Merge branch 'develop'

Author: k1o0

dlc/wheel_dlc_viewer.py

@@ -652,7 +652,7 @@ def process_key(self, event):
     import argparse
 
     docstring = """
-    Viewer to see the wheel data along side the video and DLC.
+    Viewer to see the wheel data along label the video and DLC.
 
     Below is list of key bindings:\n
         n         plot movements of next trial

tests/test_alignment_qc_gui.py

@@ -1,12 +1,16 @@
 import unittest
+from pathlib import Path
+import re
+from inspect import getmembers, isfunction
+
+import numpy as np
+
 from oneibl.one import ONE
 from ibllib.atlas import AllenAtlas
 from atlaselectrophysiology.load_data import LoadData
 from ibllib.pipes.ephys_alignment import EphysAlignment
 from ibllib.pipes.misc import create_alyx_probe_insertions
 from ibllib.pipes.histology import register_track
-from pathlib import Path
-import numpy as np
 
 
 EPHYS_SESSION = 'b1c968ad-4874-468d-b2e4-5ffa9b9964e9'
@@ -49,7 +53,16 @@ def setUp(self) -> None:
         if traj:
             self.prev_traj_id = traj[0]['id']
 
-    def test_01_no_alignment(self):
+    def test_alignments(self):
+        checks = getmembers(TestsAlignmentQcGUI,
+                            lambda x: isfunction(x) and re.match(r'^_\d{2}_.*', x.__name__))
+        # Run each function in order
+        for name, fn in sorted(checks, key=lambda x: x[0]):
+            if not name.startswith('_01_'):
+                self.setUp()
+            fn(self)
+
+    def _01_no_alignment(self):
 
         prev_align = self.ld.get_previous_alignments()
         assert (len(prev_align) == 1)
@@ -60,7 +73,7 @@ def test_01_no_alignment(self):
         assert (not self.ld.alignments)
         assert (self.ld.resolved == 0)
 
-    def test_02_one_alignment(self):
+    def _02_one_alignment(self):
         key = '2020-07-26T17:06:58_alejandro'
         feature = self.alignments[key][0]
         track = self.alignments[key][1]
@@ -86,7 +99,7 @@ def test_02_one_alignment(self):
         assert (insertion['json']['qc'] == 'NOT_SET')
         assert (self.ld.resolved == 0)
 
-    def test_03_same_user(self):
+    def _03_same_user(self):
         key = '2020-08-26T17:06:58_alejandro'
         eval_str = 'PASS: Noise and artifact'
         feature = self.alignments[key][0]
@@ -116,7 +129,7 @@ def test_03_same_user(self):
         assert (insertion['json']['qc'] == 'PASS')
         assert (self.ld.resolved == 0)
 
-    def test_04_two_alignments(self):
+    def _04_two_alignments(self):
         key = '2020-09-14T15:42:22_guido'
         feature = self.alignments[key][0]
         track = self.alignments[key][1]
@@ -147,7 +160,7 @@ def test_04_two_alignments(self):
         assert (insertion['json']['extended_qc']['alignment_qc'] < 0.8)
         assert (self.ld.resolved == 0)
 
-    def test_05_three_alignments(self):
+    def _05_three_alignments(self):
 
         key = '2020-09-14T15:44:56_nate'
         eval_str = 'WARNING: Drift'
@@ -181,7 +194,7 @@ def test_05_three_alignments(self):
         assert (insertion['json']['extended_qc']['alignment_qc'] > 0.8)
         assert(self.ld.resolved == 1)
 
-    def test_06_new_user_after_resolved(self):
+    def _06_new_user_after_resolved(self):
         key = '2020-09-16T15:44:56_mayo'
         eval_str = 'PASS: Drift'
         feature = self.alignments[key][0]
@@ -213,7 +226,7 @@ def test_06_new_user_after_resolved(self):
         assert (insertion['json']['extended_qc']['alignment_qc'] > 0.8)
         assert (self.ld.resolved == 1)
 
-    def test_07_same_user_after_resolved(self):
+    def _07_same_user_after_resolved(self):
         key = '2020-10-14T15:44:56_nate'
         eval_str = 'CRITICAL: Brain Damage'
         feature = self.alignments[key][0]
@@ -245,7 +258,7 @@ def test_07_same_user_after_resolved(self):
         assert (insertion['json']['extended_qc']['alignment_qc'] > 0.8)
         assert (self.ld.resolved == 1)
 
-    def test_08_starting_alignments(self):
+    def _08_starting_alignments(self):
         key = '2020-10-14T15:44:56_nate'
         # Starting from original
         self.ld.probe_id = self.probe_id2

viewspikes/README.md

@@ -0,0 +1,17 @@
+# View Spikes
+Electrophysiology display tools for IBL insertions.
+
+## Run instructions
+Look at the examples file at the root of the package.
+
+## Install Instructions
+
+Pre-requisites:
+-   IBL environment installed https://github.com/int-brain-lab/iblenv
+-   ONE parameters setup to download data
+
+```
+conda activate iblenv
+pip install easyqc
+pip install -U pyqtgraph
+```

viewspikes/examples.py

@@ -7,12 +7,11 @@
 from oneibl.one import ONE
 from ibllib.ephys import neuropixel
 from ibllib.dsp import voltage
-from ibllib.plots import color_cycle
 from brainbox.plot import driftmap
 
-from iblapps.needles2 import run_needles2
-from iblapps.viewspikes.data import stream, get_ks2, get_spikes
-from iblapps.viewspikes.plots import plot_insertion, show_psd, overlay_spikes
+from needles2 import run_needles2
+from viewspikes.data import stream, get_ks2, get_spikes
+from viewspikes.plots import plot_insertion, show_psd, overlay_spikes
 
 one = ONE()
 
@@ -49,14 +48,3 @@
 
 # Do the driftmap
 driftmap(spikes['times'], spikes['depths'], t_bin=0.1, d_bin=5, ax=axes[1])
-
-
-# eqc_concat = viewseis(np.r_[butt, destripe, ks2], si=1 / sr.fs, h=hhh, t0=t0, title='concat')
-# overlay_spikes(eqc_concat, spikes, clusters, channels)
-from easyqc import qt
-import datetime
-qtapp = qt.create_app()
-screenshot = qtapp.primaryScreen().grabWindow(eqc_butt.winId())
-
-fn = datetime.datetime.now().strftime('%Y-%m-%dT%H-%M-%S')
-screenshot.save(f'/home/olivier/Pictures/{fn}.png', 'png')