VEP calibration #304

lawhead · 2023-11-21T01:42:24Z

Overview

Created a new calibration task using the VEPDisplay.

Ticket

https://www.pivotaltracker.com/story/show/184564388
https://www.pivotaltracker.com/story/show/186126657

Contributions

Added a new calibration task
Updated the task registry
Refactored the target prompting and symbol animations for the VEP Display
Added functions for stimuli generation

Test

Ran unit tests, linting, and mypy
Ran VEP Calibration task

Discussion

For testing this locally, the following timing parameters worked well.
time_prompt: 4
time_fixation: 0.5
time_flash: 4

I created two followup issues:

https://www.pivotaltracker.com/story/show/186522989
https://www.pivotaltracker.com/story/show/186522657

…andling for symbols prior to putting them in boxes; updated VEP calib demo

…o boxes

…ze the rest

This reverts commit 437572ace09eb107aa09966e5a8360673131ea4d.

tab-cmd

Huge amount of effort here! I added some comments. The configurability one is the only thing I am requesting changes on before accepting.

It's ready to time test, I think? Please schedule a time to test it in the lab with me! I think we can use this with a photodiode as-is, but happy to wear the cap if that falls through.

tab-cmd · 2023-11-30T23:05:06Z

bcipy/parameters/parameters.json

+    "recommended_values": "",
+    "type": "float"
+  },
+  "vep_flicker_rates": {


I don't think we should support this kind of parameter configuration... We could do a range or discuss a different configuration strategy (task params). If this isn't a parameter we need to configure for an experiment, we can also set it ourselves. I'd support a code default and a separate PR to address configurability.

Okay, I'll do some refactoring here. I was mainly concerned about having consistent, known values between the calibration and a future copy phrase. I wasn't sure what values to use so I started with ones close the the Higger paper. I'm fine putting these elsewhere if we don't want them easily changeable.

Another option is to add List of Int or Float support to our parameters. Perhaps we can check-in with the team during demo to see what the short-term experiment needs are?

tab-cmd · 2023-12-04T19:04:45Z

bcipy/display/paradigm/vep/codes.py

+    # get the number of frames per flicker
+    length_flicker = refresh_rate / flicker_rate
+
+    if length_flicker.is_integer():


I am not sure you added this, so my apologies, but if this checks the type already, we could potentially do a if not length_flicker.is_integer() and avoid the cast?

The cast is needed below (line 62) for list generation: codes += [t] * length_flicker. If it's missing you get a TypeError that you can't multiply a sequence by a float.

tab-cmd · 2023-12-04T19:05:09Z

bcipy/display/paradigm/vep/codes.py

+    if length_flicker.is_integer():
+        length_flicker = int(length_flicker)
+    else:
+        err_message = f'flicker rate={flicker_rate} is not an integer multiple of refresh rate={refresh_rate}'


We could put the calculated value here too

tab-cmd · 2023-12-04T19:06:35Z

bcipy/display/paradigm/vep/layout.py

-            positions += [(layout.horizontal_middle, top),
-                          (layout.horizontal_middle, bottom)]
-        return positions
+        if self.num_boxes == 4:


We might consider making these a type (4by4VEP, etc) to help set other properties as well.

In this context the num_boxes refers to the number of display areas where a symbol can be sorted. The VEPStim is where the number of squares per checkerboard is defined. If we only ever want to fix this at 6 display areas, I can remove the conditional logic. The other idea here is that if we want a different layout we can provide another class with the same interface for generating these positions.

I like that last idea! Unless we are going to test 4 vs 6 in the short term, I think it would be easier to maintain cutting it out.

tab-cmd · 2023-12-04T19:08:20Z

bcipy/display/paradigm/vep/vep_stim.py

+
+        # Checkerboard is represented as a polygon with holes, backed by a
+        # simple square with the alternating color.
+        # This technique renders more efficiently and scales better than using


That's good to know. The only other VEP I could find used the GradientStim. Is the performance gain due to the decrease in objects drawn overall?

Yes, I tried various stim for this and there wasn't a significant difference. The main factor was the number of stim drawn.

tab-cmd · 2023-12-04T19:22:05Z

bcipy/task/paradigm/vep/calibration.py

+    """
+    if target == symbol:
+        return TriggerType.TARGET
+    return TriggerType.EVENT


We may need to support different TriggerTypes for this. A good question for the group at demo. What triggers will be needed for reshaping / future analysis. I added a few comments in the display that I know we will want.

tab-cmd · 2023-12-04T19:23:30Z

bcipy/task/paradigm/vep/calibration.py

+    def __init__(self, win: visual.Window, daq: ClientManager,
+                 parameters: Parameters, file_save: str):
+        super(VEPCalibrationTask, self).__init__()
+        self.num_boxes = 6


We could deprecate 4x4 until it is used if we are hardcoding. I'm thinking about long term maintainability and it would prevent some branching logic.

