calibration trigger refactor and cleanup

Makefile

@@ -32,5 +32,8 @@ clean:
 bci-gui:
 	python bcipy/gui/BCInterface.py
 
+viewer:
+	python bcipy/gui/viewer/data_viewer.py --file $(filepath)
+
 run-with-defaults:
 	bcipy

bcipy/display/rsvp/display.py

@@ -266,6 +266,7 @@ def __init__(
 
         # Trigger handling
         self.first_run = True
+        self.first_stim_time = None
         self.trigger_type = trigger_type
         self.trigger_callback = TriggerCallback()
         self.marker_writer = marker_writer or NullMarkerWriter()
@@ -326,25 +327,14 @@ def do_inquiry(self) -> List[float]:
         timing = []
 
         if self.first_run:
-            # play a inquiry start sound to help orient triggers
-            first_stim_timing = _calibration_trigger(
-                self.experiment_clock,
-                trigger_type=self.trigger_type, display=self.window,
-                on_trigger=self.marker_writer.push_marker)
-
-            timing.append(first_stim_timing)
-
-            self.first_stim_time = first_stim_timing[-1]
-            self.first_run = False
+            timing = self._trigger_pulse(timing)
 
         # generate a inquiry (list of stimuli with meta information)
         inquiry = self._generate_inquiry()
 
         # do the inquiry
         for idx in range(len(inquiry)):
 
-            self.is_first_stim = (idx == 0)
-
             # set a static period to do all our stim setting.
             #   will warn if ISI value is violated.
             self.staticPeriod.name = 'Stimulus Draw Period'
@@ -357,14 +347,15 @@ def do_inquiry(self) -> List[float]:
                 inquiry[idx]['sti_label'])
             self.window.callOnFlip(self.marker_writer.push_marker, inquiry[idx]['sti_label'])
 
+            # If this is the start of an inquiry and a callback registered for first_stim_callback evoke it
             if idx == 0 and callable(self.first_stim_callback):
                 self.first_stim_callback(inquiry[idx]['sti'])
 
             # Draw stimulus for n frames
             inquiry[idx]['sti'].draw()
             self.draw_static()
             self.window.flip()
-            core.wait((inquiry[idx]['time_to_present'] - 1) / self.refresh_rate)
+            core.wait(inquiry[idx]['time_to_present'])
 
             # End static period
             self.staticPeriod.complete()
@@ -383,6 +374,30 @@ def do_inquiry(self) -> List[float]:
 
         return timing
 
+    def _trigger_pulse(self, timing: List[str]) -> List[str]:
+        """Trigger Pulse.
+
+        This method uses a marker writer and calibration trigger to determine any functional
+            offsets needed for operation with this display. By setting the first_stim_time and searching for the
+            same stimuli output to the marker stream, the offsets between these proceses can be reconciled at the
+            beginning of an experiment. If drift is detected in your experiment, more frequent pulses and offset
+            correction may be required.
+        """
+        calibration_time = _calibration_trigger(
+            self.experiment_clock,
+            trigger_type=self.trigger_type,
+            display=self.window,
+            on_trigger=self.marker_writer.push_marker)
+
+        timing.append(calibration_time)
+
+        # set the first stim time if not present and first_run to False
+        if not self.first_stim_time:
+            self.first_stim_time = calibration_time[-1]
+            self.first_run = False
+
+        return timing
+
     def preview_inquiry(self) -> Tuple[List[float], bool]:
         """Preview Inquiry.
 
@@ -396,6 +411,9 @@ def preview_inquiry(self) -> Tuple[List[float], bool]:
         """
         # construct the timing to return and generate the content for preview
         timing = []
+        if self.first_run:
+            timing = self._trigger_pulse(timing)
+
         content = self._generate_inquiry_preview()
 
         # define the trigger callbacks. Here we use the trigger_callback to return immediately and a marker_writer
@@ -473,8 +491,7 @@ def _generate_inquiry(self):
         for idx in range(len(self.stimuli_inquiry)):
             current_stim = {}
 
