add raw data viewer from raster

Author: oliche

viewspikes/gui.py

@@ -3,13 +3,106 @@
 import numpy as np
 from PyQt5 import QtWidgets, QtCore, QtGui, uic
 import pyqtgraph as pg
-
-from iblapps import qt
+import scipy.signal
+from brainbox.processing import bincount2D
+import qt
 from iblutil.numerical import ismember
 from easyqc.gui import viewseis
-
-
-def viewephys(data, fs, channels=None, br=None, title='ephys'):
+from ibllib.io import spikeglx
+from ibllib.dsp import voltage
+
+
+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.eqcs = []
+        super(RasterView, self).__init__(*args, **kwargs)
+        # wave by Diana Militano from the Noun Projectp
+        uic.loadUi(Path(__file__).parent.joinpath('raster.ui'), self)
+        background_color = self.palette().color(self.backgroundRole())
+        self.plotItem_raster.setAspectLocked(False)
+        self.imageItem_raster = pg.ImageItem()
+        self.plotItem_raster.setBackground(background_color)
+        self.plotItem_raster.addItem(self.imageItem_raster)
+        self.viewBox_raster = self.plotItem_raster.getPlotItem().getViewBox()
+        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)
+        self.imageItem_raster.setImage(np.flip(self.raster.T))
+        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()
+
+
+
+    def mouseClick(self, event):
+        if not event.double():
+            return
+        qxy = self.imageItem_raster.mapFromScene(event.scenePos())
+        self.show_ephys(t0=self.rtimes[int(qxy.x())])
+
+    def keyPressEvent(self, e):
+        """
+        page-up / ctrl + a :  gain up
+        page-down / ctrl + z : gain down
+        :param e:
+        """
+        k, m = (e.key(), e.modifiers())
+        # page up / ctrl + a
+        if k == QtCore.Qt.Key_PageUp or (
+                m == QtCore.Qt.ControlModifier and k == QtCore.Qt.Key_A):
+            self.imageItem_raster.setLevels([0, self.imageItem_raster.levels[1] / 1.4])
+        # page down / ctrl + z
+        elif k == QtCore.Qt.Key_PageDown or (
+                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):
+
+        first = int(t0 * self.sr.fs)
+        last = first + int(self.sr.fs * len)
+
+        raw = self.sr[first:last, : - self.sr.nsync].T
+
+        butter_kwargs = {'N': 3, 'Wn': 300 / self.sr.fs * 2, 'btype': 'highpass'}
+        sos = scipy.signal.butter(**butter_kwargs, output='sos')
+        butt = scipy.signal.sosfiltfilt(sos, raw)
+        destripe = voltage.destripe(raw, fs=self.sr.fs)
+
+        # overlay spikes
+        tprobe = self.spikes.samples / self.sr.fs
+        slice_spikes = slice(np.searchsorted(tprobe, t0), np.searchsorted(tprobe, t0 + len))
+        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)
+
+
+
+
+def viewephys(data, fs, channels=None, br=None, title='ephys', t0=0, t_scalar=1e3):
     """
     :param data: [nc, ns]
     :param fs:
@@ -28,15 +121,15 @@ def viewephys(data, fs, channels=None, br=None, title='ephys'):
     from ibllib.ephys.neuropixel import trace_header
     if channels is None or br is None:
         channels = trace_header(version = 1)
-        eqc = viewseis(data.T, si=1 / fs * 1e3, h=channels, title=title, taxis=0)
+        eqc = viewseis(data.T, si=1 / fs * t_scalar, h=channels, title=title, taxis=0, t0=t0)
         return eqc
     else:
         _, ir = ismember(channels['atlas_id'], br.id)
         image = br.rgb[ir].astype(np.uint8)
         image = image[np.newaxis, :, :]
 
 
-    eqc = viewseis(data.T, si=1 / fs * 1e3, h=channels, title=title, taxis=0)
+    eqc = viewseis(data.T, si=1 / fs * t_scalar, h=channels, title=title, taxis=0)
     imitem = pg.ImageItem(image)
     eqc.plotItem_header_v.addItem(imitem)
     transform = [1, 0, 0, 0, 1, 0, -0.5, 0, 1.]

viewspikes/raster.ui

@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>810</width>
+    <height>606</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>MainWindow</string>
+  </property>
+  <widget class="QWidget" name="centralwidget">
+   <layout class="QVBoxLayout" name="verticalLayout">
+    <item>
+     <layout class="QGridLayout" name="gridLayout">
+      <item row="0" column="0">
+       <widget class="PlotWidget" name="plotItem_raster"/>
+      </item>
+     </layout>
+    </item>
+    <item>
+     <widget class="QSlider" name="horizontalSlider">
+      <property name="orientation">
+       <enum>Qt::Horizontal</enum>
+      </property>
+     </widget>
+    </item>
+   </layout>
+  </widget>
+  <widget class="QMenuBar" name="menubar">
+   <property name="geometry">
+    <rect>
+     <x>0</x>
+     <y>0</y>
+     <width>810</width>
+     <height>22</height>
+    </rect>
+   </property>
+  </widget>
+  <widget class="QStatusBar" name="statusbar"/>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>PlotWidget</class>
+   <extends>QGraphicsView</extends>
+   <header>pyqtgraph</header>
+  </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>