Update terms to glossary

README.md

@@ -3,7 +3,7 @@
 
 ### What is it?
 
-It is Brain-computer interface software written in Python. It can function as a standalone or you can take the tools you need and start coding your own system.
+It is Brain-computer interface software written in Python. It can function as a standalone or you can take the tools you need and start coding your own system. See our official BciPy documentation including affliations and more context information here: https://bcipy.github.io/  (in progress).
 
 It should, based on our dependencies, work on most recent operating systems, however it has only been verified on Windows (7 & 10 Pro) and Mac OSx (High Sierra & Mojave) at this time. It won't build as is on Linux. Some additional work will be needed to install WxPython and pylsl.
 
@@ -60,7 +60,7 @@ To use all the goodies locally (including the GUI and demo scripts)
 If wanting the latest version from PyPi:
 1. `pip install bcipy`
 
-Alternatley, if [Make](http://www.mingw.org/) is installed, you may run the follow command to run install:
+Alternatley, if [Make](http://www.mingw.org/) is installed, you may run the follow command to install:
 
 ```sh
 # install in development mode
@@ -71,7 +71,7 @@ make dev-install
 
 Start by running `python bcipy/gui/BCInterface.py` in your command prompt or terminal. You may also invoke the experiment directly using command line tools for bci_main.py.
 
-Ex.`python bci_main.py` *this will use default parameters, user, experiment and task*
+Ex. `python bci_main.py` *this will use default parameters, user, experiment and task*
 
 You can pass it attributes with flags, if desired.
 
@@ -94,7 +94,7 @@ This a list of the major modules and their functionality. Each module will conta
 - `acquisition`: acquires data, gives back desired time series, saves to file at end of session.
 - `display`: handles display of stimuli on screen and passes back stimuli timing.
 - `signal`: eeg signal models, filters, processing, evaluators and viewers. 
-- `gui`: end-user interfaces which allow running of registered bci experiments, field collection and parameter editing.
+- `gui`: end-user interface into registered bci tasks and parameter editing. See BCInterface.py.
 - `helpers`: helpful functions needed for interactions between modules, basic I/O, and data visualization. 
 - `language_model`: gives probabilities of next letters during typing.
 - `parameters`: location of json parameters.
@@ -166,7 +166,7 @@ coverage report
 coverage html
 ```
 
-Alternatley, if Make is installed, you may run the follow command to run coverage and generate the html:
+Alternatley, if Make is installed, you may run the follow command to run coverage/pytest and generate the html:
 
 ```sh
 make coverage-html
@@ -194,16 +194,29 @@ Alternatley, if Make is installed, you may run the follow command to run autopep
 make lint
 ```
 
+## Glossary
+-----------
+
+***Stimuli***: A single letter, tone or image shown (generally in an inquiry). Singular = stimulus, plural = stimuli.
+
+***Trial***: A collection of data after a stimuli is shown. A----
+
+***Inquiry***: The set of stimuli after a fixation cross in a spelling task to gather user intent. A ---- B --- C ----
+
+***Series***: Each series contains at least one inquiry. A letter/icon decision is made after a series in a spelling task.
+
+
 ## Authorship
 --------------
 
 - Tab Memmott (OHSU)
+- Matthew Lawhead (OHSU)
 - Aziz Kocanaogullari (NEU)
-- Matthew Lawhead (OHSU- OCTRI)
-- Berkan Kadioglu (NEU)
+- Shiran Dudy (OHSU)
 - Dani Smektala (OHSU)
-- Ian Jackson (OHSU/ Reed)
+- Ian Jackson (Reed)
+- Alister Cedeño (OHSU)
+- Berkan Kadioglu (NEU)
+- Basak Celik (NEU)
 - Andac Demir (NEU)
 - Shaobin Xu (NEU)
-- Shiran Dudy (OHSU)
-- Basak Celik (NEU)

bci_main.py

@@ -140,7 +140,7 @@ def _clean_up_session(display, daq, server):
     # 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.
+    # the inquiry allows acquisition to properly shutdown.
     display.close()
 
     return True

bcipy/acquisition/README.md

@@ -131,7 +131,7 @@ Sampling frequency of the hardware in Hz. Default value = 256
 Downsampling order. Default value = 2
 #### Usage:
 
