Merge branch 'release/2.10.1'

Author: juhuntenburg

brainbox/behavior/dlc.py

@@ -350,11 +350,12 @@ def plot_wheel_position(wheel_position, wheel_time, trials_df):
 
     plt.axvline(x=0, linestyle='--', c='k', label='stimOn')
     plt.axhline(y=-0.26, linestyle='--', c='g', label='reward')
+    plt.axhline(y=0.26, linestyle='--', c='g', label='reward')
     plt.ylim([-0.27, 0.27])
     plt.xlabel('time [sec]')
-    plt.ylabel('wheel position [rad]')
+    plt.ylabel('wheel position diff to first value [rad]')
     plt.legend(loc='center right')
-    plt.title('Wheel position')
+    plt.title('Wheel position trial avg\n(and individual trials)')
     plt.tight_layout()
 
     return plt.gca()
@@ -406,7 +407,7 @@ def plot_lick_hist(lick_times, trials_df):
     plt.plot(times, pd.DataFrame.from_dict(dict(zip(correct.index, incorrect.values))).mean(axis=1),
              c='gray', label='incorrect trial')
     plt.axvline(x=0, label='feedback', linestyle='--', c='purple')
-    plt.title('Lick events')
+    plt.title('Lick events trial avg')
     plt.xlabel('time [sec]')
     plt.ylabel('lick events [a.u.]')
     plt.legend(loc='lower right')
@@ -479,7 +480,7 @@ def plot_motion_energy_hist(camera_dict, trials_df):
     plt.xlabel('time [sec]')
     plt.axvline(x=0, label='stimOn', linestyle='--', c='k')
     plt.legend(loc='lower right')
-    plt.title('Motion Energy')
+    plt.title('Motion Energy trial avg\n(+/- std)')
     if len(missing_data) > 0:
         ax = plt.gca()
         ax.text(.95, .35, f"Data incomplete for\n{' and '.join(missing_data)} camera", color='r', fontsize=10,
@@ -523,7 +524,7 @@ def plot_speed_hist(dlc_df, cam_times, trials_df, feature='paw_r', cam='left', l
     plt.plot(times, pd.DataFrame.from_dict(dict(zip(incorrect.index, incorrect.values))).mean(axis=1),
              c='gray', label='incorrect trial')
     plt.axvline(x=0, label='stimOn', linestyle='--', c='r')
-    plt.title(f'{feature.split("_")[0].capitalize()} speed ({cam} cam)')
+    plt.title(f'{feature.capitalize()} speed trial avg\n({cam.upper()} cam)')
     plt.xticks([-0.5, 0, 0.5, 1, 1.5])
     plt.xlabel('time [sec]')
     plt.ylabel('speed [px/sec]')
@@ -559,8 +560,8 @@ def plot_pupil_diameter_hist(pupil_diameter, cam_times, trials_df, cam='left'):
         plt.plot(times, pupil_mean, label=align_to.split("_")[0], color=color)
         plt.fill_between(times, pupil_mean + pupil_std, pupil_mean - pupil_std, color=color, alpha=0.5)
     plt.axvline(x=0, linestyle='--', c='k')
-    plt.title(f'Pupil diameter ({cam} cam)')
+    plt.title(f'Pupil diameter trial avg\n({cam.upper()} cam)')
     plt.xlabel('time [sec]')
     plt.xticks([-0.5, 0, 0.5, 1, 1.5])
-    plt.ylabel('pupil diameter [px]')
+    plt.ylabel('z-scored smoothed pupil diameter [px]')
     plt.legend(loc='lower right', title='aligned to')

brainbox/ephys_plots.py

@@ -496,3 +496,30 @@ def histc(x, bins):
         return data.convert2dict(), fig, ax
 
