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 __init__(self, data, meta={}):
data = asarray(data)
if data is not None and not self._is_data_shape_ok(data.shape):
logger.warning('TrapData should have fields for {}'.format(self._fields))
self.data = data
self._original_data = None
self.metadata = nesteddict.from_dict(meta)
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 __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 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 __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))