-            # turn ms timing into frames! Much more accurate!
-            current_stim['time_to_present'] = int(self.stimuli_timing[idx] * self.refresh_rate)
+            current_stim['time_to_present'] = self.stimuli_timing[idx]
 
             # check if stimulus needs to use a non-default size
             if self.size_list_sti:
@@ -556,12 +573,12 @@ def wait_screen(self, message, color):
         try:
             wait_logo = visual.ImageStim(
                 self.window,
-                image='bcipy/static/images/gui_images/bci_cas_logo.png',
+                image='bcipy/static/images/gui/bci_cas_logo.png',
                 pos=(0, .5),
                 mask=None,
                 ori=0.0)
             wait_logo.size = resize_image(
-                'bcipy/static/images/gui_images/bci_cas_logo.png',
+                'bcipy/static/images/gui/bci_cas_logo.png',
                 self.window.size, 1)
             wait_logo.draw()
 

bcipy/display/tests/rsvp/test_rsvp_display.py

@@ -180,6 +180,7 @@ def test_preview_inquiry_evoked_press_to_accept_pressed(self):
         when(stim_mock).draw().thenReturn()
         when(self.rsvp).draw_static().thenReturn()
         when(self.rsvp.window).flip().thenReturn()
+        when(self.rsvp)._trigger_pulse(any()).thenReturn([])
 
         # skip the core wait for testing
         when(psychopy.core).wait(self.preview_inquiry.preview_inquiry_isi).thenReturn()
@@ -203,6 +204,7 @@ def test_preview_inquiry_evoked_press_to_skip_pressed(self):
         when(stim_mock).draw().thenReturn()
         when(self.rsvp).draw_static().thenReturn()
         when(self.rsvp.window).flip().thenReturn()
+        when(self.rsvp)._trigger_pulse(any()).thenReturn([])
 
         # skip the core wait for testing
         when(psychopy.core).wait(self.preview_inquiry.preview_inquiry_isi).thenReturn()
@@ -224,6 +226,7 @@ def test_preview_inquiry_evoked_press_to_accept_not_pressed(self):
         when(stim_mock).draw().thenReturn()
         when(self.rsvp).draw_static().thenReturn()
         when(self.rsvp.window).flip().thenReturn()
+        when(self.rsvp)._trigger_pulse(any()).thenReturn([])
 
         # skip the core wait for testing
         when(psychopy.core).wait(self.preview_inquiry.preview_inquiry_isi).thenReturn()
@@ -245,6 +248,7 @@ def test_preview_inquiry_evoked_press_to_skip_not_pressed(self):
         when(stim_mock).draw().thenReturn()
         when(self.rsvp).draw_static().thenReturn()
         when(self.rsvp.window).flip().thenReturn()
+        when(self.rsvp)._trigger_pulse(any()).thenReturn([])
 
         # skip the core wait for testing
         when(psychopy.core).wait(self.preview_inquiry.preview_inquiry_isi).thenReturn()

bcipy/gui/BCInterface.py

@@ -213,9 +213,9 @@ def build_images(self) -> None:
         Build add images needed for the UI. In this case, the OHSU and NEU logos.
         """
         self.add_image(
-            path='bcipy/static/images/gui_images/ohsu.png', position=[self.padding, 0], size=100)
+            path='bcipy/static/images/gui/ohsu.png', position=[self.padding, 0], size=100)
         self.add_image(
-            path='bcipy/static/images/gui_images/neu.png', position=[self.width - self.padding - 110, 0], size=100)
+            path='bcipy/static/images/gui/neu.png', position=[self.width - self.padding - 110, 0], size=100)
 
     def build_assets(self) -> None:
         """Build Assets.

bcipy/gui/README.md

@@ -19,7 +19,7 @@ experiments/FieldRegistry.py | GUI for creating new fields for experiment data c
 experiments/ExperimentField.py | GUI for collecting a registered experiment's field data.
 
 
-The folder 'bcipy/static/images/gui_images' contains images for the GUI.
+The folder 'bcipy/static/images/gui' contains images for the GUI.
 Parameters loaded by BCInterface parameter definition form can be found in 'bcipy/parameters/parameters.json'.
 
