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Proposed fix to allow inverted scope acquisitions #6

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Proposed fix to allow inverted scope acquisitions #6

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7 changes: 4 additions & 3 deletions scope/client_util/calibrate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,9 @@ def __init__(self, scope, min_exposure_ms=0.5, max_exposure_ms=1000, frames_to_a
self.exposure_times = []
with contextlib.ExitStack() as stack:
# set up all the scope states
stack.enter_context(scope.il.in_state(shutter_open=False))
stack.enter_context(scope.tl.in_state(shutter_open=False))
if hasattr(scope.il, 'shutter_open'): # Inverted scope doesn't have shutters.
stack.enter_context(scope.il.in_state(shutter_open=False))
stack.enter_context(scope.tl.in_state(shutter_open=False))
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I'd add a second if-block for the tl shutter open. Right now you're using hasattr(scope.il, 'shutter_open') as a proxy for "is this our inverted scope", which is a bit brittle. Here just test for each shutter and if it's present, open it.

stack.enter_context(scope.tl.lamp.in_state(enabled=False))
if hasattr(scope.il, 'spectra'):
stack.enter_context(scope.il.spectra.in_state(**{lamp+'_enabled': False for lamp in scope.il.spectra.lamp_specs.keys()}))
Expand Down Expand Up @@ -321,4 +322,4 @@ def _smooth_flat_field(image):
image = image[::2, ::2]
image = ndimage.median_filter(image, footprint=_m9)
image = ndimage.zoom(image, 2)
return ndimage.gaussian_filter(image, 5)
return ndimage.gaussian_filter(image, 5)
21 changes: 12 additions & 9 deletions scope/timecourse/timecourse_handler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,17 +153,20 @@ def configure_timepoint(self):
pass
assert self.scope.nosepiece.magnification == objective

self.scope.il.shutter_open = True
self.scope.il.spectra.lamps(**{lamp+'_enabled': False for lamp in self.scope.il.spectra.lamp_specs})
self.scope.tl.shutter_open = True
self.scope.tl.lamp.enabled = False
self.scope.tl.condenser_retracted = objective == 5 # only retract condenser for 5x objective
if self.TL_FIELD_DIAPHRAGM is not None:
self.scope.tl.field_diaphragm = self.TL_FIELD_DIAPHRAGM
if self.TL_APERTURE_DIAPHRAGM is not None:
self.scope.tl.aperture_diaphragm = self.TL_APERTURE_DIAPHRAGM
if self.IL_FIELD_WHEEL is not None:
self.scope.il.field_wheel = self.IL_FIELD_WHEEL

if hasattr(self.scope.il, 'shutter_open'): # For non-inverted scope acquisitions
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Again, it's a bit brittle to use hasattr(scope.il, 'shutter_open') in this way. I'd suggest for this change, you actually add a configuration variable to the class, like HAS_MOTORIZED_IL_TL or something. You then set that to false for acquisition scripts to be run on the inverted scope. (Putting each of the below into its own if-block seems a bit clumsy...)

Alternately, we add to the scope config a "scope name" attribute that we could test directly, rather than by proxy with the il.shutter_open thing.

self.scope.il.shutter_open = True
self.scope.tl.shutter_open = True
self.scope.tl.condenser_retracted = objective == 5 # only retract condenser for 5x objective
if self.TL_FIELD_DIAPHRAGM is not None:
self.scope.tl.field_diaphragm = self.TL_FIELD_DIAPHRAGM
if self.TL_APERTURE_DIAPHRAGM is not None:
self.scope.tl.aperture_diaphragm = self.TL_APERTURE_DIAPHRAGM
if self.IL_FIELD_WHEEL is not None:
self.scope.il.field_wheel = self.IL_FIELD_WHEEL

self.scope.il.filter_cube = self.experiment_metadata['filter_cube']
self.scope.camera.sensor_gain = '16-bit (low noise & high well capacity)'
self.scope.camera.readout_rate = self.PIXEL_READOUT_RATE
Expand Down