def linear_fit(x, y):
"""
linear fitting function with -99999 error removal
Input: x --- independent variable array
y --- dependent variable array
Output: intc --- intercept
slope--- slope
"""
#
#--- first remove error entries (which is -99999)
#
xn = []
yn = []
for i in range(0, len(x)):
if float(y[i]) != -99999:
xn.append(float(x[i]))
yn.append(float(y[i]))
if len(xn) > 3:
try:
(a, b, berr) = robust.robust_fit(xn, yn)
return [a, b]
except:
return [0, 0]
else:
return [0, 0]
def fit_line(x, y, xmin, xmax):
"""
fit robust fit line on the data on log-log plane
input: x --- x data
y --- y data
xmin --- min of x
xmax --- max of x
"""
#
#--- convert the data into log
#
xl = numpy.log10(x)
yl = numpy.log10(y)
#
#--- fit a line on log-log plane with robust fit
#
if len(xl) > 4:
[a, b, e] = robust.robust_fit(xl, yl)
else:
a = 0.0
b = 0.0
e = 0.0
#
#--- compute plotting data points on non-log plane; it is used by the plotting routine
#
xsave = []
ysave = []
step = (xmax - xmin) / 100.0
for k in range(0, 100):
xe = xmin + step * k
ye = 10**(a + b * math.log10(xe))
xsave.append(xe)
ysave.append(ye)
return [xsave, ysave, a, b]
def create_trend_data_plot(x, y, ccd, dtype, col_name, col_dname):
"""
create a trend plot
input: x --- a list of x data
y --- a list of y data
ccd --- ccd name
dytpe --- data type
col_name --- short-hand column name
col_dname --- full column name
output: <plot_dir>/<ccd>_<dtype>_<col_name>.png
"""
#
#--- fit a trend line
#
[intc, slope, err] = robust.robust_fit(x, y)
#
#--- set plotting range
#
[xmin, xmax, ymin, ymax] = set_plotting_range(x, y)
plt.close('all')
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin, xmax)
ax.set_xlim(left=xmin, right=xmax, auto=False)
ax.set_ylim(bottom=ymin, top=ymax, auto=False)
#
#--- plot data
#
plt.plot(x, y, color='blue', marker='.', markersize='1', lw=0)
#
#--- plot trending line
#
yb = intc + slope * xmin
ye = intc + slope * xmax
plt.plot([xmin, xmax], [yb, ye],
color='red',
marker='.',
markersize='1',
lw=2)
#
#--- label axes
#
plt.xlabel('Time (year)')
plt.ylabel(col_dname)
#
#--- save the plot
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10, 5)
outname = plot_dir + ccd + '_' + dtype + '_' + col_name + '.png'
plt.savefig(outname, format='png', dpi=200)
def plot_s2hvst_vt_ratio(sfile, indata):
"""
create s2hvst - valid rate/total rate plot
input: sfile --- input file name
indata --- a list of lists of data
output: <head_name>_s2hvst_vt_ratio.png
"""
#
#--- create ratio data from vald and total count rate
#
[rdata, rerr] = compute_ratio(indata[12], indata[9], indata[14],
indata[11])
#
#--- setting plotting surface
#
mpl.rcParams['font.size'] = 14
props = font_manager.FontProperties(size=12)
xmin = 4
xmax = 9
psize = 9
fsize = 14
tfsize = fsize + 2
ymin = 0.20
ymax = 0.50
a1 = plt.subplot(111)
plt.axis([xmin, xmax, ymin, ymax])
plt.plot(indata[21], rdata, lw=0, marker='+', markersize=psize)
#
#--- add fitting line
#
(sint, slope, serror) = robust.robust_fit(indata[21], rdata, iter=100)
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], lw=2.0, marker='+', markersize=psize)
xdiff = xmax - xmin
ydiff = ymax - ymin
xpos = xmin + 0.1 * xdiff
ypos = ymax - 0.1 * ydiff
text = 'Slope: ' + str(round(slope, 4)) + '+/-' + str(round(serror, 4))
plt.text(xpos, ypos, text, size=tfsize, weight='bold')
#
#--- add the legend and x axis name
#
a1.set_xlabel("S2HVST", size=fsize)
a1.set_ylabel("Valid Rate / Total Rate", size=fsize)
#
#--- save the plot in file
#
save_plot_in_file(sfile, 's2hvst_vt_ratio.png')
def get_int_slope(x, y, xl, yl):
"""
estimate a + b * x line with a robust method and then compare with a
simple two point estimate and choose a shallower slope fitting
input: x --- a list of x values
y --- a list of y values
xl --- a secondary list of x value
yl --- a seocndary list of y value
output: a --- intercept
b --- slope
"""
#
#--- choose the data only in the last one year
#
bound = ecf.current_time() - 1.0
xsave = []
ysave = []
for k in range(0, len(x)):
if x[k] < bound:
continue
xsave.append(x[k])
ysave.append(y[k])
#
#--- if there are not enough data, give up the fitting
#
if len(xsave) < 6:
return [999, 999]
try:
#
#--- robust fit
#
[a, b, err] = rfit.robust_fit(xsave, ysave)
#
#--- two point fit
#
[al, bl] = get_int_slope_supl(xl, yl)
#
#--- choose a shallower slope fit
#
if abs(bl) < abs(b):
a = al
b = bl
except:
a = 999
b = 999
return [a, b]
def get_int_slope(x, y, xl, yl):
"""
estimate a + b * x line with a robust method and then compare with a
simple two point estimate and choose a shallower slope fitting
input: x --- a list of x values
y --- a list of y values
xl --- a secondary list of x value
yl --- a seocndary list of y value
output: a --- intercept
b --- slope
"""
#
#--- choose the data only in the last one year
#
bound = ecf.current_time() - 1.0
xsave = []
ysave = []
for k in range(0, len(x)):
if x[k] < bound:
continue
xsave.append(x[k])
ysave.append(y[k])
#
#--- if there are not enough data, give up the fitting
#
if len(xsave) < 6:
return [999, 999]
try:
#
#--- robust fit
#
[a,b,err] = rfit.robust_fit(xsave, ysave)
#
#--- two point fit
#
[al, bl] = get_int_slope_supl(xl, yl)
#
#--- choose a shallower slope fit
#
if abs(bl) < abs(b):
a = al
b = bl
except:
a = 999
b = 999
return [a,b]
def linear_fit(x, y):
"""
linear fitting function with -99999 error removal
Input: x --- independent variable array
y --- dependent variable array
Output: intc --- intercept
slope--- slope
"""
#
#--- first remove error entries (which is -99999)
#
xn = []
yn = []
for i in range(0, len(x)):
if float(y[i]) != -99999:
xn.append(float(x[i]))
yn.append(float(y[i]))
if len(xn) > 3:
try:
(a, b, berr) = robust.robust_fit(xn, yn)
return [a, b]
except:
return [0,0]
#
#--- modify array to numpy array
#
# d = numpy.array(xn)
# v = numpy.array(yn)
#
#--- kmpfit
#
# param = [0, 1]
# fitobj = kmpfit.Fitter(residuals=residuals, data=(d,v))
# fitobj.fit(params0=paramsinitial)
# return fitobj.params
#
#
#--- chauvenet exclusion and linear fit
#
# try:
# [a, b, ae, be] = chauv.run_chauvenet(d, v)
# return [a, b]
# except:
# return [0, 0]
else:
return [0, 0]
def linear_fit(x, y):
"""
linear fitting function with -99999 error removal
Input: x --- independent variable array
y --- dependent variable array
Output: intc --- intercept
slope--- slope
"""
#
#--- first remove error entries
#
sum = 0
sum2 = 0
tot = 0
for i in range(0, len(y)):
if y[i] > 0:
sum += y[i]
sum2 += y[i] * y[i]
tot += 1
if tot > 0:
avg = sum / tot
sig = math.sqrt(sum2 / tot - avg * avg)
else:
avg = 3.0
lower = 0.0
upper = avg + 2.0
xn = []
yn = []
for i in range(0, len(x)):
if (y[i] > lower) and (y[i] < upper):
xn.append(x[i])
yn.append(y[i])
if len(yn) > 10:
[intc, slope, serr] = robust.robust_fit(xn, yn, iter=50)
else:
[intc, slope, serr] = [0, 0, 0]
return [intc, slope, 0.0, serr]
def plot_single_panel(xmin,
xmax,
ymin,
ymax,
xdata,
ydata,
yerror,
xname,
yname,
label,
outname,
resolution=100):
"""
plot a single data set on a single panel
Input: xmin --- min x
xmax --- max x
ymin --- min y
ymax --- max y
xdata --- independent variable
ydata --- dependent variable
yerror --- error in y axis
xname --- x axis label
ynane --- y axis label
label --- a text to indecate what is plotted
outname --- the name of output file
resolution-- the resolution of the plot in dpi
Output: png plot named <outname>
"""
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
lslope = '%2.3f' % (round(slope, 3))
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = 12
props = font_manager.FontProperties(size=9)
#
#--- set plotting range
#
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin, xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
#
#--- plot data
#
plt.plot(xdata, ydata, color='blue', marker='o', markersize=4.0, lw=0)
#
#--- plot error bar
#
plt.errorbar(xdata, ydata, yerr=yerror, lw=0, elinewidth=1)
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color='red', lw=2)
#
#--- label axes
#
plt.xlabel(xname)
plt.ylabel(yname)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.5 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.08 * ydiff
label = label + ': Slope: ' + str(lslope)
plt.text(xpos, ypos, label)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_data(t_list, d_list, fid, xlabel, outname, xs=0):
"""
create plot
input: t_list --- a list of x data
d_list --- a list of y data
fid --- fid light #
xlabel --- the label for x axis
outname --- plot file name
xs --- indicator which way to set xaxis range
output: outname --- png plot created
"""
[t_list, d_list] = remove_na_from_lists(t_list, d_list)
tarray = numpy.array(t_list)
darray = numpy.array(d_list)
idx = ~numpy.isnan(darray)
tarray = tarray[idx]
darray = darray[idx]
idx = (darray < 100) & (darray > -100)
t_list = list(tarray[idx])
d_list = list(darray[idx])
#
#--- set plotting range
#
if xs == 0:
xmin = int(min(t_list)) - 1
xmax = int(max(t_list)) + 1
else:
xmin = (int(10 * min(t_list)) - 0.5) / 10.0
xmax = (int(10 * max(t_list)) + 1.5) / 10.0
ymin = (int(10 * min(d_list)) - 0.5) / 10.0
ymax = (int(10 * max(d_list)) + 1.5) / 10.0
#
#--- y label
#
ylabel = 'MAG_I_AVG_' + str(fid)
#
#--- start plotting
#
plt.close('all')
props = font_manager.FontProperties(size=9)
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin, xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
ax.set_facecolor("lime")
#
#--- plot data
#
plt.plot(t_list, d_list, marker='D', markersize=2, lw=0)
#
#--- compute fitting line and plot a fitted line
#
try:
if len(t_list) > 3:
out = rlf.robust_fit(t_list, d_list)
pstart = out[0] + out[1] * xmin
pstop = out[0] + out[1] * xmax
plt.plot([xmin, xmax], [pstart, pstop],
markersize=0,
lw=1,
linestyle='dashed',
color='blue')
except:
pass
plt.xlabel(xlabel)
plt.ylabel(ylabel)
#
#--- set the size of the plot
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(7, 3.5)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dip=300)
plt.close('all')
def plot_multi_entries(xmin, xmax, ymin, ymax, xSets, ySets, xname, yname, entLabels, outname, yerror = 0,fsize = 9, psize = 2.0,lsize=0, resolution=100, linefit=0, connect=0):
"""
This function plots multiple data in a single panel.
