def test_hl_7():
headline("test", properties={"one": "two"})
result = "* test\n :PROPERTIES:\n :one: two\n :END:\n\n\n"
assert sys.stdout.getvalue() == result
def org(self):
'''Print an org-represention of the plate and data.
'''
from pycse.orgmode import table, figure, headline, print_redirect, link
import datetime
import json
import time
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('[%Y-%m-%d %a %H:%M:%S]')
CWD = os.getcwd()
os.chdir(os.path.join(self.base,
self.directory))
try:
import matplotlib
matplotlib.use('TkAgg')
A, B = self.metadata['A'], self.metadata['B']
print(f'#+TITLE: {A}-{B}')
print(f'#+CREATED: {st}')
print('#+STARTUP: showall')
print()
print('Generated report. Do not edit. Changes may be lost.\n')
headline('Summary',
tags=[A, B],
body=str(self))
link('file+sys', f'./primary_data/{A}col{B}rowdata.xls')
link('file+sys', './images', 'Image directory')
link('file+sys', './auxillary_data', 'auxillary_data')
print()
headline('Hydrogen data')
headline('Hydrogen production plots', level=2)
plt.figure()
self.data['mmolH'].plot_mmolH_grid_window()
plt.tight_layout()
figure('espyranto/kinetics-grid.png',
name='fig-kinetics-grid',
attributes=[['org', ':width 600']],
caption=f'Hydrogen umolH in each well for {A}-{B}.')
plt.clf()
print()
headline('Max production', level=2)
ncols, nrows = self.ncols, len(self.data['mmolH'].mmolH) // self.ncols
maxh = np.max(self.data['mmolH'].mmolH, axis=1).reshape(nrows, ncols)
data = np.round(maxh, 2)
# Add row and column labels
col_labels = self.A.reshape(nrows, ncols)[0][None, :]
row_labels = np.concatenate(([['']],
self.B.reshape(nrows, ncols)[:, 0][:, None]))
data = np.concatenate((col_labels, data))
data = np.concatenate((row_labels, data), axis=1)
data = list(data)
data.insert(1, None)
data[0][0] = f'{B}\{A}'
table(data, name='tab-maxh', caption='Maxh µmol H_{2} produced.')
print()
self.data['mmolH'].plot_mmolH_max();
plt.tight_layout()
figure('espyranto/maxh.png',
name='fig-maxh',
attributes=[['org', ':width 600']],
caption=f'Maximum hydrogen produced for {A}-{B}.')
plt.clf()
print()
tot_conc = (self.A + self.B)
# The nself.where deals with the case where A = B = 0.0
x_A = self.A / np.where(tot_conc > 0, tot_conc, 1)
plt.figure()
plt.scatter(x_A, np.max(self.data['mmolH'].mmolH, axis=1),
tot_conc * 20)
plt.xlabel(f'$x_{{{A}}}$');
plt.ylabel('$\mu molH$');
print()
figure('espyranto/maxh-scatter.png',
name='fig-maxh-scatter',
attributes=[['org', ':width 600']],
caption=f'Scatter plot for maximum hydrogen produced for {A}-{B}.')
print()
headline('Max rate', level=2)
# Heatmap of max rates
print()
self.data['mmolH'].plot_mmolH_max_derivative_window()
figure('espyranto/maxrate.png',
name='fig-maxrate',
attributes=[['org', ':width 600']],
caption=f'Maximum rate (window) of hydrogen produced for {A}-{B}.')
# Scatter plot
print()
mmolH = self.data['mmolH']
t = np.arange(0, len(mmolH[0])) * mmolH.timestep / 3600
rate_data = []
for row in self.data['mmolH'].mmolH:
ys = mmolH.smooth_window(row)
dydx = np.gradient(ys, t, edge_order=2)
rate_data += [np.max(dydx)]
# Scatter plot
plt.figure()
plt.scatter(x_A, rate_data, tot_conc * 20)
plt.xlabel(f'$x_{{{A}}}$');
plt.ylabel('$\mu molH/hr$');
print()
figure('espyranto/maxrate-scatter.png',
name='fig-maxrate-scatter',
attributes=[['org', ':width 600']],
caption=f'Scatter plot for maximum rate of hydrogen production for {A}-{B}.')
print()
# For making a table
rate_data = np.round(rate_data, 2)
rate_data = rate_data.reshape((nrows, ncols))
rate_data = np.concatenate((col_labels, rate_data))
rate_data = np.concatenate((row_labels, rate_data), axis=1)
rate_data = list(rate_data)
rate_data.insert(1, None)
rate_data[0][0] = f'{B}\{A}'
table(rate_data, name='tab-maxrate', caption='Max rate µmol/hr H_{2} produced.')
print()
headline('Metadata')
print()
print(f'''#+name: metadata
#+BEGIN_SRC json
{json.dumps(self.metadata, sort_keys=True, indent=2)}
#+END_SRC
''')
finally:
os.chdir(CWD)
plt.close('all')
def test_hl_tags():
headline("test", tags=['a', 'b'])
assert sys.stdout.getvalue() == "* test :a:b:\n\n"
def test_hl_6():
headline("test", body="some text")
assert sys.stdout.getvalue() == '* test\nsome text\n\n'
def test_hl_5():
headline("test", deadline='test')
assert sys.stdout.getvalue() == "* test\n DEADLINE: test\n\n"
def test_hl_4():
headline("test", scheduled='test', deadline='test')
result = "* test\n SCHEDULED: test DEADLINE: test\n\n"
assert sys.stdout.getvalue() == result
def test_hl_3():
headline("test", scheduled='test')
assert sys.stdout.getvalue() == "* test\n SCHEDULED: test\n\n"
def test_hl_2():
headline("test", 2)
assert sys.stdout.getvalue() == "** test\n\n"
def test_headline_1():
headline("test")
assert sys.stdout.getvalue() == "* test\n\n"