def __init__(self, parent):
# super(StocksGraphView, self).__init__(parent)
self.fatherHandle = parent
self.figure = plt.gcf()
self.ax = self.figure.gca()
self.canvas = figureCanvas(self.figure)
self.hintText = self.ax.text(-.5, -.5, "", ha="right", va="baseline", fontdict={"size": 15})
self.figure.canvas.mpl_connect('key_press_event', self._on_key_press)
self.figure.canvas.mpl_connect('button_press_event', self._on_button_press)
# figure.canvas.mpl_disconnect(figure.canvas.manager.key_press_handler_id)
self.figure.canvas.mpl_connect('motion_notify_event', self._on_mouse_move)
self._lines = {}
self._hHintLine = None
self._vHintLine = None
self.ax.fmt_date = matplotlib.dates.DateFormatter('%Y-%m-%d')
self.strpdate2num = matplotlib.dates.strpdate2num('%Y-%m-%d')
plt.subplots_adjust(left=.04, bottom=.0, right=.98, top=.97,
wspace=.0, hspace=.0)
plt.minorticks_on()
self.ax.grid()
self.ax.xaxis.set_major_formatter(matplotlib.dates.DateFormatter('%y\n-\n%m\n-\n%d'))
def SetAxes(legend=False):
# plt.axhline(y=0.165, ls='-', c='k', label=r'$\Omega_{b}$/$\Omega_{M}$ (WMAP)')
f_b = 0.164
f_star = 0.01
err_b = 0.004
err_star = 0.004
f_gas = f_b - f_star
err_gas = np.sqrt(err_b**2 + err_star**2)
plt.axhline(y=f_gas, ls='--', c='k', label='', zorder=-1)
x = np.linspace(1e+13,200e+13,1000)
plt.fill_between(x, y1=f_gas - err_gas, y2=f_gas + err_gas, color='k', alpha=0.3, zorder=-1)
plt.text(10e+13, f_gas+0.005, r'f$_{gas}$', verticalalignment='bottom', size='large')
plt.xlabel(r'M$_{vir}$ (M$_\odot$)', size='x-large')
plt.ylabel(r'f$_{gas}$ ($<$ r)', size='x-large')
plt.xscale('log')
plt.xlim([1e+13,2e+15])
plt.ylim(ymin=0.03)
plt.tick_params(length=10, which='major')
plt.tick_params(length=5, which='minor')
plt.minorticks_on()
if legend:
plt.legend(loc=0, prop={'size':'large'}, markerscale=0.7, numpoints=1)
def plot(filename):
import os
from matplotlib.pyplot import clf, tricontour, tricontourf, \
gca, savefig, rc, minorticks_on
if not os.path.exists(filename):
return -1
rc('text', usetex=True)
clf()
x, y, tri, ux, uy = load_velocity(filename)
tricontourf(x, y, tri, ux, 16)
tricontour(x, y, tri, ux, 16, linestyles='-',
colors='black', linewidths=0.5)
minorticks_on()
gca().set_aspect('equal')
gca().tick_params(direction='out', which='both')
gca().set_xticklabels([])
gca().set_yticklabels([])
name, _ = os.path.splitext(filename)
name = os.path.basename(name)
savefig('{0}.png'.format(name), dpi=300, bbox_inches='tight')
savefig('{0}.pdf'.format(name), bbox_inches='tight')
def cumulative_frequency(self):
# taken from http://stackoverflow.com/questions/15408371/cumulative-distribution-plots-python
# make the array onedimensionally
data = np.ravel(self.map)
# sort the data
sorted_data = np.sort(data) # Or data.sort(), if data can be modified
x = sorted_data
y = np.arange(sorted_data.size)/1000.0
# Cumulative distributions:
plt.step(x, y) # From 0 to the number of data points-1
# alternatively cumfreqs, lowlim, binsize, extrapoints = scipy.stats.cumfreq(data, numbins=4)
plt.title('Cumulative frequency')
plt.xlabel('e- /pix /4.4s')
plt.ylabel('1000 counts')
plt.xlim(0,100)
# see http://matplotlib.org/examples/pylab_examples/axes_demo.html
# this is another inset axes over the main axes
a = plt.axes([0.4, 0.2, .4, .5])
plt.step(x, y)
# we want to see minor ticks in the plot, disabled by default
plt.minorticks_on()
# set the limits for both axis
plt.xlim(20, 25)
plt.ylim(104,109)
plt.savefig('../ScatterMap1_cumfreq.png')
plt.savefig('../ScatterMap1_cumfreq.pdf')
plt.show()
# close the plot gracefully
plt.close()
def apcorr_plot(self):
'''
Creates a plot of delta_mag versus instru_mag to determine in which
region(s) to compute zpt_off.
'''
counts1, counts2, insmag1, insmag2, delta_mag, vegamag = \
self.mag_calc()
for image in self.imlist:
mpl.rcParams['font.family'] = 'Times New Roman'
mpl.rcParams['font.size'] = 12.0
mpl.rcParams['xtick.major.size'] = 10.0
mpl.rcParams['xtick.minor.size'] = 5.0
mpl.rcParams['ytick.major.size'] = 10.0
mpl.rcParams['ytick.minor.size'] = 5.0
mpl.minorticks_on()
mpl.ion()
mpl.title(image)
mpl.ylabel('$\Delta$ mag (r=' + self.apertures[0] + ', ' + \
self.apertures[-1] + ')')
mpl.xlabel('-2.5 log(flux)')
mpl.scatter(insmag1, delta_mag, s=1, c='k')
mpl.savefig(image[:-9] + '_apcorr.png')
left = raw_input('left: ')
right = raw_input('right: ')
bottom = raw_input('bottom: ')
top = raw_input('top: ')
mpl.close()
zpt_off_calc(left, right, top, bottom)
def plot_Nhden(elem,N,hcol,hden,bounds=False):
for i in to_plot[elem]:
plt.clf()
x = np.array(hden,dtype=np.float)
y = np.array(N[i])
#x,y,hcol = trim(x,y,hcol)
y = hcol[0] - y
xlims=[0.75*np.amin(x), 1.25*np.amax(x)]
ylims=[0.75*np.amin(y), 1.25*np.amax(y)]
try:
if bounds:
l = minNHI - observed[elem][i]["column"][2]
if observed[elem][i]["column"][0]==-30.:
u=maxNHI
else:
u = maxNHI - observed[elem][i]["column"][0]
plt.fill([-30.,30., 30., -30.], [l,l,u,u], '0.50', alpha=0.2, edgecolor='b')
#plt.fill_between(np.arange(xlims[0],xlims[1]),lower,upper,color='0.50')
except KeyError:
pass
plt.plot(x, y, color_map[i],label=ion_state(i,elem))
plt.ylabel(r"log $N_{HI}/N_{%s}$"%(str(elem)+str(roman[i])))
plt.xlabel("log $n_{H}$")
plt.minorticks_on()
makedir('hden')
f=os.path.join(paths["plot_path"],"hden", elem+roman[i]+"N_Nhden.png")
plt.xlim([-3.,0.])
#plt.ylim(ylims)
plt.savefig(f)
plt.show()
plt.close()
def make_voronoi_intens(targetSN, w1, w2):
""" Make image"""
image = "collapsed_w{0}_{1}.fits".format(w1, w2)
intens = pf.getdata(image)
extent = calc_extent(image)
vordata = pf.getdata("voronoi_sn{0}_w{1}_{2}.fits".format(targetSN, w1,
w2))
vordata = np.ma.array(vordata, mask=np.isnan(vordata))
bins = np.unique(vordata)[:-1]
combined = np.zeros_like(intens)
combined[:] = np.nan
for j, bin in enumerate(bins):
idx, idy = np.where(vordata == bin)
flux = intens[idx,idy]
combined[idx,idy] = np.nanmean(flux)
vmax = np.nanmedian(intens) + 4 * np.nanstd(intens)
fig = plt.figure(1)
plt.minorticks_on()
make_contours()
plt.imshow(combined, cmap="cubehelix_r", origin="bottom", vmax=vmax,
extent=extent, vmin=0)
plt.xlabel("X [kpc]")
plt.ylabel("Y [kpc]")
cbar = plt.colorbar()
cbar.set_label("Flux [$10^{-20}$ erg s$^{-1}$ cm$^{-2}$]")
plt.savefig("figs/intens_sn{0}.png".format(targetSN), dpi=300)
pf.writeto("figs/intens_sn{0}.fits".format(targetSN), combined,
clobber=True)
return
def make_intens_all(w1, w2):
fig = plt.figure(figsize=(6., 6.))
gs = gridspec.GridSpec(1,1)
gs.update(left=0.13, right=0.985, bottom = 0.13, top=0.988)
ax = plt.subplot(gs[0])
plt.minorticks_on()
make_contours()
labels = ["A", "B", "C", "D"]
for i, field in enumerate(fields):
os.chdir(os.path.join(data_dir, "combined_{0}".format(field)))
image = "collapsed_w{0}_{1}.fits".format(w1, w2)
intens = pf.getdata(image, verify=False)
extent = calc_extent(image)
extent = offset_extent(extent, field)
plt.imshow(intens, cmap="bone", origin="bottom", extent=extent,
vmin=-20, vmax=80)
verts = calc_verts(intens, extent)
path = Path(verts, [Path.MOVETO, Path.LINETO, Path.LINETO, Path.LINETO,
Path.CLOSEPOLY,])
patch = patches.PathPatch(path, facecolor='none', lw=2, edgecolor="r")
ax.add_patch(patch)
xtext, ytext = np.mean(verts[:-1], axis=0)
plt.text(xtext-8, ytext+8, labels[i], color="r",
fontsize=35, fontweight='bold', va='top')
plt.hold(True)
plt.xlim(26, -38)
plt.ylim(-32, 32)
plt.xlabel("X [kpc]")
plt.ylabel("Y [kpc]")
# plt.show()
plt.savefig(os.path.join(plots_dir, "muse_fields.eps"), dpi=60,
format="eps")
plt.savefig(os.path.join(plots_dir, "muse_fields.png"), dpi=200)
return
def make_lick_individual(targetSN, w1, w2):
""" Make maps for the kinematics. """
filename = "lick_corr_sn{0}.tsv".format(targetSN)
binimg = pf.getdata("voronoi_sn{0}_w{1}_{2}.fits".format(targetSN, w1, w2))
intens = "collapsed_w{0}_{1}.fits".format(w1, w2)
extent = calc_extent(intens)
bins = np.loadtxt(filename, usecols=(0,), dtype=str).tolist()
bins = np.array([x.split("bin")[1] for x in bins]).astype(int)
data = np.loadtxt(filename, usecols=np.arange(25)+1).T
labels = [r'Hd$_A$', r'Hd$_F$', r'CN$_1$', r'CN$_2$', r'Ca4227', r'G4300',
r'Hg$_A$', r'Hg$_F$', r'Fe4383', r'Ca4455', r'Fe4531', r'C4668',
r'H$_\beta$', r'Fe5015', r'Mg$_1$', r'Mg$_2$', r'Mg$_b$', r'Fe5270',
r'Fe5335', r'Fe5406', r'Fe5709', r'Fe5782', r'Na$_D$', r'TiO$_1$',
r'TiO$_2$']
mag = "[mag]"
ang = "[\AA]"
units = [ang, ang, mag, mag, ang, ang,
ang, ang, ang, ang, ang, ang,
ang, ang, mag, mag, ang, ang,
ang, ang, ang, ang, ang, mag,
mag]
lims = [[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None],
[None, None], [None, None], [None, None], [None, None]]
pdf = PdfPages("figs/lick_sn{0}.pdf".format(targetSN))
fig = plt.figure(1, figsize=(6.25,5))
plt.subplots_adjust(bottom=0.12, right=0.97, left=0.09, top=0.96)
plt.minorticks_on()
ax = plt.subplot(111)
ax.minorticks_on()
plot_indices = np.arange(12,22)
for i, vector in enumerate(data):
if i not in plot_indices:
continue
print "Making plot for {0}...".format(labels[i])
kmap = np.zeros_like(binimg)
kmap[:] = np.nan
for bin,v in zip(bins, vector):
idx = np.where(binimg == bin)
kmap[idx] = v
vmin = lims[i][0] if lims[i][0] else np.median(vector) - 2 * vector.std()
vmax = lims[i][1] if lims[i][1] else np.median(vector) + 2 * vector.std()
m = plt.imshow(kmap, cmap="inferno", origin="bottom", vmin=vmin,
vmax=vmax, extent=extent, aspect="equal")
make_contours()
plt.minorticks_on()
plt.xlabel("X [kpc]")
plt.ylabel("Y [kpc]")
plt.xlim(extent[0], extent[1])
plt.ylim(extent[2], extent[3])
cbar = plt.colorbar(m)
cbar.set_label("{0} {1}".format(labels[i], units[i]))
pdf.savefig()
plt.clf()
pdf.close()
return
def plotErrorResSize():
matplotlib.rcParams.update({'font.size': 25})
npzFile = '2016-04-28-09-57_bigRunOnlySnap.npz'
npz2 = '2016-04-28-15-18_bigRunOnlySnap.npz'
projectPath = 'C:\Users\Steve\Documents\Uni\BAThesis\\src\\errorResSize.pdf'
pp = PdfPages(projectPath)
a = np.load(getProjectPath()+npzFile)
errors = a['errors']
errors = np.mean(errors,2).squeeze()
b = np.load(getProjectPath()+npz2)
errors2 = b['errors']
errors2 = np.mean(errors2,2).squeeze()
plt.figure(figsize=(10,7.5))
plt.plot(errors, 'o', linestyle='-', linewidth=3, label='ridge para = 0.01')
#plt.plot(errors2, 'o', linestyle='-', linewidth=3, label='ridge para = 0.1')
plt.grid()
plt.minorticks_on()
plt.grid(which='minor', axis='y')
plt.xlabel('Reservoir size')
ticks = np.arange(0, 8)
labels = [25,50,100,200,400,800,1600,3200]
plt.xticks(ticks, labels)
plt.ylabel('Validation error')
plt.ylim(0,1)
plt.tight_layout()
pp.savefig()
pp.close()
def SetAxes(legend=False):
f_b = 0.164
f_star = 0.01
err_b = 0.006
err_star = 0.004
f_gas = f_b - f_star
err_gas = np.sqrt(err_b**2 + err_star**2)
plt.axhline(y=f_gas, ls='--', c='k', label='', zorder=-1)
x = np.linspace(.0,2.,1000)
plt.fill_between(x, y1=f_gas - err_gas, y2=f_gas + err_gas, color='k', alpha=0.3, zorder=-1)
plt.text(.6, f_gas+0.006, r'f$_{gas}$', verticalalignment='bottom', size='large')
plt.xlabel(r'r/r$_{vir}$', size='x-large')
plt.ylabel(r'f$_{gas}$ ($<$ r)', size='x-large')
plt.xscale('log')
plt.xticks([1./1.9, 1.33/1.9, 1, 1.5, 2.],[r'r$_{500}$', r'r$_{200}$', 1, 1.5, 2], size='large')
#plt.yticks([.1, .2], ['0.10', '0.20'])
plt.tick_params(length=10, which='major')
plt.tick_params(length=5, which='minor')
plt.xlim([0.4,1.5])
plt.minorticks_on()
if legend:
plt.legend(loc=0, prop={'size':'small'}, markerscale=0.7, numpoints=1, ncol=2)
def plotcurve(xax,f1,f2,ct):
fig, axes = plt.subplots(nrows=4, ncols=1, sharex=True)
plt.minorticks_on()
fig.subplots_adjust(hspace = 0.001)
plt.rc('font', family='serif',serif='Times')
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset=False)
axes[0].plot(xax,f1[0],'D-',c='k',mec='b',fillstyle='none')
axes[0].plot(xax,f2[0],'o-',c='g',mec='k',fillstyle='none')
axes[0].set_ylabel(r'$raw$ $RMS$',fontsize=13)
axes[0].yaxis.set_major_formatter(y_formatter)
axes[0].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[1].plot(xax,f1[1],'D-',c='k',mec='b',fillstyle='none')
axes[1].plot(xax,f2[1],'o-',c='g',mec='k',fillstyle='none')
axes[1].set_ylabel(r'$frames$ $RMS$',fontsize=13)
axes[1].yaxis.set_major_formatter(y_formatter)
axes[1].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[2].plot(xax,f1[2],'D-',c='k',mec='b',fillstyle='none')
axes[2].plot(xax,f2[2],'o-',c='g',mec='k',fillstyle='none')
axes[2].set_ylabel(r'$\sigma-clipped$',fontsize=13)
axes[2].yaxis.set_major_formatter(y_formatter)
axes[2].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[3].plot(xax,f1[3],'D-',c='k',mec='b',fillstyle='none',label='Hard')
axes[3].plot(xax,f2[3],'o-',c='g',mec='k',fillstyle='none',label='Soft')
axes[3].set_ylabel(r'$\sigma$ $clipped$ $RMS$',fontsize=13)
axes[3].set_xlabel(r'$aperture$ $(pixels)$',fontsize=13)
axes[3].yaxis.set_major_formatter(y_formatter)
axes[3].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[3].legend(numpoints=1)
plt.savefig('paneltest/'+str(ct)+'updchanges.png',bbox_inches='tight',dpi=200)
def plotshare(self):
datesaxis=mdates.date2num(self.dates)
fig0=plt.figure()
ax0=fig0.add_subplot(1,1,1)
dateFmt = mdates.DateFormatter('%Y-%m-%d')
ax0.xaxis.set_major_formatter(dateFmt)
plt.minorticks_on()
N=len(datesaxis)
#ax0.xaxis.set_major_locator(DaysLoc)
index=np.arange(N)
# dev=np.abs(self.share_prices[:,0]-self.share_prices[:,2])
# p0=plt.errorbar(index,self.share_prices,dev, fmt='.-',ecolor='green',elinewidth=0.1,linewidth=1)
p0=plt.plot(index,self.share_prices)
ax0.legend([p0],[symbol])
ax0.set_ylabel( u'Index')
ax0.xaxis.set_major_formatter(ticker.FuncFormatter(lambda x, pos=None: dates[int(x)]))
ax0.set_xticks(np.arange(0,index[-1],4))
ax0.set_xlim(index[0],index[-1])
fig0.autofmt_xdate(rotation=90)
fig0.savefig('./figures/sharesPrices.eps')
plt.show()
def avg_row_col_main(self):
'''
The main controller.
