Merge pull request #57 from BciPy/1_3_1

Version 1.4.0

CHANGELOG.md

@@ -1,3 +1,27 @@
+# 1.4.0
+
+This release focused on bug fixes, exposing parameters, and refactoring. Further dual screen configuration and testing was done to allow for simultaneous signal viewing and task operation. 
+
+## Added
+
+    - Dual screen configuration / updated support
+    - Parameters:
+            - Copy phrase decision thresholds
+            - Inter-sequence Feedback level thresholds
+
+
+## Updated
+    - RSVP Display: refactor 
+    - Decision Maker / Evidence Fusion: refactor
+    - Signal Viewer: more distinct channel names
+    - bci_main: shutdown handling and bug fix
+    - Language Model Helper: bug fix for negative probabilities
+
+## Removed
+    - Multicolor Text
+    - Old LSL viewer
+
+
 # 1.3.0
 
 This release focused on the addition of a Signal Viewer, Inter-sequence Feedback Task, Signal Processing / Decomposition Methods, and miscellaneous cleanup. 

bci_main.py

@@ -57,10 +57,10 @@ def bci_main(parameters: dict, user: str, exp_type: int, mode: str) -> bool:
 
 
 def execute_task(task_type: dict, parameters: dict, save_folder: str) -> bool:
-    """Excecute Task.
+    """Execute Task.
 
     Executes the desired task by setting up the display window and
-        data acquisition, then passing on to the start_task funtion
+        data acquisition, then passing on to the start_task function
         which will initialize experiment.
 
     Input:
@@ -82,7 +82,7 @@ def execute_task(task_type: dict, parameters: dict, save_folder: str) -> bool:
         try:
             signal_model, filename = load_signal_model()
         except Exception as e:
-            logging.debug('Cannot load signal model. Exiting')
+            print(f'Cannot load signal model. Exiting. {e}')
             raise e
 
         # if Language Model enabled init lm
@@ -116,8 +116,6 @@ def execute_task(task_type: dict, parameters: dict, save_folder: str) -> bool:
 
 def _clean_up_session(display, daq, server):
     """Clean up session."""
-    # Close the display window
-    display.close()
 
     # Stop Acquisition
     daq.stop_acquisition()
@@ -126,6 +124,12 @@ def _clean_up_session(display, daq, server):
     if server:
         server.stop()
 
+    # Close the display window
+    # NOTE: There is currently a bug in psychopy when attempting to shutdown
+    # windows when using a USB-C monitor. Putting the display close last in
+    # the sequence allows acquisition to properly shutdown.
+    display.close()
+
     return True
 
 
@@ -141,6 +145,7 @@ def _clean_up_session(display, daq, server):
                                f" {task.value}")
                               for task in ExperimentType])
     parser = argparse.ArgumentParser()
+
     # Command line utility for adding arguments/ paths via command line
     parser.add_argument('-p', '--parameters', default='bcipy/parameters/parameters.json',
                         help='Parameter location. Must be in parameters directory. Pass as parameters/parameters.json')
@@ -151,7 +156,7 @@ def _clean_up_session(display, daq, server):
                         help='BCI mode. Ex. RSVP, MATRIX, SHUFFLE')
     args = parser.parse_args()
 
-    # Load a parameters file
+    # Load parameters
     parameters = load_json_parameters(args.parameters, value_cast=True)
 
     # Start BCI Main

bcipy/display/display_main.py

@@ -40,7 +40,7 @@ def init_display_window(parameters):
     display_window = visual.Window(
         size=[window_width,
               window_height],
-        screen=0,
+        screen=int(parameters['stim_screen']),
         allowGUI=False,
         useFBO=False,
         fullscr=full_screen,
@@ -51,98 +51,3 @@ def init_display_window(parameters):
 
