Numerous fixes

added scatter plots

GradientWidget.py

@@ -163,10 +163,16 @@ class TickSlider(QtGui.QGraphicsView):
 class GradientWidget(TickSlider):
     def __init__(self, *args, **kargs):
         TickSlider.__init__(self, *args, **kargs)
+        self.currentTick = None
+        self.currentTickColor = None
         self.rectSize = 15
         self.gradRect = QtGui.QGraphicsRectItem(QtCore.QRectF(0, -self.rectSize, 100, self.rectSize))
         self.colorMode = 'rgb'
-        
+        self.colorDialog = QtGui.QColorDialog()
+        self.colorDialog.setOption(QtGui.QColorDialog.ShowAlphaChannel, True)
+        self.colorDialog.setOption(QtGui.QColorDialog.DontUseNativeDialog, True)
+        QtCore.QObject.connect(self.colorDialog, QtCore.SIGNAL('currentColorChanged(const QColor&)'), self.currentColorChanged)
+        QtCore.QObject.connect(self.colorDialog, QtCore.SIGNAL('rejected()'), self.currentColorRejected)
         
         #self.gradient = QtGui.QLinearGradient(QtCore.QPointF(0,0), QtCore.QPointF(100,0))
         self.scene.addItem(self.gradRect)
@@ -200,16 +206,27 @@ class GradientWidget(TickSlider):
         self.gradRect.setRect(0, -self.rectSize, newLen, self.rectSize)
         self.updateGradient()
         
-        
+    def currentColorChanged(self, color):
+        if color.isValid() and self.currentTick is not None:
+            self.setTickColor(self.currentTick, color)
+            self.updateGradient()
+            
+    def currentColorRejected(self):
+        self.setTickColor(self.currentTick, self.currentTickColor)
+        self.updateGradient()
         
     def tickClicked(self, tick, ev):
         if ev.button() == QtCore.Qt.LeftButton:
             if not tick.colorChangeAllowed:
                 return
-            color = QtGui.QColorDialog.getColor(tick.color, None, "Select Color", QtGui.QColorDialog.ShowAlphaChannel)
-            if color.isValid():
-                self.setTickColor(tick, color)
-                self.updateGradient()
+            self.currentTick = tick
+            self.currentTickColor = tick.color
+            self.colorDialog.setCurrentColor(tick.color)
+            self.colorDialog.open()
+            #color = QtGui.QColorDialog.getColor(tick.color, self, "Select Color", QtGui.QColorDialog.ShowAlphaChannel)
+            #if color.isValid():
+                #self.setTickColor(tick, color)
+                #self.updateGradient()
         elif ev.button() == QtCore.Qt.RightButton:
             if not tick.removeAllowed:
                 return
@@ -267,7 +284,8 @@ class GradientWidget(TickSlider):
             r = c1.red() * (1.-f) + c2.red() * f
             g = c1.green() * (1.-f) + c2.green() * f
             b = c1.blue() * (1.-f) + c2.blue() * f
-            return QtGui.QColor(r, g, b)
+            a = c1.alpha() * (1.-f) + c2.alpha() * f
+            return QtGui.QColor(r, g, b,a)
         elif self.colorMode == 'hsv':
             h1,s1,v1,_ = c1.getHsv()
             h2,s2,v2,_ = c2.getHsv()
@@ -292,6 +310,43 @@ class GradientWidget(TickSlider):
         t.removeAllowed = True
         return t
         
+    def saveState(self):
+        ticks = []
+        for t in self.ticks:
+            c = t.color
+            ticks.append((self.ticks[t], (c.red(), c.green(), c.blue(), c.alpha())))
+        state = {'mode': self.colorMode, 'ticks': ticks}
+        return state
+        
+    def restoreState(self, state):
+        self.setColorMode(state['mode'])
+        for t in self.ticks.keys():
+            self.removeTick(t)
+        for t in state['ticks']:
+            c = QtGui.QColor(*t[1])
+            self.addTick(t[0], c)
+        self.updateGradient()
+
+
+
+class BlackWhiteSlider(GradientWidget):
+    def __init__(self, parent):
+        GradientWidget.__init__(self, parent)
+        self.getTick(0).colorChangeAllowed = False
+        self.getTick(1).colorChangeAllowed = False
+        self.allowAdd = False
+        self.setTickColor(self.getTick(1), QtGui.QColor(255,255,255))
+        self.setOrientation('right')
+
+    def getLevels(self):
+        return (self.tickValue(0), self.tickValue(1))
+
+    def setLevels(self, black, white):
+        self.setTickValue(0, black)
+        self.setTickValue(1, white)
+
+
+
 
 class GammaWidget(TickSlider):
     pass
@@ -361,4 +416,31 @@ class Tick(QtGui.QGraphicsPolygonItem):
                 #self.view.tickChanged(self)
         
