Esempio n. 1
0
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()
Esempio n. 2
0
 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))
Esempio n. 3
0
 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))