Merge branch 'develop' into postdlc_local

Author: juhuntenburg

brainbox/io/spikeglx.py

@@ -116,14 +116,13 @@ def stream(pid, t0, nsecs=1, one=None, cache_folder=None, remove_cached=False, t
     :param one: An instance of ONE
     :param cache_folder:
     :param typ: 'ap' or 'lf'
-    :return: sr, dsets, t0
+    :return: sr, t0
     """
-    CHUNK_DURATION_SECS = 1  # the mtscomp chunk duration. Right now it's a constant
     if nsecs > 10:
-        ValueError(f'Streamer works only with 10 or less seconds, set nsecs to lesss than {nsecs}')
+        ValueError(f'Streamer works only with 10 or less seconds, set nsecs to less than {nsecs}')
     assert one
     assert typ in ['lf', 'ap']
-    t0 = np.floor(t0 / CHUNK_DURATION_SECS) * CHUNK_DURATION_SECS
+
     if cache_folder is None:
         samples_folder = Path(one.alyx._par.CACHE_DIR).joinpath('cache', typ)
 
@@ -134,8 +133,13 @@ def stream(pid, t0, nsecs=1, one=None, cache_folder=None, remove_cached=False, t
     ch_file = one._download_datasets(ch_rec)[0]
     one._download_datasets(meta_rec)[0]
 
-    first_chunk = int(t0 / CHUNK_DURATION_SECS)
-    last_chunk = int((t0 + nsecs) / CHUNK_DURATION_SECS) - 1
+    import json
+    with open(ch_file) as fid:
+        chinfo = json.load(fid)
+    tbounds = np.array(chinfo['chunk_bounds']) / chinfo['sample_rate']
+    first_chunk = np.maximum(0, np.searchsorted(tbounds, t0 + 0.01) - 1)
+    last_chunk = np.maximum(0, np.searchsorted(tbounds, t0 + + 0.01 + nsecs) - 2)
+    t0 = tbounds[first_chunk]
 
     samples_folder.mkdir(exist_ok=True, parents=True)
     sr = spikeglx.download_raw_partial(

ibllib/dsp/voltage.py

@@ -280,19 +280,19 @@ def destripe(x, fs, neuropixel_version=1, butter_kwargs=None, k_kwargs=None, cha
     return x
 
 
-def destripe_lfp(x, fs):
+def destripe_lfp(x, fs, channel_labels=None, **kwargs):
     """
     Wrapper around the destipe function with some default parameters to destripe the LFP band
+    See help destripe function for documentation
     :param x:
     :param fs:
     :return:
     """
-    butter_kwargs = {'N': 3, 'Wn': 2 / fs * 2, 'btype': 'highpass'}
-    k_kwargs = {'ntr_pad': 60, 'ntr_tap': 0, 'lagc': None,
-                'butter_kwargs': {'N': 3, 'Wn': 0.001, 'btype': 'highpass'}}
-    # butterworth, for display only
-    channel_labels, channel_features = detect_bad_channels(x, fs=fs, psd_hf_threshold=1.4)
-    return destripe(x, fs, butter_kwargs=butter_kwargs, channel_labels=channel_labels, k_kwargs=k_kwargs)
+    kwargs['butter_kwargs'] = {'N': 3, 'Wn': 2 / fs * 2, 'btype': 'highpass'}
+    kwargs['k_filter'] = False
+    if channel_labels is True:
+        kwargs['channel_labels'], _ = detect_bad_channels(x, fs=fs, psd_hf_threshold=1.4)
+    return destripe(x, fs, **kwargs)
 
 
 def decompress_destripe_cbin(sr_file, output_file=None, h=None, wrot=None, append=False, nc_out=None, butter_kwargs=None,