def mpld3_enable_notebook():
"""Change the default plugins, enable ipython notebook mode and return mpld3 module."""
import mpld3
from mpld3 import plugins as plugs
plugs.DEFAULT_PLUGINS = [plugs.Reset(), plugs.Zoom(), plugs.BoxZoom(), plugs.MousePosition()]
mpld3.enable_notebook()
return mpld3
def plot_vdot_race(data):
#CSS element for the tooltip label
css = """
div
{
font-family: Avenir, Helvetica, sans-serif;
border: 1px solid black;
padding-left: 5px;
padding-right: 5px;
text-align: center;
color: #000000;
background-color: #ffffff;
}
"""
#plt.style.use('seaborn-poster') #sets the size of the charts
plt.style.use('ggplot')
x_axis = []
y_axis = []
label = []
#print (data)
for key in data:
label.append("Race: " + str(data[key][1]) + "<br/>" + "VDOT: " +
str(data[key][3]))
y_axis.append(data[key][3])
datetime_obj = datetime.strptime(data[key][4],
'%Y-%m-%d %H:%M:%S+00:00')
x_axis.append(datetime_obj)
dates = matplotlib.dates.date2num(x_axis)
fig, ax = plt.subplots()
plt.xlabel("Race dates", fontsize=20)
plt.ylabel("VDOT Scores", fontsize=20)
plt.title("VDOT Score Over Time", fontsize=25)
line = plt.plot_date(dates,
y_axis,
linestyle='solid',
marker='.',
markersize=14)
plugins.clear(fig) # clear all plugins from the figure
tooltip = plugins.PointHTMLTooltip(line[0],
label,
hoffset=-60,
voffset=-70,
css=css)
plugins.connect(fig, plugins.Reset(), plugins.BoxZoom(), plugins.Zoom(),
tooltip)
return mpld3.fig_to_html(fig)
def plotConPlugins(fig):#, plot=None):
#debugPrint("El parametro plot contiene " + str(plot[0]))
plugins.connect(fig, plugins.BoxZoom(button = False))#, plugins.PointLabelTooltip(plot[0]))
debugPrint("Se logro conectar el plugin BoxZoom")
plot_url = fig_to_html(fig)
debugPrint("A punto de cerrar la figura")
pyplt.close(fig)
return plot_url
def make_html_plot_for_file(filename, my_title):
my_fontsize = 20
# read in csv file
if os.stat(filename).st_size:
data = np.genfromtxt(filename, delimiter=',')
else:
# empty data file
data = np.zeros([2, 2])
if len(data.shape) == 1:
return "<h2> " + my_title + " has no data </h2>"
x = data[:, 0]
fig, ax = plt.subplots(figsize=(10, 5))
for k in range(1, data.shape[1]):
y = data[:, k]
# sort data
x_sorted = [x1 for (x1, y1) in sorted(zip(x, y))]
y_sorted = [y1 for (x1, y1) in sorted(zip(x, y))]
lines = ax.plot(x_sorted,
y_sorted,
'.-',
markersize=15,
label='ion ' + str(k - 1))
plt.legend(fontsize=my_fontsize, loc='best')
plt.title(my_title, fontsize=my_fontsize)
ax.grid()
plt.xticks(fontsize=my_fontsize)
plt.yticks(fontsize=my_fontsize)
plt.xlim([np.min(x), np.max(x)])
#90% of the time that this function takes is taken up after this line
plugins.clear(fig)
plugins.connect(fig, plugins.Reset(), plugins.BoxZoom(),
plugins.Zoom(enabled=True),
plugins.MousePosition(fontsize=my_fontsize))
java_txt = mpld3.fig_to_html(fig)
plt.close()
return java_txt
def plot_beats_per_mile(data):
#divide meters by this factor to get in terms of miles
convert_meters_to_miles = 1609.344
#plt.style.use('seaborn-poster') #sets the size of the charts
plt.style.use('ggplot')
#Data is dictionary mapping id to (activity_name, start_date_local, average_hr, distance, total_elevation_gain)
data_by_week = {}