Input: xmin, xmax, ymin, ymax: plotting area
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
xname: a name of x-axis
yname: a name of y-axis
entLabels: a list of the names of each data
outname: a name of plotting file
yerror: a list of lists of y error, if it is '0', no error bar, default = 0
fsize: font size, default = 9
psize: plotting point size, default = 2.0
lsize: fitted line width, default = 1
resolution: plotting resolution in dpi
linefit --- if it is 1, fit a line estimated by robust method
connect: connected line size. if it is '0', no connected line
Output: a png plot: out.png
"""
colorList = ('lime', 'yellow', 'red', 'lime', 'green', 'blue', 'maroon', 'black', 'fushia', 'olive')
markerList = ('o', '*', '+', '^', 's', 'D', '1', '2', '3', '4')
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.08)
#
#---- set a panel
#
ax = plt.subplot(111)
ax.set_autoscale_on(False) #---- these three may not be needed for the new pylab, but
ax.set_xbound(xmin,xmax) #---- they are necessary for the older version to set
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
tot = len(entLabels)
#
#--- start plotting each data set
#
lnamList = []
for i in range(0, tot):
xdata = xSets[i]
ydata = ySets[i]
color = colorList[i]
marker = markerList[0]
label = entLabels[i]
if tot > 1:
lnam = 'p' + str(i)
lnamList.append(lnam)
exec '%s, = plt.plot(xdata, ydata, color="%s", lw =lsize , marker="%s", markersize=3, label=entLabels[i])' %(lnam, color, marker)
else:
#
#--- if there is only one data set, ignore legend
#
plt.plot(xdata, ydata, color=color, lw =connect , marker='o', markersize=psize)
if yerror != 0:
p, = plt.errorbar(xdata, ydata, yerr=yerror[i], lw = 0, elinewidth=1)
if linefit > 0:
(sint, slope,serror) = robust.robust_fit(xdata, ydata)
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax],[start,stop], color=color, lw =lsize )
#
#--- add legend
#
if tot > 1:
line = '['
for ent in lnamList:
if line == '[':
line = line + ent
else:
line = line +', ' + ent
line = line + ']'
exec "leg = legend(%s, entLabels, prop=props)" % (line)
leg.get_frame().set_alpha(0.5)
ax.set_xlabel(xname, size=fsize)
ax.set_ylabel(yname, size=fsize)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5.0in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_data(sdata, mdata, year, msid, oname, ymin, ymax, ydrange, msid_list):
"""
create two panel plots for tephin vs msid and its deviation
input: sdata --- a list of tephin data
mdata --- a list of msid data (mid/min/max)
year --- year of the plot
msid --- msid
oname --- output name
ymin --- y min of the first plot
ymax --- y max of the first plot
ydrange --- the range of the deviation y axis
msid_list --- msid list
output: oname in png format
"""
plt.close('all')
fig, ax = plt.subplots(1, figsize=(8,6))
props = font_manager.FontProperties(size=14)
mpl.rcParams['font.size'] = 14
mpl.rcParams['font.weight'] = 'bold'
xmin = 1.5e4
xmax = 3.5e4
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax1 = plt.subplot(211)
ax1.set_xlim(xmin, xmax)
ax1.set_ylim(ymin, ymax)
ax1.set_xlabel("Shevart (cnts)")
ax1.set_ylabel(msid.upper())
#
#--- set the size of plot
#
fig.set_size_inches(10.0, 5.0)
fig.tight_layout()
#
#---- trending plots
#
points = ax1.scatter(sdata, mdata, marker='o', s=4 ,lw=0)
#
#---- envelope
#
period = 500
[xmc, ymc, xmb, ymb, xmt, ymt] = create_trend_envelope(sdata, mdata, period)
#
#--- trending area
#
try:
ax1.fill_between(xmc, ymb, ymt, facecolor='#00FFFF', alpha=0.3, interpolate=True)
except:
pass
#
#--- center moving average
#
ax1.plot(xmc, ymc, color='#E9967A', lw=4)
plt.text(16500, ypos, str(year))
#
#---- derivative plot
#
[xd, yd, ad] = find_deriv(sdata, mdata, 'xxx', step=20)
[dymin, dymax, dypos] = set_y_plot_range(yd)
ymax = ydrange
ymin = -1.0 * abs(ymax)
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax2 = plt.subplot(212)
ax2.set_xlim(xmin, xmax)
ax2.set_ylim(ymin, ymax)
ax2.set_xlabel("Shevart (cnts)")
line = msid + '/ cnts'
ax2.set_ylabel(line)
points = ax2.scatter(xd, yd, marker='o', s=4 ,lw=0)
try:
[xx, yy] = remove_extreme_vals(xd, yd, p=96)
[a, b, e] = rbl.robust_fit(xx, yy)
except:
[a, b, e] = least_sq(xd, yd, remove=1)
ys = a + b * xmin
ye = a + b * xmax
ax2.plot([xmin, xmax], [ys, ye], color='green', lw=3)
line = 'Slope: ' + "%3.3e" % (b)
mpl.rcParams['font.size'] = 12
plt.title('dy / d(Cnts)', loc='left')
plt.text(16500, ypos, line)
#
#--- set the size of plot
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 10.0)
fig.tight_layout()
plt.savefig(oname, format='png', dpi=100)
plt.close('all')
def plot_panel2(data1,
data2,
data3,
data4,
ydpos,
ylims,
ylab,
outname,
lfit=0):
"""
plotting dtheta information
input: data1 --- data for acis-i data is a list of list and the first is a list of time
data2 --- data for acis-s
data3 --- data for hrc-i
data4 --- data for hrc-s
ydpos --- the index of the data you want to use
ylim --- a list of lists of y limits [(ymin ymax),...]
