def fret_from_image(img,
bg_pixel=(0, 0),
bg_counts=(0, 0),
beta=BETA,
gamma=GAMMA,
rois=()):
'''Returns (time,donor,acceptor,fret) calculated from an image with added ROIs
img image.Stack() or equivalent. Must have .roi dictionary with 'donor' and 'acceptor'
bg_pixel tuple of counts per pixel to substract from (donor,acceptor)
bg_counts tuple of counts to substract from (donor,acceptor)
'''
assert_all_listy(bg_pixel, bg_counts, rois)
if not img.roi:
if not rois:
raise ValueError(
'Must specify ROIs in image or provide using rois=')
else:
img.addROI(*rois)
pixel_donor, pixel_acc = bg_pixel
bg_donor, bg_acc = bg_counts
donor_roi, acceptor_roi = img.roi['donor'], img.roi['acceptor']
don = counts_from_image(img, donor_roi, pixel_donor) - bg_donor
acc = counts_from_image(img, acceptor_roi, pixel_acc) - bg_acc
dcounts, acounts, fret = fret_counts(don, acc, beta, gamma)
metadata = nesteddict.from_dict(img.metadata)
metadata.update(beta=beta,
gamma=gamma,
bg_pixel=bg_pixel,
bg_counts=bg_counts,
roi_donor=donor_roi.toDict(),
roi_acceptor=acceptor_roi.toDict())
fdata = FretData.fromFields(img.time, dcounts, acounts, fret)
fdata.metadata = metadata
return fdata
def fret(self, data):
meta = data.metadata.copy()
if self.fret:
for k, v in self.fret.metadata.iteritems():
meta.setdefault(k, v)
self._fret = FretData(data.data, meta)
self.metadata['fret.'] = self._fret.metadata
def fret_from_image(img, bg_pixel=(0,0), bg_counts=(0,0), beta=BETA, gamma=GAMMA, rois=()):
'''Returns (time,donor,acceptor,fret) calculated from an image with added ROIs
img image.Stack() or equivalent. Must have .roi dictionary with 'donor' and 'acceptor'
bg_pixel tuple of counts per pixel to substract from (donor,acceptor)
bg_counts tuple of counts to substract from (donor,acceptor)
'''
assert_all_listy(bg_pixel, bg_counts, rois)
if not img.roi:
if not rois:
raise ValueError('Must specify ROIs in image or provide using rois=')
else:
img.addROI(*rois)
pixel_donor, pixel_acc = bg_pixel
bg_donor, bg_acc = bg_counts
donor_roi,acceptor_roi = img.roi['donor'], img.roi['acceptor']
don = counts_from_image(img, donor_roi, pixel_donor) - bg_donor
acc = counts_from_image(img, acceptor_roi, pixel_acc) - bg_acc
dcounts,acounts,fret = fret_counts(don, acc, beta, gamma)
metadata = nesteddict.from_dict(img.metadata)
metadata.update(
beta=beta, gamma=gamma, bg_pixel=bg_pixel, bg_counts=bg_counts,
roi_donor=donor_roi.toDict(), roi_acceptor=acceptor_roi.toDict()
)
fdata = FretData.fromFields(img.time,dcounts,acounts,fret)
fdata.metadata = metadata
return fdata
def calculate(stack, beta=constants.beta, gamma=constants.gamma, minsub=False): """Calculates FRET of a pull from an image.Stack calculate( image.Stack, beta = constants.beta, gamma = constants.gamma) RETURNS array of calculated FRET for each frame """ donor = stack.donor - (minsub and min(stack.donor)) acceptor = stack.acceptor - donor*beta acceptor = acceptor - (minsub and min(acceptor)) return FretData.fromFields(stack.time, donor, acceptor, acceptor/(acceptor+gamma*donor))
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 fromFile(filename, **kwargs): return FretData.fromFile(filename)
def fromFile(filename, **kwargs):
return FretData.fromFile(filename)