         
+    
+    
+    
+if __name__ == '__main__':
+    app = QtGui.QApplication([])
+    w = QtGui.QMainWindow()
+    w.show()
+    w.resize(400,400)
+    cw = QtGui.QWidget()
+    w.setCentralWidget(cw)
+
+    l = QtGui.QGridLayout()
+    l.setSpacing(0)
+    cw.setLayout(l)
+
+    w1 = GradientWidget(orientation='top')
+    w2 = GradientWidget(orientation='right', allowAdd=False)
+    w2.setTickColor(1, QtGui.QColor(255,255,255))
+    w3 = GradientWidget(orientation='bottom')
+    w4 = TickSlider(orientation='left')
+
+    l.addWidget(w1, 0, 1)
+    l.addWidget(w2, 1, 2)
+    l.addWidget(w3, 2, 1)
+    l.addWidget(w4, 1, 0)
+    
+    
     
\ No newline at end of file

GradientWidgetTest.py

-# -*- coding: utf-8 -*-
-
-from GradientWidget import *
-from PyQt4 import QtGui
-
-app = QtGui.QApplication([])
-w = QtGui.QMainWindow()
-w.show()
-w.resize(400,400)
-cw = QtGui.QWidget()
-w.setCentralWidget(cw)
-
-l = QtGui.QGridLayout()
-l.setSpacing(0)
-cw.setLayout(l)
-
-w1 = GradientWidget(orientation='top')
-w2 = GradientWidget(orientation='right', allowAdd=False)
-w2.setTickColor(1, QtGui.QColor(255,255,255))
-w3 = GradientWidget(orientation='bottom')
-w4 = TickSlider(orientation='left')
-
-l.addWidget(w1, 0, 1)
-l.addWidget(w2, 1, 2)
-l.addWidget(w3, 2, 1)
-l.addWidget(w4, 1, 0)

GraphicsView.py

@@ -27,6 +27,8 @@ class GraphicsView(QtGui.QGraphicsView):
         enabled via enableMouse()."""
         
         QtGui.QGraphicsView.__init__(self, parent)
+        if 'linux' in sys.platform:  ## linux has bugs in opengl implementation
+            useOpenGL = False
         self.useOpenGL(useOpenGL)
         
         palette = QtGui.QPalette()
@@ -139,6 +141,7 @@ class GraphicsView(QtGui.QGraphicsView):
         #print "  translate:", st
         self.setMatrix(m)
         self.currentScale = scale
+        self.emit(QtCore.SIGNAL('viewChanged'), self.range)
         
         if propagate:
             for v in self.lockedViewports:
@@ -190,7 +193,6 @@ class GraphicsView(QtGui.QGraphicsView):
         #print "New Range:", self.range
         self.centralWidget.setGeometry(self.range)
         self.updateMatrix(propagate)
-        self.emit(QtCore.SIGNAL('viewChanged'), self.range)
         
         
     def lockXRange(self, v1):

ImageView.py

@@ -18,8 +18,9 @@ from graphicsItems import *
 from widgets import ROI
 from PyQt4 import QtCore, QtGui
 import sys
-from numpy import ndarray
+#from numpy import ndarray
 import ptime
+import numpy as np
 
 from SignalProxy import proxyConnect
 
@@ -52,7 +53,7 @@ class ImageView(QtGui.QWidget):
         self.ui.graphicsView.invertY()
         self.ui.graphicsView.enableMouse()
         