ylab --- a list of labels for each data set to be plotted
outname --- a name of output file
lfit --- indicator of whether to fit line lfit=1: yes
output: <web_dir>/Plots/<outname>.png
"""
plt.close('all')
dlen = len(ylab)
mlen = dlen - 1
#
#--- set panel parameters
#
plt.subplots_adjust(hspace=0.08)
props = font_manager.FontProperties(size=9)
#
#--- set xrange
#
atime = []
data = []
[xlist, xmin, xmax, xlabel, xtext] = set_x_range(data1[0])
atime.append(xlist)
data.append(data1[ydpos])
[xlist, xmin, xmax, xlabel, xtext] = set_x_range(data2[0])
atime.append(xlist)
data.append(data2[ydpos])
[xlist, xmin, xmax, xlabel, xtext] = set_x_range(data3[0])
atime.append(xlist)
data.append(data3[ydpos])
[xlist, xmin, xmax, xlabel, xtext] = set_x_range(data4[0])
atime.append(xlist)
data.append(data4[ydpos])
xrange = [xmin, xmax]
#
#--- plot each panel
#
for k in range(0, dlen):
j = k + 1
line = str(dlen) + '1' + str(j)
exec("ax%s = plt.subplot(%s)" % (str(k), line))
exec("ax%s.set_xlim(left=xmin, right=xmax, auto=False)" % (str(k)))
#
#--- if ymin and ymax are given, use them
#
if len(ylims) == dlen:
ymin = ylims[k][0]
ymax = ylims[k][1]
exec("ax%s.set_ylim(ymin=ymin, ymax=ymax, auto=False)" % (str(k)))
xdata = atime[k]
ydata = data[k]
exec(
"ax%s.plot(xdata, ydata, color='blue', marker='.', markersize=1, lw=0)"
% (str(k)))
#
#--- for the case that a fitting line is requested
if lfit == 1:
[xt, yt] = remove_out_layer(xdata, ydata, ymin, ymax)
try:
[a, b, e] = rfit.robust_fit(xt, yt)
y1 = a + b * xmin
y2 = a + b * xmax
yrange = [y1, y2]
exec("ax%s.plot(xrange, yrange, color='red', lw=2)" % (str(k)))
except:
pass
ydiff = ymax - ymin
ytext = ymax - 0.1 * ydiff
line = "Slope: " + '%3.3f' % (round(b, 3))
plt.text(xtext, ytext, line)
#
#--- y axis label
#
exec("ax%s.set_ylabel('%s')" % (str(k), ylab[k]))
#
#--- x axis label
#
exec('ax%s.set_xlabel("%s")' % (str(mlen), xlabel))
#
#--- add x ticks label only on the last panel
#
for k in range(0, dlen):
ax = 'ax' + str(k)
if k != mlen:
line = eval("%s.get_xticklabels()" % (ax))
for label in line:
label.set_visible(False)
else:
pass
#
#--- save the plot in a file
#
fig = matplotlib.pyplot.gcf()
height = 2.0 * dlen + 0.5
fig.set_size_inches(10.0, height)
outfile = web_dir + 'Plots/' + outname
plt.savefig(outfile, format='png', dpi=100.0)
def plotPanel(xmin, xmax, yMinSets, yMaxSets, xSets, ySets, eSets, xname, yname, entLabels, ydiv):
"""
This function plots multiple data in separate panels
Input: xmin, xmax, ymin, ymax: plotting area
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
eSets: a list of lists containing error values of y-axis
yMinSets: a list of ymin
yMaxSets: a list of ymax
entLabels: a list of the names of each data
ydiv: a location of dividing spot
Output: a png plot: out.png
"""
#
#--- set line color list
#
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- clean up the plotting device
#
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = 13
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.06)
tot = len(entLabels)
#
#--- start plotting each data
#
for i in range(0, len(entLabels)):
axNam = 'ax' + str(i)
#
#--- setting the panel position
#
j = i + 1
if i == 0:
line = str(tot) + '1' + str(j)
else:
line = str(tot) + '1' + str(j) + ', sharex=ax0'
line = str(tot) + '1' + str(j)
exec "%s = plt.subplot(%s)" % (axNam, line)
exec "%s.set_autoscale_on(False)" % (axNam) #---- these three may not be needed for the new pylab, but
exec "%s.set_xbound(xmin,xmax)" % (axNam) #---- they are necessary for the older version to set
exec "%s.set_xlim(xmin=xmin, xmax=xmax, auto=False)" % (axNam)
exec "%s.set_ylim(ymin=yMinSets[i], ymax=yMaxSets[i], auto=False)" % (axNam)
#
#--- since the cti seems evolving after year <ydiv>, fit two different lines before and after that point
#
xdata = xSets[i]
ydata = ySets[i]
edata = eSets[i]
xdata1 = []
ydata1 = []
edata1 = []
xdata2 = []
ydata2 = []
edata2 = []
for k in range(0, len(xdata)):
if xdata[k] < ydiv:
xdata1.append(xdata[k])
ydata1.append(ydata[k])
edata1.append(edata[k])
else:
xdata2.append(xdata[k])
ydata2.append(ydata[k])
edata2.append(edata[k])
#
#---- actual data plotting
#
p, = plt.plot(xdata, ydata, color=colorList[i], marker='*', markersize=4.0, lw =0)
errorbar(xdata, ydata, yerr=edata, color=colorList[i], markersize=4.0, fmt='*')
#
#--- fitting straight lines with robust method and plot the results
#
xdata1 = numpy.array(xdata1)
ydata1 = numpy.array(ydata1)
edata1 = numpy.array(edata1)
(intc, slope, err) = robust.robust_fit(xdata1, ydata1)
ystart = intc + slope * 2000
ystop = intc + slope * ydiv
lxdata = [2000, ydiv]
lydata = [ystart, ystop]
p, = plt.plot(lxdata, lydata, color=colorList[i], marker='', markersize=1.0, lw =2)
xdata2 = numpy.array(xdata2)
ydata2 = numpy.array(ydata2)
edata2 = numpy.array(edata2)
(intc2, slope2,err) = robust.robust_fit(xdata2, ydata2)
ystart = intc2 + slope2 * ydiv
ystop = intc2 + slope2 * xmax
lxdata = [ydiv, xmax]
lydata = [ystart, ystop]
p, = plt.plot(lxdata, lydata, color=colorList[i], marker='', markersize=1.0, lw =2)
#
#--- add legend
#
lslope = round(slope, 3)
lslope2 = round(slope2, 3)
line = entLabels[i] + ' Slope: ' + str(lslope) + ' (before '+ str(ydiv) + ') / ' + str(lslope2) + ' (after '+ str(ydiv) + ')'
leg = legend([p], [line], prop=props, loc=2)
leg.get_frame().set_alpha(0.5)
exec "%s.set_ylabel(yname, size=8)" % (axNam)
#
#--- add x ticks label only on the last panel
#
for i in range(0, tot):
ax = 'ax' + str(i)
if i != tot-1:
exec "line = %s.get_xticklabels()" % (ax)
for label in line:
label.set_visible(False)
else:
pass
xlabel(xname)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
height = (2.00 + 0.08) * tot
fig.set_size_inches(10.0, height)
#
#--- save the plot in png format
#
plt.savefig('out.png', format='png', dpi=100)
def plot_step_delta(steps, delta, outname, title):
"""
plot a single data set on a single panel
Input: steps --- translation steps
delta --- sim temperature difference before and after translation
outname --- the name of output file
title --- title of the plot
Output: png plot named <outname>
"""
fsize = 14 #--- font size
fweight = 'bold' #--- font weight
psize = 3.0 #--- plotting point size
marker = '.' #--- marker shape
pcolor = 7 #--- color of the point
lcolor = 4 #--- color of the fitted lin
lsize = 3.0 #--- fitted line width
resolution = 300 #--- the resolution of the plot
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
mpl.rcParams['font.weight'] = fweight
mpl.rcParams['axes.linewidth'] = 2
#set(0,'defaultlinelinewidth',8)
props = font_manager.FontProperties(size=12)
plt.subplots_adjust(hspace=0.05)
[xmin, xmax, ymin, ymax] = set_min_max(steps, delta)
ymin = -5
ymax = 20
#
#--- set plotting range
#
plt.subplot(111)
xlim((xmin, xmax))
ylim((ymin, ymax))
#
#--- plot data
#
plt.plot(steps, delta, color='fuchsia', marker='*', markersize=psize, lw=0)
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(steps, delta)
lslope = '%2.3f' % (round(slope * 10000, 3))
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color=colorList[lcolor], lw=lsize)
label = 'Slope: ' + str(lslope) + ' ($^o$C / 10$^4$ steps)'
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.05 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.10 * ydiff
xpos3 = xmax - 0.20 * xdiff
ypos3 = ymax + 0.005 * ydiff
xpos4 = xmin + 0.05 * xdiff
plt.text(xpos, ypos, label, size=fsize)
#
#--- label axes
#
yname = '$\Delta$ T ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- label x axis
#
xname = 'Translation Steps'
plt.xlabel(xname, size=fsize, weight=fweight)
#
#--- title
#
plt.text(xpos3, ypos3, title, size=fsize)
plt.text(xpos4, ypos3, 'TSC Motor Temp vs. Move Distance', size=fsize)
#
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_multi_entries(xmin, xmax, ymin, ymax, xSets, ySets, xname, yname, entLabels, outname, yerror = 0,fsize = 9, psize = 2.0,lsize=0, resolution=100, linefit=0, connect=0):
"""
This function plots multiple data in a single panel.
Input: xmin, xmax, ymin, ymax: plotting area
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
xname: a name of x-axis
yname: a name of y-axis
entLabels: a list of the names of each data
outname: a name of plotting file
yerror: a list of lists of y error, if it is '0', no error bar, default = 0
fsize: font size, default = 9
psize: plotting point size, default = 2.0
lsize: fitted line width, default = 1
resolution: plotting resolution in dpi
linefit --- if it is 1, fit a line estimated by robust method
connect: connected line size. if it is '0', no connected line
Output: a png plot: out.png
"""
colorList = ('green', 'blue', 'red', 'lime', 'line', 'yellow', 'maroon', 'black', 'fushia', 'olive')
markerList = ('o', '*', '+', '^', 's', 'D', '1', '2', '3', '4')
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.08)
#
#---- set a panel
#
ax = plt.subplot(111)
ax.set_autoscale_on(False) #---- these three may not be needed for the new pylab, but
ax.set_xbound(xmin,xmax) #---- they are necessary for the older version to set
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
tot = len(entLabels)
#
#--- start plotting each data set
#
lnamList = []
for i in range(0, tot):
xdata = xSets[i]
ydata = ySets[i]
color = colorList[i]
marker = markerList[0]
label = entLabels[i]
if tot > 1:
lnam = 'p' + str(i)
lnamList.append(lnam)
