BIDS DSI-24, ET Data, and 1020 support

CHANGELOG.md

@@ -3,7 +3,7 @@
 ## Contributions
 
 - BIDS
-  - Bundling support and refactor of `convert` module. See `demo_convert.py` #362
+  - Bundling support and refactor of `convert` module. See `demo_convert.py` #362 Add support for 1020 channels and eye tracker data #369
 - Library Refactor
   - Refactor `helpers` into `io` and `core` #362
 - Dependencies

README.md

@@ -190,7 +190,7 @@ This a list of the major modules and their functionality. Each module will conta
 - `feedback`: feedback mechanisms for sound and visual stimuli.
 - `gui`: end-user interface into registered bci tasks and parameter editing. See BCInterface.py.
 - `helpers`: helpful functions needed for interactions between modules and general utility.
-- `io`: load, save, and convert data files. Ex. BrainVision, EDF, MNE, CSV, JSON, etc.
+- `io`: load, save, and convert data files. Ex. BIDS, BrainVision, EDF, MNE, CSV, JSON, etc.
 - `language`: gives probabilities of next symbols during typing.
 - `main`: executor of experiments. Main entry point into the application
 - `parameters`: location of json parameters. This includes parameters.json (main experiment / app configuration) and device.json (device registry and configuration).

bcipy/core/demo/demo_report.py

@@ -31,7 +31,10 @@
     # if no path is provided, prompt for one using a GUI
     path = args.path
     if not path:
-        path = load_experimental_data()
+        path = load_experimental_data(
+            message="Select the folder containing the raw_data.csv, parameters.json and triggers.txt",
+            strict=True
+        )
 
     trial_window = (0, 1.0)
 

bcipy/core/demo/demo_session_tools.py

@@ -39,7 +39,7 @@ def main(data_dir: str):
     args = parser.parse_args()
     path = args.path
     if not path:
-        path = ask_directory()
+        path = ask_directory(strict=True)
 
     if args.db or args.csv or args.charts:
         session = read_session(Path(path, SESSION_DATA_FILENAME))

bcipy/core/raw_data.py

@@ -402,3 +402,34 @@ def sample_data(rows: int = 1000,
         data.append([timestamp] + channel_data + [trg])
 
     return data
+
+
+def get_1020_channels() -> List[str]:
+    """Returns the standard 10-20 channel names.
+
+    Note: The 10-20 system is a standard for EEG electrode placement. The following is not a complete list of all
+    possible channels, but the most common ones used in BCI research. This excludes the reference and ground channels.
+
+    Returns
+    -------
+    list of channel names
+    """
+    return [
+        'Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'T3', 'C3', 'Cz', 'C4',
+        'T4', 'T5', 'P3', 'Pz', 'P4', 'T6', 'O1', 'O2'
+    ]
+
+
+def get_1020_channel_map(channels_name: List[str]) -> List[int]:
+    """Returns a list of 1s and 0s indicating if the channel name is in the 10-20 system.
+
+    Parameters
+    ----------
+    channels_name : list of channel names
+
+    Returns
+    -------
+    list of 1s and 0s indicating if the channel name is in the 10-20 system
+    """
+    valid_channels = get_1020_channels()
+    return [1 if name in valid_channels else 0 for name in channels_name]

bcipy/core/tests/test_raw_data.py

@@ -12,7 +12,8 @@
 
 from bcipy.exceptions import BciPyCoreException
 from bcipy.core.raw_data import (RawData, RawDataReader, RawDataWriter,
-                                 load, sample_data, settings, write)
+                                 load, sample_data, settings, write,
+                                 get_1020_channel_map, get_1020_channels)
 
 
 class TestRawData(unittest.TestCase):
@@ -377,5 +378,25 @@ def test_data_by_channel_map_applies_transformation(self):
         verify(RawData, times=1).by_channel(transform)
 
 
+class Test1020(unittest.TestCase):
+    """Tests for 10-20 channel mapping functions."""
+
+    def test_get_1020_channels(self):
+        """Tests that the 10-20 channel map is correctly generated."""
+        channels = get_1020_channels()
+        self.assertEqual(19, len(channels))
+        self.assertTrue(isinstance(channels[0], str))
+
+    def test_get_1020_channel_map(self):
+        """Tests that the 10-20 channel map is correctly generated."""
+        # all but the last channel are valid 10-20 channels
+        channels = ['Fp1', 'Fp2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'invalid']
+        channel_map = get_1020_channel_map(channels)
+        self.assertEqual(10, len(channel_map))
+        self.assertEqual(0, channel_map[-1])
+        for i in range(len(channels) - 1):
+            self.assertEqual(1, channel_map[i])
+
+
 if __name__ == '__main__':
     unittest.main()

bcipy/gui/file_dialog.py

@@ -1,11 +1,13 @@
 # pylint: disable=no-name-in-module,missing-docstring,too-few-public-methods
 import sys
 from pathlib import Path
+from typing import Union
 
 from PyQt6 import QtGui
 from PyQt6.QtWidgets import QApplication, QFileDialog, QWidget
 
 from bcipy.preferences import preferences
+from bcipy.exceptions import BciPyCoreException
 