for key in data:
datetime_obj = datetime.strptime(data[key][1], '%Y-%m-%d %H:%M:%S')
year_week_val = datetime_obj.isocalendar()[:-1]
if year_week_val not in data_by_week:
#Storing average_hr, distance, total_elevation_gain
data_by_week[year_week_val] = [(data[key][2], data[key][3],
data[key][4])]
else:
data_by_week[year_week_val].append(
(data[key][2], data[key][3], data[key][4]))
x_axis = []
x_label = []
y_axis = []
for key in data_by_week:
print(key)
total_hr_each_week = 0
distance_week = 0
for activity in data_by_week[key]:
total_hr_each_week += activity[0] * (activity[1] /
convert_meters_to_miles)
distance_week += activity[1] / convert_meters_to_miles
avg_hr_per_mile = total_hr_each_week / distance_week
x_label.append(str(key[0]) + "-" + str(key[1]))
x_axis.append(key[0] * 52 + key[1])
y_axis.append(avg_hr_per_mile)
total_hr_each_week = 0
distance_week = 0
fig, ax = plt.subplots()
plt.xlabel("Weeks", fontsize=20)
plt.ylabel("Average Heartrate Per Mile", fontsize=20)
plt.title("Average Heartrate Per Mile Sorted by Week", fontsize=25)
line = plt.plot(x_axis,
y_axis,
linestyle='solid',
marker='.',
markersize=14)
x = np.asarray(x_axis)
y = np.asarray(y_axis)
b, m = polyfit(x, y, 1)
#Plots regression line
plt.plot(x, b + m * x, linestyle='solid')
plugins.clear(fig) # clear all plugins from the figure
#tooltip = plugins.PointHTMLTooltip(line[0], label,
#hoffset = -60, voffset = -70, css = css)
plugins.connect(fig, plugins.Reset(), plugins.BoxZoom(), plugins.Zoom())
return mpld3.fig_to_html(fig)
plot_rest = jitter(
reduced[rest["Membership"]]["PC1"],
reduced[rest["Membership"]]["PC2"],
c="b",
alpha=0.4,
label="Non-WMC"
)
plot_wmc = jitter(
reduced[wmc["Membership"]]["PC1"],
reduced[wmc["Membership"]]["PC2"],
c="g",
alpha=0.4,
label="WMC"
)
plt.xlabel("PC1")
plt.ylabel("PC2")
tooltip_rest = plugins.PointHTMLTooltip(plot_rest, reduced[rest["Membership"]].index.tolist())
tooltip_wmc = plugins.PointHTMLTooltip(plot_wmc, reduced[wmc["Membership"]].index.tolist())
zoom = plugins.Zoom(button=False, enabled=True)
box_zoom = plugins.BoxZoom(button=False, enabled=True)
plugins.connect(plt.gcf(), tooltip_rest)
plugins.connect(plt.gcf(), tooltip_wmc)
mpld3.save_html(plt.gcf(), "pca-2017.html")
def result():
try:
g.conn = sqlite3.connect('case_data.db')
g.curr = g.conn.cursor()
g.curr.execute("SELECT country_name FROM interval_tb")
country = g.curr.fetchone()[0]
g.curr.execute("SELECT duration FROM interval_tb")
period = g.curr.fetchall()
g.curr.execute("SELECT restriction FROM interval_tb")
restrictions = g.curr.fetchall()
g.curr.execute("SELECT * FROM cases_tb WHERE country_name=?",
(country, ))
country_statistics = g.curr.fetchone()
g.conn.commit()
g.conn.close()
plt.rcParams.update({'font.size': 12})
def differential(initial, time, *args):
# Holds initial conditions for the population
susceptible, exposed, infected, recovered = initial
# System of differential equations
# Represents changes in the susceptible, exposed, infected, and recovered population
dSdt = -(beta * susceptible * infected) / POPULATION_SIZE
dEdt = beta * susceptible * infected / POPULATION_SIZE - SIGMA * exposed
dIdt = SIGMA * exposed - GAMMA * infected
dRdt = GAMMA * infected
