def write2file(filename, string, verbosity=0):
output = open(filename, 'w')
output.write(string)
output.write('\n')
output.close()
if verbosity > 0:
mout.out("Line written to " + mcol.file + filename)
def showAll(verbosity=1):
if (verbosity > 0):
mout.out("showing all graphs"+" ... ",
printScript=True,
end='')
plt.show()
if (verbosity > 0):
mout.out("Done.")
def closeAll(verbosity=1):
if (verbosity > 0):
mout.out("closing all graphs"+" ... ",
printScript=True,
end='')
plt.close(fig='all')
if (verbosity > 0):
mout.out("Done.")
def hist2D(xdata,
ydata,
bins=10,
xlab='x',
ylab='y',
title=None,
filename=None,
show=True,
verbosity=2,
density=False,
printScript=False,
xmin=None,
xmax=None,
ymin=None,
ymax=None,
dpi=100,
figsize=[4.8, 6.4]):
if (verbosity > 0):
if title is not None:
mout.out("graphing " + mcol.varName + title + mcol.clear + " ... ",
printScript=printScript,
end='')
else:
mout.out("graphing ... ", printScript=printScript, end='')
many = any(isinstance(el, list) for el in ydata)
assert not many
if not any([thing is None for thing in [xmin, xmax, ymin, ymax]]):
range = [[xmin, xmax], [ymin, ymax]]
else:
range = None
graph, axis = plt.subplots(dpi=dpi, figsize=figsize)
plt.hist2d(xdata, ydata, bins=bins, range=range, density=density)
plt.xlabel(xlab)
plt.ylabel(ylab)
plt.suptitle(title)
if show:
plt.show()
if filename is not None:
if (verbosity > 0):
mout.out("saving as " + mcol.file + filename + mcol.clear +
" ... ",
end='')
plt.savefig(filename)
plt.close()
if (verbosity > 0):
mout.out("Done.")
def array2file(filename, list_of_things, append=False, verbosity=1):
if append:
output = open(filename, 'a')
else:
output = open(filename, 'w')
many = any(isinstance(el, list) for el in list_of_things)
if many:
counter = 0
for many_things in list_of_things:
string = ""
for thing in many_things:
string += str(thing)
string += " "
output.write(string)
output.write('\n')
counter += 1
output.close()
# mout.errorOut("Nested Lists Unsupported",fatal=True,code="mout.array2file")
else:
counter = 0
for thing in list_of_things:
try:
string = str(thing)
except:
mout.errorOut("Could not convert item to string.",
code=counter,
fatal=True)
output.write(string)
output.write('\n')
counter += 1
output.close()
if verbosity > 0:
mout.out(str(counter) + " lines written to " + mcol.file + filename)
def hist1D(ydata,
bins=10,
xlab='x',
ylab='y',
title=None,
filename=None,
show=True,
verbosity=2,
density=False,
printScript=False,
range=None):
if (verbosity > 0):
if title is not None:
mout.out("graphing " + mcol.varName + title + mcol.clear + " ... ",
printScript=printScript,
end='')
else:
mout.out("graphing ... ", printScript=printScript, end='')
many = any(isinstance(el, list) for el in ydata)
assert not many
plt.hist(ydata, bins=bins, range=range, density=density)
plt.xlabel(xlab)
plt.ylabel(ylab)
plt.suptitle(title)
if show:
plt.show()
if filename is not None:
if (verbosity > 0):
mout.out("saving as " + mcol.file + filename + mcol.clear +
" ... ",
end='')
plt.savefig(filename)
plt.close()
if (verbosity > 0):
mout.out("Done.")