 To run the GUI, do so from the root, as follows:  

bcipy/gui/gui_main.py

@@ -852,7 +852,7 @@ def start_app() -> None:
     # ex.throw_alert_message(title='title', message='test', okay_to_exit=True)
     ex.get_filename_dialog()
     ex.add_button(message='Test Button', position=[200, 300], size=[100, 100], id=1)
-    # ex.add_image(path='../static/images/gui_images/bci_cas_logo.png', position=[50, 50], size=200)
+    # ex.add_image(path='../static/images/gui/bci_cas_logo.png', position=[50, 50], size=200)
     # ex.add_static_textbox(
     #   text='Test static text',
     #   background_color='black',

bcipy/gui/viewer/README.md

@@ -28,8 +28,6 @@ In addition to its use during an experiment, the Signal Viewer can be run from t
       -f FILE, --file FILE  path to the data file
       -s SECONDS, --seconds SECONDS
                             seconds to display
-      -d DOWNSAMPLE, --downsample DOWNSAMPLE
-                            downsample factor
       -r REFRESH, --refresh REFRESH
                             refresh rate in ms                       
 

bcipy/gui/viewer/data_viewer.py

@@ -46,11 +46,6 @@ def __init__(self,
 
         self.data_source = data_source
 
-        self.refresh_rate = refresh
-        self.samples_per_second = device_info.fs
-        self.records_per_refresh = int(
-            (self.refresh_rate / 1000) * self.samples_per_second)
-
         self.channels = device_info.channels
         self.removed_channels = ['TRG', 'timestamp']
         self.data_indices = self.init_data_indices()
@@ -64,6 +59,11 @@ def __init__(self,
         # Default filter
         self.filter = Downsample(self.downsample_factor)
 
+        self.refresh_rate = refresh
+        self.samples_per_second = device_info.fs
+        self.records_per_refresh = int(
+            (self.refresh_rate / 1000) * self.samples_per_second)
+
         self.autoscale = True
         self.y_min = -y_scale
         self.y_max = y_scale
@@ -322,7 +322,7 @@ def cursor_x(self):
 
     def init_data(self):
         """Initialize the data."""
-        channel_data = self.filter(self.current_data())
+        channel_data, _ = self.filter(self.current_data())
 
         for i, _channel in enumerate(self.data_indices):
             data = channel_data[i].tolist()
@@ -351,7 +351,7 @@ def update_view(self, _evt):
         """Called by the timer on refresh. Updates the buffer with the latest
         data and refreshes the plots. This is called on every tick."""
         self.update_buffer()
-        channel_data = self.filter(self.current_data())
+        channel_data, _ = self.filter(self.current_data())
 
         # plot each channel
         for i, _channel in enumerate(self.data_indices):

bcipy/helpers/stimuli.py

@@ -12,7 +12,8 @@
 from psychopy import core
 
 # Prevents pillow from filling the console with debug info
-logging.getLogger("PIL").setLevel(logging.WARNING)
+logging.getLogger('PIL').setLevel(logging.WARNING)
+DEFAULT_FIXATION_PATH = 'bcipy/static/images/main/PLUS.png'
 
 
 class InquirySchedule(NamedTuple):
@@ -59,13 +60,10 @@ def rsvp_inq_generator(query: list,
 
     # Init some lists to construct our stimuli with
     samples, times, colors = [], [], []
-    for idx_num in range(stim_number):
+    for _ in range(stim_number):
 
         # append a fixation cross. if not text, append path to image fixation
-        if is_txt:
-            sample = ['+']
-        else:
-            sample = ['bcipy/static/images/bci_main_images/PLUS.png']
+        sample = [get_fixation(is_txt)]
 
         # construct the sample from the query
         sample += [i for i in query]
@@ -168,13 +166,10 @@ def best_case_rsvp_inq_gen(alp: list,
 
     # Init some lists to construct our stimuli with
     samples, times, colors = [], [], []
-    for idx_num in range(stim_number):
+    for _ in range(stim_number):
 