'''
self.get_image_list()
self.parse_image_info()
self.read_data()
self.calc_avg()
# Set plotting parameters
plt.rcParams['legend.fontsize'] = 10
plt.rcParams['font.family'] = 'Helvetica'
plt.minorticks_on()
# Plot the data
if self.plot_type == 'row' or self.plot_type == 'both':
self.descrip = 'Row'
self.anti_descrip = 'Column'
if self.all_switch == 'off':
self.plot_single_data(self.avg_row_list)
elif self.all_switch == 'on':
self.plot_all_data(self.avg_row_list)
elif self.plot_type == 'col' or self.plot_type == 'both':
self.descrip = 'Column'
self.anti_descrip = 'Row'
if self.all_switch == 'off':
self.plot_single_data(self.avg_col_list)
elif self.all_switch == 'on':
self.plot_all_data(self.avg_col_list)
def plotter(x, y, image, dep_var, ind_var):
"""
:param x: your dependent variable
:param y: your independent variable
:return:
"""
# todo - make little gridlines
# turn your x and y into numpy arrays
x = np.array(x)
y = np.array(y)
ETrF_vs_NDVI = plt.figure()
aa = ETrF_vs_NDVI.add_subplot(111)
aa.set_title('Bare soils/Tailings Pond - {}'.format(image), fontweight='bold')
aa.set_xlabel('{}'.format(dep_var), style='italic')
aa.set_ylabel('{}'.format(ind_var), style='italic')
aa.scatter(x, y, facecolors='none', edgecolors='blue')
plt.minorticks_on()
# aa.grid(b=True, which='major', color='k')
aa.grid(b=True, which='minor', color='white')
plt.tight_layout()
# TODO - UNCOMMENT AND CHANGE THE PATH TO SAVE THE FIGURE AS A PDF TO A GIVEN LOCATION.
# plt.savefig(
# "/Volumes/SeagateExpansionDrive/jan_metric_PHX_GR/green_river_stack/stack_output/20150728_ETrF_NDVI_gr.pdf")
plt.show()
def plot_field_corr2(cat,theta,out,err,out2,err2,label):
plt.figure()
plt.errorbar(theta,theta*out[0],yerr=theta*err[0],marker='o',linestyle='',color='r',label=r'$e_1$')
plt.errorbar(theta,theta*out2[0],yerr=theta*err2[0],marker='o',linestyle='',color='b',label=r'$e_2$')
if 'chip' not in label:
plt.axvline(x=5.25*60, linewidth=1, color='k')
elif 'corner' in label:
plt.axvline(x=0.75*60, linewidth=1, color='k')
plt.axvline(x=0.15*60, linewidth=1, color='k')
plt.axvline(x=0.765*60, linewidth=1, color='k')
elif 'centre' in label:
plt.axvline(x=0.75*60/2., linewidth=1, color='k')
plt.axvline(x=0.15*60/2., linewidth=1, color='k')
plt.axvline(x=0.765*60/2., linewidth=1, color='k')
plt.ylabel(r'$\langle e \rangle$')
plt.xlabel(r'$\theta$ (arcmin)')
plt.ylim((-.005,.005))
plt.xscale('log')
plt.minorticks_on()
plt.legend(loc='upper right',ncol=1, frameon=True,prop={'size':12})
plt.savefig('plots/xi/field_'+label+'_'+cat.name+'_mean_e.png', bbox_inches='tight')
plt.close()
return
def plot_hist(x1,bins=config.cfg.get('hbins',500),name='',label='',tile='',w=None):
print 'hist ',label,tile
if tile!='':
bins/=10
plt.figure()
if (w is None)|(tile!=''):
plt.hist(x1,bins=bins,histtype='stepfilled')
else:
plt.hist(x1,bins=bins,alpha=0.25,normed=True,label='unweighted',histtype='stepfilled')
plt.hist(x1,bins=bins,alpha=0.25,normed=True,weights=w,label='weighted',histtype='stepfilled')
plt.ylabel(r'$n$')
s=config.lbl.get(label,label.replace('_','-'))
if config.log_val.get(label,False):
s='log '+s
plt.xlabel(s+' '+tile)
plt.minorticks_on()
if tile!='':
name='tile_'+tile+'_'+name
plt.legend(loc='upper right',ncol=2, frameon=True,prop={'size':12})
plt.savefig('plots/hist/hist_'+name+'_'+label.replace('_','-')+'.png', bbox_inches='tight')
plt.close()
return
def pieces_plot(dgs, title, outfname):
"""
Plot deltaG over lambda as well as the electrostatic and vdW components.
Parameters
----------
dgs: array of energies, in order of total dG, elec, vdW
title: string name of the main title
outfname: string name of the image to be saved
"""
lambdas = np.linspace(0., 1., len(dgs[0])) # for x-axis, lambda from 0 to 1
labels = ['$\Delta$G','electrostatic','van der Waals']
plt.figure()
for y, l in zip(dgs, labels):
plt.plot(lambdas, y, label=l)
#plt.errorbar(lambdas, dgs, sds)
plt.title(title, fontsize=18)
plt.xlabel("$\lambda$",fontsize=18)
plt.ylabel("energy (kcal/mol)",fontsize=18)
plt.legend(fancybox=True, loc=2)
plt.minorticks_on()
plt.tick_params(axis='both',width=1.5,length=7,labelsize=16)
plt.tick_params(which='minor',width=1.0,length=4)
plt.savefig(outfname+'_int-decom.eps', format='eps')
plt.clf()
def prettyplot():
ticks_font = font_manager.FontProperties(family='Helvetica', style='normal',
size=16, weight='normal', stretch='normal')
font = {'family': 'Helvetica', 'size': 10}
matplotlib.rc('font',**font)
#matplotlib.rc('ylabel',fontweight='bold',fontsize=18,labelpad=20)
matplotlib.rcParams['axes.labelsize'] = 18
matplotlib.rcParams['axes.labelweight'] = 'bold'
matplotlib.rcParams['axes.titlesize'] = 20
#matplotlib.rcParams['axes.titleweight'] = 'bold'
plt.figure()
ax = plt.axes()
for label in ax.get_xticklabels():
#print label.get_text()
label.set_fontproperties(ticks_font)
for label in ax.get_yticklabels():
label.set_fontproperties(ticks_font)
plt.minorticks_on()
plt.tick_params(axis='both', which='major', labelsize=12)
plt.gcf().subplots_adjust(bottom=0.15)
plt.gcf().subplots_adjust(left=0.15)
t = plt.title('')
t.set_y(1.05)
t.set_fontweight('bold')
x = ax.set_xlabel('',labelpad=20)
y = ax.set_ylabel('',labelpad=20)
def plotSeries(key, ymin=None, ymax=None):
"""
Plot the chosen dataset key for each scanned data file.
@param key: data set key to use
@type key: L{str}
@param ymin: minimum value for y-axis or L{None} for default
@type ymin: L{int} or L{float}
@param ymax: maximum value for y-axis or L{None} for default
@type ymax: L{int} or L{float}
"""
titles = []
for title, data in sorted(dataset.items(), key=lambda x: x[0]):
titles.append(title)
x, y = zip(*[(k / 3600.0, v[key]) for k, v in sorted(data.items(), key=lambda x: x[0]) if key in v])
plt.plot(x, y)
plt.xlabel("Hours")
plt.ylabel(key)
plt.xlim(0, 24)
if ymin is not None:
plt.ylim(ymin=ymin)
if ymax is not None:
plt.ylim(ymax=ymax)
plt.xticks((1, 4, 7, 10, 13, 16, 19, 22), (18, 21, 0, 3, 6, 9, 12, 15))
plt.minorticks_on()
plt.gca().xaxis.set_minor_locator(AutoMinorLocator(n=3))
plt.grid(True, "major", "x", alpha=0.5, linewidth=0.5)
plt.grid(True, "minor", "x", alpha=0.5, linewidth=0.5)
plt.legend(titles, "upper left", shadow=True, fancybox=True)
plt.show()
def plot_comparison_numpy(params1, label1, color1='black', params2=None, label2="", color2='red', title="", plotname=""):
"""Plot same fn for 2 sets of parameters, with indiviudal labels
Uses numpy.
"""
pt = np.arange(0.5, 20, 0.5)
corrections1 = pf_func(pt, params1)
plt.plot(pt, corrections1, 'x-', color=color1, label=label1, lw=1.5)
if params2:
corrections2 = pf_func(pt, params2)
plt.plot(pt, corrections2, 'd-', color=color2, label=label2, lw=1.5)
plt.xlabel(r"$p_T^{in} \mathrm{[GeV]}$")
plt.ylabel("Corr. factor")
# plt.set_xscale('log')
plt.minorticks_on()
plt.grid(b=True, which='major', axis='both')
plt.grid(b=True, which='minor', axis='both')
plt.xlim(left=pt[0]-0.5)
# draw intersection lines for 5, 10
for p, lc in zip([0.5, 5, 10], ["purple", "blue", "green"]):
corr = pf_func(p, params1)
plt.vlines(p, ymin=plt.ylim()[0], ymax=corr, color=lc, linestyle='dashed', linewidth=1.5, label=r'$p_T^{in}$' + ' = %g GeV,\ncorr. factor = %.3f' % (p, corr))
plt.hlines(corr, xmin=0, xmax=p, color=lc, linestyle='dashed', linewidth=1.5)
plt.title(title)
plt.legend(fontsize=12, loc=0)
if plotname != "":
plt.savefig(plotname)
plt.cla()
def plot3panels(xax,p1,p2,p3,p4,ct):
fig, axes = plt.subplots(nrows=4, ncols=1, sharex=True)
plt.minorticks_on()
fig.subplots_adjust(hspace = 0.001)
plt.rc('font', family='serif',serif='Times')
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset=False)
axes[0].plot(xax,p1,'D-',c='k',mec='b',fillstyle='none')
axes[0].set_ylabel(r'$original$ $RMS$',fontsize=13)
axes[0].yaxis.set_major_formatter(y_formatter)
axes[0].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[1].plot(xax,p2,'D-',c='k',mec='b',fillstyle='none')
axes[1].set_ylabel(r'$flattened$ $RMS$',fontsize=13)
axes[1].yaxis.set_major_formatter(y_formatter)
axes[1].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[2].plot(xax,p4,'D-',c='k',mec='b',fillstyle='none')
axes[2].set_ylabel(r'$\sigma-clipped$',fontsize=13)
axes[2].yaxis.set_major_formatter(y_formatter)
axes[2].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[3].plot(xax,p3,'D-',c='k',mec='b',fillstyle='none',label='Soft')
axes[3].set_ylabel(r'$\sigma$ $clipped$ $RMS$',fontsize=13)
axes[3].set_xlabel(r'$aperture$ $(pixels)$',fontsize=13)
axes[3].yaxis.set_major_formatter(y_formatter)
axes[3].yaxis.set_major_locator(MaxNLocator(prune='both',nbins=5))
axes[3].legend(numpoints=1)
plt.savefig(str(ct)+'smoothlightS.png',bbox_inches='tight',dpi=200)
def gbar_plot(dgs, sds, title, outfname):
"""
Plot free energy change deltaG over lambda.
Parameters
----------
dgs: 1D array of dGs
sds: 1D array of standard deviations corresponding to dgs array.
If don't have this, just feed function a list of zeroes.
title: string name of the main title
outfname: string name of the image to be saved
"""
### FOR SOME REASON THE ERROR BARS ARE DISPLAYING HORIZ
### EVEN WHEN DEFINING yerr=sds ...
lambdas = np.linspace(0., 1., len(dgs)) # for x-axis, lambda from 0 to 1
plt.figure()
plt.errorbar(lambdas, dgs)
#plt.errorbar(lambdas, dgs, sds)
plt.title(title, fontsize=18)
plt.xlabel("$\lambda$",fontsize=18)
plt.ylabel("$\Delta$G (kcal/mol)",fontsize=18)
plt.minorticks_on()
plt.tick_params(axis='both',width=1.5,length=7,labelsize=16)
plt.tick_params(which='minor',width=1.0,length=4)
plt.savefig(outfname+'_summary.eps', format='eps')
plt.clf()
def plot_seeing(fwhm, tag=None):
fig = plt.figure()
plt.minorticks_on()
ax = fig.add_subplot(111)
print 'median seeing in g = ',numpy.median(fwhm['g'])
print 'median seeing in r = ',numpy.median(fwhm['r'])
print 'median seeing in i = ',numpy.median(fwhm['i'])
print 'median seeing in z = ',numpy.median(fwhm['z'])
riz = numpy.concatenate([fwhm['r'], fwhm['i'], fwhm['z']])
print 'median seeing in riz = ',numpy.median(riz)
nbins = 40
range = (0.7, 1.7)
#n, bins, p = ax.hist(riz, bins=nbins, range=range, histtype='step', fill=True,
#color='black', facecolor='cyan', label='riz')
#n, bins, p = ax.hist(fwhm['g'], bins=bins, histtype='step', color='green', label='g')
#n, bins, p = ax.hist(fwhm['r'], bins=bins, histtype='step', color='red', label='r')
#n, bins, p = ax.hist(fwhm['i'], bins=bins, histtype='step', color='magenta', label='i')
#n, bins, p = ax.hist(fwhm['z'], bins=bins, histtype='step', color='blue', label='z')
width = (range[1]-range[0])/nbins
n, bins, p = ax.hist([fwhm['z'],fwhm['i'],fwhm['r']], bins=nbins, range=range,
histtype='barstacked', fill=True,
color=['black','purple','red'], width=width)
ax.set_xlabel('Seeing FWHM (arcsec)')
ax.set_ylabel('Number of exposures')
ax.legend(reversed(p), ['r', 'i', 'z'], loc='upper right')
ax.set_xlim(*range)
plt.tight_layout()
if tag is None:
plt.savefig('seeing.pdf')
else:
plt.savefig('seeing_%s.pdf'%tag)
def plot_results(dists):
for i, d in enumerate(dists):
ax = plt.subplot(3,3,(4*i)+1)
N, bins, patches = plt.hist(d.data, color="b",ec="k", bins=30, \
range=tuple(d.lims), normed=True, \
edgecolor="k", histtype='bar',linewidth=1.)
fracs = N.astype(float)/N.max()
norm = Normalize(-.2* fracs.max(), 1.5 * fracs.max())
for thisfrac, thispatch in zip(fracs, patches):
color = cm.gray_r(norm(thisfrac))
thispatch.set_facecolor(color)
thispatch.set_edgecolor("w")
x = np.linspace(d.data.min(), d.data.max(), 100)
ylim = ax.get_ylim()
plt.plot(x, d.best.pdf(x), "-r", lw=1.5, alpha=0.7)
ax.set_ylim(ylim)
plt.axvline(d.best.MAPP, c="r", ls="--", lw=1.5)
plt.tick_params(labelright=True, labelleft=False, labelsize=10)
plt.xlim(d.lims)
plt.locator_params(axis='x',nbins=10)
if i < 2:
plt.setp(ax.get_xticklabels(), visible=False)
else:
plt.xlabel(r"[$\mathregular{\alpha}$ / Fe]")
plt.minorticks_on()
def hist2D(dist1, dist2):
""" Plot distribution and confidence contours. """
X, Y = np.mgrid[dist1.lims[0] : dist1.lims[1] : 20j,
dist2.lims[0] : dist2.lims[1] : 20j]
extent = [dist1.lims[0], dist1.lims[1], dist2.lims[0], dist2.lims[1]]
positions = np.vstack([X.ravel(), Y.ravel()])
values = np.vstack([dist1.data, dist2.data])
kernel = stats.gaussian_kde(values)
Z = np.reshape(kernel(positions).T, X.shape)
ax.imshow(np.rot90(Z), cmap="gray_r", extent=extent, aspect="auto",
interpolation="spline16")
plt.axvline(dist1.best.MAPP, c="r", ls="--", lw=1.5)
plt.axhline(dist2.best.MAPP, c="r", ls="--", lw=1.5)
plt.tick_params(labelsize=10)
ax.minorticks_on()
plt.locator_params(axis='x',nbins=10)
return
ax = plt.subplot(3,3,4)
hist2D(dists[0], dists[1])
plt.setp(ax.get_xticklabels(), visible=False)
plt.ylabel("[Z/H]")
plt.xlim(dists[0].lims)
plt.ylim(dists[1].lims)
ax = plt.subplot(3,3,7)
hist2D(dists[0], dists[2])
plt.ylabel(r"[$\mathregular{\alpha}$ / Fe]")
plt.xlabel("log Age (yr)")
plt.xlim(dists[0].lims)
plt.ylim(dists[2].lims)
ax = plt.subplot(3,3,8)
plt.xlabel("[Z/H]")
hist2D(dists[1], dists[2])
plt.xlim(dists[1].lims)
plt.ylim(dists[2].lims)
return
def plot_density(x, primary=True):
"""
Creates a density plot of the data.
Code is based on this forum message http://stackoverflow.com/a/4152016
:param x: (array like)
the data
"""
# Calculate the density points
density = gaussian_kde(x)
# TODO: COme up with a better start and end point
xs = linspace(min(x)-1, max(x)+1, 200)
density.covariance_factor = lambda : 0.25
density._compute_covariance()
plt.plot(xs,density(xs), color='#0066FF', alpha=0.7)
# Add Grid lines
plt.minorticks_on()
plt.grid(b=True, which='major', color='#666666', linestyle='-')
plt.grid(b=True, which='minor', color='#999999', linestyle='-', alpha=0.2)
# Render the plot
if primary:
plt.show()
def save(self):
result = self.bands.all()
# indexes are negative because they
# represent the number of days in the past
index = [ (i.get("index")+1)*-1 for i in result ]
close = [ i.get("close") for i in result ]
up = [ i.get("up") for i in result ]
middle = [ i.get("middle") for i in result ]
down = [ i.get("down") for i in result ]
plt.plot(index, up, label="upper band")
plt.plot(index, down, label="lower band")
plt.plot(index, middle, label="middle band")
plt.plot(index, close, label="close price")
plt.xlabel("Past days (0 = today)")
plt.ylabel("Value (USD$)")
plt.title("%s bollinger bands" % (self.bands.symbol))
# enables the grid for every single decimal value
plt.minorticks_on()
plt.grid(True, which="both")
legend = plt.legend(fancybox=True, loc="best")
legend.get_frame().set_alpha(0.5)
plt.savefig(self.bands.symbol+".png")
# the plot must be closed for otherwhise matplotlib
# will paint over previous plots
plt.close()
def disp_frame(x_data, y_data, mag_data):
'''
Show full frame.
'''
coord, x_name, y_name = prep_plots.coord_syst()
st_sizes_arr = prep_plots.star_size(mag_data)
plt.gca().set_aspect('equal')
# Get max and min values in x,y
x_min, x_max = min(x_data), max(x_data)
y_min, y_max = min(y_data), max(y_data)
# Set plot limits
plt.xlim(x_min, x_max)
plt.ylim(y_min, y_max)
# If RA is used, invert axis.
if coord == 'deg':
plt.gca().invert_xaxis()
# Set axis labels
plt.xlabel('{} ({})'.format(x_name, coord), fontsize=12)
plt.ylabel('{} ({})'.format(y_name, coord), fontsize=12)
# Set minor ticks
plt.minorticks_on()
# Set grid
plt.grid(b=True, which='major', color='k', linestyle='-', zorder=1)
plt.grid(b=True, which='minor', color='k', linestyle='-', zorder=1)
plt.scatter(x_data, y_data, marker='o', c='black', s=st_sizes_arr)
plt.draw()
print 'Plot displayed, waiting for it to be closed.'
def __init__(self,
field,
min_x, max_x, n_x,
min_y, max_y, n_y):
self.field = field
self.min_x = min_x
self.max_x = max_x
self.n_x = n_x
self.min_y = min_y
self.max_y = max_y
self.n_y = n_y
self.X = np.linspace(min_x, max_x, n_x)
self.Y = np.linspace(min_y, max_y, n_y)
points = np.empty([n_y * n_x, 3])
for i in range(0, n_y):
for j in range(0, n_x):
points[n_x * i + j, :] = np.array([self.X[j], self.Y[i], 0.])
self.B = self.field.evaluate(points)
self.legend_handles = []
plt.axis('equal')
plt.grid(b = True, which = 'major')
plt.grid(b = True, which = 'minor', color="0.75")
plt.minorticks_on()
plt.ylim([min_y, max_y])
plt.xlim([min_x, max_x])
def plot_v_of_t(volume_list,name,iteration):
"""Plots 2-volume as a function of proper time. Takes the output of
make_v_of_t.
name = name of simulation
iteration = number of spacetime in ensemble. Might be sweep# instead."""
