Merge branch 'develop' of https://github.com/int-brain-lab/iblapps into develop

Author: k1o0

atlaselectrophysiology/AdaptedAxisItem.py

@@ -0,0 +1,48 @@
+import pyqtgraph as pg
+from pyqtgraph import debug as debug
+
+
+class AdaptedAxisItem(pg.AxisItem):
+    def __init__(self, orientation, parent=None,):
+        pg.AxisItem.__init__(self, orientation, parent=parent)
+
+    def drawPicture(self, p, axisSpec, tickSpecs, textSpecs):
+        profiler = debug.Profiler()
+
+        p.setRenderHint(p.Antialiasing, False)
+        p.setRenderHint(p.TextAntialiasing, True)
+
+        # draw long line along axis
+        pen, p1, p2 = axisSpec
+        p.setPen(pen)
+        p.drawLine(p1, p2)
+        p.translate(0.5, 0)  # resolves some damn pixel ambiguity
+
+        # draw ticks
+        for pen, p1, p2 in tickSpecs:
+            p.setPen(pen)
+            p.drawLine(p1, p2)
+        profiler('draw ticks')
+
+        # Draw all text
+        if self.style['tickFont'] is not None:
+            p.setFont(self.style['tickFont'])
+        p.setPen(self.textPen())
+        for rect, flags, text in textSpecs:
+            p.drawText(rect, int(flags), text)
+
+        profiler('draw text')
+
+
+def replace_axis(plot_item, orientation='left', pos=(2, 0)):
+
+    new_axis = AdaptedAxisItem(orientation, parent=plot_item)
+    oldAxis = plot_item.axes[orientation]['item']
+    plot_item.layout.removeItem(oldAxis)
+    oldAxis.unlinkFromView()
+    #
+    new_axis.linkToView(plot_item.vb)
+    plot_item.axes[orientation] = {'item': new_axis, 'pos': pos}
+    plot_item.layout.addItem(new_axis, *pos)
+    new_axis.setZValue(-1000)
+    new_axis.setFlag(new_axis.ItemNegativeZStacksBehindParent)

atlaselectrophysiology/ephys_atlas_gui.py

@@ -12,7 +12,7 @@
 from atlaselectrophysiology.create_overview_plots import make_overview_plot
 from pathlib import Path
 import os
-
+import time
 
 class MainWindow(QtWidgets.QMainWindow, ephys_gui.Setup):
     def __init__(self, offline=False, probe_id=None, one=None):
@@ -537,6 +537,7 @@ def plot_histology(self, fig, ax='left', movable=True):
         axis = fig.getAxis(ax)
         axis.setTicks([self.hist_data['axis_label'][self.idx]])
         axis.setZValue(10)
+        self.set_axis(self.fig_hist, 'bottom', pen='w', label='blank')
 
         # Plot each histology region
         for ir, reg in enumerate(self.hist_data['region'][self.idx]):
@@ -597,7 +598,7 @@ def plot_histology_ref(self, fig, ax='right', movable=False):
         axis = fig.getAxis(ax)
         axis.setTicks([self.hist_data_ref['axis_label']])
         axis.setZValue(10)
-        self.set_axis(self.fig_hist_ref, 'bottom', pen='w')
+        self.set_axis(self.fig_hist_ref, 'bottom', pen='w', label='blank')
 
         # Plot each histology region
         for ir, reg in enumerate(self.hist_data_ref['region']):
@@ -753,6 +754,7 @@ def plot_scale_factor(self):
 
         self.fig_scale.setYRange(min=self.probe_tip - self.probe_extra,
                                  max=self.probe_top + self.probe_extra, padding=self.pad)
+        self.set_axis(self.fig_scale, 'bottom', pen='w', label='blank')
         self.fig_scale_cb.addItem(cbar)
 