-        self. ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
+        self.ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
         self.ticks[0].colorChangeAllowed = False
         self.ticks[1].colorChangeAllowed = False
         self.ui.gradientWidget.allowAdd = False
@@ -301,14 +302,14 @@ class ImageView(QtGui.QWidget):
             axes = (1, 2)
         else:
             return
-        data = self.roi.getArrayRegion(image.view(ndarray), self.imageItem, axes)
+        data = self.roi.getArrayRegion(image.view(np.ndarray), self.imageItem, axes)
         if data is not None:
             while data.ndim > 1:
                 data = data.mean(axis=1)
             self.roiCurve.setData(y=data, x=self.tVals)
             #self.ui.roiPlot.replot()
 
-    def setImage(self, img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None):
+    def setImage(self, img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None, pos=None, scale=None):
         """Set the image to be displayed in the widget.
         Options are:
           img:         ndarray; the image to be displayed.
@@ -319,16 +320,19 @@ class ImageView(QtGui.QWidget):
                        This is only needed to override the default guess.
         """
         
-        if not isinstance(img, ndarray):
+        if not isinstance(img, np.ndarray):
             raise Exception("Image must be specified as ndarray.")
         self.image = img
         
         if xvals is not None:
             self.tVals = xvals
         elif hasattr(img, 'xvals'):
-            self.tVals = img.xvals(0)
+            try:
+                self.tVals = img.xvals(0)
+            except:
+                self.tVals = np.arange(img.shape[0])
         else:
-            self.tVals = arange(img.shape[0])
+            self.tVals = np.arange(img.shape[0])
         #self.ui.timeSlider.setValue(0)
         #self.ui.normStartSlider.setValue(0)
         #self.ui.timeSlider.setMaximum(img.shape[0]-1)
@@ -346,13 +350,13 @@ class ImageView(QtGui.QWidget):
 
             
         self.imageDisp = None
-        if autoRange:
-            self.autoRange()
         if autoLevels:
             self.autoLevels()
         if levels is not None:
             self.levelMax = levels[1]
             self.levelMin = levels[0]
+            
+        self.currentIndex = 0
         self.updateImage()
         if self.ui.roiBtn.isChecked():
             self.roiChanged()
@@ -361,6 +365,7 @@ class ImageView(QtGui.QWidget):
         if self.axes['t'] is not None:
             #self.ui.roiPlot.show()
             self.ui.roiPlot.setXRange(self.tVals.min(), self.tVals.max())
+            self.timeLine.setValue(0)
             #self.ui.roiPlot.setMouseEnabled(False, False)
             if len(self.tVals) > 1:
                 start = self.tVals.min()
@@ -376,6 +381,14 @@ class ImageView(QtGui.QWidget):
         #else:
             #self.ui.roiPlot.hide()
             
+        self.imageItem.resetTransform()
+        if scale is not None:
+            self.imageItem.scale(*scale)
+        if scale is not None:
+            self.imageItem.setPos(*pos)
+            
+        if autoRange:
+            self.autoRange()
         self.roiClicked()
             
             
@@ -389,10 +402,12 @@ class ImageView(QtGui.QWidget):
         self.ui.gradientWidget.setTickValue(self.ticks[1], 1.0)
         self.imageItem.setLevels(white=self.whiteLevel(), black=self.blackLevel())
             
+
     def autoRange(self):
         image = self.getProcessedImage()
         
-        self.ui.graphicsView.setRange(QtCore.QRectF(0, 0, image.shape[self.axes['x']], image.shape[self.axes['y']]), padding=0., lockAspect=True)        
+        #self.ui.graphicsView.setRange(QtCore.QRectF(0, 0, image.shape[self.axes['x']], image.shape[self.axes['y']]), padding=0., lockAspect=True)        
+        self.ui.graphicsView.setRange(self.imageItem.sceneBoundingRect(), padding=0., lockAspect=True)
         
     def getProcessedImage(self):
         if self.imageDisp is None:
@@ -408,7 +423,7 @@ class ImageView(QtGui.QWidget):
             return image
             
         div = self.ui.normDivideRadio.isChecked()
-        norm = image.view(ndarray).copy()
+        norm = image.view(np.ndarray).copy()
         #if div:
             #norm = ones(image.shape)
         #else:
@@ -498,7 +513,7 @@ class ImageView(QtGui.QWidget):
                 return (0,0)
             totTime = xv[-1] + (xv[-1]-xv[-2])
             #t = f * totTime
-            inds = argwhere(xv < t)
+            inds = np.argwhere(xv < t)
             if len(inds) < 1:
                 return (0,t)
             ind = inds[-1,0]

