Merge pull request #2 from drammock/api_brainstorming

notes from brainstorming mtg

Author: ashtondoane

src/ilabs_streamsync/example_script.py

@@ -0,0 +1,34 @@
+import mne
+
+from ilabs_streamsync import StreamSync, extract_audio_from_video
+
+# load an MNE raw file
+raw = None
+cam1 = None
+flux1 = None
+my_events = []
+
+
+subjects = ["146a", "222b"]
+
+for subj in subjects:
+    # construct the filename/path
+    # load the Raw
+    # figure out where video files are & load them
+    audio1 = extract_audio_from_video(cam1)
+
+    ss = StreamSync(raw, "STIM001")
+    ss.add_stream(audio1)
+    ss.add_camera_events(my_events)
+    ss.add_stream(flux1)
+    result = ss.do_syncing()
+    fig = ss.plot_sync()
+    annot = ss.add_camera_events(my_events)
+    raw.set_annotations(annot)
+    fig.savefig(...)
+    if result < 0.7:
+        write_log_msg(f"subj {subj} had bad pulse syncing, aborting")
+        continue
+
+    # apply maxfilter
+    # do ICA

src/ilabs_streamsync/streamsync.py

@@ -1,3 +1,47 @@
 class StreamSync:
-    def __init__(self):
+    """Synchronize two data streams.
+
+    Inputs: `mne.io.Raw` files, audio files (TODO which formats?),
+    and additional camera events.
+
+    Outputs: `mne.Annotations` object created from the camera events and
+    time-warped to the timescale of the `Raw`.
+    """
+
+    def __init__(self, reference_object, pulse_channel):
+        self.ref_stream = reference_object.get_chan(pulse_channel)
+        self.sfreq = reference_object.info["sfreq"]  # Hz
+        self.streams = []
+
+    def add_stream(self, stream, channel=None, events=None):
+        """Add a new ``Raw`` or video stream, optionally with events.
+
+        stream : Raw | wav
+            An audio or FIF stream.
+        channel : str | int | None
+            Which channel of `stream` contains the sync pulse sequence.
+        events : array-like | None
+            Events associated with the stream. TODO: should they be integer sample
+            numbers? Timestamps? Do we support both?
+        """
+        pulses = self._extract_pulse_sequence_from_stream(stream, channel=channel)
+        self.streams.append(pulses)
+
+    def _extract_pulse_sequence_from_stream(self, stream, channel):
+        # TODO triage based on input type (e.g., if it's a Raw, pull out a stim chan,
+        # if it's audio, just add it as-is)
         pass
+
+    def do_syncing(self):
+        """Synchronize all streams with the reference stream."""
+        # TODO (waves hands) do the hard part.
+        # TODO spit out a report of correlation/association between all pairs of streams
+        pass
+
+    def plot_sync(self):
+        pass
+
+
+def extract_audio_from_video(path_to_video, channel):
+    """Path can be a regex or glob to allow batch processing."""
+    pass