Merge pull request #591 from int-brain-lab/hotfix/2.21.3

Hotfix/2.21.3

Author: juhuntenburg

brainbox/ephys_plots.py

@@ -395,7 +395,8 @@ def line_amp_plot(spike_amps, spike_depths, spike_times, chn_coords, d_bin=10, d
     return data
 
 
-def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, display=True, ax=None, title=None, label='left'):
+def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, display=True, ax=None,
+                       title=None, label='left', **kwargs):
     """
     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
@@ -404,6 +405,7 @@ def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, dis
     :param display: whether to output plot
     :param ax: axis to plot on
     :param title: title for plot
+    :param kwargs: additional keyword arguments for bar plot
     :return:
     """
 
@@ -432,8 +434,10 @@ def plot_brain_regions(channel_ids, channel_depths=None, brain_regions=None, dis
 
         for reg, col in zip(regions, region_colours):
             height = np.abs(reg[1] - reg[0])
+            bar_kwargs = dict(edgecolor='w', width=1)
+            bar_kwargs.update(**kwargs)
             color = col / 255
-            ax.bar(x=0.5, height=height, width=1, color=color, bottom=reg[0], edgecolor='w')
+            ax.bar(x=0.5, height=height, color=color, bottom=reg[0], **kwargs)
         if label == 'right':
             ax.yaxis.tick_right()
         ax.set_yticks(region_labels[:, 0].astype(int))

brainbox/io/spikeglx.py

@@ -3,6 +3,8 @@
 from pathlib import Path
 import time
 import json
+import string
+import random
 
 import numpy as np
 from one.alf.io import remove_uuid_file
@@ -141,12 +143,11 @@ def read(self, nsel=slice(0, 10000), csel=slice(None), sync=True, volts=True):
         n0 = self.chunks['chunk_bounds'][first_chunk]
         _logger.debug(f'Streamer: caching sample {n0}, (t={n0 / self.fs})')
         self.cache_folder.mkdir(exist_ok=True, parents=True)
-        sr = self._download_raw_partial(first_chunk=first_chunk, last_chunk=last_chunk)
+        sr, file_cbin = self._download_raw_partial(first_chunk=first_chunk, last_chunk=last_chunk)
         if not volts:
             data = np.copy(sr._raw[nsel.start - n0:nsel.stop - n0, csel])
         else:
             data = sr[nsel.start - n0: nsel.stop - n0, csel]
-
         sr.close()
         if self.remove_cached:
             shutil.rmtree(self.target_dir)
@@ -159,16 +160,20 @@ def _download_raw_partial(self, first_chunk=0, last_chunk=0):
         :param first_chunk:
         :param last_chunk:
         :return: spikeglx.Reader of the current chunk, Pathlib.Path of the directory where it is stored
+        :return: cbin local path
         """
         assert str(self.url_cbin).endswith('.cbin')
         webclient = self.one.alyx
         relpath = Path(self.url_cbin.replace(webclient._par.HTTP_DATA_SERVER, '.')).parents[0]
         # write the temp file into a subdirectory
         tdir_chunk = f"chunk_{str(first_chunk).zfill(6)}_to_{str(last_chunk).zfill(6)}"
-        target_dir = Path(self.cache_folder, relpath, tdir_chunk)
-        self.target_dir = target_dir
-        Path(target_dir).mkdir(parents=True, exist_ok=True)
-        ch_file_stream = target_dir.joinpath(self.file_chunks.name).with_suffix('.stream.ch')
+        # for parallel processes, there is a risk of collisions if the removed cached flag is set to True
+        # if the folder is to be removed append a unique identifier to avoid having duplicate names
+        if self.remove_cached:
+            tdir_chunk += ''.join([random.choice(string.ascii_letters) for _ in np.arange(10)])
+        self.target_dir = Path(self.cache_folder, relpath, tdir_chunk)
+        Path(self.target_dir).mkdir(parents=True, exist_ok=True)
+        ch_file_stream = self.target_dir.joinpath(self.file_chunks.name).with_suffix('.stream.ch')
 
         # Get the first sample index, and the number of samples to download.
         i0 = self.chunks['chunk_bounds'][first_chunk]
@@ -186,7 +191,7 @@ def _download_raw_partial(self, first_chunk=0, last_chunk=0):
                 cmeta_stream = json.load(f)
             if (cmeta_stream.get('chopped_first_sample', None) == i0 and
                     cmeta_stream.get('chopped_total_samples', None) == total_samples):
-                return spikeglx.Reader(ch_file_stream.with_suffix('.cbin'), ignore_warnings=True)
+                return spikeglx.Reader(ch_file_stream.with_suffix('.cbin'), ignore_warnings=True), ch_file_stream
 
         else:
             shutil.copy(self.file_chunks, ch_file_stream)
@@ -224,7 +229,7 @@ def _download_raw_partial(self, first_chunk=0, last_chunk=0):
             try:
                 cbin_local_path = webclient.download_file(
                     self.url_cbin, chunks=(first_byte, n_bytes),
-                    target_dir=target_dir, clobber=True, return_md5=False)
+                    target_dir=self.target_dir, clobber=True, return_md5=False)
                 break
             except Exception as e:
                 retries += 1
@@ -238,4 +243,4 @@ def _download_raw_partial(self, first_chunk=0, last_chunk=0):
         assert cbin_local_path_renamed.exists()
 
         reader = spikeglx.Reader(cbin_local_path_renamed, ignore_warnings=True)
-        return reader
+        return reader, cbin_local_path

ibllib/atlas/flatmaps.py

@@ -252,7 +252,7 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
     def format_coord(x, y):
         ind = sw[int(y), int(x)]
         ancestors = br.ancestors(br.id[ind])['acronym']
-        return f'sw-{ind}, x={x:1.4f}, y={y:1.4f}, aid={br.id[ind]}-{br.acronym[ind]} \n {ancestors}'
+        return f'sw-{ind}, {ancestors}, aid={br.id[ind]}-{br.acronym[ind]} \n {br.name[ind]}'
 
     ax.format_coord = format_coord
 
@@ -324,7 +324,7 @@ def plot_swanson(acronyms=None, values=None, ax=None, hemisphere=None, br=None,
     def format_coord(x, y):
         ind = s2a[int(y), int(x)]
         ancestors = br.ancestors(br.id[ind])['acronym']
-        return f'sw-{ind}, x={x:1.4f}, y={y:1.4f}, aid={br.id[ind]}-{br.acronym[ind]} \n {ancestors}'
+        return f'sw-{ind}, {ancestors}, aid={br.id[ind]}-{br.acronym[ind]} \n {br.name[ind]}'
 
     ax.format_coord = format_coord
     return ax

release_notes.md

@@ -1,3 +1,8 @@
+# Develop
+### features
+- show atlas names in swanson plot
+- allow user to define mask regions in swanson plot
+
 ## Release 2.21
 # Release Notes 2.21.2 2023-02-24
 ### bugfixes