def test_one_center_em(self):
em_band = (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)
em_bands = ((650e-9, 660e-9, 675e-9, 678e-9,
680e-9), (780e-9, 785e-9, 790e-9, 800e-9, 812e-9),
(1034e-9, 1080e-9, 1100e-9, 1200e-9, 1500e-9))
# Excitation band should be smaller than the emission band used
in_exp = [
((em_band, (490e-9, 510e-9)),
fluo.get_center(em_band)), # only one band
((em_bands, (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)),
fluo.get_center(em_bands[0])), # smallest above 500nm
((em_bands, (690e-9, 697e-9, 700e-9, 703e-9, 710e-9)),
fluo.get_center(em_bands[1])), # smallest above 700nm
((em_bands, (790e-9, 797e-9, 800e-9, 803e-9, 810e-9)),
fluo.get_center(em_bands[2])), # smallest above 800nm
((em_bands[0:2], (790e-9, 797e-9, 800e-9, 803e-9, 810e-9)),
fluo.get_center(em_bands[1])), # biggest
# Try with a pass-through
((em_band, BAND_PASS_THROUGH), 500e-9),
((em_bands, BAND_PASS_THROUGH), 1100e-9), # biggest
# ((BAND_PASS_THROUGH, (490e-9, 510e-9)), BAND_PASS_THROUGH),
]
for args, exp in in_exp:
out = fluo.get_one_center_em(*args)
self.assertEqual(
exp, out,
"Failed while running with %s and got %s" % (args, out))
def test_one_center_ex(self):
ex_band = (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)
ex_bands = ((650e-9, 660e-9, 675e-9, 678e-9, 680e-9),
(780e-9, 785e-9, 790e-9, 800e-9, 812e-9),
(1034e-9, 1080e-9, 1100e-9, 1200e-9, 1500e-9))
# Excitation band should be smaller than the emission band used
in_exp = [((ex_band, (490e-9, 510e-9)), fluo.get_center(ex_band)), # only one band
((ex_bands, (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)), fluo.get_center(ex_bands[0])), # nothing fitting, but should pick the smallest
((ex_bands, (690e-9, 697e-9, 700e-9, 703e-9, 710e-9)), fluo.get_center(ex_bands[0])), # biggest below 700nm
((ex_bands, (790e-9, 797e-9, 800e-9, 803e-9, 810e-9)), fluo.get_center(ex_bands[1])), # biggest below 800nm
]
for args, exp in in_exp:
out = fluo.get_one_center_ex(*args)
self.assertEqual(exp, out, "Failed while running with %s and got %s" % (args, out))
def test_center(self):
in_exp = [
((490e-9, 510e-9), 500e-9), # 2-float band
((490e-9, 497e-9, 500e-9, 503e-9, 510e-9), 500e-9), # 5-float band
(((490e-9, 510e-9), (820e-9, 900e-9)), (500e-9, 860e-9)
) # multi-band
]
for inp, exp in in_exp:
out = fluo.get_center(inp)
self.assertEqual(
exp, out,
"Failed while running with %s and got %s" % (inp, out))
# Special case for "pass-through": any number > 0 is fine
out = fluo.get_center(BAND_PASS_THROUGH)
self.assertGreaterEqual(out, 0)
def test_center(self):
in_exp = [((490e-9, 510e-9), 500e-9), # 2-float band
((490e-9, 497e-9, 500e-9, 503e-9, 510e-9), 500e-9), # 5-float band
(((490e-9, 510e-9), (820e-9, 900e-9)), (500e-9, 860e-9)) # multi-band
]
for inp, exp in in_exp:
out = fluo.get_center(inp)
self.assertEqual(exp, out, "Failed while running with %s and got %s" % (inp, out))
def _weight_stream(stream):
"""
Defines how much a stream is of priority (should be done first) for
acquisition.
stream (acq.stream.Stream): a stream to weight
returns (number): priority (the higher the more it should be done first)
"""
if isinstance(stream, (FluoStream, ScannedFluoMDStream)):
# Fluorescence ASAP to avoid bleaching
if isinstance(stream, ScannedFluoMDStream):
# Just take one of the streams, to keep things "simple"
stream = stream.streams[0]
