436 multiposition table focus needs to be ignored when switching from low to high res

[annie-xd-wang]

Please test to see if it works with the device. Load feature "Decoupled Focus Stage Multiposition", run in "Customized" mode. Do not select "Enable Multi-Position" on the GUI. It works as (Loop) Move To the Next Position -> Autofocus -> ZStack.
Do not merge it. If-else for the Autofocus needs to be added in the feature sequence.

[codecov-commenter]

Codecov Report

Merging #437 (1a299a2) into develop (3d17990) will decrease coverage by 0.07%.
The diff coverage is 19.56%.

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@@             Coverage Diff             @@
##           develop     #437      +/-   ##
===========================================
- Coverage    41.81%   41.74%   -0.07%     
===========================================
  Files          151      151              
  Lines        13855    13902      +47     
===========================================
+ Hits          5793     5804      +11     
- Misses        8062     8098      +36     

Flag	Coverage Δ
unittests	41.74% <19.56%> (-0.07%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/aslm/config/config.py	47.05% <0.00%> (ø)
src/aslm/controller/controller.py	0.00% <0.00%> (ø)
...oller/sub_controllers/multi_position_controller.py	22.34% <0.00%> (ø)
src/aslm/model/devices/stages/stage_pi.py	30.33% <0.00%> (-1.81%)	⬇️
src/aslm/model/features/autofocus.py	13.20% <0.00%> (-0.26%)	⬇️
src/aslm/model/features/common_features.py	38.55% <20.00%> (-2.12%)	⬇️
src/aslm/model/model.py	34.14% <57.14%> (+0.23%)	⬆️

... and 1 file with indirect coverage changes

[AdvancedImagingUTSW]

Can we keep track of just the positions, without adding this?

[annie-xd-wang]

Yes, we could keep track of positions by using a specific LoopByPosition instead of a general LoopByCount feature.

[zacsimile]

Could LoopByCount by default keep track of the number of things it iterates over? Seems like this could be useful for timepoints and channels as well as positions.

[AdvancedImagingUTSW]

Notes from our conversation:

• Move from low to high-res.
• At the first position, determine the focus position at z[0] and z[-1] so that the focus ramp is known.
• At each subsequent position, determine the central focus position. The rate of focus change should remain unchanged. If this is too complex, we could possibly measure the focus position at z[0] and z[-1] on a per position basis.

There could also be an edge case where the non-ideal focus is found (e.g., it exists out of the specified range). I guess if the range is large enough, this shouldn't be a problem (we should find it).

[zacsimile]

I ran "Volume Search" and then "Decoupled Focus Stage Multiposition". The program threw a DAQ error

Traceback (most recent call last):
  File "C:\Users\DeanLab\.conda\envs\ASLM\lib\threading.py", line 973, in _bootstrap_inner
    self.run()
  File "C:\Users\DeanLab\.conda\envs\ASLM\lib\threading.py", line 910, in run
    self._target(*self._args, **self._kwargs)
  File "c:\users\deanlab\desktop\github\aslm\src\aslm\model\model.py", line 887, in run_acquisition
    self.snap_image()
  File "c:\users\deanlab\desktop\github\aslm\src\aslm\model\model.py", line 856, in snap_image
    self.active_microscope.daq.run_acquisition()
  File "c:\users\deanlab\desktop\github\aslm\src\aslm\model\devices\daq\daq_ni.py", line 427, in run_acquisition
    if self.camera_trigger_task.is_task_done():
  File "C:\Users\DeanLab\.conda\envs\ASLM\lib\site-packages\nidaqmx\task.py", line 520, in is_task_done
    check_for_error(error_code)
  File "C:\Users\DeanLab\.conda\envs\ASLM\lib\site-packages\nidaqmx\errors.py", line 127, in check_for_error
    raise DaqError(error_buffer.value.decode("utf-8"), error_code)
nidaqmx.errors.DaqError: Task specified is invalid or does not exist.
Status Code: -200088

The stage moved to its zero position, the program took one image and then stopped. Logs attached.
model_debug.log
view_controller_debug.log

[zacsimile]

Hang on. I think this might be an issue with multiposition_count not getting copied over.

[zacsimile]

Nope, same issue.
model_debug.log

[zacsimile]

Still moving to the zero stage position and then stopping.
model_debug.log
view_controller_debug.log

[annie-xd-wang]

Please add "robust_fit: True" under "AutoFocusParameters" in experiment.yml file.

[zacsimile]

Same problem.
model_debug.log
view_controller_debug.log

[zacsimile]

Now working as expected. Let's add unit tests for the multi-position feature and the new flag in z-stack.