     return data
+
+
+def image_raw_data(raw, fs, chn_coords=None, cmap='bone', title=None, display=False, gain=-90, **kwargs):
+
+    def gain2level(gain):
+        return 10 ** (gain / 20) * 4 * np.array([-1, 1])
+
+    ylabel = 'Channel index' if chn_coords is None else 'Distance from probe tip (um)'
+    title = title or 'Raw data'
+
+    y = np.arange(raw.shape[1]) if chn_coords is None else chn_coords[:, 1]
+
+    x = np.array([0, raw.shape[0] - 1]) / fs * 1e3
+
+    data = ImagePlot(raw, y=y, cmap=cmap)
+    data.set_labels(title=title, xlabel='Time (ms)',
+                    ylabel=ylabel, clabel='Power (uV)')
+    clim = gain2level(gain)
+    data.set_clim(clim=clim)
+    data.set_xlim(xlim=x)
+    data.set_ylim()
+
+    if display:
+        ax, fig = plot_image(data.convert2dict(), **kwargs)
+        return data.convert2dict(), fig, ax
+
+    return data

brainbox/io/one.py

@@ -8,11 +8,11 @@
 import pandas as pd
 from scipy.interpolate import interp1d
 
-from one.api import ONE
+from one.api import ONE, One
 import one.alf.io as alfio
+from one.alf import cache
 
 from iblutil.util import Bunch
-
 from ibllib.io import spikeglx
 from ibllib.io.extractors.training_wheel import extract_wheel_moves, extract_first_movement_times
 from ibllib.ephys.neuropixel import SITES_COORDINATES, TIP_SIZE_UM, trace_header
@@ -872,10 +872,15 @@ def load_channels_from_insertion(ins, depths=None, one=None, ba=None):
 class SpikeSortingLoader:
     """
     Object that will load spike sorting data for a given probe insertion.
-
-
+    This class can be instantiated in several manners
+    - With Alyx database probe id:
+            SpikeSortingLoader(pid=pid, one=one)
+    - With Alyx database eic and probe name:
+            SpikeSortingLoader(eid=eid, pname='probe00', one=one)
+    - From a local session and probe name:
+            SpikeSortingLoader(session_path=session_path, pname='probe00')
     """
-    one: ONE
+    one: ONE = None
     atlas: None = None
     pid: str = None
     eid: str = ''
@@ -891,14 +896,26 @@ class SpikeSortingLoader:
     spike_sorting_path: Path = None
 
     def __post_init__(self):
+        # pid gets precedence
         if self.pid is not None:
             self.eid, self.pname = self.one.pid2eid(self.pid)
-        if self.atlas is None:
-            self.atlas = AllenAtlas()
-        self.session_path = self.one.eid2path(self.eid)
+            self.session_path = self.one.eid2path(self.eid)
+        # then eid / pname combination
+        elif self.session_path is None or self.session_path == '':
+            self.session_path = self.one.eid2path(self.eid)
+        # fully local providing a session path
+        else:
+            self.one = One(cache_dir=self.session_path.parents[2], mode='local')
+            df_sessions = cache._make_sessions_df(self.session_path)
+            self.one._cache['sessions'] = df_sessions.set_index('id')
+            self.one._cache['datasets'] = cache._make_datasets_df(self.session_path, hash_files=False)
+            self.eid = str(self.session_path.relative_to(self.session_path.parents[2]))
+        # populates default properties
         self.collections = self.one.list_collections(
             self.eid, filename='spikes*', collection=f"alf/{self.pname}*")
         self.datasets = self.one.list_datasets(self.eid)
+        if self.atlas is None:
+            self.atlas = AllenAtlas()
         self.files = {}
 
     @staticmethod

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(

brainbox/plot_base.py

@@ -185,7 +185,11 @@ def _get_scale(self, axis):
         :param axis: 'x' or 'y'
         :return:
         """
-        lim = self._set_lim(axis)
+        if axis == 'x':
+            lim = self.xlim
+        else:
+            lim = self.ylim
+        lim = self._set_lim(axis, lim=lim)
         scale = (lim[1] - lim[0]) / self.data['c'].shape[axis_dict[axis]]
         return scale