Merge branch 'develop'

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+# Recommend matching the black line length (default 88),
+# rather than using the flake8 default of 79:
+max-line-length = 88
+extend-ignore =
+    # See https://github.com/PyCQA/pycodestyle/issues/373
+    E203,

libbids/__init__.py

@@ -1,3 +1,8 @@
 from .dataset import Dataset
-from .clibbids import Subject
+from .clibbids import Subject  # type: ignore
 from .utils import qprompt
+
+
+Dataset
+Subject
+qprompt

libbids/dataset.py

@@ -2,13 +2,12 @@
 Supplemental pybids object for manipulating the dataset
 """
 import os
-import sys
 import json
 import pandas as pd  # type: ignore
 from bids.layout import BIDSLayout  # type: ignore
 from pathlib import Path
 from typing import Dict, List, Optional, cast
-from .clibbids import Subject
+from .clibbids import Subject  # type: ignore
 
 try:
     from PyQt6.QtWidgets import QMessageBox, QWidget  # type: ignore
@@ -105,11 +104,10 @@ def get_subjects(self) -> List[int]:
         -------
         List[int]
         """
-        participant_ids: List[str] = self.participant_table["participant_id"].values.tolist()
-        return [
-            int(ids[4:])
-            for ids in participant_ids
-        ]
+        participant_ids: List[str] = self.participant_table[
+            "participant_id"
+        ].values.tolist()
+        return [int(ids[4:]) for ids in participant_ids]
 
     def is_subject(self, idx: int) -> bool:
         """determins if the subject with the provided id exists

libbids/instruments/__init__.py

@@ -1,9 +1,13 @@
 from .instrument import Instrument
 from .eeg_instrument import EEGInstrument
 from .physio_instrument import PhysioInstrument
+from .read_instrument import ReadInstrument
 from .stim_instrument import StimInstrument
+from .write_instrument import WriteInstrument
 
 EEGInstrument
 Instrument
 PhysioInstrument
+ReadInstrument
 StimInstrument
+WriteInstrument

libbids/instruments/eeg_instrument.py

@@ -13,14 +13,14 @@
     cast,
 )
 
-from .instrument import Instrument
+from .read_instrument import ReadInstrument
 from ..enums import Modality
 
 if TYPE_CHECKING:
-    from ..session import Session
+    from ..session import Session  # type: ignore
 
 
-class EEGInstrument(Instrument):
+class EEGInstrument(ReadInstrument):
     """An instrumentation device capable of recording electroecephalograms"""
 
     def __init__(
@@ -105,6 +105,10 @@ def device_read(self) -> np.ndarray:
         fn, args, kwargs = cast(Tuple, self.read_fn)
         return self.device.__getattribute__(fn)(*args, **kwargs)
 
+    def flush(self) -> None:
+        """Read data from the device simply to discard"""
+        self.device_read()
+
     def read(self, remainder: bool = False) -> np.ndarray:
         """Read data from the headset and return the data
 

libbids/instruments/instrument.py

@@ -6,7 +6,7 @@
 from ..enums import Modality
 
 if TYPE_CHECKING:
-    from ..session import Session
+    from ..session import Session  # type: ignore
 
 
 class Instrument(ABC):

libbids/instruments/physio_instrument.py

@@ -5,7 +5,7 @@
 from ..enums import Modality
 
 if TYPE_CHECKING:
-    from ..session import Session
+    from ..session import Session  # type: ignore
 
 
 class PhysioInstrument(Instrument):
@@ -144,4 +144,3 @@ def _fixup_edf_metadata(self, metadata: Dict):
                     value = datetime.now()
             result.update({required_key: value})
         return result
-

libbids/instruments/read_instrument

@@ -0,0 +1 @@
+class ReadInstrument

libbids/instruments/read_instrument.py

@@ -0,0 +1,31 @@
+import numpy as np
+from abc import abstractmethod
+
+from .instrument import Instrument
+
+
+class ReadInstrument(Instrument):
+    """An instrument device capabale of recording data"""
+
+    @abstractmethod
+    def flush(self) -> None:
+        """Read from the device but throw away the data as a way to
+        clear any data buffers from the device"""
+        raise Exception("Method not implemented")
+
+    @abstractmethod
+    def read(self, remainder: bool = False) -> np.ndarray:
+        """Read data from the headset and return the data
+
+        Parameters
+        ----------
+        remainder : bool
+            Because EDFWriter only allows full seconds to be written, the last
+            time this function should be called is with remainder set to true
+
+        Returns
+        -------
+        np.ndarray
+            A 2D array of data in the shape of (channels, time)
+        """
+        raise Exception("Method not implemented")

libbids/instruments/stim_instrument.py

@@ -1,13 +1,13 @@
 from typing import Any, TYPE_CHECKING
 
-from .instrument import Instrument
+from .write_instrument import WriteInstrument
 from ..enums import Modality
 
 if TYPE_CHECKING:
-    from ..session import Session
+    from ..session import Session  # type: ignore
 
