raster viewer local server

Author: oliche

viewspikes/gui.py

@@ -1,23 +1,40 @@
 from pathlib import Path
 
 import numpy as np
+import scipy.signal
+
 from PyQt5 import QtWidgets, QtCore, QtGui, uic
 import pyqtgraph as pg
-import scipy.signal
 from brainbox.processing import bincount2D
 import qt
 from iblutil.numerical import ismember
 from easyqc.gui import viewseis
 from ibllib.io import spikeglx
 from ibllib.dsp import voltage
 
+T_BIN = .007  # time bin size in secs
+D_BIN = 10  # depth bin size in um
+
+SNS_PALETTE = [(0.12156862745098039, 0.4666666666666667, 0.7058823529411765),
+    (1.0, 0.4980392156862745, 0.054901960784313725),
+    (0.17254901960784313, 0.6274509803921569, 0.17254901960784313),
+    (0.8392156862745098, 0.15294117647058825, 0.1568627450980392),
+    (0.5803921568627451, 0.403921568627451, 0.7411764705882353),
+    (0.5490196078431373, 0.33725490196078434, 0.29411764705882354),
+    (0.8901960784313725, 0.4666666666666667, 0.7607843137254902),
+    (0.4980392156862745, 0.4980392156862745, 0.4980392156862745),
+    (0.7372549019607844, 0.7411764705882353, 0.13333333333333333),
+    (0.09019607843137255, 0.7450980392156863, 0.8117647058823529)]
+
+YMAX = 4000
 
 class RasterView(QtWidgets.QMainWindow):
     def __init__(self, bin_file, spikes, clusters, channels=None, trials=None, *args, **kwargs):
         self.sr = spikeglx.Reader(bin_file)
         self.spikes = spikes
         self.clusters = clusters
         self.channels = channels
+        self.trials = trials
         self.eqcs = []
         super(RasterView, self).__init__(*args, **kwargs)
         # wave by Diana Militano from the Noun Projectp
@@ -31,31 +48,54 @@ def __init__(self, bin_file, spikes, clusters, channels=None, trials=None, *args
         s = self.viewBox_raster.scene()
         # vb.scene().sigMouseMoved.connect(self.mouseMoveEvent)
         s.sigMouseClicked.connect(self.mouseClick)
-
-        # set image
-        t_bin = .007
-        d_bin = 10
-        self.raster, self.rtimes, self.depths = bincount2D(spikes.times, spikes.depths, t_bin, d_bin)
+        ################################################### set image
+        iok = ~np.isnan(spikes.depths)
+        self.raster, self.rtimes, self.depths = bincount2D(
+            spikes.times[iok], spikes.depths[iok], T_BIN, D_BIN)
         self.imageItem_raster.setImage(np.flip(self.raster.T))
-        transform = [t_bin, 0., 0., 0., d_bin, 0.,  - .5, - .5, 1.]
+        transform = [T_BIN, 0., 0., 0., D_BIN, 0.,  - .5, - .5, 1.]
         self.transform = np.array(transform).reshape((3, 3)).T
         self.imageItem_raster.setTransform(QtGui.QTransform(*transform))
         self.plotItem_raster.setLimits(xMin=0, xMax=self.rtimes[-1], yMin=0, yMax=self.depths[-1])
-
         # set colormap
         cm = pg.colormap.get('Greys', source='matplotlib')  # prepare a linear color map
         bar = pg.ColorBarItem(values=(0, .5), colorMap=cm)  # prepare interactive color bar
         # Have ColorBarItem control colors of img and appear in 'plot':
         bar.setImageItem(self.imageItem_raster)
-        self.show()
-
+        ################################################## plot location
+        # self.view.layers[label] = {'layer': new_scatter, 'type': 'scatter'}
+        self.line_eqc = pg.PlotCurveItem()
+        self.plotItem_raster.addItem(self.line_eqc)
+        # self.plotItem_raster.removeItem(new_curve)
+        ################################################## plot trials
+        if self.trials is not None:
+            trial_times = dict(
+                goCue_times=trials['goCue_times'],
+                error_times=trials['feedback_times'][trials['feedbackType'] == -1],
+                reward_times=trials['feedback_times'][trials['feedbackType'] == 1])
+            self.trial_lines = {}
+            for i, k in enumerate(trial_times):
+                self.trial_lines[k] = pg.PlotCurveItem()
+                self.plotItem_raster.addItem(self.trial_lines[k])
+                x = np.tile(trial_times[k][:, np.newaxis], (1, 2)).flatten()
+                y = np.tile(np.array([0, 1, 1, 0]), int(trial_times[k].shape[0] / 2 + 1))[
+                    :trial_times[k].shape[0] * 2] * YMAX
+                self.trial_lines[k].setData(x=x.flatten(), y=y.flatten(), pen=pg.mkPen(np.array(SNS_PALETTE[i]) * 256))
 