# If multiple fluorescence acquisitions: prefer the long emission
# wavelengths first because there is no chance their emission light
# affects the other dyes (and which could lead to a little bit of
# bleaching).
ewl_center = fluo.get_center(stream.emission.value)
if isinstance(ewl_center, collections.Iterable):
# multi-band filter, so fallback to guess based on excitation
xwl_center = fluo.get_center(stream.excitation.value)
if isinstance(ewl_center, collections.Iterable):
# also unguessable => just pick one "randomly"
ewl_bonus = ewl_center[0]
else:
ewl_bonus = xwl_center + 50e-6 # add 50nm as guesstimate for emission
else:
ewl_bonus = ewl_center # normally, between 0 and 1
return 100 + ewl_bonus
elif isinstance(stream, OpticalStream):
return 90 # any other kind of optical after fluorescence
elif isinstance(stream, ScannedRemoteTCStream):
return 85 # Stream for FLIM acquisition with time correlator
elif isinstance(stream, EMStream):
return 50 # can be done after any light
elif isinstance(stream,
(SEMCCDMDStream, SEMMDStream, SEMTemporalMDStream)):
return 40 # after standard (=survey) SEM
elif isinstance(stream, OverlayStream):
return 10 # after everything (especially after SEM and optical)
else:
logging.debug("Unexpected stream of type %s",
stream.__class__.__name__)
return 0
def test_center(self):
in_exp = [
((490e-9, 510e-9), 500e-9), # 2-float band
((490e-9, 497e-9, 500e-9, 503e-9, 510e-9), 500e-9), # 5-float band
(((490e-9, 510e-9), (820e-9, 900e-9)), (500e-9, 860e-9)
) # multi-band
]
for inp, exp in in_exp:
out = fluo.get_center(inp)
self.assertEqual(
exp, out,
"Failed while running with %s and got %s" % (inp, out))
def test_one_center_ex(self):
ex_band = (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)
ex_bands = ((650e-9, 660e-9, 675e-9, 678e-9,
680e-9), (780e-9, 785e-9, 790e-9, 800e-9, 812e-9),
(1034e-9, 1080e-9, 1100e-9, 1200e-9, 1500e-9))
# Excitation band should be smaller than the emission band used
in_exp = [
((ex_band, (490e-9, 510e-9)),
fluo.get_center(ex_band)), # only one band
((ex_bands, (490e-9, 497e-9, 500e-9, 503e-9, 510e-9)),
fluo.get_center(ex_bands[0])
), # nothing fitting, but should pick the smallest
((ex_bands, (690e-9, 697e-9, 700e-9, 703e-9, 710e-9)),
fluo.get_center(ex_bands[0])), # biggest below 700nm
((ex_bands, (790e-9, 797e-9, 800e-9, 803e-9, 810e-9)),
fluo.get_center(ex_bands[1])), # biggest below 800nm
]
for args, exp in in_exp:
out = fluo.get_one_center_ex(*args)
self.assertEqual(
exp, out,
"Failed while running with %s and got %s" % (args, out))
def _weight_stream(stream):
"""
Defines how much a stream is of priority (should be done first) for
acquisition.
stream (acq.stream.Stream): a stream to weight
returns (number): priority (the higher the more it should be done first)
"""
if isinstance(stream, FluoStream):
# Fluorescence ASAP to avoid bleaching
# If multiple fluorescence acquisitions: prefer the long emission
# wavelengths first because there is no chance their emission light
# affects the other dyes (and which could lead to a little bit of
# bleaching).
ewl_center = fluo.get_center(stream.emission.value)
if isinstance(ewl_center, collections.Iterable):
# multi-band filter, so fallback to guess based on excitation
xwl_center = fluo.get_center(stream.excitation.value)
if isinstance(ewl_center, collections.Iterable):
# also unguessable => just pick one "randomly"
ewl_bonus = ewl_center[0]
else:
ewl_bonus = xwl_center + 50e-6 # add 50nm as guesstimate for emission
else:
ewl_bonus = ewl_center # normally, between 0 and 1
return 100 + ewl_bonus
elif isinstance(stream, OpticalStream):
return 90 # any other kind of optical after fluorescence
elif isinstance(stream, EMStream):
return 50 # can be done after any light
elif isinstance(stream, (SEMCCDMDStream, SEMMDStream)):
return 40 # after standard (=survey) SEM
elif isinstance(stream, OverlayStream):
return 10 # after everything (especially after SEM and optical)
else:
logging.debug("Unexpected stream of type %s", stream.__class__.__name__)
return 0
def __init__(self, name, detector, dataflow, emitter, em_filter):
"""
name (string): user-friendly name of this stream
detector (Detector): the detector which has the dataflow
dataflow (Dataflow): the dataflow from which to get the data
emitter (Light): the HwComponent to modify the light excitation
filter (Filter): the HwComponent to modify the emission light filtering
"""
CameraStream.__init__(self, name, detector, dataflow, emitter)
