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 fromFile(cls, strfile, fretfile, metadata):
assert strfile or fretfile
assert isinstance(strfile, str)
assert isinstance(fretfile, (str,type(None)))
metadata = nesteddict.from_dict(metadata)
trap = TrapData.fromFile(strfile)
fret = FretData.fromFile(fretfile) if fretfile else None
trap.metadata.setdefault('date', today())
trap_datetime = trap.metadata['date']
metadata.setdefault('date', to_date(trap_datetime))
metadata.setdefault('datetime', trap_datetime)
metadata['filename'] = fileIO.splitext(strfile)[0]
newCls = cls(trap, fret, metadata)
assert isinstance(newCls, cls)
assert getattr(newCls, 'filename', None) is not None
return newCls
def fromFile(cls, strfile, fretfile, metadata):
assert strfile or fretfile
assert isinstance(strfile, str)
assert isinstance(fretfile, (str, type(None)))
metadata = nesteddict.from_dict(metadata)
trap = TrapData.fromFile(strfile)
fret = FretData.fromFile(fretfile) if fretfile else None
trap.metadata.setdefault('date', today())
trap_datetime = trap.metadata['date']
metadata.setdefault('date', to_date(trap_datetime))
metadata.setdefault('datetime', trap_datetime)
metadata['filename'] = fileIO.splitext(strfile)[0]
newCls = cls(trap, fret, metadata)
assert isinstance(newCls, cls)
assert getattr(newCls, 'filename', None) is not None
return newCls
def collapse(self, trap_sorted_by='ext', fret_sorted_by='time'):
"Collapse experiments into a single experiment with all data appended together."
assert isinstance(trap_sorted_by, str)
assert isinstance(fret_sorted_by, str)
if not self._all_elements_have_attr('trap'):
raise AttributeError(
'All experiments in ExpList must have attribute "trap"')
filtered_by_fret = self.has_attr('fret')
num_with_fret = len(filtered_by_fret)
fret_data = None
if num_with_fret == len(self):
fret_data = FretData.aggregate(self.getattrs('fret'), fret_sorted_by)
elif num_with_fret > 0:
logger.warning('Not all experiments have fret: not collapsing fret data!')
trap_data = TrapData.aggregate(self.getattrs('trap'), sort_by=trap_sorted_by)
fname = self[0].filename or ''
fname += '_collapsed' if fname else 'collapsed'
return Pulling(trap_data, fret_data, dict(filename=fname, collapsed=True))
def plot(data, pull=None, style=None, **kwargs):
"""Plot FretData and/or TrapData as stacked subplots of counts, FRET, and FEC/FDC
@data: datatypes.AbstractData
@pull: datatypes.AbstractData
@style: dict or str
"""
if isinstance(style, str):
style = Style.with_default_style(style)
elif isinstance(style, dict):
style = Style(**style)
else:
style = Style()
loc = kwargs.pop('legend', 'best')
title = kwargs.pop('title','')
label = kwargs.pop('label', '')
displayFRET = kwargs.pop('show_fret', True) and hasattr(data,'fret')
kwargs.setdefault('markersize', 2)
hold=kwargs.pop('hold', None)
if hold is not None:
plt.hold(hold)
if not pull and hasTrapData(data):
pull = TrapData.fromObject(data)
num = 0
if displayFRET:
num += 2
if pull:
num += 1
FEC = kwargs.pop('FEC', num==1)
else:
FEC = kwargs.pop('FEC', False)
if num == 0:
raise ValueError("Don't know how to plot arguments: need TrapData or FretData")
if data is None and pull is not None:
layout = iter([(num,1,num)])
else:
layout = iter((num,1,x) for x in range(1,num+1))
ax1 = None
donor, acceptor = 'donor', 'acceptor'
if displayFRET:
plt.subplot(*next(layout))
not hold and plt.cla()
plt.hold(True)
ax1 = subplot(data.time, data.donor, style[donor], label=donor, **kwargs)
subplot(data.time, data.acceptor, style[acceptor], label=acceptor, axes=('Time (s)','Counts'), **kwargs)
plt.hold(hold)
if loc is not None:
plt.legend(loc=loc,ncol=2,prop={'size':'small'})
if displayFRET:
subplot(data.time, data.fret, style['fret'], layout=next(layout),
axes=('Time (s)','FRET'), **kwargs)
plt.ylim(-0.1, 1.1)
ax2 = None
if pull:
trap_style = Style.TRAP_STYLE_NAME
x_coord,x_label = (pull.ext,'Extension (nm)') if FEC else (pull.sep,'Separation (nm)')
ax2 = subplot(x_coord, pull.f, style[trap_style], layout=next(layout), axes=(x_label,'Force (pN)'), label=label, **kwargs)
if loc is not None:
plt.legend(loc=loc,ncol=2,prop={'size':'small'})
first_plot = ax1 or ax2
if title:
first_plot.set_title(title)
def plot(data, pull=None, style=None, **kwargs):
"""Plot FretData and/or TrapData as stacked subplots of counts, FRET, and FEC/FDC
@data: datatypes.AbstractData
@pull: datatypes.AbstractData
@style: dict or str
"""
if isinstance(style, str):
style = Style.with_default_style(style)
elif isinstance(style, dict):
style = Style(**style)
else:
style = Style()
loc = kwargs.pop('legend', 'best')
title = kwargs.pop('title', '')
label = kwargs.pop('label', '')
displayFRET = kwargs.pop('show_fret', True) and hasattr(data, 'fret')
kwargs.setdefault('markersize', 2)
hold = kwargs.pop('hold', None)
if hold is not None:
plt.hold(hold)
if not pull and hasTrapData(data):
pull = TrapData.fromObject(data)
num = 0
if displayFRET:
num += 2
if pull:
num += 1
FEC = kwargs.pop('FEC', num == 1)
else:
FEC = kwargs.pop('FEC', False)
if num == 0:
raise ValueError(
"Don't know how to plot arguments: need TrapData or FretData")
if data is None and pull is not None:
layout = iter([(num, 1, num)])
else:
layout = iter((num, 1, x) for x in range(1, num + 1))
ax1 = None
donor, acceptor = 'donor', 'acceptor'
if displayFRET:
plt.subplot(*next(layout))
not hold and plt.cla()
plt.hold(True)
ax1 = subplot(data.time,
data.donor,
style[donor],
label=donor,
**kwargs)
subplot(data.time,
data.acceptor,
style[acceptor],
label=acceptor,
axes=('Time (s)', 'Counts'),
**kwargs)
plt.hold(hold)
if loc is not None:
plt.legend(loc=loc, ncol=2, prop={'size': 'small'})
if displayFRET:
subplot(data.time,
data.fret,
style['fret'],
layout=next(layout),
axes=('Time (s)', 'FRET'),
**kwargs)
plt.ylim(-0.1, 1.1)
ax2 = None
if pull:
trap_style = Style.TRAP_STYLE_NAME
x_coord, x_label = (pull.ext,
'Extension (nm)') if FEC else (pull.sep,
'Separation (nm)')
ax2 = subplot(x_coord,
pull.f,
style[trap_style],
layout=next(layout),
axes=(x_label, 'Force (pN)'),
label=label,
**kwargs)
if loc is not None:
plt.legend(loc=loc, ncol=2, prop={'size': 'small'})
first_plot = ax1 or ax2
if title:
first_plot.set_title(title)