# Defines the plot
vplot = plt.plot(volume_list, 'bo', volume_list, 'r-')
# plot title is made of name+iteration
plot_title = name+' '+str(iteration)
# Labels and Titles
plt.title(plot_title)
plt.xlabel('Proper Time')
plt.ylabel('2-Volume Per Time Slice')
# Ensure the y range is appropriate
plt.ylim([np.min(volume_list)-.5,np.max(volume_list)+.5])
# Turn on minor ticks
plt.minorticks_on()
# Show the plot
plt.show()
return
def start(self, event):
#creates DataFrame with all the data from TDMS and Raman file
d = {
'Filename': [],
'Ref_si': [],
'Elongation': [],
'Time': [],
'Force': [],
'StrainMacro': [],
'StrainSi': [],
'StressMacro': [],
'StressSi': [],
'Duration': [],
'pCov': [],
'Err_strain': [],
'Err_Stress': []
}
df = pd.DataFrame(data=d)
for r_file in self.raman_name[0]:
print("parsing {:}".format(r_file))
print('{:}'.format(self.ref_start))
print('{:}'.format(self.ref_end))
try:
r_o = rp.raman_spectrum(r_file,
orientation=self.crystalorientation,
file_type='t_scan',
ref_start=self.ref_start,
ref_end=self.ref_end,
ref_si=520.7 - self.PowerShift)
for iii, t in enumerate(r_o.time_epoch):
if self.time_coef != 1:
t = r_o.epoch + (t - r_o.epoch) * self.time_coef
if self.time_offset != 0:
t = t + self.time_offset
eps_macro = 100 * self.tdms_file.get_Elongation(
t, r_o.duration) / (self.tdms_file.Length * 1000)
df = df.append(
{
'Filename':
r_o.filename,
'Ref_si':
r_o.ref_si,
'Elongation':
self.tdms_file.get_Elongation(t, r_o.duration),
'Time':
t,
'Force':
self.tdms_file.get_value(t, r_o.duration, 'Force'),
'StrainMacro':
eps_macro,
'StrainSi':
r_o.strain[iii],
'StressMacro': [],
'StressSi':
r_o.stress[iii],
'Duration':
r_o.duration,
'pCov':
r_o.pcov_peak[iii],
'Err_strain':
r_o.err_strain[iii],
'Err_stress':
r_o.err_stress[iii]
},
ignore_index=True)
except:
r_o = rp.raman_spectrum(r_file,
orientation=self.crystalorientation,
ref_start=self.ref_start,
ref_end=self.ref_end,
ref_si=520.7 - self.PowerShift)
if self.time_offset != 0:
eps_macro = 100 * self.tdms_file.get_Elongation(
r_o.epoch + self.time_offset,
r_o.duration) / (self.tdms_file.Length * 1000)
else:
eps_macro = 100 * self.tdms_file.get_Elongation(
r_o.epoch,
r_o.duration) / (self.tdms_file.Length * 1000)
df = df.append(
{
'Filename':
r_o.filename,
'Ref_si':
r_o.ref_si,
'Elongation':
self.tdms_file.get_Elongation(r_o.epoch, r_o.duration),
'Time':
r_o.epoch,
'Force':
self.tdms_file.get_value(r_o.epoch, r_o.duration,
'Force'),
'StrainMacro':
eps_macro,
'StrainSi':
r_o.strain,
'StressMacro': [],
'StressSi':
r_o.stress,
'Duration':
r_o.duration,
'pCov':
r_o.pcov_peak,
'Err_strain':
r_o.err_strain,
'Err_stress':
r_o.err_stress
},
ignore_index=True)
print(eps_macro)
plt.figure()
plt.errorbar(df['StrainMacro'],
df['StrainSi'],
df['Err_strain'] * 3 + 0.05,
marker='o',
markerfacecolor='None',
color='k')
# df.plot(x='StrainMacro',y='StrainSi', marker='v', markerfacecolor='None', color='k')
plt.xlabel('Macroscopic strain %')
plt.ylabel('Local Silicon Strain %')
plt.gca().set_xlim(left=0)
plt.minorticks_on()
plt.title(self.tdms_file.filename)
plt.show()
# df.plot(x='StrainSi', y='Force', kind='scatter')
# plt.show()
# df.plot(x='StrainMacro',y='Force')
# plt.show()
# df.plot(x='Time',y='Elongation')
# plt.show()
# df.plot(x='Time', y='Force')
# plt.show()
# df.plot(x='StrainMacro',y='pCov',kind='scatter')
# plt.show()
# plt.figure()
# plt.errorbar(df['StrainMacro'], df['StrainSi'],df['Err_strain'])
# plt.show()
df.to_csv('results.txt', sep='\t')
p_line,
color='k',
label=r'experiment, %s $\pm$ %s' %
(np.round(pRgy, 1), np.round(errp, 1)),
linewidth=3,
alpha=0.6)
plt.plot(Q2[r1:r2],
r_line,
color='r',
label=r'fitted simulation, %s $\pm$ %s' %
(np.round(rRgy, 2), np.round(errr, 2)),
linewidth=3,
alpha=0.6)
plt.plot(Q2[r1:r2],
s_line,
color='b',
label=r'all regions simulation, %s $\pm$ %s' %
(np.round(sRgy, 2), np.round(errs, 2)),
linewidth=3,
alpha=0.6)
plt.legend(loc='lower left', frameon=False, fontsize=9)
plt.xlabel('$Q^2$ ($\AA^{-2}$)', fontsize=15)
plt.xticks([0.002, 0.004, 0.006], fontsize=12)
plt.yticks(fontsize=12)
plt.ylabel('ln[I($Q$)/I($Q_{0}$)]', fontsize=15)
plt.tight_layout()
plt.minorticks_on()
plt.savefig('figures/guinier_rgy.pdf')
plt.show()
def draw_ga_evolution(self, make_pdf=True, show_plot=False):
self.get_ga_input_from_file()
min_list = []
max_list = []
avg_list = []
for i in range(self.start_from_gen, self.num_gen + 1):
# print('reading gen ',i)
self.generation = i
try:
fpop = self.get_pop_from_pop_file()
min_, max_, avg_ = self.get_min_max_avg(fpop)
if self.conversion_function:
min_ = self.conversion_function(min_)
max_ = self.conversion_function(max_)
avg_ = self.conversion_function(avg_)
min_list.append(min_)
max_list.append(max_)
avg_list.append(avg_)
except:
if self.generation == 0:
raise ValueError('population files not found')
self.num_gen = self.generation - 1
print('generation ', self.generation, ' pop file not found')
print('results plotted until generation ', self.generation - 1)
break
fig = plt.gcf()
plt.clf()
fig.set_size_inches(12, 11)
if not self.xticks:
self.find_tick_size()
if self.fit_type == 'max':
plt.plot(min_list, color='black', lw=1, label='Minimum')
plt.plot(max_list, color='black', lw=2, label='Maximum')
loc = 4
else:
plt.plot(min_list, color='black', lw=2, label='Minimum')
plt.plot(max_list, color='black', lw=1, label='Maximum')
loc = 1
plt.plot(avg_list, color='red' , lw=1, label='Average')
plt.minorticks_on()
plt.xlim((-self.xticks / 2.0, self.num_gen - self.start_from_gen))
if self.y_bounds['y_min']:
y_min = self.y_bounds['y_min']
else:
y_min = min(min_list)
if self.y_bounds['y_max']:
y_max = self.y_bounds['y_max']
else:
y_max = max(max_list)
if self.min_fit:
plt.axhline(self.min_fit, color='red', ls=':', lw=0.5)
string = self.fit_type + ' fit'
plt.text(-self.xticks / 20, self.min_fit, string, horizontalalignment='right', color='red')
# self.min_fit,self.num_gen-self.start_from_gen
if self.min_fit < min(min_list):
y_min = self.min_fit
delta = y_max - y_min
plt.ylim((y_min - (delta * 0.1), y_max + delta * 0.1))
plt.title('Function ' + self.fit_name + ' evolution', fontsize=self.title_size)
plt.xlabel('Generation', fontsize=self.lable_size)
plt.ylabel('Function ' + self.fit_name, fontsize=self.lable_size)
labels = range(self.start_from_gen, self.num_gen, self.xticks)
x = range(0, len(labels) * self.xticks, self.xticks)
plt.xticks(x, labels)
plt.grid(True)
plt.legend(loc=loc)
if make_pdf:
plt.savefig(self.output_path + self.fit_name + '_evolution.pdf')
if show_plot:
plt.show()
print('Evolution visualisation complete')
def stackedbarplot(self,
responses,
labels,
figurename,
legend_columns=3,
samplesize=0,
title=''):
"""
Create stacked bar plots showing the proportional responses to the given question.
Parameters
----------
responses : numpy array
Array of the responses for the given question.
labels : list of strings
The possible responses for the given question.
figurename : str
Short form name of the question asked.
legend_columns : int, optional
The number of columns in the legend. Vary to control legend layout.
The default is 3.
samplesize : int, optional
The number of participants which have responded to given question.
The default is 0.
Returns
-------
Saves the figure to pdf and png files.
"""
plt.close()
print(f'Plotting the chart for {figurename} question..')
sns.set_style(
'ticks', {
'axes.spines.right': False,
'axes.spines.top': False,
'axes.spines.left': False,
'ytick.left': False
})
if responses.shape[0] == 2:
ind = [0, 1]
elif responses.shape[0] == 3:
ind = [0, 0.85, 2]
elif responses.shape[0] == 1:
ind = [0]
fig, ax = plt.subplots(figsize=(8.7, 6))
start, pos, = 0, [0, 0, 0]
for i in range(responses.shape[1]):
option = responses[:, i]
plt.barh(ind, option, left=start, label=labels[i])
for k in range(len(ind)):
xpos = pos[k] + option[k] / 2
percent = int(round(option[k] * 100))
if percent >= 10:
plt.annotate(f'{str(percent)} %',
xy=(xpos, ind[k]),
ha='center',
fontsize=15,
color='1')
elif percent < 3:
pass
else:
plt.annotate(f'{str(percent)}',
xy=(xpos, ind[k]),
ha='center',
fontsize=15,
color='1')
start = start + option
pos = start
plt.xlim(0, 1)
if responses.shape[0] == 2:
plt.yticks(ind, ('Post', 'Pre'), fontsize=18)
elif responses.shape[0] == 3:
plt.yticks(ind, ('Male', 'Female', 'All'), fontsize=18)
elif responses.shape[0] == 1:
plt.yticks(ind, '', fontsize=18)
plt.xticks(fontsize=18)
ax.xaxis.set_major_formatter(ticker.PercentFormatter(xmax=1))
plt.legend(bbox_to_anchor=(0, 0.99, 1, .05),
loc=3,
ncol=legend_columns,
borderaxespad=0,
fontsize=15)
plt.minorticks_on()
plt.figtext(0.9,
0.12, (f'Based on sample of {samplesize} participants'),
fontsize=10,
ha='right')
pdffile = 'bar_' + figurename + '.pdf'
pngfile = 'bar_' + figurename + '.png'
plt.savefig(self.save_filepath / pdffile, bbox_inches='tight')
plt.title(title,
fontsize=20,
pad=[85 if legend_columns < 3 else 50][0])
plt.savefig(self.save_filepath / pngfile, bbox_inches='tight', dpi=600)
sns.set()
def plot_xy_list(x,
y,
fmts=[],
labels=[],
xlabel='',
ylabel='',
title='',
xlim=[],
ylim=[],
minorticks=1,
grid_major=1,
grid_minor=0,
xticks=[],
yticks=[],
figsize=(4.5, 3.0),
alpha=[],
left=0.15,
bottom=0.15,
right=0.97,
top=0.97,
legend_loc='best',
xscale='linear',
yscale='linear',
savepath='',
savedpi=300,
showplot=1):
if not (len(x) == len(y)):
raise ValueError(
'number of arrays in X and Y are different. Exiting...')
n = len(x)
#### plot
legends = 1
if (labels == []):
labels = [''] * n
legends = 0
if (fmts == []):
aux = []
for i in range(n):
if (i >= 10):
i = i % 10
aux.append('-C{0:d}'.format(i))
fmts = aux
if (alpha == []):
alpha = [0.9] * n
fig, ax = plt.subplots(figsize=figsize)
plt.subplots_adjust(left, bottom, right, top)
for i in range(n):
plt.plot(x[i], y[i], fmts[i], label=labels[i], alpha=alpha[i])
plt.minorticks_on()
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title)
plt.tick_params(which='both',
axis='both',
direction='in',
top=True,
right=True)
if (legends):
plt.legend(loc=legend_loc)
if (xlim != []):
plt.xlim(xlim)
if (ylim != []):
plt.ylim(ylim)
if (xticks != []):
plt.xticks(xticks)
if (yticks != []):
plt.yticks(yticks)
if (grid_major):
plt.grid(which='major', alpha=0.5)
if (grid_minor):
plt.grid(which='minor', alpha=0.2)
if (xscale in ['log', 'logarithm']):
plt.xscale('log')
if (yscale in ['log', 'logarithm']):
plt.yscale('log')
if (savepath != ''):
plt.savefig(savepath, dpi=savedpi)
if (showplot):
plt.show()
return fig, ax
def pl_2_param_dens(_2_params, gs, min_max_p2, varIdxs, params_trace):
'''
Parameter vs parameters density map.
'''
plot_dict = {
'metal-age': [0, 2, 2, 4, 0, 1],
'metal-ext': [0, 2, 4, 6, 0, 2],
'metal-dist': [0, 2, 6, 8, 0, 3],
'metal-mass': [0, 2, 8, 10, 0, 4],
'metal-binar': [0, 2, 10, 12, 0, 5],
'age-ext': [2, 4, 4, 6, 1, 2],
'age-dist': [2, 4, 6, 8, 1, 3],
'age-mass': [2, 4, 8, 10, 1, 4],
'age-binar': [2, 4, 10, 12, 1, 5],
'ext-dist': [4, 6, 6, 8, 2, 3],
'ext-mass': [4, 6, 8, 10, 2, 4],
'ext-binar': [4, 6, 10, 12, 2, 5],
'dist-mass': [6, 8, 8, 10, 3, 4],
'dist-binar': [6, 8, 10, 12, 3, 5],
'mass-binar': [8, 10, 10, 12, 4, 5]
}
labels = [
'$z$', '$log(age)$', '$E_{(B-V)}$', '$(m-M)_o$', '$M\,(M_{{\odot}})$',
'$b_{frac}$'
]
gs_x1, gs_x2, gs_y1, gs_y2, mx, my = plot_dict[_2_params]
x_label, y_label = labels[mx], labels[my]
ax = plt.subplot(gs[gs_y1:gs_y2, gs_x1:gs_x2])
# To specify the number of ticks on both or any single axes
ax.locator_params(nbins=5)
if gs_x1 == 0:
plt.ylabel(y_label, fontsize=11)
plt.yticks(rotation=45)
else:
ax.tick_params(labelleft=False)
if gs_y2 == 12:
plt.xlabel(x_label, fontsize=11)
plt.xticks(rotation=45)
else:
ax.tick_params(labelbottom=False)
plt.minorticks_on()
if mx in varIdxs and my in varIdxs:
mx_model, my_model = varIdxs.index(mx), varIdxs.index(my)
ax.set_title(r"$\rho={:.2f}$".format(
np.corrcoef([params_trace[mx_model],
params_trace[my_model]])[0][1]),
fontsize=11)
hist2d(ax, params_trace[mx_model], params_trace[my_model])
mean_pos, width, height, theta = SigmaEllipse(
np.array([params_trace[mx_model], params_trace[my_model]]).T)
# Plot 95% confidence ellipse.
plt.scatter(mean_pos[0],
mean_pos[1],
marker='x',
c='b',
s=30,
linewidth=2,
zorder=4)
ellipse = Ellipse(xy=mean_pos,
width=width,
height=height,
angle=theta,
edgecolor='r',
fc='None',
lw=.7,
zorder=4)
ax.add_patch(ellipse)
xp_min, xp_max, yp_min, yp_max = min_max_p2
ax.set_xlim([xp_min, xp_max])
ax.set_ylim([yp_min, yp_max])