return dSdt, dEdt, dIdt, dRdt
POPULATION_SIZE = country_statistics[3]
BETA = 0.956
SIGMA = 1 / 5.2
GAMMA = 1 / 2.3
REPRODUCTION_NUMBER = BETA / GAMMA
period = list(period)
time = [0]
restrictions = list(restrictions)
contact_state = []
for i in range(len(period)):
period[i] = period[i][0]
for i in range(len(restrictions)):
restrictions[i] = restrictions[i][0]
time += list(accumulate(period))
for j in range(len(period)):
if restrictions[j] == "Lockdown":
contact_state.append(0.26)
elif restrictions[j] == "Vacation":
contact_state.append(0.46)
elif restrictions[j] == "School closure":
contact_state.append(0.8)
else:
contact_state.append(1)
susceptible_initial = POPULATION_SIZE - \
country_statistics[2] - country_statistics[1]
exposed_initial = 0
infected_initial = country_statistics[2]
recovered_initial = country_statistics[1]
infected_population = 0
current_maximum = 0
fig, ax = plt.subplots()
for graph in range(len(period)):
beta = BETA * contact_state[graph]
duration = np.linspace(time[graph], time[graph + 1],
period[graph] * 2 + 1)
solution = odeint(differential,
(susceptible_initial, exposed_initial,
infected_initial, recovered_initial),
duration,
args=(beta, SIGMA, GAMMA, POPULATION_SIZE))
susceptible_initial = solution[period[graph] * 2, 0]
exposed_initial = solution[period[graph] * 2, 1]
infected_initial = solution[period[graph] * 2, 2]
recovered_initial = solution[period[graph] * 2, 3]
current_maximum = max(solution[:, 2])
if current_maximum > infected_population:
infected_population = current_maximum
if graph == 0:
ax.plot(duration, solution[:, 0], 'r', label='Susceptible')
ax.plot(duration, solution[:, 1], 'g', label='Exposed')
ax.plot(duration, solution[:, 2], 'b', label='Infectious')
ax.plot(duration, solution[:, 3], 'y', label='Recovered')
else:
ax.plot(duration, solution[:, 0], 'r')
ax.plot(duration, solution[:, 1], 'g')
ax.plot(duration, solution[:, 2], 'b')
ax.plot(duration, solution[:, 3], 'y')
ax.set_xlim(0, time[-1])
ax.set_ylim(0, POPULATION_SIZE + POPULATION_SIZE * 0.01)
ax.legend(loc='best')
ax.set_xlabel('Time (days)')
ax.set_ylabel('Population', rotation='horizontal')
fig.set_size_inches(8, 6)
ax.yaxis.set_label_coords(-0.1, 1.02)
plugins.clear(fig)
plugins.connect(fig, plugins.Reset())
plugins.connect(fig, plugins.BoxZoom(enabled=True))
plugins.connect(fig, plugins.Zoom())
seir_graph = mpld3.fig_to_html(fig)
plt.close()
effective_reproduction_number = REPRODUCTION_NUMBER * \
susceptible_initial/POPULATION_SIZE
effective_reproduction_number = float(
"{:0.3f}".format(effective_reproduction_number))
return {
'graph': seir_graph,
'r0': REPRODUCTION_NUMBER,
'rt': effective_reproduction_number,
'susceptible_state': int(susceptible_initial),
'exposed_state': int(exposed_initial),
'infected_state': int(infected_initial),
'recovered_state': int(recovered_initial),
'max_active_cases': int(infected_population)
}
except:
return jsonify(0)
def problem_view(request, problem_id):
user = request.user
problem = get_object_or_404(Problem, id=problem_id)
if problem.user_id != user and not user.is_superuser:
raise PermissionDenied
parse_error = False
a = None
b = None
c = None
a_copy = None
b_copy = None
result = None
