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allow stack settings to be per-series #902

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barentine wants to merge 3 commits into from
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allow stack settings to be per-series #902

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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
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3 changes: 2 additions & 1 deletion PYME/Acquire/SpoolController.py
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Original file line number Diff line number Diff line change
Expand Up @@ -414,7 +414,8 @@ def StartSpooling(self, fn=None, stack=None, compLevel=None,
if stack:
protocol = protocol_z
protocol.dwellTime = z_dwell
#print(protocol)
stack_settings = stack if hasattr(stack, 'keys') else None
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@David-Baddeley David-Baddeley Feb 28, 2021

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Let me rest on it for a bit, but not 100% comfortable with the re-purposing of the boolean stack parameter. Can see arguments both ways ...

protocol.set_stack_positions(stack_settings)
else:
protocol = protocol

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18 changes: 11 additions & 7 deletions PYME/Acquire/protocol.py
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Expand Up @@ -192,11 +192,14 @@ def __init__(self, taskList, startFrame, dwellTime, metadataEntries=[], prefligh
self.slice_order = slice_order

self.require_camera_restart = require_camera_restart

def Init(self, spooler):
self.zPoss = np.arange(scope.stackSettings.GetStartPos(),
scope.stackSettings.GetEndPos() + .95 * scope.stackSettings.GetStepSize(),
scope.stackSettings.GetStepSize() * scope.stackSettings.GetDirection())

def set_stack_positions(self, stack_mdh=None):
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@David-Baddeley David-Baddeley Mar 1, 2021

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a) see PR #799 for re-factored StackSettings object. Any function to set one of these should either take a StackSettings object, or a dict of arguments (as provided by the http endpoints), not a metadata handler.

A dedicated object/handler is needed as some of the properties are computed rather than directly read, depending on stack mode (hard ends, or middle & number). It makes sense that the logic for computing these is in one place and not duplicated. Notably, this code will probably not do what you want as the default mode is middle & number. Protocol then uses it's own StackSettings object/the one that it gets passed rather than the scope one, leaving the rest of the code the same.

a) having this as a separate function (rather than in Init()) feels a bit off, but could grow on me.

stack_mdh = dict() if stack_mdh is None else stack_mdh
start = stack_mdh.get('StackSettings.StartPos', scope.stackSettings.GetStartPos())
stop = stack_mdh.get('StackSettings.EndPos', scope.stackSettings.GetEndPos())
direction = 1 if stop > start else -1
step = direction * stack_mdh.get('StackSettings.StepSize', scope.stackSettings.GetStepSize())
self.zPoss = np.arange(start, stop + .95 * step, step)

if self.slice_order != 'saw':
if self.slice_order == 'random':
Expand All @@ -208,9 +211,10 @@ def Init(self, spooler):
else:
# even
self.zPoss = np.concatenate([self.zPoss[::2], self.zPoss[-1::-2]])

self.piezoName = 'Positioning.%s' % stack_mdh.get('StackSettings.ScanPiezo', scope.stackSettings.GetScanChannel())


self.piezoName = 'Positioning.%s' % scope.stackSettings.GetScanChannel()
def Init(self, spooler):
self.startPos = scope.state[self.piezoName + '_target'] #FIXME - _target positions shouldn't be part of scope state
self.pos = 0

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