# Grid won't respect 'zorder':
# https://github.com/matplotlib/matplotlib/issues/5045
# So we plot the grid behind everything else manually.
xlocs, xlabels = plt.xticks()
ylocs, ylabels = plt.yticks()
for xt in xlocs:
plt.axvline(x=xt, linestyle='-', color='w', zorder=-4)
for yt in ylocs:
plt.axhline(y=yt, linestyle='-', color='w', zorder=-4)
def createCSV(filterSize, hashes, set1Size, set2SizeDiff, setDiff, measuring):
# Determine Graph Labels and Title
yLabel = "Time (ms)" if measuring == 1 else "Error Percent (%)"
xLabel = ""
arr = []
if type(filterSize) == list:
arr = filterSize
xLabel = "Filter Size"
elif type(hashes) == list:
arr = hashes
xLabel = "# of Hashes"
elif type(set1Size) == list:
arr = set1Size
xLabel = "Set Size"
elif type(set2SizeDiff) == list:
arr = set2SizeDiff
xLabel = "Set Size Diff"
elif type(setDiff) == list:
arr = setDiff
xLabel = "Size of Difference"
title = xLabel + str(arr) + " by " + yLabel
print(title)
# Start CSV and write first line
writer = csv.writer(open("results//" + title + ".csv", 'w', newline='' ))
writer.writerow(["", "Regular", "Method1", "Method2"])
# Define Vectors to store information
xAxis = []
regAxis = []
meth1 = []
meth2 = []
# The Main Loop Iterate through the designated variable
for i in list(range(int(arr[0]), int(arr[1]), ceil(abs(int(arr[0]) - int(arr[1])) / DATA_POINTS))):
xAxis.append(i)
# Call BloomFilter Function and save result
result = callBloomFilter(str(i) if type(filterSize) == list else filterSize,
str(i) if type(hashes) == list else hashes,
str(i) if type(set1Size) == list else set1Size,
str(i) if type(set2SizeDiff) == list else set2SizeDiff,
str(i) if type(setDiff) == list else setDiff)
info = [i, result[0 + measuring], result[2 + measuring], result[4 + measuring]]
writer.writerow(info)
regAxis.append(0)
meth1.append(result[2 + measuring] if measuring else (1-(float(result[2])/float(i if type(setDiff) == list else result[measuring]))) * 100)
meth2.append(result[4 + measuring] if measuring else (1-(float(result[4])/float(i if type(setDiff) == list else result[measuring]))) * 100)
fig, ax = plt.subplots()
plt.plot(xAxis, regAxis, label="regAxis") # plotting the points
plt.plot(xAxis, meth1, label="method 1") # plotting the points
plt.plot(xAxis, meth2, label="method 2") # plotting the points
desc = ("" if type(filterSize) == list else "M: " + filterSize + "\n") + \
("" if type(hashes) == list else "H: " + ("optimal" if hashes == '-h' else hashes) + "\n") + \
("" if type(set1Size) == list or type(set2SizeDiff) == list else
"|A|: " + set1Size + "\n" + "|B|: " + str(int(set1Size) - int(set2SizeDiff)) + "\n") + \
("" if type(setDiff) == list else "|C|: " + setDiff + "\n")
desc = desc[:-1]
plt.title(title)
plt.xlabel(xLabel) # naming the x axis
plt.ylabel(yLabel) # naming the y axis
plt.legend()
props = dict(boxstyle='round', facecolor='white', alpha=0.75)
plt.text(0.30, 0.98, desc, transform=ax.transAxes, fontsize=10, verticalalignment='top', bbox=props)
plt.minorticks_on()
plt.grid(which='major', linestyle='dashed', linewidth='0.5', color='black') # Customize the major grid
plt.grid(which='minor', linestyle=':', linewidth='0.5', color='black', alpha=.5) # Customize the minor grid
# plt.show()
plt.savefig("results//" + title + ".png")
plt.gcf().clear()
fig.clear()
ax.clear()
plt.close()
def insider_activity(other_args: List[str], stock: DataFrame, ticker: str,
start: str, interval: str):
"""Display insider activity
Parameters
----------
other_args : List[str]
argparse other args - ["-n", "10"]
stock : DataFrame
Due diligence stock dataframe
ticker : str
Due diligence ticker symbol
start : str
Start date of the stock data
interval : str
Stock data interval
"""
parser = argparse.ArgumentParser(
add_help=False,
prog="ins",
description=
"""Prints insider activity over time [Source: Business Insider]""",
)
parser.add_argument(
"-n",
"--num",
action="store",
dest="n_num",
type=check_positive,
default=10,
help="number of latest insider activity.",
)
try:
ns_parser = parse_known_args_and_warn(parser, other_args)
if not ns_parser:
return
url_market_business_insider = (
f"https://markets.businessinsider.com/stocks/{ticker.lower()}-stock"
)
text_soup_market_business_insider = BeautifulSoup(
requests.get(url_market_business_insider,
headers={
"User-Agent": get_user_agent()
}).text,
"lxml",
)
d_insider = dict()
l_insider_vals = list()
for idx, insider_val in enumerate(
text_soup_market_business_insider.findAll(
"td", {"class": "table__td text-center"})):
# print(insider_val.text.strip())
l_insider_vals.append(insider_val.text.strip())
# Add value to dictionary
if (idx + 1) % 6 == 0:
# Check if we are still parsing insider trading activity
if "/" not in l_insider_vals[0]:
break
d_insider[(idx + 1) // 6] = l_insider_vals
l_insider_vals = list()
df_insider = pd.DataFrame.from_dict(
d_insider,
orient="index",
columns=[
"Date", "Shares Traded", "Shares Held", "Price", "Type",
"Option"
],
)
df_insider["Date"] = pd.to_datetime(df_insider["Date"])
df_insider = df_insider.set_index("Date")
df_insider = df_insider.sort_index(ascending=True)
if start:
df_insider = df_insider[start:] # type: ignore
_, ax = plt.subplots()
if interval == "1440min":
plt.plot(stock.index, stock["Adj Close"].values, lw=3)
else: # Intraday
plt.plot(stock.index, stock["Close"].values, lw=3)
plt.title(f"{ticker.upper()} (Time Series) and Price Target")
plt.xlabel("Time")
plt.ylabel("Share Price ($)")
df_insider["Trade"] = df_insider.apply(
lambda row:
(1, -1)[row.Type == "Sell"] * float(row["Shares Traded"].replace(
",", "")),
axis=1,
)
plt.xlim(df_insider.index[0], stock.index[-1])
min_price, max_price = ax.get_ylim()
price_range = max_price - min_price
shares_range = (df_insider[df_insider["Type"] == "Buy"].groupby(
by=["Date"]).sum()["Trade"].max() -
df_insider[df_insider["Type"] == "Sell"].groupby(
by=["Date"]).sum()["Trade"].min())
n_proportion = price_range / shares_range
for ind in (df_insider[df_insider["Type"] == "Sell"].groupby(
by=["Date"]).sum().index):
if ind in stock.index:
ind_dt = ind
else:
ind_dt = get_next_stock_market_days(ind, 1)[0]
n_stock_price = 0
if interval == "1440min":
n_stock_price = stock["Adj Close"][ind_dt]
else:
n_stock_price = stock["Close"][ind_dt]
plt.vlines(
x=ind_dt,
ymin=n_stock_price + n_proportion *
float(df_insider[df_insider["Type"] == "Sell"].groupby(
by=["Date"]).sum()["Trade"][ind]),
ymax=n_stock_price,
colors="red",
ls="-",
lw=5,
)
for ind in (df_insider[df_insider["Type"] == "Buy"].groupby(
by=["Date"]).sum().index):
if ind in stock.index:
ind_dt = ind
else:
ind_dt = get_next_stock_market_days(ind, 1)[0]
n_stock_price = 0
if interval == "1440min":
n_stock_price = stock["Adj Close"][ind_dt]
else:
n_stock_price = stock["Close"][ind_dt]
plt.vlines(
x=ind_dt,
ymin=n_stock_price,
ymax=n_stock_price + n_proportion *
float(df_insider[df_insider["Type"] == "Buy"].groupby(
by=["Date"]).sum()["Trade"][ind]),
colors="green",
ls="-",
lw=5,
)
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True,
which="minor",
color="#999999",
linestyle="-",
alpha=0.2)
if gtff.USE_ION:
plt.ion()
plt.show()
l_names = list()
for s_name in text_soup_market_business_insider.findAll(
"a", {"onclick": "silentTrackPI()"}):
l_names.append(s_name.text.strip())
df_insider["Insider"] = l_names
print(
df_insider.sort_index(ascending=False).head(
n=ns_parser.n_num).to_string())
print("")
except Exception as e:
print(e)
print("")
return
def price_target_from_analysts(other_args: List[str], stock: DataFrame,
ticker: str, start: str, interval: str):
"""Display analysts' price targets for a given stock
Parameters
----------
other_args : List[str]
argparse other args - ["-n", "10"]
stock : DataFrame
Due diligence stock dataframe
ticker : str
Due diligence ticker symbol
start : str
Start date of the stock data
interval : str
Stock data interval
"""
parser = argparse.ArgumentParser(
add_help=False,
prog="pt",
description=
"""Prints price target from analysts. [Source: Business Insider]""",
)
parser.add_argument(
"-n",
"--num",
action="store",
dest="n_num",
type=check_positive,
default=10,
help="number of latest price targets from analysts to print.",
)
try:
ns_parser = parse_known_args_and_warn(parser, other_args)
if not ns_parser:
return
url_market_business_insider = (
f"https://markets.businessinsider.com/stocks/{ticker.lower()}-stock"
)
text_soup_market_business_insider = BeautifulSoup(
requests.get(url_market_business_insider,
headers={
"User-Agent": get_user_agent()
}).text,
"lxml",
)
d_analyst_data = None
for script in text_soup_market_business_insider.find_all("script"):
# Get Analyst data
if "window.analyseChartConfigs.push" in str(script):
# Extract config data:
s_analyst_data = (str(script).split("config: ",
1)[1].split(",\r\n", 1)[0])
d_analyst_data = json.loads(s_analyst_data)
break
df_analyst_data = pd.DataFrame.from_dict(
d_analyst_data["Markers"]) # type: ignore
df_analyst_data = df_analyst_data[[
"DateLabel", "Company", "InternalRating", "PriceTarget"
]]
df_analyst_data.columns = ["Date", "Company", "Rating", "Price Target"]
# df_analyst_data
df_analyst_data["Rating"].replace(
{
"gut": "BUY",
"neutral": "HOLD",
"schlecht": "SELL"
},
inplace=True)
df_analyst_data["Date"] = pd.to_datetime(df_analyst_data["Date"])
df_analyst_data = df_analyst_data.set_index("Date")
# Slice start of ratings
if start:
df_analyst_data = df_analyst_data[start:] # type: ignore
if interval == "1440min":
plt.plot(stock.index, stock["Adj Close"].values, lw=3)
# Intraday
else:
plt.plot(stock.index, stock["Close"].values, lw=3)
if start:
plt.plot(df_analyst_data.groupby(
by=["Date"]).mean()[start:]) # type: ignore
else:
plt.plot(df_analyst_data.groupby(by=["Date"]).mean())
plt.scatter(df_analyst_data.index,
df_analyst_data["Price Target"],
c="r",
s=40)
plt.legend(["Closing Price", "Average Price Target", "Price Target"])
plt.title(f"{ticker} (Time Series) and Price Target")
plt.xlim(stock.index[0], stock.index[-1])
plt.xlabel("Time")
plt.ylabel("Share Price ($)")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True,
which="minor",
color="#999999",
linestyle="-",
alpha=0.2)
if gtff.USE_ION:
plt.ion()
plt.show()
print("")
pd.set_option("display.max_colwidth", None)
print(
df_analyst_data.sort_index(ascending=False).head(
ns_parser.n_num).to_string())
print("")
except Exception as e:
print(e)
print("")
return
def plotHistogram(self):
# Create the figure to hold the image canvas.
self.fig = plt.figure()
# Create the canvas to hold the plot image.
self.canvas = fc(self.fig)
# Add the canvas to the box container.
# First remove any other children (previous plots).
for child in self.histBox.get_children():
self.histBox.remove(child)
self.histBox.pack_start(self.canvas, True, True, 0)
# Calculate derivatives.
# Potentially use them for detecting turning points for colour changes.
# Not being plotted at this stage.
firstDeriv = [0 for i in range(self.chaos.maxIterations)]
for i in range(1, (self.chaos.maxIterations - 1)):
firstDeriv[i - 1] = self.chaos.hist[i] - self.chaos.hist[i - 1]
# Put divergence iterations into bins for histogram plot.
self.doHistogramBins()
# Option to not include max iterations in histogram.
# Depending on the image max iterations can swamp the histogram.
# Also option to plot as bar graph or as line plot instead.
if self.chaos.incMaxIterations == True:
if self.chaos.histLinePlot == True:
plt.plot(self.chaos.bins,
self.chaos.hist,
color='blue',
linewidth=1,
marker='o',
markersize=2)
else:
plt.bar(self.chaos.bins, self.chaos.hist, color='blue')
else:
if self.chaos.histLinePlot == True:
plt.plot(self.chaos.bins[:-1],
self.chaos.hist[:-1],
color='blue',
linewidth=1,
marker='o',
markersize=2)
else:
plt.bar(self.chaos.bins[:-1],
self.chaos.hist[:-1],
color='blue')
plt.xlabel('Iteration on Divergence')
plt.ylabel('Frequency')
plt.title('Histogram of Divergence Iterations')
# Option to use log scale for iteration count axis (y).
# Depending on the plot can make it easier to read.
if self.chaos.logItsCounts == True:
plt.yscale('log')
plt.minorticks_on()
plt.tick_params(which='major', length=8, width=2, direction='out')
plt.tick_params(which='minor', length=4, width=2, direction='out')
# Show the histogram dialog.
self.winHistogram.show_all()
# Histogram present flag set.
self.chaos.histogramPresent = True
def Optimize(Item, Mode):
global Global_Power, Profile_List, Eff_Turbine, Eff_Gearbox, Eff_Generator, Startup_Cost, Payback_Time
if Item == "blade_size":
Power = []
Diameters = np.arange(1,12.5,0.5)
Profile_List = []
print("Calculating blade diameter optimization")
if Mode == "single":
Setup_Profile([[1,12],[0,5],[2,0]])
elif Mode == "double":
Setup_Profile([[3,14],[0,5],[2,0],[4,7]])
for Turbine in np.arange(1,21,1):
Power.append([])
for Diameter in np.arange(1,12.5,0.5):
Total_Mechanical_Energy = 0
Run_Simulation(step=100, tidal_function="Newport_1", turbines=Turbine, diameter=Diameter, slucies=0, sluice_size=80, profile=1, time=60*60*24*365, econ=False, output=False, graphs=False, graph_head=False, graph_QV=False, graph_P=False)
Cut_Count = 0
for Energy in Global_Power:
Total_Mechanical_Energy += Energy*100
Power[Turbine-1].append(Total_Mechanical_Energy)
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
plt.title("Energy Output Vs Blade Diameter For Different Number of Turbines In Single Effect Mode (Newport Tidal Data)")
ax.set_xlabel("Blade Diameter (m)")
ax.set_ylabel("Energy Output (J)")
Count = 0
for i in Power:
Temp = ax.plot(Diameters, Power[Count], label=("Turbines: " + str(Count+1)), linewidth=2)
Count += 1
#ax.legend("1 turbine","2 turbines","3 turbines","4 turbines","5 turbines","6 turbines","7 turbines","8 turbines","9 turbines","10 turbines","11 turbines","12 turbines","13 turbinse","14 turbines","15 turbines","16 turbines","17 turbines","18 turbines","19 turbines","20 turbines",)
ax.legend()
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
elif Item == "turbine_number":
Power = []
Turbines = np.arange(1,31,1)
Diameters = np.arange(1,12.5,0.5)
Profile_List = []
print("Calculating turbine number optimization")
if Mode == "single":
Setup_Profile([[1,12],[0,5],[2,0]])
elif Mode == "double":
Setup_Profile([[3,14],[0,5],[2,0],[4,7]])
Count = 0
for Diameter in np.arange(1,12.5,0.5):
Power.append([])
Count += 1
for Turbine in np.arange(1,31,1):
Total_Mechanical_Energy = 0
Run_Simulation(step=100, tidal_function="Newport_1", turbines=Turbine, diameter=Diameter, slucies=0, sluice_size=80, profile=1, time=60*60*24*365, econ=False, output=False, graphs=False, graph_head=False, graph_QV=False, graph_P=False)
for Energy in Global_Power:
#Global_Power_Elec.append(i*Eff_Turbine*Eff_Gearbox*Eff_Generator)
Total_Mechanical_Energy += Energy*100
Power[Count-1].append(Total_Mechanical_Energy)
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
if Mode == "single":
plt.title("Energy Output Vs Number of Turbines For Different Blade Diameters In Single Effect Mode (Newport Tidal Data)")
elif Mode == "double":
plt.title("Energy Output Vs Number of Turbines For Different Blade Diameters In Double Effect Mode (Newport Tidal Data)")
ax.set_xlabel("Number of Turbines")
ax.set_ylabel("Energy Output (J)")
Count = 0
for i in Power:
Temp = ax.plot(Turbines, Power[Count], label=("Diameter: " + str(Diameters[Count])), linewidth=2)
Count += 1
#ax.legend("1 turbine","2 turbines","3 turbines","4 turbines","5 turbines","6 turbines","7 turbines","8 turbines","9 turbines","10 turbines","11 turbines","12 turbines","13 turbinse","14 turbines","15 turbines","16 turbines","17 turbines","18 turbines","19 turbines","20 turbines",)
ax.legend()
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
elif Item == "algorithm":
Profile_List = []
Power = []
Triggers = np.arange(13,-1,-0.5)
for i in range(len(Triggers)):
Triggers[i] = (Triggers[i]/13)*100
Count = 1
Turbine_Count = 0
for Turbines in np.arange(1,26,1):
Power.append([])
Profile_List = []
Turbine_Count += 1
Count = 1
for i in np.arange(13,-1,-0.5):
Total_Mechanical_Energy = 0
Setup_Profile([[3,14],[0,i],[2,0],[4,0]])
Run_Simulation(step=100, tidal_function="sine", turbines=Turbine_Count, diameter=5.87, slucies=0, sluice_size=80, profile=Count, time=150000, econ=False, output=False, graphs=False, graph_head=False, graph_QV=False, graph_P=False)
for Energy in Global_Power:
#Global_Power_Elec.append(i*Eff_Turbine*Eff_Gearbox*Eff_Generator)
Total_Mechanical_Energy += Energy
Power[Turbine_Count-1].append(Total_Mechanical_Energy)
Count += 1
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
plt.title("Energy Output Vs Sluice Gate Triggering Height (Double Effect)")
ax.set_xlabel("Lagoon Triggering Height as (Percentage of Tidal Range)")
ax.set_ylabel("Energy Output (J)")
Count = 0
for i in Power:
Temp = ax.plot(Triggers, Power[Count], label=("Turbines: " + str(Count+1)), linewidth=2)
Count += 1
ax.legend()
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
elif Item == "power":
Power = [[],[]]
Per_Turbine = []
Turbines = np.arange(1,41,1)
for Turbine in np.arange(1,41,1):
Run_Simulation(step=100, tidal_function="Newport_1", turbines=Turbine, diameter=5.87, slucies=0, sluice_size=80, profile=1, time=60*60*24*365, econ=False, output=False, graphs=False, graph_head=False, graph_QV=False, graph_P=False)
Max_Mechanical_Power = max(Global_Power)
Max_Electrical_Power = (Max_Mechanical_Power*Eff_Gearbox*Eff_Generator)
Power[0].append(Max_Mechanical_Power)
Power[1].append(Max_Electrical_Power)
Per_Turbine.append(Max_Electrical_Power/Turbine)
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
plt.title("Max Power Output Vs Number of Turbines")
ax.set_xlabel("Number of Turbines")
ax.set_ylabel("Max Power Output (W)")
Temp = ax.plot(Turbines, Power[0], label=("Mechanical Power"), color="gold", linewidth=2)
Temp2 = ax.plot(Turbines, Power[1], "--", label=("Electrical Power"), color="y", linewidth=2)
Temp2 = ax.plot(Turbines, Per_Turbine, "--", label=("Electrical Power Per Turbine"), color="red", linewidth=2)
ax.legend()
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
elif Item == "payback":
Profile_List = []
Turbines = np.arange(3,41,1)
Startup_Costs = []
Payback_Times = []
if Mode == "single":
Setup_Profile([[1,12],[0,5],[2,0]])
elif Mode == "double":
Setup_Profile([[3,14],[0,5],[2,0],[4,7]])
for Turbine in Turbines:
Run_Simulation(step=100, tidal_function="Newport_1", turbines=Turbine, diameter=5.87, slucies=0, sluice_size=80, profile=1, time=60*60*24*365, econ=True, output=False, graphs=False, graph_head=False, graph_QV=False, graph_P=False)
Startup_Costs.append(Startup_Cost)
Payback_Times.append(Payback_Time)
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
plt.title("Number of Turbines Vs Payback Time")
ax.set_xlabel("Number of Turbines")
ax.set_ylabel("Payback Time (Years)")
Temp = ax.plot(Turbines, Payback_Times, label=("Diameter: 5.87m"), color="blue", linewidth=2)
ax.legend()
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
def getAlpha(telluric_data,lsf,continuum=True,test=False,save_path=None):
"""
Return a best alpha value from a telluric data.
"""
alpha_list = []
test_alpha = np.arange(0.1,7,0.1)
data = copy.deepcopy(telluric_data)
if continuum is True:
data = nsp.continuumTelluric(data=data, order=data.order)
for i in test_alpha:
telluric_model = nsp.convolveTelluric(lsf,data,
alpha=i)
#telluric_model.flux **= i
if data.order == 59:
# mask hydrogen absorption feature
data2 = copy.deepcopy(data)
tell_mdl = copy.deepcopy(telluric_model)
mask_pixel = 450
data2.wave = data2.wave[mask_pixel:]
data2.flux = data2.flux[mask_pixel:]
data2.noise = data2.noise[mask_pixel:]
tell_mdl.wave = tell_mdl.wave[mask_pixel:]
tell_mdl.flux = tell_mdl.flux[mask_pixel:]
chisquare = nsp.chisquare(data2,tell_mdl)
else:
chisquare = nsp.chisquare(data,telluric_model)
alpha_list.append([chisquare,i])
if test is True:
plt.plot(telluric_model.wave,telluric_model.flux+i*10,
'k-',alpha=0.5)
if test is True:
plt.plot(telluric_data.wave,telluric_data.flux,
'r-',alpha=0.5)
plt.rc('font', family='sans-serif')
plt.title("Test Alpha",fontsize=15)
plt.xlabel("Wavelength ($\AA$)",fontsize=12)
plt.ylabel("Transmission + Offset",fontsize=12)
plt.minorticks_on()
if save_path is not None:
plt.savefig(save_path+\
"/{}_O{}_alpha_data_mdl.png"\
.format(telluric_data.name,
telluric_data.order))
plt.show()
plt.close()
fig, ax = plt.subplots()
plt.rc('font', family='sans-serif')
for i in range(len(alpha_list)):
ax.plot(alpha_list[i][1],alpha_list[i][0],'k.',alpha=0.5)
ax.plot(min(alpha_list)[1],min(alpha_list)[0],'r.',
label="best alpha {}".format(min(alpha_list)[1]))
ax.set_xlabel(r"$\alpha$",fontsize=12)
ax.set_ylabel("$\chi^2$",fontsize=12)
plt.minorticks_on()
plt.legend(fontsize=10)
if save_path is not None:
plt.savefig(save_path+\
"/{}_O{}_alpha_chi2.png"\
.format(telluric_data.name,
telluric_data.order))
plt.show()
plt.close()
alpha = min(alpha_list)[1]
return alpha
def plot(args):
"""Logging format:
Epoch 0 Update 52 Cost 219.29276 G2 1483.47644 UD 2.78200 Time 127.66500 s
"""
colors = ['c', 'r', 'y', 'k', 'b', 'g']
for f_idx, filename in enumerate(args.filenames):
with open(filename, 'r') as f:
iterations = []
costs = []
valid_iterations = []
valid_costs = []
small_train_costs = []
for line in f:
if line.startswith('Epoch'):
words = line.split()
iterations.append(int(words[3]))
costs.append(float(words[5]))
elif line.startswith('Valid'):
words = line.split()
valid_iterations.append(
iterations[-1] if iterations else 0)
valid_costs.append(words[2])
small_train_costs.append(words[6])
avg_costs = [
average(costs[max(0, i - args.average):i])
for i in xrange(len(costs))
]
# Get intervals
iterations = [
iterations[i]
for i in xrange(0, len(iterations), args.interval)
]
avg_costs = [
avg_costs[i] for i in xrange(0, len(avg_costs), args.interval)
]
if args.train:
plt.plot(iterations,
avg_costs,
'{}-'.format(colors[f_idx]),
label='{}_train'.format(filename))
if args.valid:
plt.plot(valid_iterations,
valid_costs,
'{}--'.format(colors[f_idx]),
label='{}_valid'.format(filename))
if args.small_train:
plt.plot(valid_iterations,
small_train_costs,
'{}-.'.format(colors[f_idx]),
label='{}_small_train'.format(filename))
plt.xlim(xmin=args.xmin, xmax=args.xmax)
plt.ylim(ymin=args.ymin, ymax=args.ymax)
plt.minorticks_on()
plt.title('Costs')
plt.legend(loc='upper right')
plt.grid(which='both')
plt.show()
def Run_Simulation(**kwargs):
#Parameters passed:
Step_Size = kwargs["step"]
Tidal_Function = kwargs["tidal_function"]
Turbines = kwargs["turbines"]
Turbine_Diameter = kwargs["diameter"]
Sluices = kwargs["slucies"]
Sluice_Size = kwargs["sluice_size"]
Profile_Number = kwargs["profile"]
Run_Time = kwargs["time"]
Econ = kwargs["econ"]
Output = kwargs["output"]
Graphs = kwargs["graphs"]
Graph_Head = kwargs["graph_head"]
Graph_QV = kwargs["graph_QV"]
Graph_P = kwargs["graph_P"]
#Global Variables
global Civil_Price, Blade_Price, Turbine_Price, Gearbox_Price, Generator_Price, Sluice_Price, Startup_Cost, Payback_Time
global Eff_Turbine, Eff_Gearbox, Eff_Generator
global Global_Time, Global_Volume, Global_Tide, Global_Head, Global_Head_Difference, Global_Velocity, Global_Discharge, Global_Head_Loss, Global_Power, Global_Power_Elec
Global_Time = [0]
Global_Volume = [0]
Global_Tide = [0]
Global_Head = [0]
Global_Head_Difference = [0]
Global_Velocity = [0]
Global_Discharge = [0]
Global_Head_Loss = [0]
Global_Power = [0]
Global_Power_Elec = []
#Local Variables
V_0 = 18891820
Euler_Volume = [0]
Euler_Volume_Tide = [0]
Euler_Volume[0] = V_0
Euler_Volume_Tide[0] = V_0
Time = [0]
M = 1453217
G = 9.807
rho = 1029
Discharge_Coefficient= 0.8
Sluicing_Discharge_Coefficient = 0.98
Friction_Factor = 0.00035
Draft_Length = 10
Draft_Diameter = 10
State = 0 #0 = Waiting, 1 = filling sluice, 2 = draining generation, 3 = filling generation, 4 = draining sluice
Current_Time = Step_Size
Operational_Profile = Profile_List[Profile_Number-1]
Profile_Stage = 0
Total_Stages = len(Operational_Profile)
Total_Mechanical_Energy = 0
Total_Electrical_Energy = 0
#Initial Calculations
Area = np.pi*np.power((Turbine_Diameter/4),2)*Turbines
Sluice_Area = (np.pi*np.power((Turbine_Diameter/4),2)*Turbines)+(Sluice_Size*Sluices)
'''
Read operational algorithm profile, then switch between 5 different states, checking stopping conditions each time. Put Euler approximation in different function
Operational states:
-Filling_Sluice
-Filling_Generation
-Draining_Sluice
-Draining_Generation
-Transition (waiting)
Save data to global arrays
Plot graph using given parameters
If value in square root turns negative, return an error. (This should only happen if sluice gates are not shut at the right time, it means the tide is higher than the lagoon)
'''
if Output == True:
log.setLevel(logging.INFO)
else:
log.setLevel(logging.WARNING)
print("\nRunning simulation...\n")
State = Operational_Profile[0][0]
Average_Head = 0
AH_Count = 0
Runtime = 0
Flow_Rate_Average = 0
Max_Head = []
while Current_Time < Run_Time:
if State == 0:
log.info("In state 0: Waiting for tidal shift")
while State == 0:
if Current_Time > Run_Time:
State = 5
log.info("Runtime elapsed")
elif Global_Tide[-1] < Operational_Profile[Profile_Stage][1]:
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
else:
Global_Time.append(Current_Time)
Global_Tide.append(Evaluate_Tidal_Function(Tidal_Function, Current_Time))
Global_Volume.append(Global_Volume[-1])
Global_Head.append((Global_Volume[-1])/(M))
Global_Head_Difference.append(Global_Head[-1]-Global_Tide[-1])
Global_Velocity.append(0)
Global_Discharge.append(0)
Global_Head_Loss.append(0)
Global_Power.append(0)
Current_Time += Step_Size
if State == 1:
log.info("In state 1: Filling lagoon via sluicing")
while State == 1:
if Current_Time > Run_Time:
State = 5
log.info("Runtime elapsed")
elif Global_Head[-1] > Operational_Profile[Profile_Stage][1]:
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
else:
Global_Time.append(Current_Time)
Global_Tide.append(Evaluate_Tidal_Function(Tidal_Function, Current_Time))
#Global_Volume.append(Global_Volume[Current_Time-1]+Step_Size*Sluice_Area*Sluicing_Discharge_Coefficient*np.sqrt(2*G)*np.sqrt(Global_Tide[Current_Time]-((Global_Volume[Current_Time-1])/(M))-Pipe_Loss))
if (Global_Tide[-1])-((Global_Volume[-1])/(M)) < 0:
log.info("WARNING: Target value of " + str(Operational_Profile[Profile_Stage][1]) + "m in state 1 could not be met!")