PlotItem.py

@@ -23,6 +23,7 @@ from PyQt4 import QtGui, QtCore, QtSvg
 #from ObjectWorkaround import *
 #tryWorkaround(QtCore, QtGui)
 import weakref
+import numpy as np
 
 try:
     from WidgetGroup import *
@@ -37,8 +38,6 @@ except:
     HAVE_METAARRAY = False
 
 
-
-
 class PlotItem(QtGui.QGraphicsWidget):
     """Plot graphics item that can be added to any graphics scene. Implements axis titles, scales, interactive viewbox."""
     lastFileDir = None
@@ -132,6 +131,7 @@ class PlotItem(QtGui.QGraphicsWidget):
             
         self.items = []
         self.curves = []
+        self.dataItems = []
         self.paramList = {}
         self.avgCurves = {}
         
@@ -436,7 +436,7 @@ class PlotItem(QtGui.QGraphicsWidget):
         self.vb.setMouseEnabled(*state)
         
     def xRangeChanged(self, _, range):
-        if any(isnan(range)) or any(isinf(range)):
+        if any(np.isnan(range)) or any(np.isinf(range)):
             raise Exception("yRange invalid: %s. Signal came from %s" % (str(range), str(self.sender())))
         self.ctrl.xMinText.setText('%0.5g' % range[0])
         self.ctrl.xMaxText.setText('%0.5g' % range[1])
@@ -455,7 +455,7 @@ class PlotItem(QtGui.QGraphicsWidget):
         self.emit(QtCore.SIGNAL('xRangeChanged'), self, range)
 
     def yRangeChanged(self, _, range):
-        if any(isnan(range)) or any(isinf(range)):
+        if any(np.isnan(range)) or any(np.isinf(range)):
             raise Exception("yRange invalid: %s. Signal came from %s" % (str(range), str(self.sender())))
         self.ctrl.yMinText.setText('%0.5g' % range[0])
         self.ctrl.yMaxText.setText('%0.5g' % range[1])
@@ -545,6 +545,9 @@ class PlotItem(QtGui.QGraphicsWidget):
         if not item in self.items:
             return
         self.items.remove(item)
+        if item in self.dataItems:
+            self.dataItems.remove(item)
+            
         if item.scene() is not None:
             self.vb.removeItem(item)
         if item in self.curves:
@@ -571,12 +574,12 @@ class PlotItem(QtGui.QGraphicsWidget):
             params = {}
         if HAVE_METAARRAY and isinstance(data, MetaArray):
             curve = self._plotMetaArray(data, x=x)
-        elif isinstance(data, ndarray):
+        elif isinstance(data, np.ndarray):
             curve = self._plotArray(data, x=x)
         elif isinstance(data, list):
             if x is not None:
-                x = array(x)
-            curve = self._plotArray(array(data), x=x)
+                x = np.array(x)
+            curve = self._plotArray(np.array(data), x=x)
         elif data is None:
             curve = PlotCurveItem()
         else:
@@ -589,6 +592,10 @@ class PlotItem(QtGui.QGraphicsWidget):
         
         return curve
 
+    def addDataItem(self, item):
+        self.addItem(item)
+        self.dataItems.append(item)
+    
     def addCurve(self, c, params=None):
         if params is None:
             params = {}
@@ -622,7 +629,7 @@ class PlotItem(QtGui.QGraphicsWidget):
                 percentScale = [self.ctrl.xAutoPercentSpin.value(), self.ctrl.yAutoPercentSpin.value()][ax] * 0.01
                 mn = None
                 mx = None
-                for c in self.curves + [c[1] for c in self.avgCurves.values()]:
+                for c in self.curves + [c[1] for c in self.avgCurves.values()] + self.dataItems:
                     if not c.isVisible():
                         continue
                     cmn, cmx = c.getRange(ax, percentScale)
@@ -630,7 +637,7 @@ class PlotItem(QtGui.QGraphicsWidget):
                         mn = cmn
                     if mx is None or cmx > mx:
                         mx = cmx
-                if mn is None or mx is None or any(isnan([mn, mx])) or any(isinf([mn, mx])):
+                if mn is None or mx is None or any(np.isnan([mn, mx])) or any(np.isinf([mn, mx])):
                     continue
                 if mn == mx:
                     mn -= 1
@@ -1013,7 +1020,7 @@ class PlotItem(QtGui.QGraphicsWidget):
             else:
                 xv = x
         c = PlotCurveItem()
-        c.setData(x=xv, y=arr.view(ndarray))
+        c.setData(x=xv, y=arr.view(np.ndarray))
         
         if autoLabel:
             name = arr._info[0].get('name', None)