exec('%s, = plt.plot(xdata, ydata, color="%s", lw =lsize , marker="%s", markersize=3, label=entLabels[i])' %(lnam, color, marker))
else:
#
#--- if there is only one data set, ignore legend
#
plt.plot(xdata, ydata, color=color, lw =connect , marker='o', markersize=psize)
if yerror != 0:
p, = plt.errorbar(xdata, ydata, yerr=yerror[i], lw = 0, elinewidth=1)
if linefit > 0:
(sint, slope,serror) = robust.robust_fit(xdata, ydata)
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax],[start,stop], color=color, lw =lsize )
#
#--- add legend
#
if tot > 1:
line = '['
for ent in lnamList:
if line == '[':
line = line + ent
else:
line = line +', ' + ent
line = line + ']'
leg = eval("legend(%s, entLabels, prop=props)" % (line))
leg.get_frame().set_alpha(0.5)
ax.set_xlabel(xname, size=fsize)
ax.set_ylabel(yname, size=fsize)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5.0in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_multi_panel(xmin,
xmax,
yMinSets,
yMaxSets,
xSets,
ySets,
xname,
yname,
entLabels,
outname,
yerror=0,
fsize=9,
psize=2.0,
marker='o',
pcolor=7,
lcolor=7,
lsize=0,
resolution=100,
linefit=0,
connect=0):
"""
This function plots multiple data in separate panels
Input: xmin, xmax plotting range of x axis
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
yMinSets: a list of ymin
yMaxSets: a list of ymax
xname: x axis label
yname: y axis label
entLabels: a list of the names of each data
outname: a name of plotting file
yerror: a list of lists of error on y, or if it is '0' no error bar on y, default = 0
fsize: font size, default = 9
psize: plotting point size, default = 2.0
marker: marker shape, defalut = 'o'
pcolor: color of the point, default= 7 ---> 'black'
lcolor: color of the fitted line, default = 7 ---> 'black'
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia','lime', 'maroon', 'black', 'olive', 'yellow')
lsize: fitted line width, defalut = 1
resolution: plotting resolution in dpi, default = 100
linefit: if 1, linear line is fitted, default: 0
connect: connected line size. if it is '0', no connected line
Output: a png plot: outname
"""
#
#--- set line color list
#
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia', 'lime', 'maroon',
'black', 'olive', 'yellow')
#
#--- clean up the plotting device
#
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.08)
tot = len(entLabels)
#
#--- start plotting each data
#
for i in range(0, tot):
axNam = 'ax' + str(i)
#
#--- setting the panel position
#
j = i + 1
if i == 0:
line = str(tot) + '1' + str(j)
else:
line = str(tot) + '1' + str(j) + ', sharex=ax0'
line = str(tot) + '1' + str(j)
exec("%s = plt.subplot(%s)" % (axNam, line))
exec("%s.set_autoscale_on(False)" % (
axNam)) #---- these three may not be needed for the new pylab, but
exec("%s.set_xbound(xmin,xmax)" %
(axNam)) #---- they are necessary for the older version to set
exec("%s.set_xlim(xmin=xmin, xmax=xmax, auto=False)" % (axNam))
exec("%s.set_ylim(ymin=yMinSets[i], ymax=yMaxSets[i], auto=False)" %
(axNam))
xdata = xSets[i]
ydata = ySets[i]
#
#---- actual data plotting
#
p, = plt.plot(xdata,
ydata,
color=colorList[pcolor],
marker=marker,
markersize=psize,
lw=connect)
if yerror != 0:
p, = plt.errorbar(xdata, ydata, yerr=yerror[i], lw=0, elinewidth=1)
if linefit > 0:
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
start = sint + slope * xmin
stop = sint + slope * xmax
p, = plt.plot([xmin, xmax], [start, stop],
color=colorList[lcolor],
lw=lsize)
#
#--- add legend
#
leg = legend([p], [entLabels[i]], prop=props, loc=2)
leg.get_frame().set_alpha(0.5)
exec("%s.set_ylabel(yname, size=fsize)" % (axNam))
#
#--- add x ticks label only on the last panel
#
for i in range(0, tot):
ax = 'ax' + str(i)
if i != tot - 1:
exec("line = %s.get_xticklabels()" % (ax))
for label in line:
label.set_visible(False)
else:
pass
xlabel(xname)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
height = (2.00 + 0.08) * tot
fig.set_size_inches(10.0, height)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def multi_section_linear_fit(x, y, xmin, xmax, bpoints, snum=100, shift=0):
"""
compute two line fit on a data and return lists of fitted line data
input: x --- independent data
y --- dependent data
xmin --- min of x
xmax --- max of x
bpoints --- a list of breaking point e.g, [2000]
snum --- numbers of data points to return
shift --- whether shift data. useful when x is far from 0
output: int_list --- a list of intercept values
slope_list --- a list of slope values
serr_list --- a list of errors of slope
xa_list --- a list of x points for the fitted line
ya_list --- a list of y points for the fitted line
"""
#
#--- add xmax as the last "breaking" point
#
bsets = []
for ent in bpoints:
bsets.append(ent)
bsets.append(xmax)
bpnum = len(bsets)
#
#--- separate data into sections
#
xs = []
ys = []
for k in range(0, bpnum):
xs.append([])
ys.append([])
#
#--- when the x is far from 0, robust method does not work well;
#--- so add "shift" (possibly negative) to make the data near 0
#
for i in range(0, len(x)):
for k in range(0, bpnum):
if x[i] <= bsets[k]:
xs[k].append(x[i] + shift)
ys[k].append(y[i])
break
#
#--- compute intercept and slope for each section
#
int_list = []
slope_list = []
serr_list = []
xa_list = []
ya_list = []
for k in range(0, bpnum):
#
#--- if the numbers of the data is too low, skip the section
#
if len(xs[k]) < 3:
continue
try:
(sint, slope, serror) = robust.robust_fit(xs[k], ys[k])
except:
sint = 0.0
slope = 0.0
serror = 0.0
int_list.append(sint)
slope_list.append(slope)
serr_list.append(serror)
#
#--- create plotting data sets
#
smin = min(xs[k])
smax = max(xs[k])
step = (smax - smin) / float(snum)
if k > 0:
add = bsets[k - 1] + shift
else:
add = 0
tx_list = []
ty_list = []
for j in range(0, snum):
tx = step * j + add
ty = sint + slope * tx
#
#--- shift back x value
#
tx -= shift
tx_list.append(tx)
ty_list.append(ty)
xa_list.append(tx_list)
ya_list.append(ty_list)
return [int_list, slope_list, serr_list, xa_list, ya_list]
def plot_data(sdata, mdata, year, msid, oname, ymin, ymax, ydrange, msid_list,
lupdate):
"""
create two panel plots for msid vs sun angle and its deviation
input: sdata --- a list of sun angle data
mdata --- a list of msid data (mid/min/max)
year --- year of the plot
msid --- msid
oname --- output name
ymin --- y min of the first plot
ymax --- y max of the first plot
ydrange --- the range of the deviation y axis
msid_list --- msid list
lupdate --- if 1, update y plotting range.
output: oname in png format
"""
plt.close('all')
fig, ax = plt.subplots(1, figsize=(8, 6))
props = font_manager.FontProperties(size=14)
mpl.rcParams['font.size'] = 14
mpl.rcParams['font.weight'] = 'bold'
xmin = 40
xmax = 170
if ymax == -999:
[ymin, ymax, ypos] = set_y_plot_range(mdata)
#
#--- since we want to all years to be in the same plotting range, this scripts adjust
#--- the plotting range. you may need to run a couple of times for the full range to
#--- adjust plotting range for the all plot
#
[ymin, ymax, ydev] = update_yrange(msid_list,
msid,
ymin=ymin,
ymax=ymax,
ydev=ydrange)
else:
if lupdate == 2:
[ymint, ymaxt, ypos] = set_y_plot_range(mdata)
mchk = 0
if ymint < ymin:
ymin = ymint
mchk = 1
if ymaxt > ymaxt:
ymax = ymaxt
mchk = 1
if mchk == 1:
[ymin, ymax, ydev] = update_yrange(msid_list,
msid,
ymin=ymin,
ymax=ymax,
ydev=drange)
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax1 = plt.subplot(211)
ax1.set_xlim(xmin, xmax)
ax1.set_ylim(ymin, ymax)
ax1.set_xlabel("Sun Angle")
ax1.set_ylabel(msid.upper())
#
#--- set the size of plot
#
fig.set_size_inches(10.0, 5.0)
fig.tight_layout()
#
#---- trending plots
#
points = ax1.scatter(sdata, mdata, marker='o', s=20, lw=0)
#
#---- envelope
#
period = 5
[xmc, ymc, xmb, ymb, xmt,
ymt] = create_trend_envelope(sdata, mdata, period)
#
#--- trending area
#
try:
ax1.fill_between(xmc,
ymb,
ymt,
facecolor='#00FFFF',
alpha=0.3,
interpolate=True)
except:
pass
#
#--- center moving average
#
ax1.plot(xmc, ymc, color='#E9967A', lw=4)
plt.text(50, ypos, str(year))
#
#---- derivative plot
#
[xd, yd, ad] = find_deriv(sdata, mdata, step=5)
[dymin, dymax, dypos] = set_y_plot_range(yd)
if lupdate == 2:
if abs(dymin) > abs(dymax):
dymax = abs(dymin)
ymax = ydrange
ymin = -1.0 * abs(ymax)
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax2 = plt.subplot(212)
ax2.set_xlim(xmin, xmax)
ax2.set_ylim(ymin, ymax)
ax2.set_xlabel("Sun Angle")
line = msid + '/ Deg'
ax2.set_ylabel(line)
points = ax2.scatter(xd, yd, marker='o', s=20, lw=0)
try:
try:
[a, b, e] = rbl.robust_fit(xd, yd)
except:
[a, b, e] = least_sq(xd, yd, 96)
except:
a = 0
b = 0
ys = a + b * xmin
ye = a + b * xmax
ax2.plot([xmin, xmax], [ys, ye], color='green', lw=3)
line = 'Slope: ' + "%3.3e" % (b)
mpl.rcParams['font.size'] = 12
plt.title('dy / d(sun angle)', loc='left')
plt.text(50, ypos, line)
#
#--- set the size of plot
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 10.0)
fig.tight_layout()
plt.savefig(oname, format='png', dpi=100)
plt.close('all')
def linear_fit(x, y):
"""
linear fitting function with -99999 error removal
Input: x --- independent variable array
y --- dependent variable array
Output: intc --- intercept
slope--- slope
"""
#
#--- first remove error entries
#
sum = 0
sum2 = 0
tot = 0
for i in range(0, len(y)):
if y[i] > 0:
sum += y[i]
sum2 += y[i] * y[i]
tot += 1
if tot > 0:
avg = sum / tot
sig = math.sqrt(sum2 / tot - avg * avg)
