camera exposure time in lightsheet mode #808

annie-xd-wang · 2024-01-20T01:46:30Z

#630: The error has been fixed for the Hamamatsu Orca Fire camera. It was due to inaccuracies in exposure time calculation for that specific camera. If the same error occurs on other machines, I'll need to read the specific documentation.

Co-Authored-By: Annie Wang <6161065+annie-xd-wang@users.noreply.github.com>

codecov · 2024-01-20T02:14:10Z

Codecov Report

Attention: Patch coverage is 43.29897% with 110 lines in your changes are missing coverage. Please review.

Project coverage is 54.33%. Comparing base (58e6f1f) to head (05fd5c5).
Report is 4 commits behind head on develop.

Files	Patch %	Lines
.../navigate/model/devices/camera/camera_hamamatsu.py	0.00%	55 Missing ⚠️
src/navigate/view/custom_widgets/validation.py	13.33%	13 Missing ⚠️
src/navigate/controller/controller.py	30.76%	9 Missing ⚠️
src/navigate/model/microscope.py	60.86%	9 Missing ⚠️
...oller/sub_controllers/waveform_popup_controller.py	53.33%	7 Missing ⚠️
src/navigate/model/device_startup_functions.py	0.00%	5 Missing ⚠️
...troller/sub_controllers/channels_tab_controller.py	20.00%	4 Missing ⚠️
...vigate/model/devices/camera/camera_photometrics.py	0.00%	4 Missing ⚠️
...troller/sub_controllers/waveform_tab_controller.py	0.00%	2 Missing ⚠️
src/navigate/model/devices/daq/daq_ni.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #808      +/-   ##
===========================================
+ Coverage    54.26%   54.33%   +0.07%     
===========================================
  Files          154      154              
  Lines        17489    17444      -45     
===========================================
- Hits          9491     9479      -12     
+ Misses        7998     7965      -33

Flag	Coverage Δ
unittests	`54.33% <43.29%> (+0.07%)`	⬆️

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zacsimile · 2024-01-21T09:55:22Z

Awesome! That makes sense. Specs for 1H can be found for the Flash (our current assumed default) at https://www.hamamatsu.com/content/dam/hamamatsu-photonics/sites/static/sys/en/manual/C13440-20CU_IM_En.pdf, the Fusion BT at https://www.hamamatsu.com/content/dam/hamamatsu-photonics/sites/static/sys/en/manual/C15440-20UP,-20UP01_IM_En.pdf and the Lightning at https://www.hamamatsu.com/content/dam/hamamatsu-photonics/sites/static/sys/en/manual/C14120-20P_IM_En.pdf.

It's worth noting that 1H changes depending on the camera's mode of operation and a few other settings. My original thought was we could just let it throw the error, since I believe this is from our side of the code (which has a fixed rounding tolerate =/= 1H, line 1043 of HamamatsuAPI.py), since the camera automatically then does its rounding, and we pull the true exposure time for whatever the current 1H is back from the camera itself. Effectively, if we divide by a particular 1H for whatever condition we most commonly use, it will work for that condition and then still throw this error if the camera's mode of operation (and possibly exposure time, depending on the camera) is changed.

zacsimile · 2024-01-21T10:03:54Z

Looking at the code more closely, I don't fully understand why this fixes the error. Is properly_value_step as defined in line 1007 of HamamatsuAPI.py not equivalent to 1H? I think it should be.

@annie-xd-wang

@annie-xd-wang, @Sriya-235 and I were going over some of the basics of code review, and I probably went a bit too crazy. So, each type of Hamamatsu Camera has its own 1H/minimum exposure time value. Thus, it seems as if we should have this specified in their very own __init__ functions. Then we were a bit confused as well. Why is it that the methods for max_image_width, which are getters and setters, are both in the parent and child classes? It seems like we could eliminate a fair amount of code if these were only defined in the parent class. We created a new HamamatsuBase class in hopes of simplifying the children classes... For example, I think the calculate_exposure_time is only unique for the Hamamatsu Lightning camera...

annie-xd-wang · 2024-02-08T00:40:22Z

@zacsimile, I agree with you that properly_value_step, defined in line 1007 of the HamamatsuAPI, is intended to round up 1H. However, it didn't behave that way the last time I worked with the camera. I will double-check the value of properly_value_step for exposure time the next time I connect to a camera.

zacsimile · 2024-02-08T08:55:50Z

It didn't behave that way for me earlier, but I'm unclear as to why. I wondered if maybe it was returning 1H for a different exposure time. Maybe we need to set exposure time before line interval or vice versa to get the 1H to match. Or the logic is a bit different than I expect in the DCAM API.

Co-Authored-By: Annie Wang <6161065+annie-xd-wang@users.noreply.github.com>

annie-xd-wang · 2024-02-13T16:42:19Z

The minimum exposure time we get from the camera is 1H. Casting the exposure time according to the step size causes accuracy errors.