Global_Volume.append(Global_Volume[-1])
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
Global_Velocity.append(Global_Velocity[-1])
Global_Discharge.append(Global_Discharge[-1])
else:
#Global_Volume.append(Global_Volume[-1]+Step_Size*Sluice_Area*Sluicing_Discharge_Coefficient*np.sqrt(2*G)*np.sqrt((Global_Tide[-1])-((Global_Volume[-1])/(M))-Pipe_Loss))
#Global_Velocity.append(np.sqrt(2*G)*np.sqrt((Global_Tide[-1])-((Global_Volume[-1])/(M))-Pipe_Loss))
Global_Velocity.append(np.sqrt(2*G*((Global_Tide[-1])-((Global_Volume[-1])/(M)))/(1+Friction_Factor*(Draft_Length/Draft_Diameter))))
Global_Volume.append(Global_Volume[-1]+Step_Size*Sluice_Area*Sluicing_Discharge_Coefficient*Global_Velocity[-1])
Global_Discharge.append(Global_Velocity[-1]*Sluice_Area*Sluicing_Discharge_Coefficient)
Global_Head.append((Global_Volume[-1])/(M))
Global_Head_Difference.append(Global_Head[-1]-Global_Tide[-1])
Global_Head_Loss.append(0)
Global_Power.append(0)
Current_Time += Step_Size
#print("the time is: " + str(Current_Time))
if State == 2:
log.info("In state 2: Draining lagoon via energy generation")
while State == 2:
if Current_Time > Run_Time:
State = 5
log.info("Runtime elapsed")
elif Global_Head[-1] < Operational_Profile[Profile_Stage][1]:
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
#Current_Time = Run_Time+1
else:
Global_Time.append(Current_Time)
Global_Tide.append(Evaluate_Tidal_Function(Tidal_Function, Current_Time))
if (Global_Volume[-1])/(M)-(Global_Tide[-1]) < 0:
log.info("WARNING: Target value of " + str(Operational_Profile[Profile_Stage][1]) + "m in state 2 could not be met!")
Global_Volume.append(Global_Volume[-1])
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
Global_Velocity.append(Global_Velocity[-1])
Global_Discharge.append(Global_Discharge[-1])
Global_Head_Loss.append(Global_Head_Loss[-1])
Global_Power.append(Global_Power[-1])
else:
#Global_Volume.append(Global_Volume[-1]-Step_Size*Area*Discharge_Coefficient*np.sqrt(2*G)*np.sqrt((Global_Volume[-1])/(M)-(Global_Tide[-1])-Turbine_Loss-Pipe_Loss))
#Global_Velocity.append(np.sqrt(2*G)*np.sqrt((Global_Volume[-1])/(M)-(Global_Tide[-1])-Turbine_Loss-Pipe_Loss))
Global_Velocity.append(np.sqrt((2*G*((Global_Volume[-1])/(M)-(Global_Tide[-1]))*(1-Eff_Turbine))/(1-Eff_Turbine*Friction_Factor*(Draft_Length/Draft_Diameter))))
Global_Volume.append(Global_Volume[-1]-Step_Size*Area*Discharge_Coefficient*Global_Velocity[-1])
Global_Discharge.append(Global_Velocity[-1]*Area*Discharge_Coefficient)
Global_Head_Loss.append(((Global_Volume[-1])/(M)-Global_Tide[-1]-(Friction_Factor*(Draft_Length/Draft_Diameter)*(Global_Velocity[-1]**2/(2*G)))))
Global_Power.append(rho*G*Global_Discharge[-1]*Global_Head_Loss[-1])
Global_Head.append((Global_Volume[-1])/(M))
Global_Head_Difference.append(Global_Head[-1]-Global_Tide[-1])
Current_Time += Step_Size
Average_Head += abs(Global_Head_Difference[-1])
Max_Head.append(abs(Global_Head_Difference[-1]))
AH_Count += 1
if Current_Time > 50000:
Runtime += 1*Step_Size
Flow_Rate_Average += Global_Discharge[-1]
if State == 3:
log.info("In state 3: Filling lagoon via energy generation")
while State == 3:
if Current_Time > Run_Time:
State = 5
log.info("Runtime elapsed")
elif Global_Head[-1] > Operational_Profile[Profile_Stage][1]:
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
else:
Global_Time.append(Current_Time)
Global_Tide.append(Evaluate_Tidal_Function(Tidal_Function, Current_Time))
#Global_Volume.append(Global_Volume[Current_Time-1]+Step_Size*Sluice_Area*Sluicing_Discharge_Coefficient*np.sqrt(2*G)*np.sqrt(Global_Tide[Current_Time]-((Global_Volume[Current_Time-1])/(M))-Pipe_Loss))
if (Global_Tide[-1])-((Global_Volume[-1])/(M)) < 0:
log.info("WARNING: Target value of " + str(Operational_Profile[Profile_Stage][1]) + "m in state 1 could not be met!")
Global_Volume.append(Global_Volume[-1])
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
Global_Velocity.append(Global_Velocity[-1])
Global_Discharge.append(Global_Discharge[-1])
Global_Head_Loss.append(Global_Head_Loss[-1])
Global_Power.append(Global_Power[-1])
else:
#Global_Volume.append(Global_Volume[-1]+Step_Size*Sluice_Area*Sluicing_Discharge_Coefficient*np.sqrt(2*G)*np.sqrt((Global_Tide[-1])-((Global_Volume[-1])/(M))-Pipe_Loss))
#Global_Velocity.append(np.sqrt(2*G)*np.sqrt((Global_Tide[-1])-((Global_Volume[-1])/(M))-Pipe_Loss))
Global_Velocity.append(np.sqrt((2*G*((Global_Tide[-1])-(Global_Volume[-1])/(M))*(1-Eff_Turbine))/(1-Eff_Turbine*Friction_Factor*(Draft_Length/Draft_Diameter))))
Global_Volume.append(Global_Volume[-1]+Step_Size*Area*Discharge_Coefficient*Global_Velocity[-1])
Global_Discharge.append(Global_Velocity[-1]*Area*Discharge_Coefficient)
Global_Head_Loss.append(Global_Tide[-1]-((Global_Volume[-1])/(M))-(Friction_Factor*(Draft_Length/Draft_Diameter)*(Global_Velocity[-1]**2/(2*G))))
Global_Power.append(rho*G*Global_Discharge[-1]*Global_Head_Loss[-1])
Global_Head.append((Global_Volume[-1])/(M))
Global_Head_Difference.append(Global_Head[-1]-Global_Tide[-1])
Current_Time += Step_Size
Average_Head += abs(Global_Head_Difference[-1])
Max_Head.append(abs(Global_Head_Difference[-1]))
AH_Count += 1
if Current_Time > 50000:
Runtime += 1*Step_Size
Flow_Rate_Average += Global_Discharge[-1]
if State == 4:
log.info("In state 4: Waiting for tidal shift")
while State == 4:
if Current_Time > Run_Time:
State = 5
log.info("Runtime elapsed")
elif Global_Tide[-1] > Operational_Profile[Profile_Stage][1]:
Profile_Stage = (Profile_Stage+1)%Total_Stages
State = Operational_Profile[Profile_Stage][0]
else:
Global_Time.append(Current_Time)
Global_Tide.append(Evaluate_Tidal_Function(Tidal_Function, Current_Time))
Global_Volume.append(Global_Volume[-1])
Global_Head.append((Global_Volume[-1])/(M))
Global_Head_Difference.append(Global_Head[-1]-Global_Tide[-1])
Global_Velocity.append(0)
Global_Discharge.append(0)
Global_Head_Loss.append(0)
Global_Power.append(0)
Current_Time += Step_Size
log.info("Current time: " + str(Current_Time))
Average_Head = (Average_Head/AH_Count)
Flow_Rate_Average = (Flow_Rate_Average/AH_Count)
#50000 start offset, run for 86400
print("\nSimulation complete\n")
print("Average head difference across turbines (m): " + str(Average_Head))
print("Max head difference across turbines (m): " + str(max(Max_Head)))
print("Run time (s): " + str(Runtime))
print("Average discharge (m^3s^-1): " + str(Flow_Rate_Average))
#Energy generation calculations
print("\n================================================================")
print("Running energy calculations...")
for Power in Global_Power:
if np.isnan(Power) == True:
Power = 0
Global_Power_Elec.append(Power*Eff_Gearbox*Eff_Generator)
Total_Mechanical_Energy += int(Power*Step_Size)
Total_Electrical_Energy += int(Global_Power_Elec[-1]*Step_Size)
Energy_Lost = Total_Mechanical_Energy-Total_Electrical_Energy
Efficiency = (Eff_Turbine*Eff_Gearbox*Eff_Generator)
print("Total mechanical energy generated (J): " + str(Total_Mechanical_Energy))
print("Energy lost (J): " + str(Energy_Lost))
print("System efficiency: " + str(Efficiency))
print("Total electrical energy generated (J): " + str(Total_Electrical_Energy))
print("Total electrical energy generated (kWh): " + str(Total_Electrical_Energy/3.6e+6))
#Print peak power and total energy
#Print final power and energy and percentage lost
if Econ == True: #Section for calculating economic assessment.
print("\n================================================================")
print("Running economic assessment of configuration...")
Startup_Cost = Civil_Price+(Turbines*(Blade_Price+Shaft_Price+Turbine_Price+Gearbox_Price+(2*Sluice_Price)+Generator_Price+Electrical_Price))+(Sluices*Sluice_Price)
Running_Costs_Day = 823 #a day
Total_Running_Costs = Running_Costs_Day*(Run_Time/86400)
Energy_Price = 92.5/1000 #per kWh
Turnover = (Total_Electrical_Energy/(3.6e+6))*Energy_Price
Gross_Profit = Turnover-Total_Running_Costs
Net_Profit = Gross_Profit-Startup_Cost
Payback_Time = Startup_Cost/Gross_Profit
print("Startup costs: " + str(Startup_Cost))
print("Running costs: " + str(Total_Running_Costs))
print("Turnover: " + str(Turnover))
print("Gross profit: " + str(Gross_Profit))
print("Net profit: " + str(Net_Profit))
print("Pay back time in years: " + str(Payback_Time))
if Graphs == True:
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
plt.title("Break-Even Analysis")
ax.set_xlabel("Time (Years)")
ax.set_ylabel("Equity (£)")
Fixed_Costs_Plot = ax.plot([0,Payback_Time,2*Payback_Time], [Startup_Cost, Startup_Cost, Startup_Cost], "--", label="Fixed costs", color="red", linewidth=3)
Total_Costs_Plot = ax.plot([0,Payback_Time,2*Payback_Time], [Startup_Cost, (Total_Running_Costs*Payback_Time + Startup_Cost), (Total_Running_Costs*Payback_Time*2 + Startup_Cost)], "--", label="Total costs", color="darkred", linewidth=3)
Revenue_Plot = ax.plot([0,Payback_Time,2*Payback_Time], [0, (Turnover*Payback_Time), (Turnover*Payback_Time*2)], label="Revenue", color="blue", linewidth=3)
Lines = Fixed_Costs_Plot+Total_Costs_Plot+Revenue_Plot
Labels =[l.get_label() for l in Lines]
ax.legend(Lines, Labels)
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
#Take into account maintencance downtimes
if Graphs == True:
plt.figure(figsize=plt.figaspect(1)*2)
ax = plt.axes()
second_ax = ax.twinx()
plt.title("Lagoon Volume, Lagoon Height and Tide Height Vs Time (Double Effect)")
ax.set_xlabel("Time (s)")
ax.set_ylabel("Volume (m^3)")
second_ax.set_ylabel('Height (m)')
Filling_Plot = ax.plot(Global_Time, Global_Volume, label="Lagoon Volume", color="deepskyblue", linewidth=3)
Lagoon_Head_Plot = second_ax.plot(Global_Time, Global_Head, "--", label="Lagoon height", color="green", linewidth=2)
Tide_Height_Plot = second_ax.plot(Global_Time, Global_Tide, "--", label="Tide height", color ="blue", linewidth=2)
# plt.title("Lagoon Volume, Lagoon Height and Tide Height Vs Time (Double Effect)", fontsize='30', weight='bold')
# ax.set_xlabel("Time (s)", fontsize='30', weight='bold')
# ax.set_ylabel('Height (m)', fontsize='30', weight='bold')
# Lagoon_Head_Plot = ax.plot(Global_Time, Global_Head, "--", label="Lagoon height", color="green", linewidth=2)
# Tide_Height_Plot = ax.plot(Global_Time, Global_Tide, "--", label="Tide height", color ="blue", linewidth=2)
# ax.set_ylabel('Height (m)')
if Graph_Head == True:
Head_Difference_Plot = second_ax.plot(Global_Time, Global_Head_Difference, "--", label="Head difference", color ="orange", linewidth=2)
Lines = Filling_Plot+Lagoon_Head_Plot+Tide_Height_Plot+Head_Difference_Plot
else:
Lines = Filling_Plot+Lagoon_Head_Plot+Tide_Height_Plot
#Lines = Lagoon_Head_Plot+Tide_Height_Plot
Labels =[l.get_label() for l in Lines]
ax.legend(Lines, Labels)
#ax.legend(Lines, Labels, fontsize='30')
plt.minorticks_on()
ax.grid(which='major', color='black', linestyle='-', linewidth=1)
ax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
ax.set_ylim(0,2e7)
# for tick in ax.xaxis.get_major_ticks():
# tick.label.set_fontsize(30)
# tick.label.set_weight('bold')
#
# for tick in ax.yaxis.get_major_ticks():
# tick.label.set_fontsize(30)
# tick.label.set_weight('bold')
if Graph_QV == True:
#Red graphs
plt.figure(figsize=plt.figaspect(1)*2)
QVax = plt.axes()
second_QVax = QVax.twinx()
plt.title("Velocity & Discharge Vs Time")
QVax.set_xlabel("Time (s)")
QVax.set_ylabel("Velocity (ms^-1)")
second_QVax.set_ylabel('Discharge (m^3s^-1)')
Velocity_Plot = QVax.plot(Global_Time, Global_Velocity, label="Flow velocity", color="red", linewidth=2)
Discharge_Plot = second_QVax.plot(Global_Time, Global_Discharge, "--", label="Total discharge", color="maroon", linewidth=2)
Lines = Velocity_Plot+Discharge_Plot
Labels =[l.get_label() for l in Lines]
QVax.legend(Lines, Labels)
plt.minorticks_on()
QVax.grid(which='major', color='black', linestyle='-', linewidth=1)
QVax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
if Graph_P == True:
plt.figure(figsize=plt.figaspect(1)*2)
Pax = plt.axes()
plt.title("Mechanical & Electrical Power Vs Time")
Pax.set_xlabel("Time (s)")
Pax.set_ylabel("Power (w)")
Mech_Power_Plot = Pax.plot(Global_Time, Global_Power, label="Mechanical Power", color="gold", linewidth=2)
Elec_Power_Plot = Pax.plot(Global_Time, Global_Power_Elec, "--", label="Electrical Power", color="y", linewidth=2)
Lines = Mech_Power_Plot+Elec_Power_Plot
Labels =[l.get_label() for l in Lines]
Pax.legend(Lines, Labels)
plt.minorticks_on()
Pax.grid(which='major', color='black', linestyle='-', linewidth=1)
Pax.grid(which='minor', color='black', linestyle='--', linewidth=0.5)
def main():
assert_banknote_threshold(0)
# parse args
save = False
arg_error = False
if len(sys.argv) > 2:
arg_error = True
if len(sys.argv) == 2:
if sys.argv[1] not in ["-s", "--save"]:
arg_error = True
else:
save = True
if arg_error:
print_help(os.path.basename(sys.argv[0]))
sys.exit(1)
# get all directories (classes) in the test directory
(dirpath, dirnames, _) = next(os.walk(os.path.join(TEST_DIR)))
errors = []
# true positives
true_positive_confidences = []
for dirname in dirnames:
# ignore 'bg' class
if dirname == 'bg':
continue
# for each directory (class), run the inference on all images
images = load_base64(dirname, os.path.join(dirpath, dirname))
for (response_json, _) in predict(images):
if response_json["status"] == "error":
errors.append(f"{dirname}: {response_json['error_message']}")
continue
if response_json["status"] == "ok":
if response_json["response"] == dirname:
true_positive_confidences.append(
response_json["confidence"]
)
# false positives
false_positive_confidences = []
images = load_base64('bg', os.path.join(dirpath, 'bg'))
for (response_json, _) in predict(images):
if response_json["status"] == "error":
errors.append(f"bg: {response_json['error_message']}")
continue
if response_json["status"] == "ok":
false_positive_confidences.append(response_json["confidence"])
if errors:
print("\nErrors:")
for error in errors:
print(error)
if save:
print("\nSaving confidences...")