def fit(xdata,
ydata,
rank=0,
verbosity=1,
printScript=False,
title="",
fitMin=None,
fitMax=None,
precision=4,
errorPrecision=2,
xUnit="",
yUnit="",
dataFile=None):
# if there are nested ydatas:
many = any(isinstance(el, list) for el in ydata)
if xdata is None:
if many:
xdata = [i for i in range(len(ydata[0]))]
else:
xdata = [i for i in range(len(ydata))]
if title is None: title = ""
# initialise arrays
combined_xdata = []
combined_ydata = []
combined_data = []
# check if multiple ydata sets
if not many:
# if just one set of data
for index, xpoint in enumerate(xdata):
if fitMin is not None and xpoint < fitMin:
continue
if fitMax is not None and xpoint > fitMax:
break
combined_xdata.append(xpoint)
combined_ydata.append(ydata[index])
else:
# loop over ydata sets
for data in ydata:
for index, ypoint in enumerate(data):
if fitMin is not None and xdata[index] < fitMin:
continue
if fitMax is not None and xdata[index] > fitMax:
break
combined_xdata.append(xdata[index])
combined_ydata.append(ypoint)
# get the number of datapoints
num_points = len(combined_ydata)
# user output
if verbosity > 0:
mout.out("fitting " + mcol.varName + title + mcol.clear + " (rank " +
str(rank) + ", " + str(num_points) + " points) " +
mcol.clear + "...",
printScript=printScript,
end=' ')
if fitMin is not None or fitMax is not None:
mout.out("fitrange=[" + str(fitMin) + ":" + str(fitMax) + "]",
printScript=False,
end=' ')
# the actual fitting:
coeffs, variance = np.polyfit(combined_xdata,
combined_ydata,
rank,
cov=True)
# user output
if verbosity > 0:
mout.out("Done.")
# get list of letters in the alphabet
alphabet_string = string.ascii_uppercase
# alphabet_string = string.ascii_lowercase
alphabet_list = list(alphabet_string)
# write out the function type:
if verbosity > 1:
mout.out(mcol.func + "f" + mcol.clear + "(" + mcol.arg + "x" +
mcol.clear + ") = ",
end='')
for i in range(rank, -1, -1):
if i == 0:
x_string = " "
elif i == 1:
x_string = mcol.arg + "x" + mcol.clear + " + "
else:
x_string = mcol.arg + "x^" + str(i) + mcol.clear + " + "
mout.out(mcol.varName + alphabet_list[rank - i] + x_string +
mcol.clear,
end='')
mout.out("")
# initialise arrays
vals = []
errs = []
# process the coefficients
for i in range(rank, -1, -1):
# append the current coefficient
vals.append(coeffs[i])
errs.append(np.sqrt(variance[i, i]))
if yUnit != "" and xUnit != "":
for i in range(rank, -1, -1):
# write out the results
unitString = yUnit
if i == 1:
unitString = unitString + "/(" + xUnit + ")"
elif i > 1:
unitString = unitString + "/(" + xUnit + "^" + str(i) + ")"
mout.varOut(alphabet_list[rank - i],
vals[i],
unit=unitString,
error=errs[i],
valCol=mcol.result,
precision=precision,
errorPrecision=errorPrecision,
printScript=printScript,
dataFile=dataFile,
verbosity=verbosity)
# get the resulting fit function
fit_func = np.poly1d(coeffs)
if rank == 0:
vals = vals[0]
errs = errs[0]
# return the necessary
return vals, errs, fit_func
def graph2D(xdata,
ydata,
fitFunc=None,
printScript=False,
ytitles=None,
fitTitle=None,
style=None,
filename=None,
show=True,
xmin=None,
xmax=None,
ymin=None,
ymax=None,
xlab='x',
ylab='y',
title=None,
subtitle=None,
verbosity=2,
colour=None,
yerrors=None,
xerrors=None,
alpha=1.0,
xticrot=None,
xticsize=None,
xSci=False,
ySci=False,
xLog=False,
yLog=False,
xtics=None,
ytics=None,
dpi=100,
figsize=[6.4, 4.8],
bar_width=0.8,
zeroaxis=False,
points=None):
# graph = plt.figure(dpi=dpi,figsize=figsize)
graph, axis = plt.subplots(dpi=dpi, figsize=figsize)
if (verbosity > 0):
if title is not None:
mout.out("graphing " + mcol.varName + title + mcol.clear + " ... ",
printScript=printScript,
end='')
else:
mout.out("graphing ... ", printScript=printScript, end='')
y_many = any(isinstance(el, list) for el in ydata)
if xdata is not None:
x_many = any(isinstance(el, list) for el in xdata)
else:
x_many = False
style_many = isinstance(style, list)
if xdata is None:
if y_many:
xdata = [i for i in range(len(ydata[0]))]
else:
xdata = [i for i in range(len(ydata))]
# plot the normal data
if y_many:
# ydata is a list of lists!
if ytitles is not None:
# for curve, label in zip(ydata,ytitles):
for index, curve in enumerate(ydata):
if x_many:
this_xdata = xdata[index]
else:
this_xdata = xdata
if style_many:
this_style = style[index]
else:
this_style = style
if ytitles[index] is None:
label = "ydata[" + str(index) + "]"
else:
label = ytitles[index]
if style is None:
if colour is None or colour[index] is None:
plt.plot(this_xdata, curve, label=label)
else:
plt.plot(this_xdata, curve, colour[index], label=label)
elif this_style == "bar":
if colour is None or colour[index] is None:
plt.bar(this_xdata,
curve,
align='center',
label=label,
alpha=alpha)
else:
plt.bar(this_xdata,
curve,
align='center',
label=label,
color=colour[index],
alpha=alpha)
else:
if colour is None or colour[index] is None:
plt.plot(this_xdata, curve, this_style, label=label)
else:
plt.plot(this_xdata,
curve,
colour[index] + this_style,
label=label)
else:
for index, curve in enumerate(ydata):
if x_many:
this_xdata = xdata[index]
else:
this_xdata = xdata
if style_many:
this_style = style[index]
else:
this_style = style
if this_style is None:
if colour is None or colour[index] is None:
plt.plot(this_xdata,
curve,
label="ydata[" + str(index) + "]")
else:
plt.plot(this_xdata,
curve,
colour[index],
label="ydata[" + str(index) + "]")
elif this_style == "bar":
if colour is None or colour[index] is None:
plt.bar(this_xdata,
curve,
align='center',
label="ydata[" + str(index) + "]",
alpha=alpha)
else:
plt.bar(this_xdata,
curve,
colour[index],
align='center',
label="ydata[" + str(index) + "]",
alpha=alpha)
else:
if colour is None or colour[index] is None:
plt.plot(this_xdata,
curve,
this_style,
label="ydata[" + str(index) + "]")
else:
plt.plot(this_xdata,
curve,
colour[index] + this_style,
label="ydata[" + str(index) + "]")
else:
if ytitles is not None:
label = ytitles
print(label)
else:
label = None
if colour is None:
colour = "k"
