def execute(self, namespace):
from PYME.experimental import labview_spooling_hacks
from PYME.Analysis import piecewiseMapping
im = namespace[self.inputImage]
position, frames = labview_spooling_hacks.spoof_focus_from_metadata(im.mdh)
frame_nums = np.arange(im.data.shape[2])
zm = piecewiseMapping.piecewiseMap(0, frames, position, im.mdh['Camera.CycleTime'], xIsSecs=False)
z = zm[frame_nums]
namespace[self.outputName] = tabular.ColumnSource(z=z)
def _processEvents(ds, events, mdh):
"""Read data from events table and translate it into mappings for,
e.g. z position"""
eventCharts = []
ev_mappings = {}
if not events is None:
evKeyNames = set()
for e in events:
evKeyNames.add(e['EventName'])
if b'ProtocolFocus' in evKeyNames:
zm = piecewiseMapping.GeneratePMFromEventList(
events,
mdh,
mdh['StartTime'],
mdh['Protocol.PiezoStartPos'],
eventName=b'ProtocolFocus')
ev_mappings['z_command'] = zm
if b'PiezoOnTarget' in evKeyNames:
# Sometimes we also emit PiezoOnTarget events with the actual piezo position, rather than where we
# told it to go, use these preferentially
# TODO - deprecate in favour of, e.g. 'FocusOnTarget' events which are offset-corrected - see issue 766
from PYME.Analysis import piezo_movement_correction
spoofed_evts = piezo_movement_correction.spoof_focus_events_from_ontarget(
events, mdh)
zm = piecewiseMapping.GeneratePMFromEventList(
spoofed_evts,
mdh,
mdh['StartTime'],
mdh['Protocol.PiezoStartPos'],
eventName=b'ProtocolFocus')
ev_mappings['z_ontarget'] = zm
ev_mappings[
'piezo_moving'] = piecewiseMapping.bool_map_between_events(
events,
mdh,
b'ProtocolFocus',
b'PiezoOnTarget',
default=False)
# the z position we use for localizations gets the ontarget info if present
ev_mappings['zm'] = zm
eventCharts.append(('Focus [um]', zm, b'ProtocolFocus'))
if b'ScannerXPos' in evKeyNames:
x0 = 0
if 'Positioning.Stage_X' in mdh.getEntryNames():
x0 = mdh.getEntry('Positioning.Stage_X')
xm = piecewiseMapping.GeneratePMFromEventList(
events, mdh, mdh['StartTime'], x0, b'ScannerXPos', 0)
ev_mappings['xm'] = xm
eventCharts.append(('XPos [um]', xm, 'ScannerXPos'))
if b'ScannerYPos' in evKeyNames:
y0 = 0
if 'Positioning.Stage_Y' in mdh.getEntryNames():
y0 = mdh.getEntry('Positioning.Stage_Y')
ym = piecewiseMapping.GeneratePMFromEventList(
events, mdh, mdh.getEntry('StartTime'), y0, b'ScannerYPos', 0)
ev_mappings['ym'] = ym
eventCharts.append(('YPos [um]', ym, 'ScannerYPos'))
if b'ShiftMeasure' in evKeyNames:
driftx = piecewiseMapping.GeneratePMFromEventList(
events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure', 0)
drifty = piecewiseMapping.GeneratePMFromEventList(
events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure', 1)
driftz = piecewiseMapping.GeneratePMFromEventList(
events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure', 2)
ev_mappings['driftx'] = driftx
ev_mappings['drifty'] = drifty
ev_mappings['driftz'] = driftz
eventCharts.append(('X Drift [px]', driftx, 'ShiftMeasure'))
eventCharts.append(('Y Drift [px]', drifty, 'ShiftMeasure'))
eventCharts.append(('Z Drift [px]', driftz, 'ShiftMeasure'))
# self.eventCharts = eventCharts
# self.ev_mappings = ev_mappings
elif all(k in mdh.keys() for k in [
'StackSettings.FramesPerStep', 'StackSettings.StepSize',
'StackSettings.NumSteps', 'StackSettings.NumCycles'
]):
# TODO - Remove this code - anytime we get here it's generally the result of an error in the input data
# This should be handled upstream when spooling
logger.warning(