+        self.show()
 
     def mouseClick(self, event):
+        """Draws a line on the raster and display in EasyQC"""
         if not event.double():
             return
         qxy = self.imageItem_raster.mapFromScene(event.scenePos())
-        self.show_ephys(t0=self.rtimes[int(qxy.x())])
+        x = qxy.x()
+        self.show_ephys(t0=self.rtimes[int(x - .5)])
+        ymax = np.max(self.depths) + 50
+        self.line_eqc.setData(x=x + np.array([-.5, -.5, .5, .5]),
+                              y=np.array([0, ymax, ymax, 0]),
+                              pen=pg.mkPen((0, 255, 0)))
+
 
     def keyPressEvent(self, e):
         """
@@ -73,10 +113,10 @@ def keyPressEvent(self, e):
                 m == QtCore.Qt.ControlModifier and k == QtCore.Qt.Key_Z):
             self.imageItem_raster.setLevels([0, self.imageItem_raster.levels[1] * 1.4])
 
-    def show_ephys(self, t0, len=1):
+    def show_ephys(self, t0, tlen=1):
 
         first = int(t0 * self.sr.fs)
-        last = first + int(self.sr.fs * len)
+        last = first + int(self.sr.fs * tlen)
 
         raw = self.sr[first:last, : - self.sr.nsync].T
 
@@ -85,19 +125,21 @@ def show_ephys(self, t0, len=1):
         butt = scipy.signal.sosfiltfilt(sos, raw)
         destripe = voltage.destripe(raw, fs=self.sr.fs)
 
+        self.eqc_raw = viewephys(butt, self.sr.fs, channels=None, br=None, title='butt', t0=t0, t_scalar=1)
+        self.eqc_des = viewephys(destripe, self.sr.fs, channels=None, br=None, title='destripe', t0=t0, t_scalar=1)
+
+        eqc_xrange = [t0 + tlen / 2 - 0.01, t0 + tlen / 2 + 0.01]
+        self.eqc_des.viewBox_seismic.setXRange(*eqc_xrange)
+        self.eqc_raw.viewBox_seismic.setXRange(*eqc_xrange)
+
+        # eqc2 = viewephys(butt - destripe, self.sr.fs, channels=None, br=None, title='diff')
         # overlay spikes
         tprobe = self.spikes.samples / self.sr.fs
-        slice_spikes = slice(np.searchsorted(tprobe, t0), np.searchsorted(tprobe, t0 + len))
+        slice_spikes = slice(np.searchsorted(tprobe, t0), np.searchsorted(tprobe, t0 + tlen))
         t = tprobe[slice_spikes]
         c = self.clusters.channels[self.spikes.clusters[slice_spikes]]
-
-        self.eqc_raw = viewephys(butt, self.sr.fs, channels=None, br=None, title='butt', t0=t0, t_scalar=1)
-        self.eqc_des = viewephys(destripe, self.sr.fs, channels=None, br=None, title='destripe', t0=t0, t_scalar=1)
-        # eqc2 = viewephys(butt - destripe, self.sr.fs, channels=None, br=None, title='diff')
-
         self.eqc_raw.ctrl.add_scatter(t, c)
         self.eqc_des.ctrl.add_scatter(t, c)
-        # eqc2.ctrl.add_scatter(t, c)
 
 
 

viewspikes/raster.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>810</width>
-    <height>606</height>
+    <width>999</width>
+    <height>656</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -36,12 +36,24 @@
     <rect>
      <x>0</x>
      <y>0</y>
-     <width>810</width>
+     <width>999</width>
      <height>22</height>
     </rect>
    </property>
+   <widget class="QMenu" name="menuFile">
+    <property name="title">
+     <string>File</string>
+    </property>
+    <addaction name="actionopen"/>
+   </widget>
+   <addaction name="menuFile"/>
   </widget>
   <widget class="QStatusBar" name="statusbar"/>
+  <action name="actionopen">
+   <property name="text">
+    <string>open...</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>