tab-cmd · 2023-12-04T19:24:02Z

bcipy/task/paradigm/vep/calibration.py

+
+
+def init_calibration_display(parameters: Parameters,
+                             window,


tab-cmd · 2023-12-04T19:25:49Z

bcipy/task/paradigm/vep/stim_generation.py

+            timing(list[list[float]]): list of timings
+            color(list(list[str])): list of colors)): scheduled inquiries
+    """
+    if timing is None:


I think it would be okay to fail without these instead of making optional.

tab-cmd · 2023-12-04T19:26:27Z

bcipy/task/paradigm/vep/stim_generation.py

+
+def generate_vep_inquiries(symbols: List[str],
+                           num_boxes: int = 6,
+                           inquiry_count: int = 20,


same here on defaults, it would make sense to have the caller define.

tab-cmd

The task runs as expected! Left a few cleanup items. This still needs to be tested more fully in the lab, but I'd be okay merging with some clean up and making follow-up VEP PRs to the rc or closing this and making future VEP PRs to this branch.

tab-cmd · 2023-12-22T19:54:41Z

bcipy/display/paradigm/vep/codes.py

+
+log = logging.getLogger(__name__)
+
+DEFAULT_FLICKER_RATES = [4, 5, 6, 10, 12, 15]


Having tested this now in lab, having these calculated or a default dictionary for different Hz would be helpful! This could live in config.py

I added more details for this to https://www.pivotaltracker.com/story/show/186641183.

tab-cmd · 2023-12-22T21:08:22Z

bcipy/task/paradigm/vep/calibration.py

+                                      stim_color=colors,
+                                      inquiry=[],
+                                      stim_length=1,
+                                      animation_seconds=1.0)


pull from parameters?

tab-cmd · 2023-12-22T21:13:38Z

bcipy/task/paradigm/vep/calibration.py

+                                  height=parameters['task_height'])
+
+    # issue #186641183 ; determine a better configuration strategy
+    flicker_rates = DEFAULT_FLICKER_RATES


We should log these

tab-cmd · 2023-12-22T21:14:36Z

bcipy/task/paradigm/vep/stim_generation.py

+                                   random_target_positions)
+
+
+def generate_vep_calibration_inquiries(alp: List[str],


These could go in helpers with the others. I'd be okay breaking our old pattern but wanna be consistent or make some tickets to clean up.

The stimuli module is getting pretty large and these functions seemed specific to this task. I also think they are more likely to change, so it made sense to me to split these out. I think it would be good to revisit the stimuli module and see if some of the things in there would make sense elsewhere. I'll create a ticket for that.

…than codes; added logging

lawhead added 21 commits October 20, 2023 09:59

Initial work on generating calibration inquiries for VEP

31ae2fd

Stubs for VEP calibration task

d1a0878

Updated stimuli generation for VEP; updated VEP display with better h…

071b83e

…andling for symbols prior to putting them in boxes; updated VEP calib demo

Merged latest from upstream

55c2a4f

Fixed error resulting from upstream merge

f854e76

VEP display changes for presenting a target and animating symbols int…

3b94689

…o boxes

Added code to highlight the box with the target symbol and de-emphasi…

0956e74

…ze the rest

Fix typing issues

5372445

Fix issue with VEP stimuli generation

dca547c

Add VEP calibration task

ac382b7

Refactor for clarity; fix typing issues

2352c46

Refactoring

630481b

New parameter for vep animation time

27d1ad0

New parameter for vep animation time

2423c42

Revert "New parameter for vep animation time"

7ae1f4e

This reverts commit 437572ace09eb107aa09966e5a8360673131ea4d.

Merged upstream changes

7f57016

Added missing import

348f671

Merged latest upstream

efba06a

Added configuration for VEP codes

df3673d

Added configuration for VEP codes

0418f64

Fixed issues with refresh rates

6e9f344

lawhead requested a review from tab-cmd November 21, 2023 01:44

tab-cmd requested changes Dec 4, 2023

View reviewed changes

lawhead added 7 commits December 7, 2023 17:17

Removed parameter for VEP flicker rate configuration

8cf0ce7

Removed option to layout VEP with 4 boxes

8e58b5b

Add missing property

e3510b2

Added typings; fixed linting; fixed broken tests

7381588

Merged latest upstream

a9e9ed6

Added debugging for frame rate

90aa3f2

Fixed bug in highlighting target box

b3371fe

lawhead added 3 commits December 12, 2023 14:40

Hide all letters before showing checkerboard stim

9283658

Merged latest upstream

11010ea

Merged latest upstream

29268f7

tab-cmd approved these changes Jan 8, 2024

View reviewed changes

Refactored VEP display to take a parameter for flicker_rates, rather …

172bedf

…than codes; added logging

lawhead merged commit a8856a0 into 2.0.0rc4 Jan 10, 2024
4 of 6 checks passed

lawhead deleted the vep-calib branch January 10, 2024 00:20

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VEP calibration #304

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		log = logging.getLogger(__name__)

		DEFAULT_FLICKER_RATES = [4, 5, 6, 10, 12, 15]

		random_target_positions)


		def generate_vep_calibration_inquiries(alp: List[str],

VEP calibration #304

VEP calibration #304

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lawhead commented Nov 21, 2023

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