alpha = 0.5
# ydata is just a list!
if label is not None:
if style is None:
plt.plot(xdata, ydata, colour, label=label)
elif style == "bar":
plt.bar(xdata,
ydata,
color=colour,
label=label,
align='center',
alpha=alpha,
width=bar_width)
else:
plt.plot(xdata, ydata, colour + style, label=label)
else:
if style is None:
plt.plot(xdata, ydata, colour)
elif style == "bar":
plt.bar(xdata,
ydata,
color=colour,
align='center',
alpha=alpha,
width=bar_width)
else:
plt.plot(xdata, ydata, colour + style)
if xSci:
plt.ticklabel_format(axis='x', style='sci', scilimits=(0, 0))
if ySci:
plt.ticklabel_format(axis='y', style='sci', scilimits=(0, 0))
# plot the yerrorbars
if yerrors is not None:
if y_many:
for index, curve in enumerate(ydata):
if yerrors[index] is not None:
if style == "bar":
this_colour = "k"
if colour is None or colour[index] is None:
this_colour = None
else:
this_colour = colour[index]
if colour is None or colour[index] is None:
plt.errorbar(xdata,
curve,
yerrors[index],
fmt='none',
capsize=3,
capthick=2,
color='C' + str(index))
else:
plt.errorbar(xdata,
curve,
yerrors[index],
fmt='none',
capsize=3,
capthick=2,
color=colour[index])
else:
if style == "bar":
colour = "k"
if colour is None:
plt.errorbar(xdata,
ydata,
yerrors,
fmt='none',
capsize=3,
capthick=2,
color='C' + str(index),
colour="k")
else:
plt.errorbar(xdata,
ydata,
yerrors,
fmt='none',
color=colour,
capsize=3,
capthick=2)
# plot the xerrorbars
if xerrors is not None:
if y_many:
for index, curve in enumerate(ydata):
if xerrors[index] is not None:
if style == "bar":
this_colour = "k"
if colour is None or colour[index] is None:
this_colour = None
else:
this_colour = colour[index]
if colour is None or colour[index] is None:
plt.errorbar(xdata,
curve,
xerr=xerrors[index],
fmt='none',
capsize=3,
capthick=2,
color='C' + str(index))
else:
plt.errorbar(xdata,
curve,
xerr=xerrors[index],
fmt='none',
capsize=3,
capthick=2,
color=colour[index])
else:
if style == "bar":
colour = "k"
if colour is None:
plt.errorbar(xdata,
ydata,
xerr=xerrors,
fmt='none',
capsize=3,
capthick=2,
color='C' + str(index))
else:
plt.errorbar(xdata,
ydata,
xerr=xerrors,
fmt='none',
color=colour,
capsize=3,
capthick=2)
# plot extra points:
if points is not None:
y_many_points = any(isinstance(el, list) for el in points)
if y_many_points:
for pair in points:
plt.plot(pair[0], pair[1], 'ko')
else:
plt.plot(points[0], points[1], 'ko')
# plot the fitting function
if x_many:
this_xdata = xdata[0]
else:
this_xdata = xdata
if fitFunc is not None:
if fitTitle is None or fitTitle == "":
if ytitles is None or fitTitle == "":
plt.plot(this_xdata, fitFunc(this_xdata), 'k--')
else:
plt.plot(this_xdata,
fitFunc(this_xdata),
'k--',
label="f(x) " + str(fitFunc))
else:
plt.plot(this_xdata, fitFunc(this_xdata), 'k--', label=fitTitle)
plt.axis([xmin, xmax, ymin, ymax])
plt.xlabel(xlab)
plt.ylabel(ylab)
plt.suptitle(title)
if zeroaxis:
axis.axhline(y=0, color='k')
axis.axvline(x=0, color='k')
if xLog:
plt.xscale('log')
if yLog:
plt.yscale('log')
if xticrot is not None:
plt.xticks(rotation=xticrot)
if xticsize is not None:
plt.xticks(fontsize=xticsize)
if xtics is not None:
start, end = axis.get_xlim()
# print(start, end, xtics)
xtics = round((end - start) / xtics)
axis.xaxis.set_ticks(np.arange(start, end, xtics))
if ytics is not None:
start, end = axis.get_xlim()
ytics = round((end - start) / ytics)
axis.yaxis.set_ticks(np.arange(start, end, ytics))
if subtitle is not None:
plt.figtext(0.5, 0.91, subtitle, horizontalalignment='center')
if y_many or ytitles is not None:
plt.legend()
if show:
if (verbosity > 1):
mout.out("showing ... ", end='')
plt.show()
if filename is not None:
if (verbosity > 0):
mout.out("saving as " + mcol.file + filename + mcol.clear +
" ... ",
end='')
plt.savefig(filename)
plt.close(fig=graph)
if (verbosity > 0):
mout.out("Done.")