Merge branch 'release/2.3.0'

Author: oliche

brainbox/ephys_plots.py

@@ -1,9 +1,10 @@
 import numpy as np
 from matplotlib import cm
-
+import matplotlib.pyplot as plt
 from brainbox.plot_base import (ImagePlot, ScatterPlot, ProbePlot, LinePlot, plot_line,
                                 plot_image, plot_probe, plot_scatter, arrange_channels2banks)
 from brainbox.processing import bincount2D, compute_cluster_average
+from ibllib.atlas.regions import BrainRegions
 
 
 def image_lfp_spectrum_plot(lfp_power, lfp_freq, chn_coords, chn_inds, freq_range=(0, 300),
@@ -372,3 +373,100 @@ def line_amp_plot(spike_amps, spike_depths, spike_times, chn_coords, d_bin=10, d
         fig, ax = plot_line(data.convert2dict())
         return data.convert2dict(), fig, ax
     return data
+
+
+def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, display=True, ax=None):
+    """
+    Plot brain regions along probe, if channel depths is provided will plot along depth otherwise along channel idx
+    :param channel_ids: atlas ids for each channel
+    :param channel_depths: depth along probe for each channel
+    :param brain_regions: BrainRegions object
+    :param display: whether to output plot
+    :param ax: axis to plot on
+    :return:
+    """
+
+    if channel_depths is not None:
+        assert channel_ids.shape[0] == channel_depths.shape[0]
+
+    br = brain_regions or BrainRegions()
+
+    region_info = br.get(channel_ids)
+    boundaries = np.where(np.diff(region_info.id) != 0)[0]
+    boundaries = np.r_[0, boundaries, region_info.id.shape[0] - 1]
+
+    regions = np.c_[boundaries[0:-1], boundaries[1:]]
+    if channel_depths is not None:
+        regions = channel_depths[regions]
+    region_labels = np.c_[np.mean(regions, axis=1), region_info.acronym[boundaries[1:]]]
+    region_colours = region_info.rgb[boundaries[1:]]
+
+    if display:
+        if ax is None:
+            fig, ax = plt.subplots()
+
+        for reg, col in zip(regions, region_colours):
+            height = np.abs(reg[1] - reg[0])
+            color = col / 255
+            ax.bar(x=0.5, height=height, width=1, color=color, bottom=reg[0], edgecolor='w')
+        ax.set_yticks(region_labels[:, 0].astype(int))
+        ax.yaxis.set_tick_params(labelsize=8)
+        ax.get_xaxis().set_visible(False)
+        ax.set_yticklabels(region_labels[:, 1])
+        ax.spines['right'].set_visible(False)
+        ax.spines['top'].set_visible(False)
+        ax.spines['bottom'].set_visible(False)
+
+        return fig, ax
+    else:
+        return regions, region_labels, region_colours
+
+
+def plot_cdf(spike_amps, spike_depths, spike_times, n_amp_bins=10, d_bin=40, amp_range=None, d_range=None,
+             display=False, cmap='hot'):
+    """
+    Plot cumulative amplitude of spikes across depth
+    :param spike_amps:
+    :param spike_depths:
+    :param spike_times:
+    :param n_amp_bins: number of amplitude bins to use
+    :param d_bin: the value of the depth bins in um (default is 40 um)
+    :param amp_range: amp range to use [amp_min, amp_max], if not given automatically computed from spike_amps
+    :param d_range: depth range to use, by default [0, 3840]
+    :param display: whether or not to display plot
+    :param cmap:
+    :return:
+    """
+
+    amp_range = amp_range or np.quantile(spike_amps, (0, 0.9))
+    amp_bins = np.linspace(amp_range[0], amp_range[1], n_amp_bins)
+    d_range = d_range or [0, 3840]
+    depth_bins = np.arange(d_range[0], d_range[1] + d_bin, d_bin)
+    t_bin = np.max(spike_times)
+
+    def histc(x, bins):
+        map_to_bins = np.digitize(x, bins)  # Get indices of the bins to which each value in input array belongs.
+        res = np.zeros(bins.shape)
+
+        for el in map_to_bins:
+            res[el - 1] += 1  # Increment appropriate bin.
+        return res
+
+    cdfs = np.empty((len(depth_bins) - 1, n_amp_bins))
+    for d in range(len(depth_bins) - 1):
+        spikes = np.bitwise_and(spike_depths > depth_bins[d], spike_depths <= depth_bins[d + 1])
+        h = histc(spike_amps[spikes], amp_bins) / t_bin
+        hcsum = np.cumsum(h[::-1])
+        cdfs[d, :] = hcsum[::-1]
+
+    cdfs[cdfs == 0] = np.nan
+
+    data = ImagePlot(cdfs.T, x=amp_bins * 1e6, y=depth_bins[:-1], cmap=cmap)
+    data.set_labels(title='Cumulative Amplitude', xlabel='Spike amplitude (uV)',
+                    ylabel='Distance from probe tip (um)', clabel='Firing Rate (Hz)')
+
+    if display:
+        fig, ax = plot_image(data.convert2dict(), fig_kwargs={'figsize': [3, 7]})
+        return data.convert2dict(), fig, ax
+
+    return data