figure = None
parse_result = parse_problem(problem.problem_text)
print parse_result
if parse_result is not None:
a, b, c, x = parse_result
if a and b and c and x:
result = simple_simplex(copy.deepcopy(a), copy.deepcopy(b),
copy.deepcopy(c))
b.pop(0)
a_copy = copy.deepcopy(a)
b_copy = copy.deepcopy(b)
if len(x) is 2:
tmp = [0, 0]
tmp[1] = 1
a.insert(0, copy.deepcopy(tmp))
tmp[0] = 1
tmp[1] = 0
a.insert(0, copy.deepcopy(tmp))
b.insert(0, 0)
b.insert(0, 0)
dots = []
for i in range(len(b)):
dots.append([])
shape_x = []
for i in xrange(0, len(b)):
for j in xrange(i + 1, len(b)):
if a[i][0] == a[j][0] and a[i][1] == a[j][1]:
continue
shape_a = np.array([[a[i][0], a[i][1]],
[a[j][0], a[j][1]]])
shape_b = np.array([b[i], b[j]])
res = np.linalg.solve(shape_a, shape_b)
dots[i].append(res)
dots[j].append(res)
# fig, ax = plt.subplots()
fig = plt.figure()
ax = fig.add_subplot(111)
for dot in dots:
ax.plot(
[float(dot[0][0]), float(dot[1][0])],
[float(dot[0][1]), float(dot[1][1])],
ls='-',
color='green',
marker='o',
lw=2)
# print([dot[0], dot[1]])
ax.set_xlabel('X axis')
ax.set_ylabel('Y axis')
ax.set_title('Plot of 2D Problem!', size=14)
plugins.clear(fig)
plugins.connect(fig, plugins.Reset(),
plugins.Zoom(enabled=True), plugins.BoxZoom())
figure = fig_to_html(fig,
d3_url=STATIC_URL + 'js/d3.min.js',
mpld3_url=STATIC_URL + 'js/mpld3.v0.2.js',
use_http=True)
else:
figure = 'Larger than 2D!'
else:
parse_error = True
return render_to_response(
'problems/view.html', {
'user': user,
'problem': problem,
'parse_error': parse_error,
'figure': figure,
'a': a_copy,
'b': b_copy,
'c': c,
'result': result,
'view_name': 'Problem - %s' % problem.id,
})
def render(self, idf, filename='output.html'):
progress_inst = helpers.Progress(idf.opt)
self.progress = progress_inst.progress
if idf.opt['outputFilename']:
filename = idf.opt['outputFilename']
if idf.opt['outputAs'] == 'html':
# write matplotlib/d3 plots to html file
import matplotlib
import matplotlib.pyplot as plt, mpld3
import matplotlib.axes
from mpld3 import plugins
from jinja2 import Environment, FileSystemLoader
elif idf.opt['outputAs'] in ['pdf', 'interactive', 'tikz']:
# show plots in separate matplotlib windows
import matplotlib
if idf.opt['outputAs'] == 'pdf':
from matplotlib.backends.backend_pdf import PdfPages
pp = PdfPages(filename)
import matplotlib.pyplot as plt
import matplotlib.axes
else:
print("No proper output method given. Not plotting.")
return
font_size = 10
if idf.opt['outputAs'] in ['pdf', 'tikz']:
if idf.opt['plotPerJoint']:
font_size = 30
else:
font_size = 12
matplotlib.rcParams.update({'font.size': font_size})
matplotlib.rcParams.update({'axes.labelsize': font_size - 5})
matplotlib.rcParams.update({'axes.linewidth': font_size / 15.})
matplotlib.rcParams.update({'axes.titlesize': font_size - 2})
matplotlib.rcParams.update({'legend.fontsize': font_size - 2})
matplotlib.rcParams.update({'xtick.labelsize': font_size - 5})
matplotlib.rcParams.update({'ytick.labelsize': font_size - 5})
matplotlib.rcParams.update({'lines.linewidth': font_size / 15.})
matplotlib.rcParams.update({'patch.linewidth': font_size / 15.})
matplotlib.rcParams.update({'grid.linewidth': font_size / 20.})
