docs and test

Author: mayofaulkner

brainbox/ephys_plots.py

@@ -376,6 +376,15 @@ def line_amp_plot(spike_amps, spike_depths, spike_times, chn_coords, d_bin=10, d
 
 
 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]
@@ -414,7 +423,20 @@ def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, dis
 
 
 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'):
+             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)

ibllib/atlas/regions.py

@@ -152,9 +152,9 @@ def _mapping_from_regions_list(self, new_map, lateralize=False):
     def remap(self, region_ids, source_map='Allen', target_map='Beryl'):
         """
         Remap atlas regions ids from source map to target map
-        :param region_ids:
-        :param source_map:
-        :param 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]])

ibllib/tests/test_atlas.py

@@ -57,6 +57,13 @@ def test_mappings_not_lateralized(self):
         inds_[0] = 0
         assert np.all(inds == inds_)
 
+    def test_remap(self):
+        # Test mapping atlas ids from one map to another
+        atlas_id = np.array([463, 685])  # CA3 and PO
+        cosmos_atlas_id = self.brs.remap(atlas_id, source_map='Allen', target_map='Cosmos')
+        expectd_cosmos_id = [1089, 549]  # HPF and TH
+        assert np.all(cosmos_atlas_id == expectd_cosmos_id)
+
 
 class TestAtlasSlicesConversion(unittest.TestCase):