with open(os.path.join(os.path.dirname(__file__), "output/tp.json"), "w") as out_file:
out_file.write(json.dumps(true_positive_confidences))
with open(os.path.join(os.path.dirname(__file__), "output/fp.json"), "w") as out_file:
out_file.write(json.dumps(false_positive_confidences))
print("\nPlotting results...")
plt.boxplot([true_positive_confidences,
false_positive_confidences], widths=0.7)
plt.xticks([1, 2], ["True positives", "False positives"])
plt.minorticks_on()
plt.grid(which='major', axis='y')
plt.grid(which='minor', axis='y', linestyle=':', alpha=0.3)
plt.ylim(0, 1)
plt.ylabel("Confidence level")
plt.title('Confidence statistics')
plt.show()
label=
r'$\mathcal{A}(\ell=%1.1f nm)=%3.2f, \,\,\, \mathcal{A}(\ell=%1.1f nm)=%3.2f$'
% (1e9 * Ls[0], 1e21 * sum_A[0], 1e9 * Ls[1], 1e21 * sum_A[1]))
pl.xlabel(x_ax)
pl.ylabel(y_ax_par)
pl.title(title('6', '5', 'parallel'))
pl.legend(loc='best')
pl.savefig(svfig('65pk', '65', 'loglog_parallel'))
pl.show()
# Semilog
pl.figure()
pl.semilogy(
1e9 * Ls,
1e21 * sum_A,
label=
r'$\mathcal{A}(\ell=%1.1f nm)=%3.2f, \,\,\, \mathcal{A}(\ell=%1.1f nm)=%3.2f$'
% (1e9 * Ls[0], 1e21 * sum_A[0], 1e9 * Ls[1], 1e21 * sum_A[1]))
pl.xlabel(x_ax)
pl.ylabel(y_ax_per)
pl.title(title('6', '5', 'parallel'))
pl.legend(loc='best')
pl.axis([0.0, 500, 1e1, 1e3])
pl.minorticks_on()
pl.ticklabel_format(axis='both')
pl.grid(which='both')
pl.tick_params(which='both', labelright=True)
pl.savefig(svfig('65pk', '65', 'parallel'))
pl.legend(loc='best')
pl.show()
def mlp(l_args, s_ticker, df_stock):
parser = argparse.ArgumentParser(prog="mlp",
description="""Multilayer Perceptron. """)
parser.add_argument(
"-d",
"--days",
action="store",
dest="n_days",
type=check_positive,
default=5,
help="prediction days.",
)
parser.add_argument(
"-i",
"--input",
action="store",
dest="n_inputs",
type=check_positive,
default=40,
help="number of days to use for prediction.",
)
parser.add_argument(
"-e",
"--epochs",
action="store",
dest="n_epochs",
type=check_positive,
default=200,
help="number of training epochs.",
)
parser.add_argument(
"-j",
"--jumps",
action="store",
dest="n_jumps",
type=check_positive,
default=1,
help="number of jumps in training data.",
)
parser.add_argument(
"-p",
"--pp",
action="store",
dest="s_preprocessing",
default="normalization",
choices=["normalization", "standardization", "none"],
help="pre-processing data.",
)
parser.add_argument(
"-o",
"--optimizer",
action="store",
dest="s_optimizer",
default="adam",
choices=[
"adam",
"adagrad",
"adadelta",
"adamax",
"ftrl",
"nadam",
"optimizer",
"rmsprop",
"sgd",
],
help="optimization technique.",
)
parser.add_argument(
"-l",
"--loss",
action="store",
dest="s_loss",
default="mae",
choices=["mae", "mape", "mse", "msle"],
help="loss function.",
)
try:
ns_parser = parse_known_args_and_warn(parser, l_args)
# Pre-process data
if ns_parser.s_preprocessing == "standardization":
scaler = StandardScaler()
stock_train_data = scaler.fit_transform(
np.array(df_stock["5. adjusted close"].values.reshape(-1, 1)))
elif ns_parser.s_preprocessing == "normalization":
scaler = MinMaxScaler()
stock_train_data = scaler.fit_transform(
np.array(df_stock["5. adjusted close"].values.reshape(-1, 1)))
else: # No pre-processing
stock_train_data = np.array(
df_stock["5. adjusted close"].values.reshape(-1, 1))
# Split training data for the neural network
stock_x, stock_y = splitTrain.split_train(
stock_train_data,
ns_parser.n_inputs,
ns_parser.n_days,
numJumps=ns_parser.n_jumps,
)
stock_x = np.array(stock_x)
stock_x = np.reshape(stock_x, (stock_x.shape[0], stock_x.shape[1]))
stock_y = np.array(stock_y)
stock_y = np.reshape(stock_y, (stock_y.shape[0], stock_y.shape[1]))
# Build Neural Network model
model = build_neural_network_model(cfg_nn_models.MultiLayer_Perceptron,
ns_parser.n_inputs,
ns_parser.n_days)
model.compile(optimizer=ns_parser.s_optimizer, loss=ns_parser.s_loss)
# Train our model
model.fit(stock_x, stock_y, epochs=ns_parser.n_epochs, verbose=1)
print("")
print(model.summary())
print("")
# Prediction
yhat = model.predict(
stock_train_data[-ns_parser.n_inputs:].reshape(
1, ns_parser.n_inputs),
verbose=0,
)
# Re-scale the data back
if (ns_parser.s_preprocessing
== "standardization") or (ns_parser.s_preprocessing
== "normalization"):
y_pred_test_t = scaler.inverse_transform(yhat.tolist())
else:
y_pred_test_t = yhat
l_pred_days = get_next_stock_market_days(
last_stock_day=df_stock["5. adjusted close"].index[-1],
n_next_days=ns_parser.n_days,
)
df_pred = pd.Series(y_pred_test_t[0].tolist(),
index=l_pred_days,
name="Price")
# Plotting
plt.figure()
plt.plot(df_stock.index, df_stock["5. adjusted close"], lw=3)
plt.title(f"MLP on {s_ticker} - {ns_parser.n_days} days prediction")
plt.xlim(df_stock.index[0],
get_next_stock_market_days(df_pred.index[-1], 1)[-1])
plt.xlabel("Time")
plt.ylabel("Share Price ($)")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True,
which="minor",
color="#999999",
linestyle="-",
alpha=0.2)
plt.plot(
[df_stock.index[-1], df_pred.index[0]],
[df_stock["5. adjusted close"].values[-1], df_pred.values[0]],
lw=1,
c="tab:green",
linestyle="--",
)
plt.plot(df_pred.index, df_pred, lw=2, c="tab:green")
plt.axvspan(df_stock.index[-1],
df_pred.index[-1],
facecolor="tab:orange",
alpha=0.2)
_, _, ymin, ymax = plt.axis()
plt.vlines(
df_stock.index[-1],
ymin,
ymax,
colors="k",
linewidth=3,
linestyle="--",
color="k",
)
plt.ion()
plt.show()
# Print prediction data
print_pretty_prediction(df_pred,
df_stock["5. adjusted close"].values[-1])
print("")
except Exception as e:
print(e)
print("")
def getLSF(telluric_data, alpha=1.0, continuum=True,test=False,save_path=None):
"""
Return a best LSF value from a telluric data.
"""
lsf_list = []
test_lsf = np.arange(3.0,13.0,0.1)
data = copy.deepcopy(telluric_data)
if continuum is True:
data = nsp.continuumTelluric(data=data)
data.flux **= alpha
for i in test_lsf:
telluric_model = nsp.convolveTelluric(i,data)
if telluric_data.order == 59:
telluric_model.flux **= 3
# mask hydrogen absorption feature
data2 = copy.deepcopy(data)
tell_mdl = copy.deepcopy(telluric_model)
mask_pixel = 450
data2.wave = data2.wave[mask_pixel:]
data2.flux = data2.flux[mask_pixel:]
data2.noise = data2.noise[mask_pixel:]
tell_mdl.wave = tell_mdl.wave[mask_pixel:]
tell_mdl.flux = tell_mdl.flux[mask_pixel:]
chisquare = nsp.chisquare(data2,tell_mdl)
else:
chisquare = nsp.chisquare(data,telluric_model)
lsf_list.append([chisquare,i])
if test is True:
plt.plot(telluric_model.wave,telluric_model.flux+(i-3)*10+1,
'r-',alpha=0.5)
if test is True:
plt.plot(data.wave,data.flux,
'k-',label='telluric data',alpha=0.5)
plt.title("Test LSF",fontsize=15)
plt.xlabel("Wavelength ($\AA$)",fontsize=12)
plt.ylabel("Transmission + Offset",fontsize=12)
plt.minorticks_on()
if save_path is not None:
plt.savefig(save_path+\
"/{}_O{}_lsf_data_mdl.png"\
.format(data.name, data.order))
#plt.show()
plt.close()
fig, ax = plt.subplots()
for i in range(len(lsf_list)):
ax.plot(lsf_list[i][1],lsf_list[i][0],'k.',alpha=0.5)
ax.plot(min(lsf_list)[1],min(lsf_list)[0],'r.',
label="best LSF {} km/s".format(min(lsf_list)[1]))
ax.set_xlabel("LSF (km/s)",fontsize=12)
ax.set_ylabel("$\chi^2$",fontsize=11)
plt.minorticks_on()
plt.legend(fontsize=10)
if save_path is not None:
plt.savefig(save_path+\
"/{}_O{}_lsf_chi2.png"\
.format(data.name, data.order))
#plt.show()
plt.close()
lsf = min(lsf_list)[1]
if telluric_data.order == 61 or telluric_data.order == 62 \
or telluric_data.order == 63: #or telluric_data.order == 64:
lsf = 5.5
print("The LSF is obtained from orders 60 and 65 (5.5 km/s).")
return lsf
def arima(l_args, s_ticker, s_interval, df_stock):
parser = argparse.ArgumentParser(
prog='arima',
description="""In statistics and econometrics, and in particular in time
series analysis, an autoregressive integrated moving average (ARIMA) model
is a generalization of an autoregressive moving average (ARMA) model. Both
of these models are fitted to time series data either to better understand
the data or to predict future points in the series (forecasting).
ARIMA(p,d,q) where parameters p, d, and q are non-negative integers, p is
the order (number of time lags) of the autoregressive model, d is the degree
of differencing (the number of times the data have had past values subtracted),
and q is the order of the moving-average model."""
)
parser.add_argument('-d',
"--days",
action="store",
dest="n_days",
type=check_positive,
default=5,
help='prediction days.')
parser.add_argument('-i',
"--ic",
action="store",
dest="s_ic",
type=str,
default='aic',
choices=['aic', 'aicc', 'bic', 'hqic', 'oob'],
help='information criteria.')
parser.add_argument('-s',
"--seasonal",
action="store_true",
default=False,
dest="b_seasonal",
help='Use weekly seasonal data.')
parser.add_argument('-o',
"--order",
action="store",
dest="s_order",
type=str,
help='arima model order (p,d,q) in format: pdq.')
parser.add_argument('-r',
"--results",
action="store_true",
dest="b_results",
default=False,
help='results about ARIMA summary flag.')
(ns_parser, l_unknown_args) = parser.parse_known_args(l_args)
if l_unknown_args:
print(
f"The following args couldn't be interpreted: {l_unknown_args}\n")
return
# Machine Learning model
if ns_parser.s_order:
t_order = tuple([int(ord) for ord in list(ns_parser.s_order)])
model = ARIMA(df_stock['5. adjusted close'].values,
order=t_order).fit()
l_predictions = model.predict(
start=len(df_stock['5. adjusted close']) + 1,
end=len(df_stock['5. adjusted close']) + ns_parser.n_days)
else:
if ns_parser.b_seasonal:
model = pmdarima.auto_arima(df_stock['5. adjusted close'].values,
error_action='ignore',
seasonal=True,
m=5,
information_criteria=ns_parser.s_ic)
else:
model = pmdarima.auto_arima(df_stock['5. adjusted close'].values,
error_action='ignore',
seasonal=False,
information_criteria=ns_parser.s_ic)
l_predictions = model.predict(n_periods=ns_parser.n_days)
# Prediction data
l_pred_days = get_next_stock_market_days(
last_stock_day=df_stock['5. adjusted close'].index[-1],
n_next_days=ns_parser.n_days)
df_pred = pd.Series(l_predictions, index=l_pred_days, name='Price')
if ns_parser.b_results:
print(model.summary())
print("")
# Plotting
plt.plot(df_stock.index, df_stock['5. adjusted close'], lw=2)
if ns_parser.s_order:
plt.title(
f"ARIMA {str(t_order)} on {s_ticker} - {ns_parser.n_days} days prediction"
)
else:
plt.title(
f"ARIMA {model.order} on {s_ticker} - {ns_parser.n_days} days prediction"
)
plt.xlim(df_stock.index[0],
get_next_stock_market_days(df_pred.index[-1], 1)[-1])
plt.xlabel('Time')
plt.ylabel('Share Price ($)')
plt.grid(b=True, which='major', color='#666666', linestyle='-')
plt.minorticks_on()
plt.grid(b=True, which='minor', color='#999999', linestyle='-', alpha=0.2)
plt.plot([df_stock.index[-1], df_pred.index[0]],
[df_stock['5. adjusted close'].values[-1], df_pred.values[0]],
lw=1,
c='tab:green',
linestyle='--')
plt.plot(df_pred.index, df_pred, lw=2, c='tab:green')
plt.axvspan(df_stock.index[-1],
df_pred.index[-1],
facecolor='tab:orange',
alpha=0.2)
xmin, xmax, ymin, ymax = plt.axis()
plt.vlines(df_stock.index[-1],
ymin,
ymax,
linewidth=1,
linestyle='--',
color='k')
plt.show()
# Print prediction data
print("Predicted share price:")
df_pred = df_pred.apply(lambda x: f"{x:.2f} $")
print(df_pred.to_string())
print("")
def plot_scale_height_distribution(dataframe,
cut=None,
title=None,
histcolor=plt.cm.Blues,
savename=None):
if type(cut) != type(None):
dataframe = dataframe[cut]
## calculate and store scale heights for a given selection of stars
dz = 0.1
dr1 = 0.5
dr2 = 1.0
dr3 = 2.0
dr4 = 5.0
rbins1 = np.arange(0.0, 7, dr1)
rbins2 = np.arange(7, 10, dr2)
rbins3 = np.arange(10, 20, dr3)
rbins4 = np.arange(20, 40 + dr4, dr4)
scalerads = np.concatenate((rbins1, rbins2, rbins3, rbins4))
zbins = np.arange(0, 3 + dz, dz)
scaleheights1 = np.zeros(len(scalerads) - 1)
scaleheights2 = np.zeros(len(scalerads) - 1)
norms1 = np.zeros(len(scalerads) - 1)
norms2 = np.zeros(len(scalerads) - 1)
err_array = np.zeros(len(scalerads) - 1)
for ii in range(len(scalerads) - 1):
cut = (dataframe.R > scalerads[ii]) & (dataframe.R < scalerads[ii + 1])
err_array[ii] = (scalerads[ii + 1] - scalerads[ii]) / 2.
zvals = dataframe.Z[cut]
coeffs = exponential_fit_coeffs(zvals)
scaleheights1[ii] = coeffs[0]
scaleheights2[ii] = coeffs[2]
norms1[ii] = coeffs[1]
norms2[ii] = coeffs[3]
for ii in range(len(scaleheights1)):
if str(scaleheights1[ii]) == 'nan':
scaleheights1[ii] = 0
else:
scaleheights1[ii] = 1. / abs(scaleheights1[ii])
if str(scaleheights2[ii]) == 'nan':
scaleheights2[ii] = 0
else:
scaleheights2[ii] = 1. / abs(scaleheights2[ii])
## plot scale height distribution
dr = 0.25
dz = 0.1
radbins = np.arange(0, 40 + dr, dr)
zbins = np.arange(0, 5 + dz, dz)
fig = plt.figure(figsize=(12, 6))
H, xed, yed = np.histogram2d(dataframe.R,
abs(dataframe.Z),
bins=(radbins, zbins))
extent = [xed[0], xed[-1], yed[0], yed[-1]]
ax = plt.subplot(111)
im = plt.imshow(np.log10(H.T),
extent=extent,
origin='lower',
aspect='auto',
interpolation='nearest',
cmap=histcolor)
plt.scatter(scalerads[6:-1] + err_array[6:], scaleheights1[6:], c='r')
plt.errorbar(scalerads[6:-1] + err_array[6:],
scaleheights1[6:],
xerr=err_array[6:],
linewidth=0,
ecolor='r',
elinewidth=1)
plt.scatter(scalerads[6:-1] + err_array[6:],
scaleheights2[6:],
c='#00FF40')
plt.errorbar(scalerads[6:-1] + err_array[6:],
scaleheights2[6:],
xerr=err_array[6:],
linewidth=0,
ecolor='#00FF40',
elinewidth=1)
plt.fill_between([0, 3], [-1, -1], [3, 3], color='k', alpha=0.75)
plt.minorticks_on()
plt.xlabel('Radius (kpc)')
plt.ylabel('Z (kpc)')
plt.xlim(0, 40)
plt.ylim(-0.05, 3.)
cax = fig.add_axes([0.91, 0.125, 0.03, 0.775])
cbar = fig.colorbar(im, cax=cax)
cbar.ax.set_ylabel('log$_{10}$(N)')
ax.minorticks_on()
if savename != None:
plt.savefig(savename)
plt.show()
def plot_xy_with_subregions(dataframe,
cut=None,
slopes=None,
title=None,
savename=None,
contours=False):
if type(cut) != type(None):
dataframe = dataframe[cut]
x = dataframe.X
y = dataframe.Y
z = dataframe.Z
if slopes == None:
slopes = [-np.inf, -1, 1, np.inf]
dlev = 0.75
levs = np.arange(0, 3.5 + dlev, dlev)
## Plot to confirm
dh = 401
xbins = np.linspace(-100, 100, dh)
ybins = np.linspace(-100, 100, dh)
fig = plt.figure(figsize=(6, 6))
if title != None:
plt.suptitle(title)
## contours
if contours == True:
H, xedges, yedges = np.histogram2d(x, y, bins=(xbins, ybins))
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]
im = plt.contour(np.log10(H.T),
extent=extent,
cmap=plt.cm.Reds_r,
levels=levs)
plt.subplot(111)
plt.scatter(x, y, s=1, edgecolor='None', c='k')
the_colors = [
'#00FF40', 'b', 'r', 'y', 'orange', '#00FF40', 'b', 'r', 'y', 'orange'
]
for ii in range(len(slopes) - 1):
slope1 = slopes[ii]
slope2 = slopes[ii + 1]
select = (y > slope1 * x) & (y < slope2 * x)
## sample
plt.scatter(x[select],
y[select],
s=1,
edgecolor='None',
c=the_colors[ii])
plt.scatter(the_sun.X, the_sun.Y, s=50, c='y')
## crosshairs on (0,0)
plt.plot([-1E5, 1E5], [0, 0], linestyle='--', color='grey')
plt.plot([0, 0], [-1E5, 1E5], linestyle='--', color='grey')
plt.xlim(-39, 39)
## Flip the Y-axis
plt.ylim(39, -39)
plt.xlabel('X (kpc)')
plt.ylabel('Y (kpc)')
plt.minorticks_on()
if savename != None:
plt.savefig(savename)
plt.show()
b0 = popt0[1] # Intercept value
yy = m0 * x + b0
m, b = Gradient_descent(x, y) # Inacting the Gradient decent above
Y = Line(x, m, b) # For Gradient decent calc
# Plotting
plt.scatter(x, y, color="red", label='Real data', marker=".") # Plot Real Data
plt.title("Linear Model using Gradient descent") # Plot title
plt.xlabel('Age of guest (Years)') # Plot x axis name
plt.ylabel('Fare (pounds)') # Plot y axis label
plt.grid() # Plot grid lines
plt.plot(x, Y, color="blue",
label='Grad line') # Plot Best fit line for Gradient Des
plt.plot(x, yy, color="green",
label='Scipy line') # Plot Best fit line from Scipy
plt.legend()
plt.minorticks_on() # adds small ticks on main axis
"""
Your turn
The scipy line is the best way to get an accurate line and we see that the Grad and Scipy line are similar.