# skip some samples so graphs don't get too large/detailed TODO: change skip so that some
# maximum number of points is plotted (determined by screen etc.)
skip = 5
#create figures and plots
figures = list()
for ds in self.progress(range(len(self.datasets))):
group = self.datasets[ds]
fig, axes = plt.subplots(len(group['dataset']),
sharex=True,
sharey=True)
# scale unified scaling figures to same ranges and add some margin
if group['unified_scaling']:
ymin = 0
ymax = 0
for i in range(len(group['dataset'])):
ymin = np.min(
(np.min(group['dataset'][i]['data']), ymin)) * 1.05
ymax = np.max(
(np.max(group['dataset'][i]['data']), ymax)) * 1.05
#plot each group of data
for d_i in range(len(group['dataset'])):
d = group['dataset'][d_i]
if not issubclass(type(axes), matplotlib.axes.SubplotBase):
ax = axes[d_i]
else:
ax = axes
axes = [axes]
if idf.opt['outputAs'] != 'tikz':
ax.set_title(d['title'])
if group['unified_scaling']:
ax.set_ylim([ymin, ymax])
for data_i in range(0, len(d['data'])):
if len(d['data'][data_i].shape) > 1:
#data matrices
for i in range(0, d['data'][data_i].shape[1]):
l = group['labels'][i] if data_i == 0 else ''
if i < 6 and 'contains_base' in group and group[
'contains_base']:
ls = 'dashed'
else:
ls = '-'
dashes = () # type: Tuple
if idf.opt['plotErrors']:
if idf.opt['plotPrioriTorques']:
n = 3
else:
n = 2
if i == n:
ls = 'dashed'
dashes = (3, 0.5)
ax.plot(d['time'][::skip],
d['data'][data_i][::skip, i],
label=l,
color=colors[i],
alpha=1 - (data_i / 2.0),
linestyle=ls,
dashes=dashes)
else:
#data vector
ax.plot(d['time'][::skip],
d['data'][data_i][::skip],
label=group['labels'][d_i],
color=colors[0],
alpha=1 - (data_i / 2.0))
ax.grid(which='both', linestyle="dotted", alpha=0.8)
if 'y_label' in group:
ax.set_ylabel(group['y_label'])
if idf.opt['outputAs'] != 'tikz':
ax.set_xlabel("Time (s)")
plt.setp([a.get_xticklabels() for a in axes[:-1]], visible=False)
#plt.setp([a.get_yticklabels() for a in axes], fontsize=8)
if idf.opt['plotLegend']:
handles, labels = ax.get_legend_handles_labels()
if idf.opt['outputAs'] == 'html':
#TODO: show legend properly (see mpld3 bug #274)
#leg = fig.legend(handles, labels, loc='upper right', fancybox=True, fontsize=10, title='')
leg = axes[0].legend(handles,
labels,
loc='upper right',
fancybox=True,
fontsize=10,
title='',
prop={'size': 8})
else:
leg = plt.figlegend(handles,
labels,
loc='upper right',
fancybox=True,
fontsize=font_size,
title='',
prop={'size': font_size - 3})
leg.draggable()
fig.subplots_adjust(hspace=2)
fig.set_tight_layout(True)
if idf.opt['outputAs'] == 'html':
plugins.clear(fig)
plugins.connect(fig, plugins.Reset(), plugins.BoxZoom(),
plugins.Zoom(enabled=False),
plugins.MousePosition(fontsize=14, fmt=".5g"))
figures.append(mpld3.fig_to_html(fig))
elif idf.opt['outputAs'] == 'interactive':
plt.show(block=False)
elif idf.opt['outputAs'] == 'pdf':
pp.savefig(plt.gcf())
elif idf.opt['outputAs'] == 'tikz':
from matplotlib2tikz import save as tikz_save
tikz_save('{}_{}_{}.tex'.format(
filename, group['dataset'][0]['title'].replace('_', '-'),
ds // idf.model.num_dofs),
figureheight='\\figureheight',
figurewidth='\\figurewidth',
show_info=False)
if idf.opt['outputAs'] == 'html':
path = os.path.dirname(os.path.abspath(__file__))
template_environment = Environment(
autoescape=False,
loader=FileSystemLoader(os.path.join(path, '../output')),
trim_blocks=False)
context = {'figures': figures, 'text': self.text}
outfile = os.path.join(path, '..', 'output', filename)
import codecs
with codecs.open(outfile, 'w', 'utf-8') as f:
html = template_environment.get_template(
"templates/index.html").render(context)
f.write(html)
print("Saved output at file://{}".format(outfile))
elif idf.opt['outputAs'] == 'interactive':
#keep non-blocking plot windows open
plt.show()
elif idf.opt['outputAs'] == 'pdf':
pp.close()
