattr=="actual_psiN":
global_xlabel=r"$\psi_N$"
elif xattr=="psi_index":
global_xlabel=r"$i_\psi$"
elif xattr==None:
global_xlabel=r"$i$"
perfect_visualizer(psp_list,gridspec_list[i_li],global_xlabel=global_xlabel,dimensions=1,global_ylabel=global_ylabel)
if same_plot:
plt.savefig(outputname+".pdf")
else:
plt.savefig(attribs[i_li]+".pdf")
if interactive:
#dangerous, since it will (for some reason) be executed after all 1d_plot calls and show everything plotted in the given script.
datacursor(display='multiple', draggable=True)
plt.show()