     def plot_fit(self):
@@ -778,19 +780,19 @@ def plot_slice(self, data, img_type):
         self.slice_lines = []
         img = pg.ImageItem()
         img.setImage(data[img_type])
+        transform = [data['scale'][0], 0., 0., 0., data['scale'][1], 0., data['offset'][0],
+                     data['offset'][1], 1.]
+        img.setTransform(QtGui.QTransform(*transform))
 
         if img_type == 'label':
-            img.translate(data['offset'][0], data['offset'][1])
-            img.scale(data['scale'][0], data['scale'][1])
             self.fig_slice_layout.removeItem(self.slice_item)
             self.fig_slice_layout.addItem(self.fig_slice_hist_alt, 0, 1)
             self.slice_item = self.fig_slice_hist_alt
         else:
-            img.translate(data['offset'][0], data['offset'][1])
-            img.scale(data['scale'][0], data['scale'][1])
             color_bar = cb.ColorBar('cividis')
             lut = color_bar.getColourMap()
             img.setLookupTable(lut)
+
             self.fig_slice_layout.removeItem(self.slice_item)
             self.fig_slice_hist = pg.HistogramLUTItem()
             self.fig_slice_hist.axis.hide()
@@ -867,9 +869,11 @@ def plot_scatter(self, data):
             [self.fig_img_cb.removeItem(cbar) for cbar in self.img_cbars]
             self.img_plots = []
             self.img_cbars = []
-            connect = np.zeros(data['x'].size, dtype=int)
+            start = time.time()
             size = data['size'].tolist()
             symbol = data['symbol'].tolist()
+            end = time.time()
+            print(end-start)
 
             color_bar = cb.ColorBar(data['cmap'])
             cbar = color_bar.makeColourBar(20, 5, self.fig_img_cb, min=np.min(data['levels'][0]),
@@ -878,13 +882,22 @@ def plot_scatter(self, data):
             self.img_cbars.append(cbar)
 
             if type(np.any(data['colours'])) == QtGui.QColor:
+                start = time.time()
                 brush = data['colours'].tolist()
+                plot = pg.ScatterPlotItem()
+                plot.setData(x=data['x'], y=data['y'],
+                             symbol=symbol, size=size, brush=brush, pen=data['pen'])
+                end = time.time()
+                print(end-start)
             else:
                 brush = color_bar.map.mapToQColor(data['colours'])
+                plot = pg.ScatterPlotItem()
+                start = time.time()
+                plot.setData(x=data['x'], y=data['y'],
+                             symbol=symbol, size=size, brush=brush, pen=data['pen'])
+                end = time.time()
+                print(end - start)
 
-            plot = pg.PlotDataItem()
-            plot.setData(x=data['x'], y=data['y'], connect=connect,
-                         symbol=symbol, symbolSize=size, symbolBrush=brush, symbolPen=data['pen'])
             self.fig_img.addItem(plot)
             self.fig_img.setXRange(min=data['xrange'][0], max=data['xrange'][1],
                                    padding=0)
@@ -898,7 +911,8 @@ def plot_scatter(self, data):
 
             if data['cluster']:
                 self.data = data['x']
-                self.data_plot.sigPointsClicked.connect(self.cluster_clicked)
+                #self.data_plot.sigPointsClicked.connect(self.cluster_clicked)
+                self.data_plot.sigClicked.connect(self.cluster_clicked)
 
     def plot_line(self, data):
         """
@@ -957,8 +971,9 @@ def plot_probe(self, data, bounds=None):
             for img, scale, offset in zip(data['img'], data['scale'], data['offset']):
                 image = pg.ImageItem()
                 image.setImage(img)
-                image.translate(offset[0], offset[1])
-                image.scale(scale[0], scale[1])
+                transform = [scale[0], 0., 0., 0., scale[1], 0., offset[0],
+                             offset[1], 1.]
+                image.setTransform(QtGui.QTransform(*transform))
                 image.setLookupTable(lut)
                 image.setLevels((data['levels'][0], data['levels'][1]))
                 self.fig_probe.addItem(image)
@@ -972,6 +987,8 @@ def plot_probe(self, data, bounds=None):
             self.fig_probe.setXRange(min=data['xrange'][0], max=data['xrange'][1], padding=0)
             self.fig_probe.setYRange(min=self.probe_tip - self.probe_extra,
                                      max=self.probe_top + self.probe_extra, padding=self.pad)
+            # so stupid!!!!!
+            self.set_axis(self.fig_probe, 'bottom', pen='w', label='blank')
             if bounds is not None:
                 # add some infinite line stuff
                 for bound in bounds:
@@ -1005,8 +1022,9 @@ def plot_image(self, data):
 