     # Return display window to caller
     return display_window
-
-
-class MultiColorText(object):
-    """Multi Color Text.
-
-    Implementation of multi color Text Stimuli. Psychopy does not
-        support multiple color texts. Draws multiple TextStim elements on
-        the screen with different colors.
-
-    Attr:
-        texts(list[TextStim]): characters that form the string
-    """
-
-    def __init__(self, win, list_color=['red'] * 5, height=0.2,
-                 text='dummy_text', font='Times', pos=(0, 0), wrap_width=None,
-                 color_space='rgb', opacity=1, depth=-6.0):
-        """Initialize Multi Color Text.
-
-        Args:
-            win(visual_window): display window
-            text(string): string to be displayed
-            list_color(list[string]): list of colors of the string
-            height(float): height of each character
-            pos(tuple): center position of the multi color text
-
-            wrap_width, color_space, opacity, depth : to keep consistency
-                 of the visual object definition (required in TextStim)
-        """
-        self.win = win
-        self.pos = pos
-        self.text = text
-        self.font = font
-        self.height = height
-        self.list_color = list_color
-        self.wrap_width = wrap_width
-        self.color_space = color_space
-        self.opacity = opacity
-        self.depth = depth
-
-        self.texts = []
-
-        # Align characters using pixel wise operations
-        width_total_in_pix = 0
-        for idx in range(len(list_color)):
-            self.texts.append(
-                visual.TextStim(win=win, color=list_color[idx], height=height,
-                                text=text[idx], font=font, pos=(0, 0),
-                                wrapWidth=self.wrap_width,
-                                colorSpace=self.color_space,
-                                opacity=opacity, depth=depth))
-            # Bounding box provides pixel information of each letter
-            width_total_in_pix += self.texts[idx].boundingBox[0]
-
-        # Window goes from [-1,1], therefore we need to multiply by 2
-        x_pos_text = pos[0] - (width_total_in_pix / win.size[0])
-        for idx in range(len(list_color)):
-            len_txt = self.texts[idx].boundingBox[0] / win.size[0]
-            self.texts[idx].pos = (x_pos_text + len_txt, pos[1])
-            x_pos_text += len_txt * 2
-
-    def draw(self):
-        """Draw Multi Color Text."""
-        for idx in range(len(self.texts)):
-            self.texts[idx].draw()
-
-    def update(self, text, color_list, pos):
-        """Update (Re-creates) Multicolor Text Object.
-
-        It is more
-            compact to erase the previous one and recreate a new object.
-            Args:
-                text(string): string to be displayed
-                color_list(list[string]): list of colors of the string
-                pos(tuple): position of the multicolor text
-        """
-        # Align characters using pixel wise operations
-        width_total_in_pix = 0
-        self.texts = []
-        for idx in range(len(color_list)):
-            self.texts.append(
-                visual.TextStim(win=self.win, color=color_list[idx],
-                                height=self.height,
-                                text=text[idx], font=self.font, pos=(0, 0),
-                                wrapWidth=self.wrap_width,
-                                colorSpace=self.color_space,
-                                opacity=self.opacity, depth=self.depth))
-            # Bounding box provides pixel information of each letter
-            width_total_in_pix += self.texts[idx].boundingBox[0]
-
-        # Window goes from [-1,1], therefore we need to multiply by 2
-        x_pos_text = pos[0] - (width_total_in_pix / self.win.size[0])
-        for idx in range(len(color_list)):
-            len_txt = self.texts[idx].boundingBox[0] / self.win.size[0]
-            self.texts[idx].pos = (x_pos_text + len_txt, pos[1])
-            x_pos_text += len_txt * 2

bcipy/display/matrix/__init__.py

@@ -0,0 +1,3 @@
+import sys
+from os.path import dirname
+sys.path.append(dirname(__file__))

bcipy/display/matrix/matrix_disp.py → bcipy/display/matrix/display.py

@@ -6,7 +6,7 @@
 import logging
 
 
-class DisplayMatrix(object):
+class MatrixDisplay:
     """ Matrix Display Object for Sequence Presentation. Animates a sequence
         in Matrix. Mode should be determined outside.
         Attr:
@@ -16,36 +16,37 @@ class DisplayMatrix(object):
             sti(visual_Text_Stimuli): stimuli text
             trialClock(core_clock): timer for presentation """
 
