def SetScientificFmt(axis='y', min_order=-3, max_order=3):
"""
Scalar format for axes
======================
"""
# applies to current axis
fmt = ScalarFormatter(useOffset=True)
fmt.set_powerlimits((min_order, max_order))
if axis == 'y': gca().yaxis.set_major_formatter(fmt)
else: gca().xaxis.set_major_formatter(fmt)
def SetScientificFmt(axis='y', min_order=-3, max_order=3):
"""
Scalar format for axes
======================
"""
# applies to current axis
fmt = ScalarFormatter(useOffset=True)
fmt.set_powerlimits((min_order,max_order))
if axis=='y': gca().yaxis.set_major_formatter(fmt)
else: gca().xaxis.set_major_formatter(fmt)
def create_bar(filename, emfretmax, emfretmax_error, a, units):
# Creates x locations to place the bars
ind = arange(len(emfretmax))
fig, ax = subplots()
width = 0.35
unit_label = 'p'
if (units == 'u'):
#add micro symbol
unit_label = u"\u00B5"
unit_label = unit_label + 'M'
elif (units == 'n'):
#add nano symbol
unit_label = 'nM'
elif (units == 'p'):
#pico
unit_label = 'pM'
ax.bar(ind, emfretmax, width, color='r', yerr=emfretmax_error)
ax.set_ylabel("Em$_{FRETMAX}$", fontsize=14)
ax.set_xticks(ind + width / 2)
ax.set_xticklabels(a)
xlabel('Concentration of Donor [' + unit_label + ']')
gca().yaxis.set_major_formatter(ScalarFormatter(useMathText=True))
ax.ticklabel_format(axis='y', style='sci', scilimits=(0, 0))
savefig(filename, bbox_inches='tight', dpi=200)
def plot_best_light_curve(field_id, ccd_id):
field = pdb.Field(field_id, "R")
lc = get_best_light_curve(field, ccd_id)
fig = plt.figure(figsize=(15,5))
ax = fig.add_subplot(111)
lc.plot(ax)
#ax.yaxis.set_ticks([])
from pylab import ScalarFormatter
ax.yaxis.set_major_formatter(ScalarFormatter(False))
ax.set_xlabel("MJD", fontsize=20)
ax.set_ylabel("$R$ [mag]", fontsize=20)
fig.savefig("plots/new_detection_efficiency/example_light_curve_f{}_ccd{}.pdf".format(field.id, ccd_id), bbox_inches="tight")
def __init__(self, everyother=False):
self.everyother = everyother
ScalarFormatter.__init__(self)
# Plot throughput
# ax2 = ax1.twinx()
# ax2.plot(throughput_data, 'o-', color=paleblue, linewidth=2, markersize=8)
# Label the axis
ax1.set_title(label)
ax1.set_xlabel('Number of concurrent requests')
# ax2.set_ylabel('Requests per second')
ax1.set_ylabel('Milliseconds')
ax1.set_xticks(range(1, len(plot_labels) + 1, 1))
ax1.set_xticklabels(plot_labels[0::1])
fig.subplots_adjust(top=0.9, bottom=0.15, right=0.85, left=0.15)
# Turn off scientific notation for Y axis
ax1.yaxis.set_major_formatter(ScalarFormatter(False))
# Set the lower y limit to the match the first column
ax1.set_ylim(bottom=bp['boxes'][0].get_ydata()[0])
_, yend = ax1.get_ylim()
yend = int(yend)
step = 50
if yend < 50:
step = 5
print(yend)
if yend > 1000:
step = 100
if yend > 2000:
step = 200
if yend > 10000:
step = 500
def create_scatter(filename, result, x, y, a, stddev, i, units):
xx = linspace(
x.min(), x.max(), 50
) #so this returns 50 evenly spaced values between the start and stop points
yy = emfret(
result.params, xx,
a) #it uses each of these to calculate emfretmax (one per xx value)
z = linspace(x.min(), x.max(), 50)
#this plots all the values contained in Y
points = ['b.', 'r.', 'g.', 'c.',
'm.'] #colors are: Blue, Red, Green, Cyan, Magenta.
#Do not use yellow, too hard to see against white background
stddev_points = ['b_', 'r_', 'g_', 'c_',
'm_'] #will plot colored horizontal lines for std dev
line_style = ['b-', 'r-', 'g-', 'c-', 'm-'
] #uses dashes, but generally connects into a straight line
#tracks the number of colors used in the lists above. Rotate through this list as necessary
num_colors = len(points)
#note that markersize is completely arbitrary
#this plots the points of the given data, the calculated line is done below
plot(x, y, points[i % num_colors], markersize=15)
#plot the std dev ( point +/- std dev)
#again, markersize/width are arbitrary. Markeredgewith increases the size of the dashes used by expanding the border.
#the border is the same color as the interior of the marker, so it appears only the dashes got thicker
plot(x,
y - stddev,
stddev_points[i % num_colors],
markersize=7,
markeredgewidth=3)
plot(x,
y + stddev,
stddev_points[i % num_colors],
markersize=7,
markeredgewidth=3)
plot([x, x], [y - stddev, y + stddev],
line_style[i % num_colors],
linewidth=1) #this plots a vertical line between stddev values
unit_label = 'p'
if (units == 'u'):
#add micro symbol
unit_label = u"\u00B5"
unit_label = unit_label + 'M'
elif (units == 'n'):
#add nano symbol
unit_label = 'nM'
elif (units == 'p'):
#pico
unit_label = 'pM'
#this plots the calcualted EMfret (xx,yy), and a black horizontal line through the origin (xx, z) for orientation of the axis
line = plot(xx,
yy,
line_style[i % num_colors],
linewidth=3,
label='Donor [{}] = {}'.format(unit_label, str(a)))
plot(xx, z, 'k-')
gca().yaxis.set_major_formatter(ScalarFormatter(useMathText=True))
ticklabel_format(axis='y', style='sci', scilimits=(
0, 0)) #this forces labels on the y axis into scientific format
# appropriately labels the x and y axis, fontsize is arbitary
xlabel('Concentration of Acceptor [' + unit_label + ']')
ylabel("Em$_{FRET}$ (RFU)", fontsize=14)
legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
savefig(filename, bbox_inches='tight', dpi=200)