brainbox/io/one.py

@@ -95,14 +95,24 @@ def _channels_traj2bunch(xyz_chans, brain_atlas):
     return channels
 
 
+def _channels_bunch2alf(channels):
+    channels_ = {
+        'mlapdv': np.c_[channels['x'], channels['y'], channels['z']] * 1e6,
+        'brainLocationIds_ccf_2017': channels['atlas_id'],
+        'localCoordinates': np.c_[channels['lateral_um'], channels['axial_um']]}
+    return channels_
+
+
 def _channels_alf2bunch(channels, brain_regions=None):
     # reformat the dictionary according to the standard that comes out of Alyx
     channels_ = {
         'x': channels['mlapdv'][:, 0].astype(np.float64) / 1e6,
         'y': channels['mlapdv'][:, 1].astype(np.float64) / 1e6,
         'z': channels['mlapdv'][:, 2].astype(np.float64) / 1e6,
         'acronym': None,
-        'atlas_id': channels['brainLocationIds_ccf_2017']
+        'atlas_id': channels['brainLocationIds_ccf_2017'],
+        'axial_um': channels['localCoordinates'][:, 1],
+        'lateral_um': channels['localCoordinates'][:, 0],
     }
     if brain_regions:
         channels_['acronym'] = brain_regions.get(channels_['atlas_id'])['acronym']
@@ -207,24 +217,33 @@ def _load_channels_locations_from_disk(eid, collection=None, one=None, revision=
             channels_aligned = one.load_object(eid, 'channels', collection=ac_collection)
             channels[probe] = channel_locations_interpolation(channels_aligned, channels[probe])
             # only have to reformat channels if we were able to load coordinates from disk
-            channels[probe] = _channels_alf2bunch(channels[probe], brain_regions=brain_regions)
+        channels[probe] = _channels_alf2bunch(channels[probe], brain_regions=brain_regions)
     return channels
 