             image = pg.ImageItem()
             image.setImage(data['img'])
-            image.translate(data['offset'][0], data['offset'][1])
-            image.scale(data['scale'][0], data['scale'][1])
+            transform = [data['scale'][0], 0., 0., 0., data['scale'][1], 0., data['offset'][0],
+                         data['offset'][1], 1.]
+            image.setTransform(QtGui.QTransform(*transform))
             cmap = data.get('cmap', [])
             if cmap:
                 color_bar = cb.ColorBar(data['cmap'])

atlaselectrophysiology/ephys_gui_setup.py

@@ -3,6 +3,7 @@
 import pyqtgraph.exporters
 import numpy as np
 from random import randrange
+from atlaselectrophysiology.AdaptedAxisItem import replace_axis
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('foreground', 'k')
 
@@ -643,7 +644,8 @@ def init_figures(self):
         self.fig_hist.setMouseEnabled(x=False)
         self.fig_hist.setYRange(min=self.probe_tip - self.probe_extra, max=self.probe_top +
                                 self.probe_extra, padding=self.pad)
-        self.set_axis(self.fig_hist, 'bottom', pen='w', ticks=False)
+        self.set_axis(self.fig_hist, 'bottom', pen='w')
+        replace_axis(self.fig_hist)
         self.ax_hist = self.set_axis(self.fig_hist, 'left', pen=None)
         self.ax_hist.setWidth(0)
         self.ax_hist.setStyle(tickTextOffset=-70)
@@ -652,7 +654,7 @@ def init_figures(self):
         self.fig_scale.setMaximumWidth(50)
         self.fig_scale.setMouseEnabled(x=False)
         self.scale_label = pg.LabelItem(color='k')
-        self.set_axis(self.fig_scale, 'bottom', pen='w', ticks=False)
+        self.set_axis(self.fig_scale, 'bottom', pen='w')
         self.set_axis(self.fig_scale, 'left', show=False)
         (self.fig_scale).setYLink(self.fig_hist)
 
@@ -672,6 +674,7 @@ def init_figures(self):
                                     self.probe_extra, padding=self.pad)
         self.set_axis(self.fig_hist_ref, 'bottom', pen='w')
         self.set_axis(self.fig_hist_ref, 'left', show=False)
+        replace_axis(self.fig_hist_ref, orientation='right', pos=(2, 2))
         self.ax_hist_ref = self.set_axis(self.fig_hist_ref, 'right', pen=None)
         self.ax_hist_ref.setWidth(0)
         self.ax_hist_ref.setStyle(tickTextOffset=-70)

data_exploration_gui/data_class.py

@@ -104,8 +104,8 @@ def compute_depth_and_amplitudes(self):
         self.amps = []
         self.nspikes = []
         for clu in self.ids:
-            self.depths = np.append(self.depths, np.mean(units_b.depths[str(clu)]))
-            self.amps = np.append(self.amps, np.mean(units_b.amps[str(clu)]) * 1e6)
+            self.depths = np.append(self.depths, np.nanmean(units_b.depths[str(clu)]))
+            self.amps = np.append(self.amps, np.nanmean(units_b.amps[str(clu)]) * 1e6)
             self.nspikes = np.append(self.nspikes, len(units_b.amps[str(clu)]))
 
         np.save((self.gui_path + '/cluster_depths'), self.depths)