 
-class StimInstrument(Instrument):
+class StimInstrument(WriteInstrument):
     """Ann instrument device capable of sending a stimulus"""
 
     def __init__(
@@ -38,6 +38,6 @@ def start(self, task: str, run_id: str):
     def stop(self):
         self.device.stop()
 
-    def write(self, command: str):
+    def write(self, command: str) -> None:
         """a string command to send to the device"""
         self.device.write(command)

libbids/instruments/write_instrument.py

@@ -0,0 +1,17 @@
+from abc import abstractmethod
+
+from .instrument import Instrument
+
+
+class WriteInstrument(Instrument):
+
+    @abstractmethod
+    def write(self, command: str) -> None:
+        """A string command to send to the device
+
+        Parameters
+        ----------
+        command : str
+            The command to send to the device
+        """
+        raise Exception("Method not implemented")

libbids/run.py

@@ -4,8 +4,9 @@
 from pathlib import Path
 from typing import Any, List, Optional, TYPE_CHECKING, cast
 
-from .clibbids import Entity
+from .clibbids import Entity  # type: ignore
 from .event import Event
+from .instruments import ReadInstrument
 
 if TYPE_CHECKING:
     from .task import Task
@@ -55,6 +56,12 @@ def end_current_event(self) -> None:
             self.previous_event = self.current_event
             self.current_event = None
 
+    def flush_instruments(self) -> None:
+        """Flushes Read instruments"""
+        for ins in self.task.instruments:
+            if isinstance(ins, ReadInstrument):
+                ins.flush()
+
     def initialize_event_file(self) -> None:
         """Initializes the event file for writing"""
         if self.event_filepath.exists():
@@ -106,7 +113,7 @@ def start(self) -> None:
             self.task.on_event_start(self.current_event)
 
         # Throw away any samples collected during setup
-        self.task.process()
+        self.flush_instruments()
         while not self.done:
             # Handle events
             if self.is_current_event_finished():

libbids/task.py

@@ -4,7 +4,7 @@
 from datetime import timedelta
 from pathlib import Path
 from typing import Dict, List, Optional, TYPE_CHECKING
-from .clibbids import Entity
+from .clibbids import Entity  # type: ignore
 from .event import Event
 from .instruments import Instrument
 from .notes import Notes

libbids/utils.py

@@ -1,7 +1,7 @@
 try:
     from PyQt6.QtWidgets import QMessageBox, QPushButton  # type: ignore
 except ModuleNotFoundError:
-    from PyQt5.QtWidgets import QMessageBox, QPushButton # type: ignore
+    from PyQt5.QtWidgets import QMessageBox, QPushButton  # type: ignore
 
 
 def qprompt(msg: str, yes_button_text: str = "Yes", no_button_text: str = "No"):
@@ -29,7 +29,9 @@ def qprompt(msg: str, yes_button_text: str = "Yes", no_button_text: str = "No"):
 
     msgbox: QMessageBox = QMessageBox()
     msgbox.setText(msg)
-    yes_button: QPushButton = msgbox.addButton(yes_button_text, QMessageBox.YesRole)
-    msgbox.addButton(no_button_text, QMessageBox.NoRole)
-    QMessageBox.exec_(msgbox)
+    yes_button: QPushButton = msgbox.addButton(
+        yes_button_text, QMessageBox.YesRole  # type: ignore
+    )
+    msgbox.addButton(no_button_text, QMessageBox.NoRole)  # type: ignore
+    QMessageBox.exec_(msgbox)  # type: ignore
     return msgbox.clickedButton() == yes_button

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "libbids"
-version = "0.1.3"
+version = "0.1.4"
 description = "Library for generating data using the Brain Imaging Data Structure"
 authors = [ { name = "Kevin Davis", email = "[email protected]" } ]
 dependencies = [