else:
avg = 3.0
lower = 0.0
upper = avg + 2.0
xn = []
yn = []
for i in range(0, len(x)):
# if (y[i] > 0) and (y[i] < yupper): #--- removing -99999/9999 error
if (y[i] > lower) and (y[i] < upper):
xn.append(x[i])
yn.append(y[i])
if len(yn) > 10:
# [intc, slope, serr] = robust.robust_fit(xn, yn, iter=50)
[intc, slope, serr] = robust.robust_fit(xn, yn, iter=1)
else:
[intc, slope, serr] = [0, 0, 0]
#
#--- modify array to numpy array
#
# d = numpy.array(xn)
# v = numpy.array(yn)
#
#--- kmpfit
#
# param = [0, 1]
# fitobj = kmpfit.Fitter(residuals=residuals, data=(d,v))
# fitobj.fit(params0=param)
#
# [intc, slope] = fitobj.params
# [ierr, serr] = fitobj.stderr
#
#--- chauvenet exclusion of outlyers and linear fit
#
# [intc, slope, ierr, serr] = chauv.run_chauvenet(d,v)
return [intc, slope, 0.0, serr]
def plot_data(x, y, xmin, xmax, ymin, ymax, inst, ychoice):
"""
plot data
input: x --- a list of independent variable
y --- a list of dependent variable
xmin --- x min
xmax --- x max
ymin --- y min
ymax --- y max
inst --- instrument name
ychoice --- y or z
output: <web_dir>/Plots/inst_<ychoice>.png
"""
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = 16
props = font_manager.FontProperties(size=16)
#
#--- set plotting range
#
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin,xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
#
#--- plot data
#
plt.plot(x, y, color='blue', marker='.', markersize=8, lw=0)
#
#--- put y = 0 line
#
plt.plot([xmin, xmax], [0, 0], color='black', linestyle='-.', lw=1)
#
#--- fit a line
#
(sint, slope, serr) = robust.robust_fit(x, y)
ybeg = sint + slope * xmin
yend = sint + slope * xmax
plt.plot([xmin, xmax], [ybeg, yend], color='red', lw=2)
#
#--- add text
#
line = 'Slope: %3.2f' % (slope)
xpos = xmin + 0.05 * (xmax - xmin)
ypos = 1.6
plt.text(xpos, ypos, line, color='red')
plt.xlabel('Time (Year)')
ylabel = ychoice.upper() + ' Axis Error (arcsec)'
plt.ylabel(ylabel)
#
#--- save the plot in png format
#
width = 10.0
height = 5.0
resolution = 200
outname = web_dir + 'Plots/' + inst + '_' + ychoice + '.png'
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(width, height)
plt.tight_layout()
plt.savefig(outname, format='png', dpi=resolution)
plt.close('all')
def plot_single_panel(xmin,
xmax,
ymin,
ymax,
xdata,
ydata,
yerror,
xname,
yname,
label,
outname,
fsize=9,
psize=2.0,
marker='o',
pcolor=7,
lcolor=7,
lsize=1,
resolution=100,
linefit=1,
connect=0):
"""
plot a single data set on a single panel
Input: xmin --- min x
xmax --- max x
ymin --- min y
ymax --- max y
xdata --- independent variable
ydata --- dependent variable
yerror --- error in y axis; if it is '0', no error bar
xname --- x axis label
ynane --- y axis label
label --- a text to indecate what is plotted
outname --- the name of output file
fsize --- font size, default = 9
psize --- plotting point size, default = 2.0
marker --- marker shape, defalut = 'o'
pcolor --- color of the point, default= 7 ---> 'black'
lcolor --- color of the fitted line, default = 7 ---> 'black'
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia','lime', 'maroon', 'black', 'olive', 'yellow')
lsize: fitted line width, defalut = 1
resolution-- the resolution of the plot in dpi
linefit --- if it is 1, fit a line estimated by robust method
connect --- if it is > 0, lsize data point with a line, the larger the value thinker the line
Output: png plot named <outname>
"""
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon',
'black', 'yellow', 'olive')
#
#--- fit line --- use robust method
#
if linefit == 1:
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
lslope = '%2.3f' % (round(slope, 3))
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
#
#--- set plotting range
#
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin, xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
#
#--- plot data
#
plt.plot(xdata,
ydata,
color=colorList[pcolor],
marker=marker,
markersize=psize,
lw=connect)
#
#--- plot error bar
#
if yerror != 0:
plt.errorbar(xdata, ydata, yerr=yerror, lw=0, elinewidth=1)
#
#--- plot fitted line
#
if linefit == 1:
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop],
color=colorList[lcolor],
lw=lsize)
#
#--- label axes
#
plt.xlabel(xname, size=fsize)
plt.ylabel(yname, size=fsize)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.5 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.08 * ydiff
if linefit == 1:
label = label + ': Slope: ' + str(lslope)
plt.text(xpos, ypos, label, size=fsize)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_single_panel(xmin, xmax, ymin, ymax, xdata, ydata, yerror, xname, yname, label, outname, fsize = 9, psize = 2.0, marker = 'o', pcolor =7, lcolor=7,lsize=1, resolution=100, linefit=1, connect=0):
"""
plot a single data set on a single panel
Input: xmin --- min x
xmax --- max x
ymin --- min y
ymax --- max y
xdata --- independent variable
ydata --- dependent variable
yerror --- error in y axis; if it is '0', no error bar
xname --- x axis label
ynane --- y axis label
label --- a text to indecate what is plotted
outname --- the name of output file
fsize --- font size, default = 9
psize --- plotting point size, default = 2.0
marker --- marker shape, defalut = 'o'
pcolor --- color of the point, default= 7 ---> 'black'
lcolor --- color of the fitted line, default = 7 ---> 'black'
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia','lime', 'maroon', 'black', 'olive', 'yellow')
lsize: fitted line width, defalut = 1
resolution-- the resolution of the plot in dpi
linefit --- if it is 1, fit a line estimated by robust method
connect --- if it is > 0, lsize data point with a line, the larger the value thinker the line
Output: png plot named <outname>
"""
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- fit line --- use robust method
#
if linefit == 1:
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
lslope = '%2.3f' % (round(slope, 3))
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
#
#--- set plotting range
#
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin,xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
#
#--- plot data
#
plt.plot(xdata, ydata, color=colorList[pcolor], marker=marker, markersize=psize, lw = connect)
#
#--- plot error bar
#
if yerror != 0:
plt.errorbar(xdata, ydata, yerr=yerror, lw = 0, elinewidth=1)
#
#--- plot fitted line
#
if linefit == 1:
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color=colorList[lcolor], lw = lsize)
#
#--- label axes
#
plt.xlabel(xname, size=fsize)
plt.ylabel(yname, size=fsize)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.5 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.08 * ydiff
if linefit == 1:
label = label + ': Slope: ' + str(lslope)
plt.text(xpos, ypos, label, size=fsize)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plotPanel(xmin, xmax, yMinSets, yMaxSets, xSets, ySets, eSets, xname, yname, entLabels, ydiv):
"""
This function plots multiple data in separate panels
Input: xmin, xmax, ymin, ymax: plotting area
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
eSets: a list of lists containing error values of y-axis
yMinSets: a list of ymin
yMaxSets: a list of ymax
entLabels: a list of the names of each data
ydiv: a location of dividing spot
Output: a png plot: out.png
"""
#
#--- set line color list
#
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- clean up the plotting device
#
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = 13
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.06)
tot = len(entLabels)
#
#--- start plotting each data
#
for i in range(0, len(entLabels)):
axNam = 'ax' + str(i)
#
#--- setting the panel position
#
j = i + 1
if i == 0:
line = str(tot) + '1' + str(j)
else:
line = str(tot) + '1' + str(j) + ', sharex=ax0'
line = str(tot) + '1' + str(j)
exec "%s = plt.subplot(%s)" % (axNam, line)
exec "%s.set_autoscale_on(False)" % (axNam) #---- these three may not be needed for the new pylab, but
exec "%s.set_xbound(xmin,xmax)" % (axNam) #---- they are necessary for the older version to set
exec "%s.set_xlim(xmin=xmin, xmax=xmax, auto=False)" % (axNam)
exec "%s.set_ylim(ymin=yMinSets[i], ymax=yMaxSets[i], auto=False)" % (axNam)
#
#--- since the cti seems evolving after year <ydiv>, fit two different lines before and after that point
#
xdata = xSets[i]
ydata = ySets[i]
edata = eSets[i]
xdata1 = []
ydata1 = []
edata1 = []
xdata2 = []
ydata2 = []
edata2 = []
for k in range(0, len(xdata)):
if xdata[k] < ydiv:
xdata1.append(xdata[k])
ydata1.append(ydata[k])
edata1.append(edata[k])
else:
xdata2.append(xdata[k])
ydata2.append(ydata[k])
edata2.append(edata[k])
#
#---- actual data plotting
#
p, = plt.plot(xdata, ydata, color=colorList[i], marker='*', markersize=4.0, lw =0)
errorbar(xdata, ydata, yerr=edata, color=colorList[i], markersize=4.0, fmt='*')
#
#--- fitting straight lines with robust method and plot the results
#
xdata1 = numpy.array(xdata)
ydata1 = numpy.array(ydata)
edata1 = numpy.array(edata)
(intc, slope, err) = robust.robust_fit(xdata1, ydata1)
ystart = intc + slope * 2000
ystop = intc + slope * xmax
lxdata = [2000, xmax]
lydata = [ystart, ystop]
p, = plt.plot(lxdata, lydata, color=colorList[i], marker='', markersize=1.0, lw =2)
#
#--- add legend
#
lslope = round(slope, 3)
line = entLabels[i] + ' Slope: ' + str(lslope)
leg = legend([p], [line], prop=props, loc=2)