Evaluating new light-sheet calculation for ORCA FIRE

zacsimile · 2024-02-14T07:00:58Z

Nice find! Super weird that rounding to integer multiples the step size doesn't work, but glad it's working with the minimum now.

This reverts commit 387e583.

…ure_time_error

AdvancedImagingUTSW · 2024-03-12T05:43:58Z

I quickly tried to test it on a Mac, and I got the following error when running it in the continuous mode. However, when I tried to get the same error again, it did not happen. Seems somewhat random. Was in continuous mode, 3 channels selected, hit stop, and it threw the error.

Exception in thread live signal:
Traceback (most recent call last):
  File "/opt/miniconda3/envs/navigate/lib/python3.9/threading.py", line 973, in _bootstrap_inner
    self.run()
  File "/opt/miniconda3/envs/navigate/lib/python3.9/threading.py", line 910, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/S155475/Desktop/GitHub/navigate/src/navigate/model/model.py", line 1094, in run_live_acquisition
    self.signal_container.reset()
AttributeError: 'Model' object has no attribute 'signal_container'

AdvancedImagingUTSW · 2024-03-12T05:46:24Z

src/navigate/controller/sub_controllers/camera_setting_controller.py


        elif sensor_mode == "Light-Sheet":
            #  Progressive sensor mode operation
-            readout_time = exposure_time - 1 / (exposure_time + (vn + 10) * h)
+            readout_time = 0


Is this always the case? What happens if the exposure time is very short (e.g., 1 ms)?

AdvancedImagingUTSW · 2024-03-12T05:48:29Z

src/navigate/model/device_startup_functions.py

-                    devices["camera"][build_ref_name("_", device["type"], int(camera_serial_number, 8))] = camera
+                    try:
+                        oct_num = int(camera_serial_number, 8)
+                        devices["camera"][build_ref_name("_", device["type"], oct_num)] = camera


I still need to test this.

camera exposure time in lightsheet mode

08c4a7f

Co-Authored-By: Annie Wang <6161065+annie-xd-wang@users.noreply.github.com>

AdvancedImagingUTSW self-requested a review February 6, 2024 21:04

AdvancedImagingUTSW and others added 2 commits February 6, 2024 15:49

refactor

97c06b2

annie-xd-wang and others added 5 commits February 8, 2024 14:21

Merge branch 'develop' into fix_exposure_time_error

2b3d9c4

keep x_pixels and y_pixels

a29124a

exposure time in light-sheet mode

4d501bd

Co-Authored-By: Annie Wang <6161065+annie-xd-wang@users.noreply.github.com>

small fix

da3be65

Co-Authored-By: Annie Wang <6161065+annie-xd-wang@users.noreply.github.com>

update the line interval calculation for Hamamatsu Fire

0c5f13b

Quick updates

cc84b65

Evaluating new light-sheet calculation for ORCA FIRE

annie-xd-wang added 13 commits February 16, 2024 15:07

using fixed time

ff3966c

use milliseconds as the delay unit

90fa1df

calculate framerate in controller side

c1d6c2a

remove get_readout_function()

bdf0b4c

rename calculate_readout_time in controllers

6ed823a

update readout time and line interval calculation for Hamamatsu Fire

a16a157

using seconds in camera functions

36913b3

update exposure time in light-sheet mode

60fb75e

Merge branch 'develop' into fixed-timing

134acd2

automatically use minimum camera delay

387e583

verify configuration

d9c5869

Revert "automatically use minimum camera delay"

93aedf7

This reverts commit 387e583.

add fly back time in waveform popup window

6e14cf4

annie-xd-wang added 11 commits March 1, 2024 09:27

round up displaying exposure time

9f2389f

update tests

27cbf6d

Update test_model.py

7ab1e6d

Merge branch 'develop' into fix_exposure_time_error

a155a1e

update tests

243b791

update tests

a72fc2c

update tests

0aeb0ef

fix bug: serial number with leading zero but not an octal number

d21755a

update line interval calculation for Hamamatsu Lightning and Fusion

b118721

galvo frequency

d04f4bd

Merge branch 'camera_serial_number_with_leading_zeros' into fix_expos…

05fd5c5

…ure_time_error

AdvancedImagingUTSW reviewed Mar 12, 2024

View reviewed changes

AdvancedImagingUTSW approved these changes Mar 12, 2024

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AdvancedImagingUTSW merged commit c1c0d11 into develop Mar 12, 2024
1 check passed

This was referenced Mar 12, 2024

Cleanup Readout Time in Hamamatsu #823

Closed

Timing observations #817

Closed

Leading zeros (again) #836

Closed

annie-xd-wang mentioned this pull request Mar 12, 2024

828 save waveform constants with acquisition and generate method to load it #841

Merged

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camera exposure time in lightsheet mode #808

camera exposure time in lightsheet mode #808

annie-xd-wang commented Jan 20, 2024

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camera exposure time in lightsheet mode #808

camera exposure time in lightsheet mode #808

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