VEP display #296

lawhead · 2023-09-28T01:04:46Z

Overview

Modified VEP Display to support a configurable number of text areas with provided positions, as well as configurable VEP stimulus that can use any size of checkerboard pattern.

Ticket

https://www.pivotaltracker.com/story/show/184564386

Contributions

Added a module for computing box positions and checkerboard patterns.
Updated the vep demo code.
Refactored the display code to use the new positions, simplifying stim creation.
Refactored the layout utilities to support computing square shapes in 'norm' units. Also refactored to support 'height' units.
Created a demo module for demonstrating various positional elements.

Test

Ran all demo code
Created unit tests for computations. Ran all unit tests.

Discussion

With just 4 text areas and a 2x2 checkerboard to represent each VEPStimuli, the flicker rate was able to render in the allotted 1 second. However, with 6 text areas, this increased the total number of stimuli to be rendered in each frame and the rendering of a single flicker took longer than 1 second. This problem was worse when the checkerboard size was increased to 3x3 or above. This is because each square on the checkerboard was represented using two shapes, a GratingStim for 'on' and one for 'off'. With 6 areas, this resulted in 48 visual shapes just to represent the stim.

I was able to reduce the number of stimuli by rendering each VEP Stim (checkerboard) as two visual shapes, a polygon with the primary color that has holes for each alternating square, and a backing square with the secondary color. On my local machine with 6 text boxes and 6 corresponding 5x5 checkerboards, the timing was able to complete in the allowed second. I put logging in place to confirm that this will work on other machines. If not, we can reduce the checkerboard size or draw fewer static elements.

vep_display.mov

…base

…ing layout elements.

…d as the responsibility of a VEPStim object. Added some debugging to report on stim timing

…cept demo for constructing a complex polygon with holes that may be used to generate a checkerboard using fewer visual stim.

…rboard, making rendering more efficient

celikbasak · 2023-10-04T18:47:42Z

bcipy/display/demo/components/demo_layouts.py

+    circle.draw()
+
+
+def draw_positions(win: visual.Window,


It seems like we decide the boundaries of the boxes here. Is there any way to extract the coordinates of individual symbols in a box?

This demo code is useful for visualizing a list of positions to se where they are at in the window. For example, I used this to confirm the checkerboard positions and layouts. It could also be used for matrix symbol positions. But to extract coordinates within a box I think you would need to add some interactivity.

I think it's probably better, though, to compute positions whenever possible. The layout module is useful for this. For instance, I could create a Layout based on the box corners and used its functions to compute the center, etc.

celikbasak

A lot of great work here!

celikbasak · 2023-10-04T19:06:48Z

bcipy/display/demo/vep/demo_calibration_vep.py

-    stim_font='Consolas',
-    timing=(1, 0.5, 4),  # prompt, fixation, stimuli
+    stim_font='Arial',
+    timing=(1, 0.5, 2, 4),  # prompt, fixation, animation, stimuli


Can we test these in a timing test? Only asking because I am worried there might be a lag as in Matrix case, where we set the stimulus duration as 0.25 but it ends up ~0.30s

We probably want to create a timing task specific to VEP. I had to modify how I represented the checkerboards because it was taking more than the 1 second to display the sequence. However, I based this decision on the experiment clock timings. It would be better to confirm these values with the photodiode.

This is more about how the do_inquiry method is implemented in the displays. We will time-test this code 👍🏼

tab-cmd

This is an excellent start for VEP. Thanks for the PR! Should the next task be a time-test calibration?

tab-cmd · 2023-10-09T18:09:57Z

bcipy/display/components/layout.py

+                units: str = 'norm') -> Tuple[float, float]:
+    """Scales the provided height value to reflect the aspect ratio of a
+    visual.Window. Used for creating squared stimulus. Returns (w,h) tuple"""
+    if units == 'height':


We should standardize to one unit type and assert that in our display... I use height in the inquiry preview, but it might be worth a refactor.

In practice I have been using norms for everything. When I finish working on the ticket for matrix row heights it should be easy to refactor Inquiry Preview to use that function to compute positions in 'norm' units.

tab-cmd · 2023-10-09T18:13:00Z

bcipy/display/demo/vep/demo_calibration_vep.py


 info = InformationProperties(
    info_color=['White'],
    info_pos=[(-.5, -.75)],
    info_height=[0.1],
-    info_font=['Consolas'],
+    info_font=['Arial'],


We want to use monospaced fonts—another possible display type assertion.

tab-cmd · 2023-10-09T18:14:56Z

bcipy/display/demo/vep/demo_calibration_vep.py

-win = visual.Window(size=[700, 700], fullscr=False, screen=1, allowGUI=False,
-                    allowStencil=False, monitor='testMonitor', color='black',
-                    colorSpace='rgb', blendMode='avg',
+win = visual.Window(size=[700, 700],