self._em_filter = em_filter
# Emission and excitation are based on the hardware capacities.
# For excitation, compared to the hardware, only one band at a time can
# be selected. The difficulty comes to pick the default value. The best
# would be to use the current hardware value, but if the light is off
# there is no default value. In that case, we pick the emission value
# and try to pick a compatible excitation value: the first excitation
# wavelength below the emission. However, the emission value might also
# be difficult to know if there is a multi-band filter. In that case we
# just pick the lowest value.
# TODO: once the streams have their own version of the hardware settings
# and in particular light.power, it should be possible to turn off the
# light just by stopping the power, and so leaving the emissions as is.
em_choices = em_filter.axes["band"].choices.copy()
# convert any list into tuple, as lists cannot be put in a set
for k, v in em_choices.items():
em_choices[k] = conversion.ensureTuple(v)
# invert the dict, to directly convert the emission to the position value
self._emission_to_idx = dict((v, k) for k, v in em_choices.items())
cur_pos = em_filter.position.value["band"]
current_em = em_choices[cur_pos]
if isinstance(current_em[0], collections.Iterable):
# if multiband => pick the first one
em_band = current_em[0]
else:
em_band = current_em
center_em = fluo.get_center(em_band)
exc_choices = set(emitter.spectra.value)
current_exc = self._get_current_excitation()
if current_exc is None:
# pick the closest below the current emission
current_exc = min(exc_choices, key=lambda b: b[2]) # default to the smallest
for b in exc_choices:
# Works because exc_choices only contains 5-float tuples
if (b[2] < center_em and
center_em - b[2] < center_em - current_exc[2]):
current_exc = b
logging.debug("Guessed excitation is %s, based on emission %s",
current_exc, current_em)
self.excitation = model.VAEnumerated(current_exc, choices=exc_choices,
unit="m")
self.excitation.subscribe(self.onExcitation)
# The wavelength band on the out path (set when emission changes)
self.emission = model.VAEnumerated(current_em, choices=set(em_choices.values()),
unit="m")
self.emission.subscribe(self.onEmission)
# colouration of the image
default_tint = conversion.wave2rgb(center_em)
self.tint = model.ListVA(default_tint, unit="RGB") # 3-tuple R,G,B
self.tint.subscribe(self.onTint)
def __init__(self, name, detector, dataflow, emitter, em_filter, **kwargs):
"""
name (string): user-friendly name of this stream
detector (Detector): the detector which has the dataflow
dataflow (Dataflow): the dataflow from which to get the data
emitter (Light): the HwComponent to modify the light excitation
em_filter (Filter): the HwComponent to modify the emission light filtering
"""
super(FluoStream, self).__init__(name, detector, dataflow, emitter, **kwargs)
self._em_filter = em_filter
# Emission and excitation are based on the hardware capacities.
# For excitation, compared to the hardware, only one band at a time can
# be selected. The difficulty comes to pick the default value. The best
# would be to use the current hardware value, but if the light is off
# there is no default value. In that case, we pick the emission value
# and try to pick a compatible excitation value: the first excitation
# wavelength below the emission. However, the emission value might also
# be difficult to know if there is a multi-band filter. In that case we
# just pick the lowest value.
# TODO: once the streams have their own version of the hardware settings
# and in particular light.power, it should be possible to turn off the
# light just by stopping the power, and so leaving the emissions as is.
em_choices = em_filter.axes["band"].choices.copy()
# convert any list into tuple, as lists cannot be put in a set
for k, v in em_choices.items():
em_choices[k] = conversion.ensure_tuple(v)
# invert the dict, to directly convert the emission to the position value
self._emission_to_idx = {v: k for k, v in em_choices.items()}
cur_pos = em_filter.position.value["band"]
current_em = em_choices[cur_pos]
if isinstance(current_em[0], collections.Iterable):
# if multiband => pick the first one
em_band = current_em[0]
else:
em_band = current_em
center_em = fluo.get_center(em_band)
exc_choices = set(emitter.spectra.value)
current_exc = self._get_current_excitation()
if current_exc is None:
# pick the closest below the current emission
current_exc = min(exc_choices, key=lambda b: b[2]) # default to the smallest
for b in exc_choices:
# Works because exc_choices only contains 5-float tuples
if (b[2] < center_em and
center_em - b[2] < center_em - current_exc[2]):
current_exc = b
logging.debug("Guessed excitation is %s, based on emission %s",
current_exc, current_em)
self.excitation = model.VAEnumerated(current_exc, choices=exc_choices,
unit="m")
self.excitation.subscribe(self.onExcitation)
# The wavelength band on the out path (set when emission changes)
self.emission = model.VAEnumerated(current_em, choices=set(em_choices.values()),
unit="m")
self.emission.subscribe(self.onEmission)
# colouration of the image
self.tint.value = conversion.wave2rgb(center_em)