-Pass an input eeg np.array that is a matrix where every row is a channels data. For example a two channel EEG sequence could be:
+Pass an input eeg np.array that is a matrix where every row is a channels data. For example a two channel EEG inquiry could be:
 
 ```python
 input_seq = np.array([[1, 4, ...],

bcipy/display/matrix/display.py

@@ -7,7 +7,7 @@
 
 
 class MatrixDisplay:
-    """ Matrix Display Object for Sequence Presentation. Animates a sequence
+    """ Matrix Display Object for inquiry Presentation. Animates a inquiry
         in Matrix. Mode should be determined outside.
         Attr:
             task(visual_Text_Stimuli): task bar
@@ -124,8 +124,8 @@ def make_spelling_grid(self):
                     stim.draw()
                     self.stimuli.append(stim)
 
-    def do_sequence(self):
-        """ implements grid sequence """
+    def do_inquiry(self):
+        """ implements grid inquiry """
 
         # Stimulate rows
         for x in self.uniform_grid_values_row:
@@ -202,6 +202,6 @@ def determine_position_on_grid(row_idx, col_idx,
         matrix.draw_static()
 
         # animate!
-        matrix.do_sequence()
+        matrix.do_inquiry()
 
         time.sleep(2)

bcipy/display/rsvp/demo/demo_calibration_rsvp.py

@@ -81,7 +81,7 @@
     stim_font=font_sti,
     stim_pos=pos_sti,
     stim_height=sti_height,
-    stim_sequence=['a'] * 10,
+    stim_inquiry=['a'] * 10,
     stim_colors=['white'] * 10,
     stim_timing=[3] * 10,
     is_txt_stim=is_txt_stim)
@@ -95,18 +95,18 @@
     win.flip()
     rsvp.sti.height = sti_height
 
-    # Schedule a sequence
-    rsvp.stimuli_sequence = ele_sti[idx_o]
+    # Schedule a inquiry
+    rsvp.stimuli_inquiry = ele_sti[idx_o]
 
     if is_txt_stim:
         rsvp.stimuli_colors = color_sti[idx_o]
 
     rsvp.stimuli_timing = timing_sti[idx_o]
 
     core.wait(.4)
-    sequence_timing = rsvp.do_sequence()
+    inquiry_timing = rsvp.do_inquiry()
 
-    # _write_triggers_from_sequence_calibration(sequence_timing, trigger_file)
+    # _write_triggers_from_inquiry_calibration(inquiry_timing, trigger_file)
 
     core.wait(.5)
 

bcipy/display/rsvp/demo/demo_copyphrase_rsvp.py

@@ -82,7 +82,7 @@
     task_height=height_task,
     stim_font=font_sti, stim_pos=pos_sti,
     stim_height=sti_height,
-    stim_sequence=['a'] * 10, stim_colors=['white'] * 10,
+    stim_inquiry=['a'] * 10, stim_colors=['white'] * 10,
     stim_timing=[3] * 10,
     is_txt_stim=is_txt_stim)
 
@@ -98,29 +98,29 @@
     rsvp.sti.height = sti_height
 
     for idx in range(int(len(ele_sti) / 2)):
-        # Schedule a sequence
-        rsvp.stimuli_sequence = ele_sti[counter]
+        # Schedule a inquiry
+        rsvp.stimuli_inquiry = ele_sti[counter]
         if is_txt_stim:
             rsvp.stimuli_colors = color_sti[counter]
 
         rsvp.stimuli_timing = timing_sti[counter]
 
         #
         core.wait(.4)
-        sequence_timing = rsvp.do_sequence()
+        inquiry_timing = rsvp.do_inquiry()
 
-        # _write_triggers_from_sequence_copy_phrase(sequence_timing,
+        # _write_triggers_from_inquiry_copy_phrase(inquiry_timing,
         #                                           trigger_file, text_task,
         #                                           task_text[idx_o])
 
         core.wait(.5)
         counter += 1
 
     # Get stimuli parameters
-    rsvp.stim_sequence = ele_list_dec[idx_o]
+    rsvp.stim_inquiry = ele_list_dec[idx_o]
     rsvp.color_list_sti = ['green']
     rsvp.time_list_sti = [2]
-    rsvp.do_sequence()
+    rsvp.do_inquiry()
 
 win.close()
 # trigger_file.close()

bcipy/display/rsvp/display.py

@@ -12,9 +12,9 @@
 
 
 class RSVPDisplay(object):
-    """RSVP Display Object for Sequence Presentation.
+    """RSVP Display Object for inquiry Presentation.
 
