def plot(data, pull=None, **kwargs):
loc = kwargs.get('legend', 'best')
title = kwargs.get('title','')
FEC = kwargs.get('FEC',False)
displayFRET = kwargs.get('show_fret', hasattr(data,'fret'))
hold=kwargs.pop('hold', None)
if hold is not None:
plt.hold(hold)
if hasattr(data, '_to_plot'):
args, kwargs = data._to_plot()
return _subplot(*args, **kwargs)
if not pull and hasTrapData(data):
pull = TrapData.fromObject(data)
if not displayFRET and data is not None: num = 1
elif hasFretData(data): num = 2
else: num = 0
if pull: num += 1
if num==0:
raise ValueError("Don't know how to plot argument: missing named fields")
layout = iter((num,1,x) for x in range(1,num+1))
ax1 = None
if hasFretData(data):
plt.subplot(*next(layout))
not hold and plt.cla()
plt.hold(True)
ax1 = _subplot(data.time, data.donor, label='donor')
_subplot(data.time, data.acceptor, label='acceptor', axes=('','counts'))
plt.hold(hold)
plt.legend(loc=loc,ncol=2,prop={'size':'small'})
if displayFRET:
_subplot(data.time, data.fret, layout=next(layout),
axes=('Seconds','FRET'))
ax2 = None
if pull:
x_coord,x_label = (pull.ext,'Extension (nm)') if FEC else (pull.sep,'Separation (nm)')
ax2 = _subplot(x_coord, pull.f, '.', layout=next(layout), axes=(x_label,'Force (pN)'))
first_plot = ax1 if ax1 else ax2
first_plot.set_title(title)
plt.show()
def __init__(self, trap, fret, metadata):
if trap and not hasTrapData(trap):
raise ValueError(
"__init__ argument 'trap' <{}> does not have trap data".format(trap))
if fret and not hasFretData(fret):
raise ValueError(
"__init__ argument 'fret' <{}> does not have fret data".format(fret))
self.trap = trap
self._fret = fret
self.metadata = nesteddict.from_dict(metadata)
self.metadata['trap'] = getattr(trap, 'metadata', nesteddict())
self.metadata['fret'] = getattr(fret, 'metadata', nesteddict())
# Move 'fret' metadata fields found in trap metadata (recorded in .str files)
# to the fret.metadata dictionary
for key in ifilter(lambda s: s.startswith('fret'), self.metadata['trap'].keys()):
self['fret'].update(self.metadata['trap'].pop(key))
def __init__(self, trap, fret, metadata):
if trap and not hasTrapData(trap):
raise ValueError(
"__init__ argument 'trap' <{}> does not have trap data".format(
trap))
if fret and not hasFretData(fret):
raise ValueError(
"__init__ argument 'fret' <{}> does not have fret data".format(
fret))
self.trap = trap
self._fret = fret
self.metadata = nesteddict.from_dict(metadata)
self.metadata['trap'] = getattr(trap, 'metadata', nesteddict())
self.metadata['fret'] = getattr(fret, 'metadata', nesteddict())
# Move 'fret' metadata fields found in trap metadata (recorded in .str files)
# to the fret.metadata dictionary
for key in ifilter(lambda s: s.startswith('fret'),
self.metadata['trap'].keys()):
self['fret'].update(self.metadata['trap'].pop(key))