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determine z range for localization stacks from widefield stacks and queue them #906

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determine z range for localization stacks from widefield stacks and queue them #906

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cad2667
use state set and saw step in htsms-cal
barentine Feb 19, 2021
1df064f
stepped sparse-bead registration
barentine Feb 19, 2021
2a13c47
Merge branch 'htsmscal' of https://github.com/barentine/python-micros…
barentine Feb 27, 2021
ef03cba
swap to square scan instead of circular
barentine Feb 27, 2021
f6cb728
set stack settings for each series and allow them to be passed in dic…
barentine Feb 27, 2021
52da6ce
fix getScanChannel call
barentine Feb 27, 2021
d59149d
allow direction in scan without adding metadata key
barentine Feb 27, 2021
6de0363
add stack settings estimation
barentine Feb 27, 2021
86d5024
add focus
barentine Feb 27, 2021
86c295e
add z acquisition recipe
barentine Feb 27, 2021
5f8d62e
masked laplace metric
barentine Feb 28, 2021
0c68e80
dwelltime hack for widefield
barentine Feb 28, 2021
2d3c53e
fix subdir / metadata passing
barentine Feb 28, 2021
9848b2f
jitter cycles
barentine Feb 28, 2021
084586c
allow setting step size
barentine Feb 28, 2021
7198af3
update curr_cycle
barentine Feb 28, 2021
09ea5fa
Merge branch 'htsmscal' of https://github.com/barentine/python-micros…
barentine Feb 28, 2021
c45c908
set minimum range
barentine Feb 28, 2021
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stepped sparse-bead registration
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@barentine
barentine committed Feb 19, 2021
commit 1df064feebc0301cc13467bfc0e9fed1f8bcb185
0 PYME/Acquire/Protocols/htsms-calibration.py → PYME/Acquire/Protocols/htsms-cal-psf.py
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52 changes: 52 additions & 0 deletions PYME/Acquire/Protocols/htsms-cal-registration.py
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Original file line number Diff line number Diff line change
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from PYME.Acquire.protocol import *
from PYME.Acquire.Utils.pointScanner import PointScanner
import numpy as np
import logging

logger = logging.getLogger(__name__)

class Scanner(PointScanner):
def __init__(self, steps=10):
self._steps = radial_steps

def setup(self):
fs = np.array((scope.cam.size_x, scope.cam.size_y))
fov_size = np.mean(fs * np.array(scope.GetPixelSize()))

CircularPointScanner.__init__(self, scope, self._steps,
fov_size/self._steps, 1, 0,
False, True, trigger=True,
stop_on_complete=True,
return_to_start=True)
self.on_stop.connect(scope.spoolController.StopSpooling)
self.genCoords()

scanner = Scanner()

taskList = [
T(-1, scope.state.update, {
'Lasers.MPB560.On': True,
'Lasers.MPB560.Power': 0.0,
'Lasers.MPB642.On': True,
'Lasers.MPB642.Power': 0.0,
'Lasers.OBIS405.On': False,
'Lasers.OBIS488.On': False,
'Multiview.ActiveViews': [0, 1, 2, 3],
'Multiview.ROISize': [256, 256],
'Camera.IntegrationTime': 0.1,
}),
T(-1, scanner.setup),
T(0, scanner.start),
T(maxint, scope.turnAllLasersOff),
]

metaData = [
('Protocol.DataStartsAt', 0),
]

preflight = [] # no preflight checks

# must be defined for protocol to be discovered
PROTOCOL = TaskListProtocol(taskList, metaData, preflight, filename=__file__)
PROTOCOL_STACK = ZStackTaskListProtocol(taskList, 1, 3, metaData, preflight, slice_order='saw',
require_camera_restart=True, filename=__file__)