-    Animates a sequence in RSVP. Mode should be determined outside.
+    Animates a inquiry in RSVP. Mode should be determined outside.
     """
 
     def __init__(
@@ -36,7 +36,7 @@ def __init__(
             stim_font='Times',
             stim_pos=(-.8, .9),
             stim_height=0.2,
-            stim_sequence: List[str] = ['a'] * 10,
+            stim_inquiry: List[str] = ['a'] * 10,
             stim_colors: List[str] = ['white'] * 10,
             stim_timing: List[float] = [1] * 10,
             is_txt_stim: bool = True,
@@ -74,7 +74,7 @@ def __init__(
         stim_height(float): height of the stimuli object
         stim_pos(tuple): position of stimuli
         stim_font(string): font of the stimuli
-        stim_sequence(list[string]): list of elements to flash
+        stim_inquiry(list[string]): list of elements to flash
         stim_colors(list[string]): list of colors for stimuli
         stim_timing(list[float]): timing for each letter flash
         """
@@ -83,7 +83,7 @@ def __init__(
 
         self.logger = logging.getLogger(__name__)
 
-        self.stimuli_sequence = stim_sequence
+        self.stimuli_inquiry = stim_inquiry
         self.stimuli_colors = stim_colors
         self.stimuli_timing = stim_timing
 
@@ -97,7 +97,7 @@ def __init__(
         self.marker_writer = marker_writer or NullMarkerWriter()
 
         # Length of the stimuli (number of flashes)
-        self.stim_length = len(stim_sequence)
+        self.stim_length = len(stim_inquiry)
 
         # Informational Parameters
         self.info_text = info_text
@@ -171,7 +171,7 @@ def schedule_to(self, ele_list=[], time_list=[], color_list=[]):
                 time_list(list[float]): list of timings of stimuli
                 color_list(list[string]): colors of elements of stimuli
         """
-        self.stimuli_sequence = ele_list
+        self.stimuli_inquiry = ele_list
         self.stimuli_timing = time_list
         self.stimuli_colors = color_list
 
@@ -188,17 +188,17 @@ def update_task(self, text: str, color_list: List[str], pos: Tuple[float]):
         self.task.color = color_list[0]
         self.task.pos = pos
 
-    def do_sequence(self):
-        """Do Sequence.
+    def do_inquiry(self):
+        """Do inquiry.
 
-        Animates a sequence of flashing letters to achieve RSVP.
+        Animates a inquiry of flashing letters to achieve RSVP.
         """
 
         # init an array for timing information
         timing = []
 
         if self.first_run:
-            # play a sequence start sound to help orient triggers
+            # 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,
@@ -209,11 +209,11 @@ def do_sequence(self):
             self.first_stim_time = first_stim_timing[-1]
             self.first_run = False
 
-        # generate a sequence (list of stimuli with meta information)
-        sequence = self._generate_sequence()
+        # generate a inquiry (list of stimuli with meta information)
+        inquiry = self._generate_inquiry()
 
-        # do the sequence
-        for idx in range(len(sequence)):
+        # do the inquiry
+        for idx in range(len(inquiry)):
 
             self.is_first_stim = (idx == 0)
 
@@ -226,17 +226,17 @@ def do_sequence(self):
             self.window.callOnFlip(
                 self.trigger_callback.callback,
                 self.experiment_clock,
-                sequence[idx]['sti_label'])
-            self.window.callOnFlip(self.marker_writer.push_marker, sequence[idx]['sti_label'])
+                inquiry[idx]['sti_label'])
+            self.window.callOnFlip(self.marker_writer.push_marker, inquiry[idx]['sti_label'])
 
             if idx == 0 and callable(self.first_stim_callback):
-                self.first_stim_callback(sequence[idx]['sti'])