leg.get_frame().set_alpha(0.5)
exec "%s.set_ylabel(yname, size=8)" % (axNam)
#
#--- add x ticks label only on the last panel
#
for i in range(0, tot):
ax = 'ax' + str(i)
if i != tot-1:
exec "line = %s.get_xticklabels()" % (ax)
for label in line:
label.set_visible(False)
else:
pass
xlabel(xname)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
height = (2.00 + 0.08) * tot
fig.set_size_inches(10.0, height)
#
#--- save the plot in png format
#
plt.savefig('out.png', format='png', dpi=100)
def plot_multi_panel(xmin, xmax, yMinSets, yMaxSets, xSets, ySets, xname, yname, entLabels, outname, yerror=0, fsize = 9, psize = 2.0, marker = 'o', pcolor =7, lcolor=7,lsize=0, resolution=100, linefit=0, connect=0):
"""
This function plots multiple data in separate panels
Input: xmin, xmax plotting range of x axis
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
yMinSets: a list of ymin
yMaxSets: a list of ymax
xname: x axis label
yname: y axis label
entLabels: a list of the names of each data
outname: a name of plotting file
yerror: a list of lists of error on y, or if it is '0' no error bar on y, default = 0
fsize: font size, default = 9
psize: plotting point size, default = 2.0
marker: marker shape, defalut = 'o'
pcolor: color of the point, default= 7 ---> 'black'
lcolor: color of the fitted line, default = 7 ---> 'black'
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia','lime', 'maroon', 'black', 'olive', 'yellow')
lsize: fitted line width, defalut = 1
resolution: plotting resolution in dpi, default = 100
linefit: if 1, linear line is fitted, default: 0
connect: connected line size. if it is '0', no connected line
Output: a png plot: outname
"""
#
#--- set line color list
#
colorList = ('blue', 'red', 'green', 'aqua', 'fuchsia','lime', 'maroon', 'black', 'olive', 'yellow')
#
#--- clean up the plotting device
#
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = fsize
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.08)
tot = len(entLabels)
#
#--- start plotting each data
#
for i in range(0, tot):
axNam = 'ax' + str(i)
#
#--- setting the panel position
#
j = i + 1
if i == 0:
line = str(tot) + '1' + str(j)
else:
line = str(tot) + '1' + str(j) + ', sharex=ax0'
line = str(tot) + '1' + str(j)
exec "%s = plt.subplot(%s)" % (axNam, line)
exec "%s.set_autoscale_on(False)" % (axNam) #---- these three may not be needed for the new pylab, but
exec "%s.set_xbound(xmin,xmax)" % (axNam) #---- they are necessary for the older version to set
exec "%s.set_xlim(xmin=xmin, xmax=xmax, auto=False)" % (axNam)
exec "%s.set_ylim(ymin=yMinSets[i], ymax=yMaxSets[i], auto=False)" % (axNam)
xdata = xSets[i]
ydata = ySets[i]
#
#---- actual data plotting
#
p, = plt.plot(xdata, ydata, color=colorList[pcolor], marker= marker, markersize=psize, lw =connect)
if yerror != 0:
p, = plt.errorbar(xdata, ydata, yerr=yerror[i], lw = 0, elinewidth=1)
if linefit > 0:
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
start = sint + slope * xmin
stop = sint + slope * xmax
p, = plt.plot([xmin, xmax],[start,stop], color=colorList[lcolor], lw =lsize)
#
#--- add legend
#
leg = legend([p], [entLabels[i]], prop=props, loc=2)
leg.get_frame().set_alpha(0.5)
exec "%s.set_ylabel(yname, size=fsize)" % (axNam)
#
#--- add x ticks label only on the last panel
#
for i in range(0, tot):
ax = 'ax' + str(i)
if i != tot-1:
exec "line = %s.get_xticklabels()" % (ax)
for label in line:
label.set_visible(False)
else:
pass
xlabel(xname)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
height = (2.00 + 0.08) * tot
fig.set_size_inches(10.0, height)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_sim_temp_data(xmin, xmax, simtx, simtl, simth, mxs, mys, mxe, mye,\
delta, stime, angle, outname, yind, title,skip):
"""
plot sim trend, temp delta, and pitch angle trends
Input: xmin --- starting date, either in year or yday
xmax --- ending date, either in year or yday
simtx --- time in either year or yday
simtl --- starting sim temperature
simth --- ending sim temperature
mxs --- moving average time
mys --- moving average of simtl
mye --- moving average of simth
delta --- <sim ending temp> - <sim starting temp>
stime --- time in either year or yday of picthc angle data
angle --- pitch angle
outname --- output file name
yind --- whether this is a full range plot or yearly plot
title --- title of the plot
skip --- if 1, skip moving averge plots
Output: png plot named <outname>
"""
#
#--- several setting for plotting
#
fsize = 14 #--- font size
fweight = 'bold' #--- font weight
psize = 3.0 #--- plotting point size
marker = '.' #--- marker shape
pcolor = 7 #--- color of the point
lcolor = 4 #--- color of the fitted lin
lsize = 3.0 #--- fitted line width
resolution = 300 #--- the resolution of the plot
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
mpl.rcParams['font.weight'] = fweight
mpl.rcParams['axes.linewidth'] = 2
#set(0,'defaultlinelinewidth',8)
props = font_manager.FontProperties(size=12)
plt.subplots_adjust(hspace=0.05)
#
#--- set grid to 3 rows or height rtio 3:1:1
#
gs = gridspec.GridSpec(3, 1, height_ratios=[3, 1, 1])
#
#
#--- first panel: moter temperature trend ------------------------------
#
#
#---- set ymin and ymax
#
ymin = -40
ymax = 60
#
#--- set plotting range
#
#plt.subplot(311)
ax0 = plt.subplot(gs[0])
line = ax0.get_xticklabels()
for label in line:
label.set_visible(False)
xlim((xmin, xmax))
ylim((ymin, ymax))
#
#--- plot data
#
plt.plot(simtx,
simtl,
color=colorList[0],
marker=marker,
markersize=psize,
lw=0)
plt.plot(simtx,
simth,
color=colorList[2],
marker=marker,
markersize=psize,
lw=0)
for i in range(0, len(simtx)):
xset = [simtx[i], simtx[i]]
yset = [simtl[i], simth[i]]
plt.plot(xset, yset, color=colorList[3], marker='', markersize=0, lw=1)
#
#--- plot moving average
#
if skip == 0:
plt.plot(mxs, mys, color=colorList[0], marker='', markersize=0, lw=2)
plt.plot(mxe, mye, color=colorList[2], marker='', markersize=0, lw=2)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.05 * xdiff
ydiff = ymax - ymin
ypos1 = ymax - 0.08 * ydiff
ypos2 = ymax - 0.12 * ydiff
xpos3 = xmax - 0.20 * xdiff
ypos3 = ymax + 0.005 * ydiff
xpos4 = xmin + 0.05 * xdiff
val1 = numpy.mean(simtl)
val1 = '%2.2f' % round(val1, 2)
val2 = numpy.mean(simth)
val2 = '%2.2f' % round(val2, 2)
label = 'T Stop Average: ' + str(val2) + ' $^o$C'
plt.text(xpos, ypos1, label, size=fsize, color=colorList[2])
label = 'T Start Average: ' + str(val1) + ' $^o$C'
plt.text(xpos, ypos2, label, size=fsize, color=colorList[0])
plt.text(xpos3, ypos3, title, size=fsize)
plt.text(xpos4, ypos3, 'SIM TSC Moter Temperatures', size=fsize)
#
#--- label axes
#
yname = 'TSC Motor Temp ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#
#--- second panel: temperature delta trend -----------------------------
#
#
#--- set plotting range
#
ymin = -20
ymax = 20
#plt.subplot(312)
ax1 = plt.subplot(gs[1])
line = ax1.get_xticklabels()
for label in line:
label.set_visible(False)
xlim((xmin, xmax))
ylim((ymin, ymax))
#
#--- plot data
#
plt.plot(simtx,
delta,
color=colorList[0],
marker=marker,
markersize=3,
lw=0)
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(simtx, delta)
lslope = '%2.3f' % (round(slope, 3))
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color=colorList[lcolor], lw=lsize)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.1 * xdiff
ydiff = ymax - ymin
ypos = ymin + 0.10 * ydiff
label = 'Slope: ' + str(lslope)
plt.text(xpos, ypos, label, size=fsize)
#
#--- label axes
#
yname = '$\Delta$ T ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- third panel: pitch angle trend -------------------------------
#
#--- set plotting range
#
ymin = 0
ymax = 180
#plt.subplot(313)
plt.subplot(gs[2])
xlim((xmin, xmax))
ylim((ymin, ymax))
#
#--- plot data
#
plt.plot(stime, angle, color=colorList[4], marker='', markersize=0, lw=0.5)
#
#--- label axes
#
yname = 'Pitch Angle'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- label x axis
#
if yind == 0:
xname = 'Time (year)'
else:
xname = 'Time (yday)'
plt.xlabel(xname, size=fsize, weight=fweight)
#
#
#--- set the size of the plotting area in inch (width: 10.0in, height 15 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 15.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_sim_temp_data(xmin, xmax, simtx, simtl, simth, mxs, mys, mxe, mye, delta, stime, angle, outname, yind, title,skip):
"""
plot sim trend, temp delta, and pitch angle trends
Input: xmin --- starting date, either in year or yday
xmax --- ending date, either in year or yday
simtx --- time in either year or yday
simtl --- starting sim temperature
simth --- ending sim temperature
mxs --- moving average time
mys --- moving average of simtl
mye --- moving average of simth
delta --- <sim ending temp> - <sim starting temp>
stime --- time in either year or yday of picthc angle data
angle --- pitch angle
outname --- output file name
yind --- whether this is a full range plot or yearly plot
title --- title of the plot
skip --- if 1, skip moving averge plots
Output: png plot named <outname>
"""
#
#--- several setting for plotting
#
fsize = 14 #--- font size
fweight = 'bold' #--- font weight
psize = 3.0 #--- plotting point size
marker = '.' #--- marker shape
pcolor = 7 #--- color of the point
lcolor = 4 #--- color of the fitted lin
lsize = 3.0 #--- fitted line width
resolution = 300 #--- the resolution of the plot