Up the interations of the Gradient descent model what do you see happen?
Up the learning rate of the Gradient descent model what do you see happen?
Try Gradient Descent on x = sib and y = parents
# BONUS used One Hot encoder to compare gender = x to fare = y
"""
def plot_knn_f1scores(plot_label=''):
# Plots F1-score for each source from the nearest neighbours found using knn_closest. Input is a list of indices.
# If dim==1 knn found in 1-D. If dim==10, knn found in 10-D. (see later half of this function for details)
# Choose to plot as function of 1D feature or r magnitude.
# Load output from previous run:
print('Loading knn indices from previous run saved on disk...')
filename1d = 'knn_f1scores_1D'
filename10d = 'knn_f1scores_10D'
try:
knn_f1scores_1d = load_obj(filename1d)
knn_f1scores_10d = load_obj(filename10d)
except:
print(
'Failed to load knn_f1scores_*.pkl from disk - did you run "get_knn_accuracy()" yet?'
)
exit()
# combine list of dicts into single dictionary
knn_f1scores_1d = {
k: [d.get(k) for d in knn_f1scores_1d]
for k in {k
for d in knn_f1scores_1d for k in d}
}
knn_f1scores_10d = {
k: [d.get(k) for d in knn_f1scores_10d]
for k in {k
for d in knn_f1scores_10d for k in d}
}
df1d = pd.DataFrame(knn_f1scores_1d)
df10d = pd.DataFrame(knn_f1scores_10d)
# 1D
df1d_g = df1d[[
'galaxy_xvar_mean', 'galaxy_xvar_std', 'galaxy_probs_mean',
'galaxy_probs_std', 'f1g', 'f1gerr', 'correct_source'
]].copy()
df1d_q = df1d[[
'quasar_xvar_mean', 'quasar_xvar_std', 'quasar_probs_mean',
'quasar_probs_std', 'f1q', 'f1qerr', 'correct_source'
]].copy()
df1d_s = df1d[[
'star_xvar_mean', 'star_xvar_std', 'star_probs_mean', 'star_probs_std',
'f1s', 'f1serr', 'correct_source'
]].copy()
df1d_g['class'] = 'GALAXY'
df1d_g.columns = [
'feature1d_mean', 'feature1d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df1d_q['class'] = 'QSO'
df1d_q.columns = [
'feature1d_mean', 'feature1d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df1d_s['class'] = 'STAR'
df1d_s.columns = [
'feature1d_mean', 'feature1d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df_all_1d = pd.concat([df1d_g, df1d_q, df1d_s], axis=0)
df_all_1d['class'] = df_all_1d['class'].astype(
'category') # datashader wants categorical class
df10d_g = df10d[[
'galaxy_xvar_mean', 'galaxy_xvar_std', 'galaxy_probs_mean',
'galaxy_probs_std', 'f1g', 'f1gerr', 'correct_source'
]].copy()
df10d_q = df10d[[
'quasar_xvar_mean', 'quasar_xvar_std', 'quasar_probs_mean',
'quasar_probs_std', 'f1q', 'f1qerr', 'correct_source'
]].copy()
df10d_s = df10d[[
'star_xvar_mean', 'star_xvar_std', 'star_probs_mean', 'star_probs_std',
'f1s', 'f1serr', 'correct_source'
]].copy()
df10d_g['class'] = 'GALAXY'
df10d_g.columns = [
'feature10d_mean', 'feature10d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df10d_q['class'] = 'QSO'
df10d_q.columns = [
'feature10d_mean', 'feature10d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df10d_s['class'] = 'STAR'
df10d_s.columns = [
'feature10d_mean', 'feature10d_std', 'probs_mean', 'probs_std', 'f1',
'f1err', 'correct_source', 'class'
]
df_all_10d = pd.concat([df10d_g, df10d_q, df10d_s], axis=0)
df_all_10d['class'] = df_all_10d['class'].astype(
'category') # datashader wants categorical class
# Did we fit the knn in 1-D or in 10-D?
# In 1-D a few thousand nearest neighbours will likely be a healthy mix of the 3 classes throughout most/all of the feature space. So you will get reliable numbers for F1 scores per class (perhaps with differring error bars). These are basically a round-about way of getting F1 scores shown in the histogram created by the function plot_histogram_matrix_f1. It is nice they agree (they most definately should). The mannor in which they agree is interesting - since knn effectively uses variable bin widths to get enough nearest neighbours, whilst plot_histogram_matrix_f1 uses fixed bin widths and averages within that bin.
# select correct sources only?
# Only plot f1-score for correct object type in question. e.g. If it's a galaxy, nearest 10000 objects will likely only be galaxies, so f1 for star and quasar will be very poor or zero because there are no True Positives in this area of 1-D feature space. In 1-D feature space the 10000 nearest neighbours were a healthy mix of all three classes so we didn't have this problem.
print(df_all_1d.correct_source.value_counts())
print(df_all_10d.correct_source.value_counts())
df_all_1d = df_all_1d[df_all_1d.correct_source == 1]
df_all_10d = df_all_10d[df_all_10d.correct_source == 1]
# only 5000 sources are wrong, not so bad.
# Create datashader pngs for each plot, since we have too much data for matplotlib to handle
# 1D - 1dfeature vs f1
xmin1d = df1d.star_xvar_mean.min() - 0.1 # padd for plotting later
xmax1d = df1d.star_xvar_mean.max() + 0.1
print(xmin1d, xmax1d)
ymin = 0
ymax = 1.05
cvs = ds.Canvas(plot_width=1000,
plot_height=600,
x_range=(xmin1d, xmax1d),
y_range=(ymin, ymax),
x_axis_type='linear',
y_axis_type='linear')
agg = cvs.points(df_all_1d, 'feature1d_mean', 'f1', ds.count_cat('class'))
ckey = dict(GALAXY=(101, 236, 101), QSO='hotpink', STAR='dodgerblue')
img = tf.shade(agg, color_key=ckey, how='log')
export_image(img, 'knn1d_1d_vs_f1', fmt='.png', background='white')
# 10D - 1dfeature vs f1
xmin10d = df10d.star_xvar_mean.min() - 0.1 # padd for plotting later
xmax10d = df10d.star_xvar_mean.max() + 0.1
print(xmin10d, xmax10d)
ymin = 0
ymax = 1.05
cvs = ds.Canvas(plot_width=200,
plot_height=120,
x_range=(xmin10d, xmax10d),
y_range=(ymin, ymax),
x_axis_type='linear',
y_axis_type='linear')
agg = cvs.points(df_all_10d, 'feature10d_mean', 'f1',
ds.count_cat('class'))
ckey = dict(GALAXY=(101, 236, 101), QSO='hotpink', STAR='dodgerblue')
img = tf.shade(agg, color_key=ckey, how='log')
export_image(img, 'knn10d_1d_vs_f1', fmt='.png', background='white')
# 1D - prob vs f1
xmin1d_probs = 0 # padd for plotting later
xmax1d_probs = 1.05
ymin = 0
ymax = 1.05
cvs = ds.Canvas(plot_width=300,
plot_height=300,
x_range=(xmin1d_probs, xmax1d_probs),
y_range=(ymin, ymax),
x_axis_type='linear',
y_axis_type='linear')
agg = cvs.points(df_all_1d, 'probs_mean', 'f1', ds.count_cat('class'))
ckey = dict(GALAXY=(101, 236, 101), QSO='hotpink', STAR='dodgerblue')
img = tf.shade(agg, color_key=ckey, how='log')
export_image(img, 'knn1d_probs_vs_f1', fmt='.png', background='white')
# 10D - 1dfeature vs f1
xmin10d_probs = 0 # padd for plotting later
xmax10d_probs = 1.05
ymin = 0
ymax = 1.05
cvs = ds.Canvas(plot_width=200,
plot_height=200,
x_range=(xmin10d_probs, xmax10d_probs),
y_range=(ymin, ymax),
x_axis_type='linear',
y_axis_type='linear')
agg = cvs.points(df_all_10d, 'probs_mean', 'f1', ds.count_cat('class'))
ckey = dict(GALAXY=(101, 236, 101), QSO='hotpink', STAR='dodgerblue')
img = tf.shade(agg, color_key=ckey, how='log')
export_image(img, 'knn10d_probs_vs_f1', fmt='.png', background='white')
# ----------------- plotting -----------------
# get datashader pngs, and plot a small sample of points over the top to guide eye with error bars.
img_1d_1d = mpimg.imread('knn1d_1d_vs_f1.png')
img_1d_probs = mpimg.imread('knn1d_probs_vs_f1.png')
mpl.rcParams.update({'font.size': 10})
markeredgewidth = 0.5
mew = 0.5
elinewidth = 0.5
fig, axs = plt.subplots(1, 2, figsize=(14.5, 4))
# --- 1D --- 1d ---
plt.sca(axs[0])
plt.imshow(img_1d_1d, extent=[xmin1d, xmax1d, ymin * 10,
ymax * 10]) # make yaxis 10 times larger
# fix ylabels after scaling the axis
ylabels = axs[0].get_yticks()
new_ylabels = [l / 10
for l in ylabels] # account for factor of 10 increase
axs[0].set_yticklabels(new_ylabels)
axs[0].xaxis.set_major_formatter(FormatStrFormatter('%.1f'))
# plot sample over the top to get a feel for error bars
samp = 2500
plt.errorbar(df1d_g[0::samp]['feature1d_mean'],
df1d_g[0::samp]['f1'] * 10,
xerr=df1d_g[0::samp]['feature1d_std'],
yerr=df1d_g[0::samp]['f1err'] * 10,
color=galaxy_c,
elinewidth=elinewidth,
markeredgewidth=mew,
ls='none',
label='Galaxies')
plt.errorbar(df1d_q[0::samp]['feature1d_mean'],
df1d_q[0::samp]['f1'] * 10,
xerr=df1d_q[0::samp]['feature1d_std'],
yerr=df1d_q[0::samp]['f1err'] * 10,
color=quasar_c,
elinewidth=elinewidth,
markeredgewidth=mew,
ls='none',
label='Quasars')
plt.errorbar(df1d_s[0::samp]['feature1d_mean'],
df1d_s[0::samp]['f1'] * 10,
xerr=df1d_s[0::samp]['feature1d_std'],
yerr=df1d_s[0::samp]['f1err'] * 10,
color=star_c,
elinewidth=elinewidth,
markeredgewidth=mew,
ls='none',
label='Stars')
plt.tick_params(axis='y', which='both', right=True)
plt.minorticks_on()
plt.xlabel('1D feature')
plt.ylabel('F1 score in 1 dimensions')
#axs[1].text(0.95, 0.01, 'calculated from 10000 nearest neighbours in 10 dimensions', verticalalignment='bottom', horizontalalignment='right', transform=axs[1].transAxes, color='black', fontsize=8)
plt.xlim(-7, 12.5)
plt.legend(frameon=False, loc='lower right')
plt.tight_layout()
fig.tight_layout()
# --- 1D --- probs ---
plt.sca(axs[1])
xf = 2
plt.imshow(img_1d_probs,
extent=[xmin1d_probs * xf, xmax1d_probs * xf, ymin,
ymax]) # make xaxis larger
# fix ylabels after scaling the axis
#xlabels = axs[0].get_xticks()
#new_xlabels = [l/xf for l in xlabels] # account for scaling axis
axs[1].set_xticks(np.arange(0, 2.1, step=0.2))
axs[1].set_xticklabels(np.arange(0, 1.1, step=0.1))
#axs[0].xaxis.set_major_formatter(FormatStrFormatter('%.1f')) # doesn't work
# getting some labels with 8 F****** decimal places without these two lines:
labels = [item.get_text() for item in axs[1].get_xticklabels()]
axs[1].set_xticklabels([str(round(float(label), 2)) for label in labels])
# plot sample over the top to get a feel for error bars
df1d_g2 = df1d_g[(df1d_g.f1 < 0.85) & (df1d_g.probs_mean < 0.85)][0::3000]
plt.errorbar(df1d_g2['probs_mean'] * xf,
df1d_g2['f1'],
xerr=df1d_g2['probs_std'] * xf,
yerr=df1d_g2['f1err'],
color=galaxy_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Galaxies')
df1d_q2 = df1d_q[(df1d_q.f1 < 0.85) & (df1d_q.probs_mean < 0.85)][0::3000]
plt.errorbar(df1d_q2['probs_mean'] * xf,
df1d_q2['f1'],
xerr=df1d_q2['probs_std'] * xf,
yerr=df1d_q2['f1err'],
color=quasar_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Quasars')
df1d_q2 = df1d_q[(df1d_q.f1 < 0.85) & (df1d_q.probs_mean < 0.75)][
0::800] # plot more at lower values in undersampled region
plt.errorbar(df1d_q2['probs_mean'] * xf,
df1d_q2['f1'],
xerr=df1d_q2['probs_std'] * xf,
yerr=df1d_q2['f1err'],
color=quasar_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew)
df1d_s2 = df1d_s[(df1d_s.f1 < 0.85) & (df1d_s.probs_mean < 0.85)][0::3000]
plt.errorbar(df1d_s2['probs_mean'] * xf,
df1d_s2['f1'],
xerr=df1d_s2['probs_std'] * xf,
yerr=df1d_s2['f1err'],
color=star_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Stars')
plt.tick_params(axis='y', which='both', right=True)
plt.minorticks_on()
plt.xlabel('Classification probability')
plt.ylabel('F1 score in 1 dimension')
#axs[0].text(0.95, 0.01, 'calculated from 10000 nearest neighbours in 1 dimension', verticalalignment='bottom', horizontalalignment='right', transform=axs[0].transAxes, color='black', fontsize=8)
#plt.xlim(0.66,2)
plt.tight_layout()
#fig.subplots_adjust(wspace=0.1, hspace=0.1) # Must come after tight_layout to work! ... doesn't seem to work when using imshow :(
fig.savefig('knn_plot_1D' + plot_label + '.pdf')
plt.clf()
# ---------------- 10-d ----------------
# ----------------- plotting -----------------
elinewidth = 0.2
mpl.rcParams.update({'font.size':
10}) # else its really small in the paper
img_10d_1d = mpimg.imread('knn10d_1d_vs_f1.png')
img_10d_probs = mpimg.imread('knn10d_probs_vs_f1.png')
fig, axs = plt.subplots(1, 2, figsize=(14.5, 4))
xf = 2 # make x-axis twice as long as y.
# --- 10D ---
plt.sca(axs[0])
plt.imshow(img_10d_1d, extent=[xmin10d, xmax10d, ymin * 10,
ymax * 10]) # make yaxis 10 times larger
# fix ylabels after scaling the axis
ylabels = axs[0].get_yticks()
new_ylabels = [l / 10
for l in ylabels] # account for factor of 10 increase
axs[0].set_yticklabels(new_ylabels)
axs[0].xaxis.set_major_formatter(FormatStrFormatter('%.1f'))
# plot sample over the top to get a feel for error bars
df10d_g2 = df10d_g[df10d_g.f1 < 0.95][
0::
500] # only plot error bars below 0.95 because above this they are v small.
plt.errorbar(df10d_g2['feature10d_mean'],
df10d_g2['f1'] * 10,
xerr=df10d_g2['feature10d_std'],
yerr=df10d_g2['f1err'] * 10,
color=galaxy_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Galaxies')
df10d_q2 = df10d_q[df10d_q.f1 < 0.95][0::500]
plt.errorbar(df10d_q2['feature10d_mean'],
df10d_q2['f1'] * 10,
xerr=df10d_q2['feature10d_std'],
yerr=df10d_q2['f1err'] * 10,
color=quasar_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Quasars')
df10d_s2 = df10d_s[df10d_s.f1 < 0.95][0::500]
plt.errorbar(df10d_s2['feature10d_mean'],
df10d_s2['f1'] * 10,
xerr=df10d_s2['feature10d_std'],
yerr=df10d_s2['f1err'] * 10,
color=star_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Stars')
plt.tick_params(axis='y', which='both', right=True)
plt.minorticks_on()
plt.xlabel('1D feature')
plt.ylabel('F1 score in 10 dimensions')
#axs[1].text(0.95, 0.01, 'calculated from 10000 nearest neighbours in 10 dimensions', verticalalignment='bottom', horizontalalignment='right', transform=axs[1].transAxes, color='black', fontsize=8)
plt.xlim(-7, 12.5)
plt.tight_layout()
# --- 10D --- probs ---
plt.sca(axs[1])
plt.imshow(img_10d_probs,
extent=[xmin10d_probs * xf, xmax10d_probs * xf, ymin,
ymax]) # make xaxis larger
# fix ylabels after scaling the axis
#xlabels = axs[1].get_xticks()
#new_xlabels = [l/xf for l in xlabels] # account for scaling axis
#axs[1].set_xticklabels(new_xlabels)
axs[1].set_xticks(np.arange(0, 2.1, step=0.2))
axs[1].set_xticklabels(np.arange(0, 1.1, step=0.1))
#axs[0].xaxis.set_major_formatter(FormatStrFormatter('%.1f')) # doesn't work
labels = [item.get_text() for item in axs[1].get_xticklabels()]
axs[1].set_xticklabels([str(round(float(label), 2)) for label in labels])
# plot sample over the top to get a feel for error bars
df10d_g2 = df10d_g[(df10d_g.f1 < 0.85) & (
df10d_g.probs_mean < 0.85
)][0::
1000] # only plot error bars below 0.95 because above this they are v small, and overcrowd the plot.
plt.errorbar(df10d_g2['probs_mean'] * xf,
df10d_g2['f1'],
xerr=df10d_g2['probs_std'] * xf,
yerr=df10d_g2['f1err'],
color=galaxy_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Galaxy')
df10d_q2 = df10d_q[(df10d_q.f1 < 0.85)
& (df10d_q.probs_mean < 0.85)][0::1000]
plt.errorbar(df10d_q2['probs_mean'] * xf,
df10d_q2['f1'],
xerr=df10d_q2['probs_std'] * xf,
yerr=df10d_q2['f1err'],
color=quasar_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Quasar')
df10d_s2 = df10d_s[(df10d_s.f1 < 0.85)
& (df10d_s.probs_mean < 0.85)][0::1000]
plt.errorbar(df10d_s2['probs_mean'] * xf,
df10d_s2['f1'],
xerr=df10d_s2['probs_std'] * xf,
yerr=df10d_s2['f1err'],
color=star_c,
elinewidth=elinewidth,
ls='none',
markeredgewidth=mew,
label='Star')
plt.tick_params(axis='y', which='both', right=True)
plt.minorticks_on()
plt.xlabel('Classification probability')
plt.ylabel('F1 score in 10 dimensions')
plt.legend(frameon=False, loc='upper left')
#axs[1].text(0.95, 0.01, 'calculated from 10000 nearest neighbours in 10 dimensions', verticalalignment='bottom', horizontalalignment='right', transform=axs[1].transAxes, color='black', fontsize=8)
plt.tight_layout()
fig.tight_layout()
#plt.xlim(0.66,2)
fig.savefig('knn_plot_10D' + plot_label + '.pdf')
def obv(l_args, s_ticker, s_interval, df_stock):
parser = argparse.ArgumentParser(
add_help=False,
prog="obv",
description="""
The On Balance Volume (OBV) is a cumulative total of the up and
down volume. When the close is higher than the previous close, the volume is added
to the running total, and when the close is lower than the previous close, the volume
is subtracted from the running total. \n \n To interpret the OBV, look for the OBV
to move with the price or precede price moves. If the price moves before the OBV,
then it is a non-confirmed move. A series of rising peaks, or falling troughs, in the
OBV indicates a strong trend. If the OBV is flat, then the market is not trending.
