Output stim positions, capture screenshots, more cleanup #303

tab-cmd · 2023-11-20T22:09:11Z

Overview

Add functionality to output stimuli positions and capture a screenshot. The output also contains the screen size, and can be used to further adjust visualizations for greater accuracy (currently unused).

In addition, further typing and cleanup.

Ticket

Contributions

bcipy/config.py: add new matrix options
visualization.py: use new config path
offline_analysis.py: use new config path, extract from the session folder, and fix argument passing to visualization.
save.py: add a stimuli position export method
task.py: add export of positions, cleanup on tasks, remove unneeded abc method on task, typing, add calibration tests
feedback.py: deprecate level feedback (no tests and unused). We could potentially deprecate the Audio feedback for now as well...
matrix/display.py add capture screenshot method
.coveragerc: ignore the exceptions
requirements.txt: upgraded to lock PyQt6 dependancies failing Windows builds. See PyQt6: DLL load failed while importing QtGui: The specified procedure could not be found. altendky/pyqt-tools#105

Test

make test-all
bcipy --fake --task "Matrix Calibration" and ensured the output looked correct

Documentation

Are documentation updates required? In-line, README, or documentation? in-line and task/README.md updated.

Changelog

Is the CHANGELOG.md updated with your detailed changes? TODO!

tab-cmd · 2023-11-20T22:10:57Z

bcipy/task/paradigm/matrix/calibration.py

+                time = client.offset(
+                    self.matrix.first_stim_time) - self.matrix.first_stim_time
+                triggers.append(Trigger(label, TriggerType.OFFSET, time))
+            self.trigger_handler.add_triggers(triggers)

        # make sure triggers are written for the inquiry
        self.trigger_handler.add_triggers(convert_timing_triggers(timing, timing[0][0], self.trigger_type))

    def write_offset_trigger(self) -> None:


Updated this to match the recent update to support multiple device offsets.. I think this is correct @lawhead

Thanks, I just noticed this missing. Looks right to me.

tab-cmd · 2023-11-20T22:11:28Z

bcipy/task/tests/paradigm/rsvp/test_copy_phrase.py

@@ -23,7 +22,6 @@
 from bcipy.task.paradigm.rsvp.copy_phrase import RSVPCopyPhraseTask


-@pytest.mark.slow


I added this to help me on the typing PR. It was merged by accident!

celikbasak

Great additions! Thank you for including the calibration tests!
For symbol positions, maybe we can introduce a parameter/saving option in helpers/save.py for saving the units in Tobii for ease of use.

celikbasak · 2023-11-20T23:00:54Z

bcipy/display/paradigm/matrix/display.py

            grid[sym] = visual.TextStim(win=self.window,
                                        text=sym,
                                        color=self.grid_color,
                                        opacity=self.start_opacity,
-                                        pos=self.positions[pos_index],
+                                        pos=pos,


Is this the position in psychopy?

Yes, the visual.TextStim is a psychopy display component, so the position information is expected to be a valid psychopy format, depending on the units. When no units are provided it uses the default 'norm' units.

celikbasak · 2023-11-20T23:03:02Z

bcipy/helpers/save.py

+        screen_info: dict) -> str:
+    """Save stimuli positions and screen info to `path`
+
+   stimuli_position_info: {'A': (0, 0)}


Same question here, I think it would be more informative if we mentioned the units here (pyschopy, Tobii or maybe just the screen limits like (0,0), (1,1), (-1,-1))

Good idea, I'm happy to put those in the export as well. We will need to to some testing to see how these line up. I should have data to look at by EOD today.

celikbasak · 2023-11-20T23:05:09Z

bcipy/signal/model/offline_analysis.py

                show=show_figures,
-                raw_plot=True,
+                raw_plot=plot_points,


Good catch!

lawhead · 2023-11-21T00:14:18Z

bcipy/display/paradigm/matrix/display.py

+        """
+        # draw the grid and flip the window
+        self.draw_grid(opacity=self.full_grid_opacity)
+        self.task_bar.current_index = 0


I would't expect this method to mutate the object state. It seems like this has the potential to lead to some unexpected bugs. Maybe have a temp variable here and set it back to its previous value after the screenshot?

lawhead · 2023-11-21T00:20:52Z

bcipy/task/paradigm/matrix/calibration.py

+                time = client.offset(
+                    self.matrix.first_stim_time) - self.matrix.first_stim_time
+                triggers.append(Trigger(label, TriggerType.OFFSET, time))
+            self.trigger_handler.add_triggers(triggers)

        # make sure triggers are written for the inquiry
        self.trigger_handler.add_triggers(convert_timing_triggers(timing, timing[0][0], self.trigger_type))

    def write_offset_trigger(self) -> None:


Thanks, I just noticed this missing. Looks right to me.

lawhead · 2023-11-21T00:26:43Z

bcipy/helpers/save.py

+    assert 'screen_size_pixels' in screen_info.keys(), \
+        'screen_size_pixels must be a key in screen_info'
+    assert isinstance(screen_info['screen_size_pixels'], list), \
+        'screen_size_pixels must be a list'


Given the amount of input validation required would it make sense to have some stricter parameter types?

That's true with the new typing it should be mostly caught... I will remove some of this (minus key:value assert) and avoid a more explicit data structure for now.

lawhead · 2023-11-21T00:28:56Z

bcipy/display/paradigm/matrix/display.py

            grid[sym] = visual.TextStim(win=self.window,
                                        text=sym,
                                        color=self.grid_color,
                                        opacity=self.start_opacity,
-                                        pos=self.positions[pos_index],
+                                        pos=pos,


Yes, the visual.TextStim is a psychopy display component, so the position information is expected to be a valid psychopy format, depending on the units. When no units are provided it uses the default 'norm' units.

…on Windows

… a screen capture

tab-cmd added 3 commits November 18, 2023 21:55

stimuli position export + capture matrix grid

eb5529b

update offline analysis and gaze visualization

bc8907e

remove unneeded class variable

555a4dd

tab-cmd commented Nov 20, 2023

View reviewed changes

tab-cmd requested review from lawhead and celikbasak November 20, 2023 22:11

celikbasak approved these changes Nov 20, 2023

View reviewed changes

lawhead approved these changes Nov 21, 2023

View reviewed changes

tab-cmd added 7 commits November 21, 2023 14:15

dsi-flex and better starting parameters

6c05cb1

update the calibration tests to mock open and prevent testing issues …

a923063

…on Windows

revert parameter change

8b0df0b

update to workflow to fix Windows build

2dcf154

revert actions change, lock a pyqt6 dep

65d129c

remove unneeded assertions and save the current task bar index before…

c362ed8

… a screen capture

add more info to output, update CHANGELOG

b2e8e2a

tab-cmd merged commit 4102a83 into 2.0.0rc4 Dec 5, 2023
6 checks passed

tab-cmd deleted the output_stim_positions branch December 5, 2023 01:51

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Output stim positions, capture screenshots, more cleanup #303

Output stim positions, capture screenshots, more cleanup #303

tab-cmd commented Nov 20, 2023 •

edited

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lawhead Nov 21, 2023

		@@ -23,7 +22,6 @@
		from bcipy.task.paradigm.rsvp.copy_phrase import RSVPCopyPhraseTask


		@pytest.mark.slow

Output stim positions, capture screenshots, more cleanup #303

Output stim positions, capture screenshots, more cleanup #303

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tab-cmd commented Nov 20, 2023 • edited Loading

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tab-cmd commented Nov 20, 2023 •

edited

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