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
mpl.rcParams['font.weight'] = fweight
mpl.rcParams['axes.linewidth'] = 2
#set(0,'defaultlinelinewidth',8)
props = font_manager.FontProperties(size=12)
plt.subplots_adjust(hspace=0.05)
#
#--- set grid to 3 rows or height rtio 3:1:1
#
gs = gridspec.GridSpec(3,1,height_ratios=[3,1,1])
#
#
#--- first panel: moter temperature trend ------------------------------
#
#
#---- set ymin and ymax
#
ymin = -40
ymax = 60
#
#--- set plotting range
#
#plt.subplot(311)
ax0 = plt.subplot(gs[0])
line = ax0.get_xticklabels()
for label in line:
label.set_visible(False)
xlim((xmin,xmax))
ylim((ymin,ymax))
#
#--- plot data
#
plt.plot(simtx, simtl, color=colorList[0], marker=marker, markersize=psize, lw = 0)
plt.plot(simtx, simth, color=colorList[2], marker=marker, markersize=psize, lw = 0)
for i in range (0, len(simtx)):
xset = [simtx[i], simtx[i]]
yset = [simtl[i], simth[i]]
plt.plot(xset, yset, color=colorList[3], marker='', markersize=0, lw = 1)
#
#--- plot moving average
#
if skip == 0:
plt.plot(mxs, mys, color=colorList[0], marker='', markersize=0, lw=2)
plt.plot(mxe, mye, color=colorList[2], marker='', markersize=0, lw=2)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.05 * xdiff
ydiff = ymax - ymin
ypos1 = ymax - 0.08 * ydiff
ypos2 = ymax - 0.12 * ydiff
xpos3 = xmax - 0.20 * xdiff
ypos3 = ymax + 0.005 * ydiff
xpos4 = xmin + 0.05 * xdiff
val1 = numpy.mean(simtl)
val1 = '%2.2f' %round(val1, 2)
val2 = numpy.mean(simth)
val2 = '%2.2f' %round(val2, 2)
label = 'T Stop Average: ' + str(val2) + ' $^o$C'
plt.text(xpos, ypos1, label, size=fsize, color=colorList[2])
label = 'T Start Average: ' + str(val1) + ' $^o$C'
plt.text(xpos, ypos2, label, size=fsize, color=colorList[0])
plt.text(xpos3, ypos3, title, size=fsize)
plt.text(xpos4, ypos3, 'SIM TSC Moter Temperatures', size=fsize)
#
#--- label axes
#
yname = 'TSC Motor Temp ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#
#--- second panel: temperature delta trend -----------------------------
#
#
#--- set plotting range
#
ymin = -20
ymax = 20
#plt.subplot(312)
ax1 = plt.subplot(gs[1])
line = ax1.get_xticklabels()
for label in line:
label.set_visible(False)
xlim((xmin,xmax))
ylim((ymin,ymax))
#
#--- plot data
#
plt.plot(simtx, delta, color=colorList[0], marker=marker, markersize=3, lw = 0)
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(simtx, delta)
lslope = '%2.3f' % (round(slope, 3))
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color=colorList[lcolor], lw = lsize)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.1 * xdiff
ydiff = ymax - ymin
ypos = ymin + 0.10 * ydiff
label = 'Slope: ' + str(lslope)
plt.text(xpos, ypos, label, size=fsize)
#
#--- label axes
#
yname = '$\Delta$ T ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- third panel: pitch angle trend -------------------------------
#
#--- set plotting range
#
ymin = 0
ymax = 180
#plt.subplot(313)
plt.subplot(gs[2])
xlim((xmin,xmax))
ylim((ymin,ymax))
#
#--- plot data
#
plt.plot(stime, angle, color=colorList[4], marker='', markersize=0, lw = 0.5)
#
#--- label axes
#
yname = 'Pitch Angle'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- label x axis
#
if yind == 0:
xname = 'Time (year)'
else:
xname = 'Time (yday)'
plt.xlabel(xname, size=fsize, weight=fweight)
#
#
#--- set the size of the plotting area in inch (width: 10.0in, height 15 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 15.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_data(sdata, mdata, year, msid, oname, ymin, ymax, ydrange, msid_list,
lupdate):
"""
create two panel plots for tephin vs msid and its deviation
input: sdata --- a list of tephin data
mdata --- a list of msid data (mid/min/max)
year --- year of the plot
msid --- msid
oname --- output name
ymin --- y min of the first plot
ymax --- y max of the first plot
ydrange --- the range of the deviation y axis
msid_list --- msid list
lupdate --- if 1, update y plotting range.
output: oname in png format
"""
plt.close('all')
fig, ax = plt.subplots(1, figsize=(8, 6))
props = font_manager.FontProperties(size=14)
mpl.rcParams['font.size'] = 14
mpl.rcParams['font.weight'] = 'bold'
xmin = 260
xmax = 360
if ymax == -999:
[ymin, ymax, ypos] = set_y_plot_range(mdata)
#
#--- since we want to all years to be in the same plotting range, this scripts adjust
#--- the plotting range. you may need to run a couple of times for the full range to
#--- adjust plotting range for the all plot
#
[ymin, ymax, ydev] = update_yrange(msid_list,
msid,
ymin=ymin,
ymax=ymax,
ydev=ydrange)
else:
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax1 = plt.subplot(211)
ax1.set_xlim(xmin, xmax)
ax1.set_ylim(ymin, ymax)
ax1.set_xlabel("5ephin (K)")
ax1.set_ylabel(msid.upper())
#
#--- set the size of plot
#
fig.set_size_inches(10.0, 5.0)
fig.tight_layout()
#
#---- trending plots
#
points = ax1.scatter(sdata, mdata, marker='o', s=4, lw=0)
#
#---- envelope
#
period = 1.0
[xmc, ymc, xmb, ymb, xmt,
ymt] = create_trend_envelope(sdata, mdata, period)
#
#--- trending area
#
try:
ax1.fill_between(xmc,
ymb,
ymt,
facecolor='#00FFFF',
alpha=0.3,
interpolate=True)
except:
pass
#
#--- center moving average
#
ax1.plot(xmc, ymc, color='#E9967A', lw=4)
plt.text(270, ypos, str(year))
#
#---- derivative plot
#
[xd, yd, ad] = find_deriv(sdata, mdata, 'xxx', step=20)
[dymin, dymax, dypos] = set_y_plot_range(yd)
if lupdate == 1:
if abs(dymin) > abs(dymax):
dymax = abs(dymin)
if dymax > ydrange:
update_yrange(msid_list, msid, ymin=ymin, ymax=ymax, ydev=dymax)
ydrange = dymax
ymax = ydrange
ymin = -1.0 * abs(ymax)
#
#---------------------------------------------------------
#---- temporarily set ymin <--> ymax value (Jan 24, 2018)
#
ymin = -50.0
ymax = 50.0
mc = re.search('sc', msid)
if mc is not None:
ymin = -300.0
ymax = 300.0
if msid in ['scp25gm', 'scp4gm', 'scp8gm']:
ymin = -3000.0
ymax = 3000.0
elif msid in ['sce150', 'sce300']:
ymin = -30000.0
ymax = 30000.0
#---------------------------------------------------------
ydiff = ymax - ymin
ypos = ymax - 0.1 * ydiff
ax2 = plt.subplot(212)
ax2.set_xlim(xmin, xmax)
ax2.set_ylim(ymin, ymax)
ax2.set_xlabel("5ephin (K)")
line = msid + '/ K'
ax2.set_ylabel(line)
points = ax2.scatter(xd, yd, marker='o', s=4, lw=0)
if mc is not None:
try:
#[xs, ys] = remove_extreme_vals(xd, yd, 96)
[xs, ys] = remove_extreme_vals(xd, yd, 75)
[a, b, e] = rbl.robust_fit(xs, ys)
except:
[a, b, e] = least_sq(xd, yd, remove=1)
else:
try:
[a, b, e] = rbl.robust_fit(xd, yd)
except:
[a, b, e] = least_sq(xd, yd)
#
#--- if b == 999, it means that it could not get the slope; so set it to 0
#
if b == 999.0:
a = 0
b = 0
ys = a + b * xmin
ye = a + b * xmax
ax2.plot([xmin, xmax], [ys, ye], color='green', lw=3)
line = 'Slope: ' + "%3.3e" % (b)
mpl.rcParams['font.size'] = 12
plt.title('dy / d(Temp)', loc='left')
plt.text(270, ypos, line)
#
#--- set the size of plot
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 10.0)
fig.tight_layout()
plt.savefig(oname, format='png', dpi=100)
plt.close('all')
def plot_step_delta(steps, delta, outname, title):
"""
plot a single data set on a single panel
Input: steps --- translation steps
delta --- sim temperature difference before and after translation
outname --- the name of output file
title --- title of the plot
Output: png plot named <outname>
"""
fsize = 14 #--- font size
fweight = 'bold' #--- font weight
psize = 3.0 #--- plotting point size
marker = '.' #--- marker shape
pcolor = 7 #--- color of the point
lcolor = 4 #--- color of the fitted lin
lsize = 3.0 #--- fitted line width
resolution = 300 #--- the resolution of the plot
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = fsize
mpl.rcParams['font.weight'] = fweight
mpl.rcParams['axes.linewidth'] = 2
#set(0,'defaultlinelinewidth',8)
props = font_manager.FontProperties(size=12)
plt.subplots_adjust(hspace=0.05)
[xmin, xmax, ymin, ymax ] = set_min_max(steps, delta)
ymin = -5
ymax = 20
#
#--- set plotting range
#
plt.subplot(111)
xlim((xmin,xmax))
ylim((ymin,ymax))
#
#--- plot data
#
plt.plot(steps, delta, color='fuchsia', marker='*', markersize=psize, lw = 0)
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(steps, delta)
lslope = '%2.3f' % (round(slope * 10000, 3))
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color=colorList[lcolor], lw = lsize)
label = 'Slope: ' + str(lslope) + ' ($^o$C / 10$^4$ steps)'
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.05 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.10 * ydiff
xpos3 = xmax - 0.20 * xdiff
ypos3 = ymax + 0.005 * ydiff
xpos4 = xmin + 0.05 * xdiff
plt.text(xpos, ypos, label, size=fsize)
#
#--- label axes
#
yname = '$\Delta$ T ($^o$C)'
plt.ylabel(yname, size=fsize, weight=fweight)
#
#--- label x axis
#
xname = 'Translation Steps'
plt.xlabel(xname, size=fsize, weight=fweight)
#
#--- title
#
plt.text(xpos3, ypos3, title, size=fsize)
plt.text(xpos4, ypos3, 'TSC Motor Temp vs. Move Distance', size=fsize)
#
#
#--- set the size of the plotting area in inch (width: 10.0in, height 5 in)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
def plot_panel(data, ylims, ylab, outname, lfit=0):
"""
plot sim twist and sim information trends
input: data --- data: [time, dy, dz, dthera] for sim twist plots
[time, sim_x, sim_y, sim_z, pithcamp, yawamp] for sim infor plot
ylims --- a list of y limits [(ymin, ymax),....]