 
-def channel_locations_interpolation(channels_aligned, channels):
+def channel_locations_interpolation(channels_aligned, channels, brain_regions=None):
     """
     oftentimes the channel map for different spike sorters may be different so interpolate the alignment onto
     if there is no spike sorting in the base folder, the alignment doesn't have the localCoordinates field
     so we reconstruct from the Neuropixel map. This only happens for early pykilosort sorts
     :param channels_aligned: Bunch or dictionary of aligned channels containing at least keys
-     'mlapdv' and 'brainLocationIds_ccf_2017' - those are the guide for the interpolation
+     'localCoordinates', 'mlapdv' and 'brainLocationIds_ccf_2017'
+     OR
+      'x', 'y', 'z', 'acronym', 'axial_um'
+      those are the guide for the interpolation
     :param channels: Bunch or dictionary of aligned channels containing at least keys 'localCoordinates'
-    :return: Bunch or dictionary of channels with extra keys 'mlapdv' and 'brainLocationIds_ccf_2017'
+    :param brain_regions: None (default) or ibllib.atlas.BrainRegions object
+     if None will return a dict with keys 'localCoordinates', 'mlapdv', 'brainLocationIds_ccf_2017
+     if a brain region object is provided, outputts a dict with keys
+      'x', 'y', 'z', 'acronym', 'atlas_id', 'axial_um', 'lateral_um'
+    :return: Bunch or dictionary of channels with brain coordinates keys
     """
     nch = channels['localCoordinates'].shape[0]
+    if set(['x', 'y', 'z']).issubset(set(channels_aligned.keys())):
+        channels_aligned = _channels_bunch2alf(channels_aligned)
     if 'localCoordinates' in channels_aligned.keys():
         aligned_depths = channels_aligned['localCoordinates'][:, 1]
-    else:
+    else:  # this is a edge case for a few spike sorting sessions
         assert channels_aligned['mlapdv'].shape[0] == 384
         NEUROPIXEL_VERSION = 1
         from ibllib.ephys.neuropixel import trace_header
@@ -238,7 +257,10 @@ def channel_locations_interpolation(channels_aligned, channels):
     # the brain locations have to be interpolated by nearest neighbour
     fcn_interp = interp1d(depth_aligned, channels_aligned['brainLocationIds_ccf_2017'][ind_aligned], kind='nearest')
     channels['brainLocationIds_ccf_2017'] = fcn_interp(depths)[iinv].astype(np.int32)
-    return channels
+    if brain_regions is not None:
+        return _channels_alf2bunch(channels, brain_regions=brain_regions)
+    else:
+        return channels
 
 
 def _load_channel_locations_traj(eid, probe=None, one=None, revision=None, aligned=False,
@@ -531,7 +553,7 @@ def merge_clusters_channels(dic_clus, channels, keys_to_add_extra=None):
     dic_clus : dict of one.alf.io.AlfBunch
         1 bunch per probe, containing cluster information
     channels : dict of one.alf.io.AlfBunch
-        1 bunch per probe, containing channels bunch with keys ('acronym', 'atlas_id')
+        1 bunch per probe, containing channels bunch with keys ('acronym', 'atlas_id', 'x', 'y', z', 'localCoordinates')
     keys_to_add_extra : list of str
         Any extra keys to load into channels bunches
 
@@ -541,7 +563,7 @@ def merge_clusters_channels(dic_clus, channels, keys_to_add_extra=None):
         clusters (1 bunch per probe) with new keys values.
     """
     probe_labels = list(channels.keys())  # Convert dict_keys into list
-    keys_to_add_default = ['acronym', 'atlas_id', 'x', 'y', 'z']
+    keys_to_add_default = ['acronym', 'atlas_id', 'x', 'y', 'z', 'axial_um', 'lateral_um']
 
     if keys_to_add_extra is None:
         keys_to_add = keys_to_add_default
@@ -550,10 +572,9 @@ def merge_clusters_channels(dic_clus, channels, keys_to_add_extra=None):
         keys_to_add = list(set(keys_to_add_extra + keys_to_add_default))
 
     for label in probe_labels:
-        try:
-            clu_ch = dic_clus[label]['channels']
-
-            for key in keys_to_add:
+        clu_ch = dic_clus[label]['channels']
+        for key in keys_to_add:
+            try:
                 assert key in channels[label].keys()  # Check key is in channels
                 ch_key = channels[label][key]
                 nch_key = len(ch_key) if ch_key is not None else 0
@@ -564,11 +585,9 @@ def merge_clusters_channels(dic_clus, channels, keys_to_add_extra=None):
                         f'Probe {label}: merging channels and clusters for key "{key}" has {nch_key} on channels'
                         f' but expected {max(clu_ch)}. Data in new cluster key "{key}" is returned empty.')
                     dic_clus[label][key] = []
-        except AssertionError:
-            _logger.warning(
-                f'Either clusters or channels does not have key {label}, could not'
-                f' merge')
-            continue
+            except AssertionError:
+                _logger.warning(f'Either clusters or channels does not have key {key}, could not merge')
+                continue
 