""",
)
parser.add_argument(
"-o",
"--offset",
action="store",
dest="n_offset",
type=check_positive,
default=0,
help="offset",
)
try:
ns_parser = parse_known_args_and_warn(parser, l_args)
if not ns_parser:
return
# Daily
if s_interval == "1440min":
df_ta = ta.obv(
close=df_stock["5. adjusted close"],
volume=df_stock["6. volume"],
offset=ns_parser.n_offset,
).dropna()
# Intraday
else:
df_ta = ta.obv(
close=df_stock["4. close"],
volume=df_stock["5. volume"],
offset=ns_parser.n_offset,
).dropna()
plt.figure(figsize=plot_autoscale(), dpi=PLOT_DPI)
axPrice = plt.subplot(211)
if s_interval == "1440min":
plt.plot(df_stock.index, df_stock["5. adjusted close"].values, "k", lw=2)
else:
plt.plot(df_stock.index, df_stock["4. close"].values, "k", lw=2)
plt.title(f"On-Balance Volume (OBV) on {s_ticker}")
plt.xlim(df_stock.index[0], df_stock.index[-1])
plt.ylabel("Share Price ($)")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True, which="minor", color="#999999", linestyle="-", alpha=0.2)
_ = axPrice.twinx()
if s_interval == "1440min":
plt.bar(
df_stock.index,
df_stock["6. volume"].values,
color="k",
alpha=0.8,
width=0.3,
)
else:
plt.bar(
df_stock.index,
df_stock["5. volume"].values,
color="k",
alpha=0.8,
width=0.3,
)
plt.subplot(212)
plt.plot(df_ta.index, df_ta.values, "b", lw=1)
plt.xlim(df_stock.index[0], df_stock.index[-1])
plt.legend(["OBV"])
plt.xlabel("Time")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True, which="minor", color="#999999", linestyle="-", alpha=0.2)
if gtff.USE_ION:
plt.ion()
plt.show()
print("")
except Exception as e:
print(e)
print("")
#Set delta for linmix array which says what are upper limits. 1 is a measured value. 0 is an upper limit.
#Brooke's galaxies have measured B/T, SDSS are all upper limits and INT values have 2 measured, 3 upper limits (set to a B/T =1)
delta = N.append(N.ones(len(brooke_mtot)),
N.append(N.zeros(len(bt[is_sdss])), int_delta))
# plot a histogram of B/T ratios, just a check (as almost all, but not all, are upper limits)
P.figure(figsize=(6, 3))
P.hist(N.append(brooke_BT, N.array(bt[BTcol])),
range=(-0.05, 1.05),
bins=15,
histtype='step',
color='k')
P.xlabel(r'$[\rm{B}/\rm{T}]_r$')
P.ylabel(r'$\rm{number}$')
P.ylim(0, 20)
P.minorticks_on()
P.tight_layout()
P.savefig('bulge_to_total_r_ratio_hist_with_INT_simmons13.pdf',
frameon=False,
transparent=True)
# the x values we'll be using for all the linmix fits
# (finely sampled so they don't look jagged)
xs = N.linspace(0, 15, 500)
# Now either load the linmix parameters from a file or re-fit the data
# depending on what was specified when the program started
if read_from_file:
lmhr_chain = N.load('%s_haringrixfit.npy' % linmixfilebase)
lmhr_alpha = lmhr_chain['alpha']
lmhr_beta = lmhr_chain['beta']
def collectData(pandaID):
logFiles = []
logFiles.extend(
Filestable4.objects.filter(pandaid=pandaID, type='log').values())
if len(logFiles) == 0:
logFiles.extend(
FilestableArch.objects.filter(pandaid=pandaID,
type='log').values())
if not len(logFiles) == 1:
return HttpResponse('Log files for pandaid=%s not found' % pandaID)
logfile = logFiles[0]
guid = logfile['guid']
lfn = logfile['lfn']
scope = logfile['scope']
http = urllib3.PoolManager()
resp = http.request('GET',
filebrowserURL,
fields={
'guid': guid,
'lfn': lfn,
'scope': scope,
'json': 1
})
if resp and len(resp.data) > 0:
try:
data = json.loads(resp.data)
HOSTNAME = data['HOSTNAME']
tardir = data['tardir']
MEDIA_URL = data['MEDIA_URL']
dirprefix = data['dirprefix']
files = data['files']
files = [
f for f in files if 'memory_monitor_output.txt' in f['name']
]
except:
return -2
else:
return -2
urlBase = "http://" + HOSTNAME + "/" + MEDIA_URL + "/" + dirprefix + "/" + tardir
dfl = []
pd.set_option('display.max_columns', 1000)
for f in files:
url = urlBase + f['dirname'] + "/" + f['name']
resp = http.request('GET', url)
TESTDATA = StringIO.StringIO(resp.data)
dfl.append(pd.read_csv(TESTDATA, sep="\t").iloc[:, range(9)])
if len(dfl) > 0:
df = pd.concat(dfl)
df.columns = [
'Time', 'VMEM', 'PSS', 'RSS', 'Swap', 'rchar', 'wchar', 'rbytes',
'wbytes'
]
df = df.sort_values(by='Time')
tstart = df['Time'].min()
df['Time'] = df['Time'].apply(lambda x: x - tstart)
df['PSS'] = df['PSS'].apply(lambda x: x / 1024.0 / 1024.0)
df['RSS'] = df['RSS'].apply(lambda x: x / 1024.0 / 1024.0)
df['VMEM'] = df['VMEM'].apply(lambda x: x / 1024.0 / 1024.0)
df['Swap'] = df['Swap'].apply(lambda x: x / 1024.0 / 1024.0)
df['rchar'] = df['rchar'].apply(lambda x: x / 1024.0 / 1024.0)
df['wchar'] = df['wchar'].apply(lambda x: x / 1024.0 / 1024.0)
df['rbytes'] = df['rbytes'].apply(lambda x: x / 1024.0 / 1024.0)
df['wbytes'] = df['wbytes'].apply(lambda x: x / 1024.0 / 1024.0)
# Make plot for memory consumption
f1 = plt.figure(figsize=(15, 10))
ax1 = f1.add_subplot(111)
ax1.plot(df['Time'], df['PSS'], label="PSS")
ax1.legend(loc="upper right")
ax2 = f1.add_subplot(111)
ax2.plot(df['Time'], df['RSS'], label="RSS")
ax2.legend(loc="upper right")
ax3 = f1.add_subplot(111)
ax3.plot(df['Time'], df['Swap'], label="Swap")
ax3.legend(loc="upper right")
ax4 = f1.add_subplot(111)
ax4.plot(df['Time'], df['VMEM'], label="VMEM")
ax4.legend(loc="upper right")
plt.title("Memory consumption, job " + str(pandaID))
plt.xlabel("time (s)")
plt.ylabel("memory usage (GB)")
plt.ylim(ymin=0)
plt.xlim(xmin=0)
plt.grid()
minor_ticks = np.arange(0, plt.ylim()[1], 1)
plt.minorticks_on()
plt.yticks(minor_ticks)
plot1img = StringIO.StringIO()
plt.savefig(plot1img, format='png')
plot1img.seek(0)
#Make plot for IO
f1 = plt.figure(figsize=(15, 10))
ax1 = f1.add_subplot(111)
ax1.plot(df['Time'], df['rchar'], label="rchar")
ax1.legend(loc="upper right")
ax2 = f1.add_subplot(111)
ax2.plot(df['Time'], df['wchar'], label="wchar")
ax2.legend(loc="upper right")
ax3 = f1.add_subplot(111)
ax3.plot(df['Time'], df['rbytes'], label="rbytes")
ax3.legend(loc="upper right")
ax4 = f1.add_subplot(111)
ax4.plot(df['Time'], df['wbytes'], label="wbytes")
ax4.legend(loc="upper right")
plt.title("IO, job " + str(pandaID))
plt.xlabel("time (s)")
plt.ylabel("IO (MB)")
plt.grid()
plt.ylim(ymin=0)
plt.xlim(xmin=0)
plot2img = StringIO.StringIO()
plt.savefig(plot2img, format='png')
plot2img.seek(0)
#Make plot for IO rate
lasttime = 0
lastrchar = 0
lastwchar = 0
lastrbytes = 0
lastwbytes = 0
drchar = [0]
dwchar = [0]
drbytes = [0]
dwbytes = [0]
for index, row in df.iterrows():
if index > 0:
dt = row['Time'] - lasttime
drchar.append((row['rchar'] - lastrchar) / dt)
dwchar.append((row['wchar'] - lastwchar) / dt)
drbytes.append((row['rbytes'] - lastrbytes) / dt)
dwbytes.append((row['wbytes'] - lastwbytes) / dt)
lasttime = row['Time']
lastrchar = row['rchar']
lastwchar = row['wchar']
lastrbytes = row['rbytes']
lastwbytes = row['wbytes']
df['drchar'] = drchar
df['dwchar'] = dwchar
df['drbytes'] = drbytes
df['dwbytes'] = dwbytes
f1 = plt.figure(figsize=(15, 10))
ax1 = f1.add_subplot(111)
ax1.plot(df['Time'], drchar, label="rchar")
ax1.legend(loc="upper right")
ax2 = f1.add_subplot(111)
ax2.plot(df['Time'], dwchar, label="wchar")
ax2.legend(loc="upper right")
ax3 = f1.add_subplot(111)
ax3.plot(df['Time'], drbytes, label="rbytes")
ax3.legend(loc="upper right")
ax4 = f1.add_subplot(111)
ax4.plot(df['Time'], dwbytes, label="wbytes")
ax4.legend(loc="upper right")
plt.title("IO rate, job " + str(pandaID))
plt.xlabel("time (s)")
plt.ylabel("IO rate (MB/S)")
plt.grid()
plt.ylim(ymin=0)
plt.xlim(xmin=0)
plot3img = StringIO.StringIO()
plt.savefig(plot3img, format='png')
plot3img.seek(0)
#Here we combine few plots
images = map(Image.open, [plot1img, plot2img, plot3img])
widths, heights = zip(*(i.size for i in images))
max_width = max(widths)
total_height = sum(heights)
new_im = Image.new('RGB', (max_width, total_height))
y_offset = 0
for im in images:
new_im.paste(im, (0, y_offset))
y_offset += im.size[1]
finPlotData = StringIO.StringIO()
new_im.save(finPlotData, format='png')
finPlotData.seek(0)
if plot1img is not None:
return HttpResponse(finPlotData.buf, content_type="image/png")
return HttpResponse('')
print('\n----------------------------')
print('spacing: ', space)
print('time: ', opdays / opfact) # real time: ',tm(space))
print('F_lim: ', Flimval)
print('difference: ', -(Fset - Flimval) / Fset)
spacelst.append(space)
timelst.append(opdays / opfact)
Flimlst.append(7 * Flimval)
space = space - dsp
#print(space,Fset,Flimval,-(Fset - Flimval)/Fset)
c1 = (0, 102 / 256, 204 / 256)
c2 = (1, 0, 0)
plt.axvline(0, color=(0, 0, 0), linewidth=0.8)
plt.axhline(0, color=(0, 0, 0), linewidth=0.8)
plt.minorticks_on() # set minor ticks
plt.grid(which='major', linestyle='-', linewidth='0.3',
color='black') # customise major grid
plt.grid(which='minor', linestyle=':', linewidth='0.3',
color='grey') # customise minor grid
plt.axvline(200, color=(0, 153 / 256, 44 / 256), linestyle='--')
plt.plot(spacelst, timelst, color=c1)
#plt.xscale('log')
plt.xlabel('Mesh Spacing [m]')
plt.ylabel('Operational Time [Days]')
plt.show()
def imss(fdic,
key,
cut=None,
ax=None,
extent=None,
cbar=None,
smth=None,
nolabels=None,
lblsz='small',
**kwargs):
"""
A wrapper function for imshow to do most
tedious stuff for my simulations
"""
old_ax = plt.gca() # Get Current Axis
if ax is None:
ax = old_ax
else:
plt.sca(ax) # Set Current Axis
if type(key) is str: plt_val = fdic[key]
else : plt_val = key
if smth is not None:
plt_val = gf(plt_val,sigma=smth)
if cut is None:
if len(plt_val.shape) == 2:
IDX=np.s_[:,:]
else:
IDX=np.s_[:,:,0]
else:
if len(plt_val.shape) == 2:
IDX=compute2didx([fdic['xx'],fdic['yy']],cut)
else:
IDX=compute2didx([fdic['xx'],fdic['yy'],fdic['zz']],cut)
# Use the dict values of xx and yy to set extent
ext = [fdic['xx'][IDX[0]][0],
fdic['xx'][IDX[0]][-1],
fdic['yy'][IDX[1]][0],
fdic['yy'][IDX[1]][-1]]
if kwargs.has_key('cmap'): cmap=kwargs.pop('cmap')
else: cmap='PuOr'
im = ax.imshow(plt_val[IDX].T,
origin='low',
extent=ext,
cmap=cmap, # I just love this color map
aspect='equal',
**kwargs)
if extent is not None:
ax.set_xlim(extent[:2])
ax.set_ylim(extent[2:])
ax.autoscale(False)
if nolabels is None:
ax.set_xlabel(r'$X (d_i)$',size=lblsz)
ax.set_ylabel(r'$Y (d_i)$',size=lblsz)
ax.xaxis.set_tick_params(which='both',labelsize=lblsz)
#minorLocator = AutoMinorLocator() # Note the second call is so that the minor x ticks are not
#ax.xaxis.set_minor_locator(minorLocator) # the same as the y ticks
ax.yaxis.set_tick_params(which='both',labelsize=lblsz)
#minorLocator = AutoMinorLocator()
#ax.yaxis.set_minor_locator(minorLocator)
plt.minorticks_on()
plt.sca(old_ax)
# Code to implement for a cbar
if cbar:
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", "3%", pad="1.5%")
plt.colorbar(im, cax=cax)
cax.xaxis.set_tick_params(which='both',labelsize=lblsz)
cax.yaxis.set_tick_params(which='both',labelsize=lblsz)
plt.draw()
return im,cax
else:
return im
def plot_raman(yscale="linear",
figname="Raman.png",
relative=False,
w_min=None,
w_max=None,
ramanname=None):
"""
Plots a given Raman spectrum
Input:
yscale: Linear or logarithmic yscale
figname: Name of the generated figure
relative: Scale to the highest peak
w_min, w_max: The plotting range wrt the Raman shift
ramanname: Suffix used for the file containing the Raman spectrum
Output:
ramanname: image containing the Raman spectrum.
"""
import matplotlib
matplotlib.use('Agg') # FIXME: Evil, none of this function's business
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as cmx
from ase.parallel import world
# Plotting function
if world.rank == 0:
legend = isinstance(ramanname, (list, tuple))
if ramanname is None:
RI_name = ["RI.npy"]
elif type(ramanname) == list:
RI_name = ["RI_{}.npy".format(name) for name in ramanname]
else:
RI_name = ["RI_{}.npy".format(ramanname)]
ylabel = "Intensity (arb. units)"
inferno = cm = plt.get_cmap('inferno')
cNorm = colors.Normalize(vmin=0, vmax=len(RI_name))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cm)
peaks = None
for i, name in enumerate(RI_name):
RI = np.real(np.load(name))
if w_min == None:
w_min = np.min(RI[0])
if w_max == None:
w_max = np.max(RI[0])
r = RI[1][np.logical_and(RI[0] >= w_min, RI[0] <= w_max)]
w = RI[0][np.logical_and(RI[0] >= w_min, RI[0] <= w_max)]
cval = scalarMap.to_rgba(i)
if relative:
ylabel = "I/I_max"
r = r / np.max(r)
if peaks is None:
peaks = signal.find_peaks(r[np.logical_and(
w >= w_min, w <= w_max)])[0]
locations = np.take(w[np.logical_and(w >= w_min, w <= w_max)],
peaks)
intensities = np.take(
r[np.logical_and(w >= w_min, w <= w_max)], peaks)
if legend:
plt.plot(w, r, color=cval, label=ramanname[i])
else:
plt.plot(w, r, color=cval)
for i, loc in enumerate(locations):
if intensities[i] / np.max(intensities) > 0.05:
plt.axvline(x=loc, color="grey", linestyle="--")
# FIXME: usage of pyplot API
plt.yscale(yscale)
plt.minorticks_on()
if legend:
plt.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
plt.title("Raman intensity")
plt.xlabel("Raman shift (cm$^{-1}$)")
plt.ylabel(ylabel)
if not relative:
plt.yticks([])
plt.savefig(figname, dpi=300)
plt.clf()
def ad(l_args, s_ticker, s_interval, df_stock):
parser = argparse.ArgumentParser(
add_help=False,
prog="ad",
description="""
The Accumulation/Distribution Line is similar to the On Balance
Volume (OBV), which sums the volume times +1/-1 based on whether the close is
higher than the previous close. The Accumulation/Distribution indicator, however
multiplies the volume by the close location value (CLV). The CLV is based on the
movement of the issue within a single bar and can be +1, -1 or zero. \n \n
The Accumulation/Distribution Line is interpreted by looking for a divergence in
the direction of the indicator relative to price. If the Accumulation/Distribution
Line is trending upward it indicates that the price may follow. Also, if the
Accumulation/Distribution Line becomes flat while the price is still rising (or falling)
then it signals an impending flattening of the price.
""",
)
parser.add_argument(
"-o",
"--offset",
action="store",
dest="n_offset",
type=check_positive,
default=0,
help="offset",
)
parser.add_argument(
"--open",
action="store_true",
default=False,
dest="b_use_open",
help="uses open value of stock",
)
try:
ns_parser = parse_known_args_and_warn(parser, l_args)
if not ns_parser:
return
# Daily
if s_interval == "1440min":
# Use open stock values
if ns_parser.b_use_open:
df_ta = ta.ad(
high=df_stock["2. high"],
low=df_stock["3. low"],
close=df_stock["5. adjusted close"],
volume=df_stock["6. volume"],
offset=ns_parser.n_offset,
open_=df_stock["1. open"],
).dropna()
# Do not use open stock values
else:
df_ta = ta.ad(
high=df_stock["2. high"],
low=df_stock["3. low"],
close=df_stock["5. adjusted close"],
volume=df_stock["6. volume"],
offset=ns_parser.n_offset,
).dropna()
# Intraday
else:
# Use open stock values
if ns_parser.b_use_open:
df_ta = ta.ad(
high=df_stock["2. high"],
low=df_stock["3. low"],
close=df_stock["4. close"],
volume=df_stock["5. volume"],
offset=ns_parser.n_offset,
open_=df_stock["1. open"],
).dropna()
# Do not use open stock values
else:
df_ta = ta.ad(
high=df_stock["2. high"],
low=df_stock["3. low"],
close=df_stock["4. close"],
volume=df_stock["5. volume"],
offset=ns_parser.n_offset,
).dropna()
plt.figure(figsize=plot_autoscale(), dpi=PLOT_DPI)
axPrice = plt.subplot(211)
if s_interval == "1440min":
plt.plot(df_stock.index, df_stock["5. adjusted close"].values, "k", lw=2)
else:
plt.plot(df_stock.index, df_stock["4. close"].values, "k", lw=2)
plt.title(f"Accumulation/Distribution Line (AD) on {s_ticker}")
plt.xlim(df_stock.index[0], df_stock.index[-1])
plt.ylabel("Share Price ($)")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True, which="minor", color="#999999", linestyle="-", alpha=0.2)
_ = axPrice.twinx()
if s_interval == "1440min":
plt.bar(
df_stock.index,
df_stock["6. volume"].values,
color="k",
alpha=0.8,
width=0.3,
)
else:
plt.bar(
df_stock.index,
df_stock["5. volume"].values,
color="k",
alpha=0.8,
width=0.3,
)
plt.subplot(212)
plt.plot(df_ta.index, df_ta.values, "b", lw=1)
plt.xlim(df_stock.index[0], df_stock.index[-1])
plt.axhline(0, linewidth=2, color="k", ls="--")
plt.legend(["Chaikin Oscillator"])
plt.xlabel("Time")
plt.grid(b=True, which="major", color="#666666", linestyle="-")
plt.minorticks_on()
plt.grid(b=True, which="minor", color="#999999", linestyle="-", alpha=0.2)
if gtff.USE_ION:
plt.ion()
plt.show()
print("")
except Exception as e:
print(e)
print("")
return