'Spoofing focus from metadata: this usually implies an error in the input data (missing events) and results might vary'
)
try:
# if we dont have events file, see if we can use metadata to spoof focus
from PYME.experimental import labview_spooling_hacks
position, frames = labview_spooling_hacks.spoof_focus_from_metadata(
mdh)
zm = piecewiseMapping.piecewiseMap(0,
frames,
position,
mdh['Camera.CycleTime'],
xIsSecs=False)
ev_mappings['z_command'] = zm
eventCharts.append(('Focus [um]', zm, b'ProtocolFocus'))
except:
# It doesn't really matter if this fails, print our traceback anyway
logger.exception('Error trying to fudge focus positions')
return ev_mappings, eventCharts
def _processEvents(ds, events, mdh):
"""Read data from events table and translate it into mappings for,
e.g. z position"""
eventCharts = []
ev_mappings = {}
if not events is None:
evKeyNames = set()
for e in events:
evKeyNames.add(e['EventName'])
if b'ProtocolFocus' in evKeyNames:
zm = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh['StartTime'], mdh['Protocol.PiezoStartPos'])
ev_mappings['zm'] = zm
eventCharts.append(('Focus [um]', zm, b'ProtocolFocus'))
if b'ScannerXPos' in evKeyNames:
x0 = 0
if 'Positioning.Stage_X' in mdh.getEntryNames():
x0 = mdh.getEntry('Positioning.Stage_X')
xm = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh['StartTime'], x0, b'ScannerXPos', 0)
ev_mappings['xm'] = xm
eventCharts.append(('XPos [um]', xm, 'ScannerXPos'))
if b'ScannerYPos' in evKeyNames:
y0 = 0
if 'Positioning.Stage_Y' in mdh.getEntryNames():
y0 = mdh.getEntry('Positioning.Stage_Y')
ym = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh.getEntry('StartTime'), y0, b'ScannerYPos', 0)
ev_mappings['ym'] = ym
eventCharts.append(('YPos [um]', ym, 'ScannerYPos'))
if b'ShiftMeasure' in evKeyNames:
driftx = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure',
0)
drifty = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure',
1)
driftz = piecewiseMapping.GeneratePMFromEventList(events, mdh, mdh.getEntry('StartTime'), 0, b'ShiftMeasure',
2)
ev_mappings['driftx'] = driftx
ev_mappings['drifty'] = drifty
ev_mappings['driftz'] = driftz
eventCharts.append(('X Drift [px]', driftx, 'ShiftMeasure'))
eventCharts.append(('Y Drift [px]', drifty, 'ShiftMeasure'))
eventCharts.append(('Z Drift [px]', driftz, 'ShiftMeasure'))
# self.eventCharts = eventCharts
# self.ev_mappings = ev_mappings
elif all(k in mdh.keys() for k in ['StackSettings.FramesPerStep', 'StackSettings.StepSize',
'StackSettings.NumSteps', 'StackSettings.NumCycles']):
# TODO - Remove this code - anytime we get here it's generally the result of an error in the input data
# This should be handled upstream when spooling
logger.warning('Spoofing focus from metadata: this usually implies an error in the input data (missing events) and results might vary')
try:
# if we dont have events file, see if we can use metadata to spoof focus
from PYME.experimental import labview_spooling_hacks
position, frames = labview_spooling_hacks.spoof_focus_from_metadata(mdh)
zm = piecewiseMapping.piecewiseMap(0, frames, position, mdh['Camera.CycleTime'], xIsSecs=False)
ev_mappings['zm'] = zm
eventCharts.append(('Focus [um]', zm, b'ProtocolFocus'))
except:
# It doesn't really matter if this fails, print our traceback anyway
logger.exception('Error trying to fudge focus positions')
return ev_mappings, eventCharts