 DEFAULT_FILE_TYPES = "All Files (*)"
 
@@ -61,18 +63,22 @@ def ask_directory(self, directory: str = "", prompt: str = "Select Directory") -
 def ask_filename(
         file_types: str = DEFAULT_FILE_TYPES,
         directory: str = "",
-        prompt: str = "Select File") -> str:
-    """Prompt for a file.
+        prompt: str = "Select File",
+        strict: bool = False) -> Union[str, BciPyCoreException]:
+    """Prompt for a file using a GUI.
 
     Parameters
     ----------
     - file_types : optional file type filters; Examples: 'Text files (*.txt)'
     or 'Image files (*.jpg *.gif)' or '*.csv;;*.pkl'
     - directory : optional directory
+    - prompt : optional prompt message to display to users
+    - strict : optional flag to raise an exception if the user cancels the dialog. Default is False.
+        If False, an empty string is returned.
 
     Returns
     -------
-    path to file or None if the user cancelled the dialog.
+    path to file or raises an exception if the user cancels the dialog.
     """
     app = QApplication(sys.argv)
     dialog = FileDialog()
@@ -84,18 +90,29 @@ def ask_filename(
     if filename and path.is_file():
         preferences.last_directory = str(path.parent)
 
-    # Alternatively, we could use `app.closeAllWindows()`
-    app.quit()
+        # Alternatively, we could use `app.closeAllWindows()`
+        app.quit()
+
+        return filename
+
+    if strict:
+        raise BciPyCoreException('No file selected.')
+
+    return ''
 
-    return filename
 
+def ask_directory(prompt: str = "Select Directory", strict: bool = False) -> Union[str, BciPyCoreException]:
+    """Prompt for a directory using a GUI.
 
-def ask_directory(prompt: str = "Select Directory") -> str:
-    """Prompt for a directory.
+    Parameters
+    ----------
+    prompt : optional prompt message to display to users
+    strict : optional flag to raise an exception if the user cancels the dialog. Default is False.
+        If False, an empty string is returned.
 
     Returns
     -------
-    path to directory or None if the user cancelled the dialog.
+    path to directory or raises an exception if the user cancels the dialog.
     """
     app = QApplication(sys.argv)
 
@@ -107,7 +124,12 @@ def ask_directory(prompt: str = "Select Directory") -> str:
     if name and Path(name).is_dir():
         preferences.last_directory = name
 
-    # Alternatively, we could use `app.closeAllWindows()`
-    app.quit()
+        # Alternatively, we could use `app.closeAllWindows()`
+        app.quit()
+
+        return name
+
+    if strict:
+        raise BciPyCoreException('No directory selected.')
 
-    return name
+    return ''

bcipy/helpers/demo/demo_visualization.py

@@ -42,7 +42,10 @@
 
     path = args.path
     if not path:
-        path = load_experimental_data()
+        path = load_experimental_data(
+            message="Select the folder containing the raw_data.csv, parameters.json and triggers.txt",
+            strict=True
+        )
 
     parameters = load_json_parameters(f'{path}/{DEFAULT_PARAMETERS_FILENAME}',
                                       value_cast=True)

bcipy/helpers/offset.py

@@ -340,7 +340,7 @@ def extract_data_latency_calculation(
     args = parser.parse_args()
     data_path = args.data_path
     if not data_path:
-        data_path = ask_directory()
+        data_path = ask_directory(prompt="Please select a BciPy time test directory..", strict=True)
 
     # grab the stim length from the data directory parameters
     stim_length = load_json_parameters(f'{data_path}/{DEFAULT_PARAMETERS_FILENAME}', value_cast=True)['stim_length']

bcipy/io/README.md

@@ -2,6 +2,6 @@
 
 The BciPy IO module contains functionality for loading and saving data in various formats. This includes the ability to convert data to BIDS format, load and save raw data, and load and save triggers.
 
-- `convert`: functionality for converting the bcipy raw data output to other formats (currently, EDF)
-- `load`: methods for loading most BciPy data. For loading of triggers, see triggers.py
-- `save`: methods for saving BciPy data in supported formats. For saving of triggers, see triggers.py
+- `convert`: functionality for converting the bcipy raw data output to other formats (currently, BrainVision and EDF), and for converting the raw data to BIDS format.
+- `load`: methods for loading most BciPy data formats, including raw data and triggers.
+- `save`: methods for saving BciPy data in supported formats.