Merge pull request #37 from int-brain-lab/develop

Develop

Author: mayofaulkner

atlaselectrophysiology/ephys_gui_setup.py

@@ -4,6 +4,8 @@
 import numpy as np
 from random import randrange
 from atlaselectrophysiology.AdaptedAxisItem import replace_axis
+from ibllib.qc.critical_reasons import REASONS_INS_CRIT_GUI
+
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('foreground', 'k')
 
@@ -490,7 +492,7 @@ def init_interaction_features(self):
             self.desc_layout = QtWidgets.QVBoxLayout()
             self.desc_layout.setSpacing(5)
             self.desc_buttons.setExclusive(False)
-            options = ["Noise and artifact", "Drift", "Poor neural yield", "Brain Damage", "Other"]
+            options = REASONS_INS_CRIT_GUI
             for i, val in enumerate(options):
 
                 button = QtWidgets.QCheckBox(val)

atlaselectrophysiology/extract_files.py

@@ -27,8 +27,7 @@ def rmsmap(fbin, spectra=True):
     :return: a dictionary with amplitudes in channeltime space, channelfrequency space, time
      and frequency scales
     """
-    if not isinstance(fbin, spikeglx.Reader):
-        sglx = spikeglx.Reader(fbin)
+    sglx = spikeglx.Reader(fbin, open=True)
     rms_win_length_samples = 2 ** np.ceil(np.log2(sglx.fs * RMS_WIN_LENGTH_SECS))
     # the window generator will generates window indices
     wingen = dsp.WindowGenerator(ns=sglx.ns, nswin=rms_win_length_samples, overlap=0)
@@ -58,6 +57,7 @@ def rmsmap(fbin, spectra=True):
         # print at least every 20 windows
         if (iw % min(20, max(int(np.floor(wingen.nwin / 75)), 1))) == 0:
             print_progress(iw, wingen.nwin)
+    sglx.close()
     return win
 
 

atlaselectrophysiology/load_data.py

@@ -10,6 +10,7 @@
 import glob
 import os
 from atlaselectrophysiology.load_histology import download_histology_data, tif2nrrd
+import ibllib.qc.critical_reasons as usrpmt
 
 ONE_BASE_URL = "https://alyx.internationalbrainlab.org"
 
@@ -430,6 +431,9 @@ def upload_dj(self, align_qc, ephys_qc, ephys_desc):
                         allow_direct_insert=True, replace=True)
         self.alyx_str = ephys_qc.upper() + ': ' + ephys_desc_str
 
+        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):
         # if resolved just update the alignment_number
         align_qc = AlignmentQC(self.probe_id, one=self.one, brain_atlas=self.brain_atlas)