ylab ----a list of ylabel
outname --- output file name (without png)
lfit --- the indicator to show whether to fit a line. 1: yes
output: <web_dir>/Plots/<outname>.png
"""
#
#--- data are separated into a few sections. here we set the end of the each
#--- section in fractional year. the last closing data is set to year 4000
#--- see b_period for the starting date (in fractional year)
#
s_period = b_period
r_len = len(b_period)
e_period = []
for k in range(1, r_len):
e_period.append(b_period[k])
e_period.append(4000.0)
plt.close('all')
dlen = len(ylab)
mlen = dlen - 1
#
#--- set panel parameters
#
plt.subplots_adjust(hspace=0.08)
props = font_manager.FontProperties(size=9)
#
#--- set xrange
#
[atime, xmin, xmax, xlabel, xtext] = set_x_range(data[0])
xrange = [xmin, xmax]
#
#--- plot each panel
#
for k in range(0, dlen):
j = k + 1
line = str(dlen) + '1' + str(j)
exec("ax%s = plt.subplot(%s)" % (str(k), line))
exec("ax%s.set_xlim(left=xmin, right=xmax, auto=False)" % (str(k)))
#
#--- if ymin and ymax are given, use them
#
if len(ylims) == dlen:
ymin = ylims[k][0]
ymax = ylims[k][1]
exec("ax%s.set_ylim(bottom=ymin, top=ymax, auto=False)" % (str(k)))
ydata = data[k + 1]
exec(
"ax%s.plot(atime, ydata, color='blue', marker='.', markersize=1, lw=0)"
% (str(k)))
#
#--- for the case that a fitting line is requested
if lfit == 1:
[a, b, e] = rfit.robust_fit(atime, ydata)
y1 = a + b * xmin
y2 = a + b * xmax
yrange = [y1, y2]
exec("ax%s.plot(xrange, yrange, color='red', lw=2)" % (str(k)))
ydiff = ymax - ymin
ytext = ymax - 0.1 * ydiff
line = "Slope: " + '%3.3f' % (round(b, 3))
plt.text(xtext, ytext, line)
elif lfit > 1:
for m in range(0, r_len):
[xrange, yrange, ytext, line] \
= fit_line_period(atime, ydata, b_period[m], e_period[m], m, ymin, ymax, bot=0)
exec("ax%s.plot(xrange, yrange, color='red', lw=2)" % (str(k)))
plt.text(xtext, ytext, line)
#
#--- y axis label
#
exec("ax%s.set_ylabel('%s')" % (str(k), ylab[k]))
#
#--- x axis label
#
exec('ax%s.set_xlabel("%s")' % (str(mlen), xlabel))
#
#--- add x ticks label only on the last panel
#
for k in range(0, dlen):
ax = 'ax' + str(k)
if k != mlen:
line = eval("%s.get_xticklabels()" % (ax))
for label in line:
label.set_visible(False)
else:
pass
#
#--- save the plot in a file
#
fig = matplotlib.pyplot.gcf()
height = 2.0 * dlen + 0.5
fig.set_size_inches(10.0, height)
outfile = web_dir + 'Plots/' + outname
plt.savefig(outfile, format='png', dpi=100.0)
def plotPanel(xmin, xmax, yMinSets, yMaxSets, xSets, ySets, xname, yname, entLabels, outname, psize=1.0):
"""
This function plots multiple data in separate panels
Input: xmin, xmax, ymin, ymax: plotting area
xSets: a list of lists containing x-axis data
ySets: a list of lists containing y-axis data
yMinSets: a list of ymin
yMaxSets: a list of ymax
entLabels: a list of the names of each data
Output: a png plot: out.png
"""
#
#--- set line color list
#
colorList = ('blue', 'green', 'red', 'aqua', 'lime', 'fuchsia', 'maroon', 'black', 'yellow', 'olive')
#
#--- clean up the plotting device
#
plt.close('all')
#
#---- set a few parameters
#
mpl.rcParams['font.size'] = 9
props = font_manager.FontProperties(size=9)
plt.subplots_adjust(hspace=0.08)
tot = len(entLabels)
#
#--- start plotting each data
#
for i in range(0, len(entLabels)):
axNam = 'ax' + str(i)
#
#--- setting the panel position
#
j = i + 1
if i == 0:
line = str(tot) + '1' + str(j)
else:
line = str(tot) + '1' + str(j) + ', sharex=ax0'
line = str(tot) + '1' + str(j)
exec "%s = plt.subplot(%s)" % (axNam, line)
exec "%s.set_autoscale_on(False)" % (axNam) #---- these three may not be needed for the new pylab, but
exec "%s.set_xbound(xmin,xmax)" % (axNam) #---- they are necessary for the older version to set
exec "%s.set_xlim(xmin=xmin, xmax=xmax, auto=False)" % (axNam)
exec "%s.set_ylim(ymin=yMinSets[i], ymax=yMaxSets[i], auto=False)" % (axNam)
xdata = xSets[i]
ydata = ySets[i]
#
#---- actual data plotting
#
p, = plt.plot(xdata, ydata, color=colorList[i], marker='.', markersize=psize, lw =0)
#
#---- compute fitting line
#
(intc, slope, berr) = robust.robust_fit(xdata, ydata)
cslope = str('%.4f' % round(slope, 4))
ystart = intc + slope * xmin
yend = intc + slope * xmax
plt.plot([xmin, xmax], [ystart, yend], color=(colorList[i+2]), lw=1)
#
#--- add legend
#
tline = entLabels[i] + ' Slope: ' + cslope
leg = legend([p], [tline], prop=props, loc=2)
leg.get_frame().set_alpha(0.5)
exec "%s.set_ylabel(yname, size=8)" % (axNam)
#
#--- add x ticks label only on the last panel
#
for i in range(0, tot):
ax = 'ax' + str(i)
if i != tot-1:
exec "line = %s.get_xticklabels()" % (ax)
for label in line:
label.set_visible(False)
else:
pass
xlabel(xname)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
height = (2.00 + 0.08) * tot
fig.set_size_inches(10.0, height)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=100)
def fit_line_period(x, y, x_start, x_stop, m, ymin, ymax, bot=0):
"""
fit a line on the given data section and return the result
input: x --- x data
y --- y data
x_start --- a list of the starting points
x_stop --- a list of the stopping points
m --- section position of the lists above
ymin --- y min
yax --- y max
bot --- an indicator of where to print the text. bot =1 to bottom side
output: xrange --- a list of start and stop position of the line in x
yrange --- a list of start and stop position of the line in y
ytext --- y position of the text
line --- a line to be printed
"""
dlen = len(x)
xn = []
yn = []
#
#--- select data for the limited range
#
for k in range(0, dlen):
if x[k] >= x_start and x[k] < x_stop:
if y[k] >= ymin and y[k] <= ymax:
xn.append(x[k])
yn.append(y[k])
try:
#
#--- compute the fitted line with robust method
#
[a, b, e] = rfit.robust_fit(list(xn), list(yn))
y1 = a + b * x_start
y2 = a + b * x_stop
xrange = [x_start, x_stop]
yrange = [y1, y2]
#
#--- set the text postion and create the text to be printed
#
ydiff = ymax - ymin
if bot == 0:
ytext = ymax - 0.1 * ydiff * (m + 1)
else:
ytext = ymax - 0.1 * ydiff * (m + 1) - 0.5 * ydiff
if x_start < 2000:
line = "Slope (%4.1f < year): %3.3f" % (x_stop, round(b, 3))
elif x_stop > 3000:
line = "Slope (year > %4.1f): %3.3f" % (x_start, round(b, 3))
else:
line = "Slope (%4.1f < year < %4.1f): %3.3f" % (x_start, x_stop,
round(b, 3))
#
#--- for the case the fitting failed
#
except:
ydiff = ymax - ymin
if bot == 0:
ytext = ymax - 0.1 * ydiff * (m + 1)
else:
ytext = ymax - 0.1 * ydiff * (m + 1) - 0.5 * ydiff
xrange = [0, 0]
yrange = [0, 0]
line = 'NA'
return [xrange, yrange, ytext, line]
def plot_single_panel(xmin, xmax, ymin, ymax, xdata, ydata, yerror, xname, yname, label, outname, resolution=100):
"""
plot a single data set on a single panel
Input: xmin --- min x
xmax --- max x
ymin --- min y
ymax --- max y
xdata --- independent variable
ydata --- dependent variable
yerror --- error in y axis
xname --- x axis label
ynane --- y axis label
label --- a text to indecate what is plotted
outname --- the name of output file
resolution-- the resolution of the plot in dpi
Output: png plot named <outname>
"""
#
#--- fit line --- use robust method
#
(sint, slope, serr) = robust.robust_fit(xdata, ydata)
lslope = '%2.3f' % (round(slope, 3))
#
#--- close everything opened before
#
plt.close('all')
#
#--- set font size
#
mpl.rcParams['font.size'] = 12
props = font_manager.FontProperties(size=9)
#
#--- set plotting range
#
ax = plt.subplot(111)
ax.set_autoscale_on(False)
ax.set_xbound(xmin,xmax)
ax.set_xlim(xmin=xmin, xmax=xmax, auto=False)
ax.set_ylim(ymin=ymin, ymax=ymax, auto=False)
#
#--- plot data
#
plt.plot(xdata, ydata, color='blue', marker='o', markersize=4.0, lw =0)
#
#--- plot error bar
#
plt.errorbar(xdata, ydata, yerr=yerror, lw = 0, elinewidth=1)
#
#--- plot fitted line
#
start = sint + slope * xmin
stop = sint + slope * xmax
plt.plot([xmin, xmax], [start, stop], color='red', lw = 2)
#
#--- label axes
#
plt.xlabel(xname)
plt.ylabel(yname)
#
#--- add what is plotted on this plot
#
xdiff = xmax - xmin
xpos = xmin + 0.5 * xdiff
ydiff = ymax - ymin
ypos = ymax - 0.08 * ydiff
label = label + ': Slope: ' + str(lslope)
plt.text(xpos, ypos, label)
#
#--- set the size of the plotting area in inch (width: 10.0in, height 2.08in x number of panels)
#
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(10.0, 5.0)
#
#--- save the plot in png format
#
plt.savefig(outname, format='png', dpi=resolution)