+                self.first_stim_callback(inquiry[idx]['sti'])
 
             # Draw stimulus for n frames
-            sequence[idx]['sti'].draw()
+            inquiry[idx]['sti'].draw()
             self.draw_static()
             self.window.flip()
-            core.wait((sequence[idx]['time_to_present'] - 1) / self.refresh_rate)
+            core.wait((inquiry[idx]['time_to_present'] - 1) / self.refresh_rate)
 
             # End static period
             self.staticPeriod.complete()
@@ -255,13 +255,13 @@ def do_sequence(self):
 
         return timing
 
-    def _generate_sequence(self):
-        """Generate Sequence.
+    def _generate_inquiry(self):
+        """Generate inquiry.
 
-        Generate stimuli for next RSVP sequence.
+        Generate stimuli for next RSVP inquiry.
         """
         stim_info = []
-        for idx in range(len(self.stimuli_sequence)):
+        for idx in range(len(self.stimuli_inquiry)):
             current_stim = {}
 
             # turn ms timing into frames! Much more accurate!
@@ -274,17 +274,17 @@ def _generate_sequence(self):
                 this_stimuli_size = self.stimuli_height
 
             # Set the Stimuli attrs
-            if self.stimuli_sequence[idx].endswith('.png'):
+            if self.stimuli_inquiry[idx].endswith('.png'):
                 current_stim['sti'] = self.create_stimulus(mode='image', height_int=this_stimuli_size)
-                current_stim['sti'].image = self.stimuli_sequence[idx]
+                current_stim['sti'].image = self.stimuli_inquiry[idx]
                 current_stim['sti'].size = resize_image(
                     current_stim['sti'].image, current_stim['sti'].win.size, this_stimuli_size)
                 current_stim['sti_label'] = path.splitext(
-                    path.basename(self.stimuli_sequence[idx]))[0]
+                    path.basename(self.stimuli_inquiry[idx]))[0]
             else:
                 # text stimulus
                 current_stim['sti'] = self.create_stimulus(mode='text', height_int=this_stimuli_size)
-                txt = self.stimuli_sequence[idx]
+                txt = self.stimuli_inquiry[idx]
                 # customize presentation of space char.
                 current_stim['sti'].text = txt if txt != SPACE_CHAR else self.space_char
                 current_stim['sti'].color = self.stimuli_colors[idx]

bcipy/display/rsvp/mode/calibration.py

@@ -23,7 +23,7 @@ def __init__(self,
                  stim_font='Times',
                  stim_pos=(-.8, .9),
                  stim_height=0.2,
-                 stim_sequence=['a'] * 10,
+                 stim_inquiry=['a'] * 10,
                  stim_colors=['white'] * 10,
                  stim_timing=[1] * 10,
                  is_txt_stim=True,
@@ -57,7 +57,7 @@ def __init__(self,
             stim_font=stim_font,
             stim_pos=stim_pos,
             stim_height=stim_height,
-            stim_sequence=stim_sequence,
+            stim_inquiry=stim_inquiry,
             stim_colors=stim_colors,
             stim_timing=stim_timing,
             is_txt_stim=is_txt_stim,

bcipy/display/rsvp/mode/copy_phrase.py

@@ -41,7 +41,7 @@ def __init__(
             stim_font='Times',
             stim_pos=(-.8, .9),
             stim_height=0.2,
-            stim_sequence=['a'] * 10,
+            stim_inquiry=['a'] * 10,
             stim_colors=['white'] * 10,
             stim_timing=[1] * 10,
             is_txt_stim=True,
@@ -83,7 +83,7 @@ def __init__(
             stim_font=stim_font,
             stim_pos=stim_pos,
             stim_height=stim_height,
-            stim_sequence=stim_sequence,
+            stim_inquiry=stim_inquiry,
             stim_colors=stim_colors,
             stim_timing=stim_timing,
             is_txt_stim=is_txt_stim,