     return dic_clus
 

brainbox/io/spikeglx.py

@@ -128,9 +128,9 @@ def stream(pid, t0, nsecs=1, one=None, cache_folder=None, remove_cached=False, t
         samples_folder = Path(one.alyx._par.CACHE_DIR).joinpath('cache', typ)
 
     eid, pname = one.pid2eid(pid)
-    cbin_rec = one.list_datasets(eid, collection=f"*{pname}", filename='*ap.*bin', details=True)
-    ch_rec = one.list_datasets(eid, collection=f"*{pname}", filename='*ap.ch', details=True)
-    meta_rec = one.list_datasets(eid, collection=f"*{pname}", filename='*ap.meta', details=True)
+    cbin_rec = one.list_datasets(eid, collection=f"*{pname}", filename=f'*{typ}.*bin', details=True)
+    ch_rec = one.list_datasets(eid, collection=f"*{pname}", filename=f'*{typ}.ch', details=True)
+    meta_rec = one.list_datasets(eid, collection=f"*{pname}", filename=f'*{typ}.meta', details=True)
     ch_file = one._download_datasets(ch_rec)[0]
     one._download_datasets(meta_rec)[0]
 

brainbox/task/passive.py

@@ -200,12 +200,14 @@ def get_stim_aligned_activity(stim_events, spike_times, spike_depths, z_score_fl
     stim_activity = {}
     for stim_type, stim_times in stim_events.items():
 
+        # Get rid of any nan values
+        stim_times = stim_times[~np.isnan(stim_times)]
         stim_intervals = np.c_[stim_times - pre_stim, stim_times + post_stim]
         base_intervals = np.c_[stim_times - base_stim, stim_times - pre_stim]
         out_intervals = stim_intervals[:, 1] > times[-1]
 
-        idx_stim = np.searchsorted(times, stim_intervals)[np.invert(out_intervals)]
-        idx_base = np.searchsorted(times, base_intervals)[np.invert(out_intervals)]
+        idx_stim = np.searchsorted(times, stim_intervals, side='right')[np.invert(out_intervals)]
+        idx_base = np.searchsorted(times, base_intervals, side='right')[np.invert(out_intervals)]
 
         stim_trials = np.zeros((depths.shape[0], n_bins, idx_stim.shape[0]))
         noise_trials = np.zeros((depths.shape[0], n_bins_base, idx_stim.shape[0]))

ibllib/atlas/regions.py

@@ -149,6 +149,17 @@ def _mapping_from_regions_list(self, new_map, lateralize=False):
             mapind = mapind[iregion]
         return mapind
 
+    def remap(self, region_ids, source_map='Allen', target_map='Beryl'):
+        """
+        Remap atlas regions ids from source map to target map
+        :param region_ids: atlas ids to map
+        :param source_map: map name which original region_ids are in
+        :param target_map: map name onto which to map
+        :return:
+        """
+        _, inds = ismember(region_ids, self.id[self.mappings[source_map]])
+        return self.id[self.mappings[target_map][inds]]
+
 
 def regions_from_allen_csv():
     """

ibllib/dsp/voltage.py

@@ -206,7 +206,8 @@ def destripe(x, fs, tr_sel=None, neuropixel_version=1, butter_kwargs=None, k_kwa
     x = scipy.signal.sosfiltfilt(sos, x)
     # apply ADC shift
     if neuropixel_version is not None:
-        x = fshift(x, h['sample_shift'], axis=1)
+        sample_shift = h['sample_shift'] if (30000 / fs) < 10 else h['sample_shift'] * fs / 30000
+        x = fshift(x, sample_shift, axis=1)
     # apply spatial filter on good channel selection only
     x_ = kfilt(x, **k_kwargs)
     return x_