-    def __init__(self, window, clock, experiment_clock, color_task='white',
-                 font_task='Times', pos_task=(-.75, .75), task_height=0.1,
+    def __init__(self, window, clock, experiment_clock, task_color='white',
+                 task_font='Times', task_pos=(-.75, .75), task_height=0.1,
                  grid_rows=6, grid_columns=6, time_flash=.25,
-                 text_task='1/100', color_text=['white'],
-                 font_text='Times', height_text=0.25,
-                 font_sti='Times', pos_sti=(0, .0), sti_height=0.25,
-                 is_txt_sti=True, alp=None):
+                 task_text='1/100',
+                 stim_font='Times',
+                 stim_pos=(0, .0),
+                 stim_height=0.25,
+                 is_txt_stim=True, alp=None):
 
         self.win = window
         self.logger = log = logging.getLogger(__name__)
 
         # TASK TEXT
-        self.font_task_text = font_task
+        self.task_font_text = task_font
         self.task_height = task_height
-        self.pos_task_text = pos_task
-        self.text_task = text_task
-        self.color_task = color_task
+        self.task_pos = task_pos
+        self.task_text = task_text
+        self.task_color = task_color
 
         # STIM / GRID
-        self.is_txt_sti = is_txt_sti
+        self.is_txt_stim = is_txt_stim
         self.stimuli = []
         self.rows = grid_rows
-        self.font = font_sti
+        self.stimuli_font = stim_font
         self.columns = grid_columns
-        self.sti_height = sti_height
+        self.stim_height = stim_height
 
         self.stim_number = grid_rows + grid_columns
 
-        self.max_height_grid = -1 + sti_height
-        self.max_width_grid = 1 - sti_height
+        self.max_height_grid = -1 + stim_height
+        self.max_width_grid = 1 - stim_height
         self.uniform_grid_values_row = sorted(
             np.linspace(
                 start=self.max_height_grid,
@@ -70,7 +71,7 @@ def __init__(self, window, clock, experiment_clock, color_task='white',
         self.expClock = experiment_clock
 
         # Length of the stimuli (number of stimuli on screen)
-        self.len_sti = len(self.stimuli)
+        self.stim_length = len(self.stimuli)
 
     def draw_static(self):
         """ Draws static elements in a stimulus. """
@@ -83,11 +84,11 @@ def draw_static(self):
             stim.draw()
 
         # Next, Draw the task text
-        task_text = visual.TextStim(win=self.win, color=self.color_task,
+        task_text = visual.TextStim(win=self.win, color=self.task_color,
                                     height=self.task_height,
-                                    text=self.text_task,
-                                    font=self.font_task_text,
-                                    pos=self.pos_task_text,
+                                    text=self.task_text,
+                                    font=self.task_font_text,
+                                    pos=self.task_pos,
                                     wrapWidth=None, colorSpace='rgb',
                                     opacity=1, depth=-6.0)
         task_text.draw()
@@ -100,7 +101,7 @@ def make_spelling_grid(self):
 
         # Loop through each row
         for idx in range(self.rows):
-            if self.is_txt_sti:
+            if self.is_txt_stim:
 
                 # loop through each column
                 for x in range(self.columns):
@@ -113,9 +114,9 @@ def make_spelling_grid(self):
                         self.uniform_grid_values_row)
 
                     stim = visual.TextStim(win=self.win,
-                                           height=self.sti_height,
+                                           height=self.stim_height,
                                            text=self.alp[alp_idx],
-                                           font=self.font, pos=pos,
+                                           font=self.stimuli_font, pos=pos,
                                            wrapWidth=None, colorSpace='rgb',
                                            opacity=1, depth=-6.0)
                     alp_idx += 1
@@ -183,11 +184,11 @@ def determine_position_on_grid(row_idx, col_idx,
         color='black')
 
     # Create a Display Matrix Object
-    matrix = DisplayMatrix(
+    matrix = MatrixDisplay(
         display_window,
         clock.MonotonicClock(),
         clock.MonotonicClock(),
-        text_task='')
+        task_text='')
 
     # draw matrix grid and other static
     matrix.draw_static()
@@ -196,7 +197,7 @@ def determine_position_on_grid(row_idx, col_idx,
     for i in range(task_length):
         task_index += 1
 
-        matrix.text_task = '%s/5' % task_index
+        matrix.task_text = '%s/5' % task_index
         matrix.draw_static()
 
         # animate!