Merge pull request #96 from int-brain-lab/develop

Develop

atlaselectrophysiology/load_data.py

@@ -582,7 +582,7 @@ def upload_dj(self, align_qc, ephys_qc, ephys_desc):
         if ephys_qc.upper() == 'CRITICAL':
             usrpmt.main_gui(eid=self.probe_id, reasons_selected=ephys_desc, one=self.one)
 
-    def update_qc(self, upload_alyx=True, upload_flatiron=True):
+    def update_qc(self, upload_alyx=True, upload_flatiron=False):
         # if resolved just update the alignment_number
         align_qc = AlignmentQC(self.probe_id, one=self.one, brain_atlas=self.brain_atlas,
                                collection=self.probe_collection)

ephysfeatures/features_across_region.py

@@ -1,16 +1,21 @@
+import copy
+from pathlib import Path
+import sys
+
 import pyqtgraph as pg
 from PyQt5 import QtCore, QtGui, QtWidgets
-import sys
 import pandas as pd
 import numpy as np
+
 from ibllib.atlas import AllenAtlas
 import atlaselectrophysiology.ColorBar as cb
 from ibllib.pipes.ephys_alignment import EphysAlignment
 from atlaselectrophysiology.AdaptedAxisItem import replace_axis
 from ephysfeatures.qrangeslider import QRangeSlider
-import copy
 from one.remote import aws
 from one.api import ONE
+from pathlib import Path
+
 
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('foreground', 'k')
@@ -49,10 +54,15 @@ def __init__(self, one, region_ids=None, ba=None, download=True, size=(1600, 800
         self.ba = ba or AllenAtlas()
         br = self.ba.regions
 
-        table_path = self.one.cache_dir.joinpath('bwm_features')
+        table_path = self.one.cache_dir.joinpath('bwm_features')  #TODO NOTE THIS FOLDER DOES NOT EXIST ON S3
         if download:
             s3, bucket_name = aws.get_s3_from_alyx(alyx=self.one.alyx)
-            aws.s3_download_folder("aggregates/bwm/latest", table_path, s3=s3, bucket_name=bucket_name)
+            # Download file
+            base_path = Path("aggregates/atlas")  # TODO THIS FOLDER DOES NOT CONTAIN PROBES
+            file_list = ['channels.pqt', 'probes.pqt', 'raw_ephys_features.pqt']
+            for file_name in file_list:
+                aws.s3_download_file(base_path.joinpath(file_name), table_path.joinpath(file_name),
+                                     s3=s3, bucket_name=bucket_name)
 
         channels = pd.read_parquet(table_path.joinpath('channels.pqt'))
         probes = pd.read_parquet(table_path.joinpath('probes.pqt'))
@@ -71,16 +81,36 @@ def __init__(self, one, region_ids=None, ba=None, download=True, size=(1600, 800
         self.data = pd.merge(data, depths, left_on=['pid', 'axial_um'], right_on=['pid', 'depths'], how='outer')
         self.data.loc[self.data['histology'] == 'alf', 'histology'] = 'resolved'
 
-        del data, depths, channels, probes, features, df_voltage
-
         # Initialise region combobox
         if region_ids is not None:
             self.region_ids = region_ids
         else:
-            self.region_ids = self.data.atlas_id.unique()
+            # self.region_ids = self.data.atlas_id.unique()
+
+            # Get the unique region IDs appearing in the data as int64
+            ids = np.sort(data.atlas_id.dropna().astype(np.int64).unique())
+            # Find the region indices within the BrainAtlas, to keep the atlas order.
+            indata = np.isin(br.id, ids)
+            self.region_ids = br.id[indata]
+
+        del data, depths, channels, probes, features, df_voltage
+
         acronyms = br.id2acronym(self.region_ids)
+        level = br.level[indata]
+
+        # Show hierarchy
+        acro_h = [((' ' * level) + acro) for (level, acro) in zip(level, acronyms)]
 
-        for id, acro in enumerate(acronyms):
+        # NOTE: this does not work well as is because of the hierarchy spaces at the beginning
+        # of the strings. You can't type "FRP" but need to type "      FRP" which is impractical!
+
+        # # Completion.
+        # completer = QtWidgets.QCompleter(acro_h, self)
+        # completer.setCaseSensitivity(QtCore.Qt.CaseInsensitive)
+        # completer.setCompletionMode(QtWidgets.QCompleter.PopupCompletion)
+        # self.region_combobox.setCompleter(completer)
+
+        for id, acro in enumerate(acro_h):
             item = QtGui.QStandardItem(id)
             item.setText(acro)
             item.setEditable(False)
@@ -120,6 +150,13 @@ def layout(self, size):
         options_widget.setLayout(options_layout)
 
         region_combobox = QtWidgets.QComboBox()
+
+        # NOTE: uncomment if users may want to type the acronym with autocompletion
+        # but that does not work well at the moment because of the spaces prefix (to show
+        # hierarchical information).
+        # region_combobox.setEditable(True)
+
+        self.region_combobox = region_combobox
         self.region_list = QtGui.QStandardItemModel()
         region_combobox.setModel(self.region_list)
         region_combobox.activated.connect(self.on_region_chosen)