         # append a fixation cross. if not text, append path to image fixation
-        if is_txt:
-            sample = ['+']
-        else:
-            sample = ['bcipy/static/images/bci_main_images/PLUS.png']
+        sample = [get_fixation(is_txt)]
 
         # construct the sample from the query
         sample += [i for i in query]
@@ -217,13 +212,13 @@ def random_rsvp_calibration_inq_gen(alp,
     len_alp = len(alp)
 
     samples, times, colors = [], [], []
-    for idx_num in range(stim_number):
+    for _ in range(stim_number):
         idx = np.random.permutation(np.array(list(range(len_alp))))
         rand_smp = (idx[0:stim_length])
         if not is_txt:
             sample = [
                 alp[rand_smp[0]],
-                'bcipy/static/images/bci_main_images/PLUS.png']
+                get_fixation(is_txt=False)]
         else:
             sample = [alp[rand_smp[0]], '+']
         rand_smp = np.random.permutation(rand_smp)
@@ -268,12 +263,9 @@ def target_rsvp_inquiry_generator(alp,
     # initialize our arrays
     samples, times, colors = [], [], []
     rand_smp = random.sample(range(len_alp), stim_length)
-    if is_txt:
-        sample = ['+']
-    else:
-        sample = ['bcipy/static/images/bci_main_images/PLUS.png']
-        target_letter = parameters['path_to_presentation_images'] + \
-            target_letter + '.png'
+    sample = [get_fixation(is_txt)]
+    target_letter = parameters['path_to_presentation_images'] + \
+        target_letter + '.png'
     sample += [alp[i] for i in rand_smp]
 
     # if the target isn't in the array, replace it with some random index that
@@ -419,7 +411,7 @@ def generate_icon_match_images(
                 image_array[target_image_numbers[inquiry]])
         # Add PLUS.png to image array TODO: get this from parameters file
         return_array[inquiry].append(
-            'bcipy/static/images/bci_main_images/PLUS.png')
+            get_fixation(is_txt=False))
 
         # Add target image to inquiry, if it is not already there
         if not target_image_numbers[inquiry] in random_number_array[
@@ -507,13 +499,10 @@ def play_sound(sound_file_path: str,
 
     #  if timing is wanted, get trigger timing for this sound stimuli
     if track_timing:
-        timing.append(trigger_name)
-        timing.append(experiment_clock.getTime())
-
-        # if there is a timing callback for sound, evoke it with the timing
-        # list
+        # if there is a timing callback for sound, evoke it
         if sound_callback is not None:
-            sound_callback(timing)
+            sound_callback(experiment_clock, trigger_name)
+        timing.append([trigger_name, experiment_clock.getTime()])
 
     # play our loaded sound and wait for some time before it's finished
     # NOTE: there is a measurable delay for calling sd.play. (~ 0.1 seconds;
@@ -544,3 +533,14 @@ def soundfiles(directory: str) -> Iterator[str]:
     if not directory.endswith(sep):
         directory += sep
     return itertools.cycle(glob.glob(directory + '*.wav'))
+
+
+def get_fixation(is_txt: bool) -> str:
+    """Get Fixation.
+
+    Return the correct stimulus fixation given the type (text or image).
+    """
+    if is_txt:
+        return '+'
+    else:
+        return DEFAULT_FIXATION_PATH

bcipy/helpers/tests/resources/mock_session/parameters.json

@@ -445,10 +445,10 @@
     "type": "str"
   },
   "alert_sounds_path": {
-    "value": "bcipy/static/sounds/rsvp_sounds/",
+    "value": "bcipy/static/sounds/rsvp/",
     "section": "bci_config",
     "readableName": "Alert sounds directory",
-    "helpTip": "Specifies the location of audio files to be presented with visual stimuli during the Alert Tone Calibration Task. This must be a directory ending with /. Default: bcipy/static/sounds/rsvp_sounds/",
+    "helpTip": "Specifies the location of audio files to be presented with visual stimuli during the Alert Tone Calibration Task. This must be a directory ending with /. Default: bcipy/static/sounds/rsvp/",
     "recommended_values": "",
     "type": "directorypath"
   },