I know you didn't add this (feel free to kick to a ticket), but we should use:

window_parameters = { 'full_screen': False, 'window_height': 500, 'window_width': 500, 'stim_screen': 0, 'background_color': 'black' } win = init_display_window(window_parameters)

tab-cmd · 2023-10-09T18:15:26Z

bcipy/display/demo/vep/demo_calibration_vep.py

                    waitBlanking=False,
                    winType='pyglet')
 win.recordFrameIntervals = True
 frameRate = win.getActualFrameRate()

 print(f'Monitor refresh rate: {frameRate} Hz')

-clock = core.Clock()
+box_colors = ['#00FF80', '#FFFFB3', '#CB99FF', '#FB8072', '#80B1D3', '#FF8232']


What are these colors?

These were in the pivotal tracker ticket. I think when we implement the calibration task we should add a parameter for these.

tab-cmd · 2023-10-09T18:16:38Z

bcipy/display/demo/vep/demo_calibration_vep.py

-    stim_font='Consolas',
-    timing=(1, 0.5, 4),  # prompt, fixation, stimuli
+    stim_font='Arial',
+    timing=(1, 0.5, 2, 4),  # prompt, fixation, animation, stimuli


This is more about how the do_inquiry method is implemented in the displays. We will time-test this code 👍🏼

tab-cmd · 2023-10-09T18:17:55Z

bcipy/display/paradigm/vep/display.py

                self.window.flip()
+        ended_at = self.static_clock.getTime()
+        # TODO: should we have a trigger for VEP_STIM_END?


No, we know the stim length

We do know the stim length and how long this should take, but the issue that I encountered is that rendering was possibly taking longer than this. I got the timing on my local machine to mostly within the allotted stim length by using the multi-polygon checkerboards, but there is always some variation and I haven't yet tested with the full alphabet. Another trigger here would allow us to confirm that all stim happened with the correct timing, though maybe this should only be used in the timing task.

If we need to make adjustments, there are a couple ways to resolve this:

We could render fewer things: omit the static elements; use simpler checkerboard patterns such as 4x4 or 3x3, or use fewer boxes (4 instead of 6).

We could do a time check after every frame to ensure that we're still within the stim length. However, this may cut the pattern short and the check adds a little overhead to each frame.

tab-cmd · 2023-10-09T18:23:05Z

bcipy/display/paradigm/vep/layout.py

+
+    def validate(self):
+        """Validate invariants"""
+        assert self.num_boxes == 4 or self.num_boxes == 6, 'Number of boxes must be 4 or 6'


Is this still needed?

It's needed because it's possible to change these values between constructing the config and getting the positions. However, the code was repeated. I refactored to have the constructor use this method as well.

lawhead added 15 commits September 13, 2023 14:44

Updated VEP display and calibration demo to work with the latest code…

c81b4e3

…base

VEP Display cleanup

18daec4

Added functions to support height layout calculations

b3e1914

Added module for VEP layout calculations. Added a module for visualiz…

9bb1680

…ing layout elements.

Updated VEP layout to use the new calculated position information

da9ad0f

Code cleanup; clarified the use of timing parameters

9be5b06

Refactored VEP display to put the details of which visual stim is use…

b7efdac

…d as the responsibility of a VEPStim object. Added some debugging to report on stim timing

Added layout code for computing the envelope of a shape; proof of con…

ae68d96

…cept demo for constructing a complex polygon with holes that may be used to generate a checkerboard using fewer visual stim.

Refactored API of VEPStim

074e997

Refactored VEP stim to use a polygon with holes to represent a checke…

149560c

…rboard, making rendering more efficient

Cleaned up API for computing coordinates relative to another value

56493a4

Type fix

1dd5657

Cleanup and unit tests

195a058

Demo cleanup

5cbc5bd

Code cleanup and documentation

924c97f

lawhead requested review from tab-cmd and celikbasak September 28, 2023 01:04

celikbasak reviewed Oct 4, 2023

View reviewed changes

celikbasak approved these changes Oct 4, 2023

View reviewed changes

tab-cmd approved these changes Oct 9, 2023

View reviewed changes

lawhead added 2 commits October 9, 2023 13:55

Address PR feedback

dfef540

Fix lint error

ed81600

lawhead merged commit cd9e344 into 2.0.0rc4 Oct 9, 2023

lawhead deleted the vep-calib-display branch October 23, 2023 20:23

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VEP display #296

VEP display #296

lawhead commented Sep 28, 2023

celikbasak Oct 4, 2023

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VEP display #296

VEP display #296

Conversation

lawhead commented Sep 28, 2023

Overview

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Test

Discussion

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