Point.py

@@ -20,7 +20,10 @@ class Point(QtCore.QPointF):
     
     def __init__(self, *args):
         if len(args) == 1:
-            if hasattr(args[0], '__getitem__'):
+            if isinstance(args[0], QtCore.QSizeF):
+                QtCore.QPointF.__init__(self, float(args[0].width()), float(args[0].height()))
+                return
+            elif hasattr(args[0], '__getitem__'):
                 QtCore.QPointF.__init__(self, float(args[0][0]), float(args[0][1]))
                 return
             elif type(args[0]) in [float, int]:
@@ -31,6 +34,9 @@ class Point(QtCore.QPointF):
             return
         QtCore.QPointF.__init__(self, *args)
         
+    def __reduce__(self):
+        return (Point, (self.x(), self.y()))
+        
     def __getitem__(self, i):
         if i == 0:
             return self.x()

SignalProxy.py

@@ -24,14 +24,17 @@ class SignalProxy(QtCore.QObject):
         self.args = None
         self.timers = 0
         self.signal = signal
+        self.block = False
         
     def setDelay(self, delay):
         self.delay = delay
         
     def flush(self):
         """If there is a signal queued up, send it now."""
-        if self.args is None:
+        if self.args is None or self.block:
             return False
+        if self.block:
+            return
         self.emit(self.signal, *self.args)
         self.args = None
         return True
@@ -39,6 +42,8 @@ class SignalProxy(QtCore.QObject):
         
     def signal(self, *args):
         """Received signal, queue to be forwarded later."""
+        if self.block:
+            return
         self.waitUntil = time() + self.delay
         self.args = args
         self.timers += 1
@@ -46,7 +51,7 @@ class SignalProxy(QtCore.QObject):
         
     def tryEmit(self):
         """Emit signal if it has been long enougn since receiving the last signal."""
-        if self.args is None:
+        if self.args is None or self.block:
             return False
         self.timers -= 1
         t = time()
@@ -59,4 +64,6 @@ class SignalProxy(QtCore.QObject):
         return True
                 
         
+    def disconnect(self):
+        self.block = True
     
\ No newline at end of file

examples/test_ImageItem.py

@@ -14,6 +14,7 @@ app = QtGui.QApplication([])
 ## Create window with GraphicsView widget
 win = QtGui.QMainWindow()
 view = GraphicsView()
+#view.useOpenGL(True)
 win.setCentralWidget(view)
 win.show()
 

examples/test_draw.py

+# -*- coding: utf-8 -*-
+## Add path to library (just for examples; you do not need this)
+import sys, os
+sys.path = [os.path.join(os.path.dirname(__file__), '..', '..')] + sys.path
+
+from pyqtgraph.GraphicsView import *
+from pyqtgraph.graphicsItems import *
+#from numpy import random
+from PyQt4 import QtCore, QtGui
+from scipy.ndimage import *
+import numpy as np
+
+app = QtGui.QApplication([])
+
+## Create window with GraphicsView widget
+win = QtGui.QMainWindow()
+view = GraphicsView()
+#view.useOpenGL(True)
+win.setCentralWidget(view)
+win.show()
+
+## Allow mouse scale/pan
+view.enableMouse()
+
+## ..But lock the aspect ratio
+view.setAspectLocked(True)
+
+## Create image item
+img = ImageItem(np.zeros((200,200)))
+view.scene().addItem(img)
+
+## Set initial view bounds
+view.setRange(QtCore.QRectF(0, 0, 200, 200))
+
+img.setDrawKernel(1)
+img.setLevels(10,0)
+
+#app.exec_()

examples/test_scatterPlot.py

+# -*- coding: utf-8 -*-
+import sys, os
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', '..'))
+
+from PyQt4 import QtGui, QtCore
+from pyqtgraph.PlotWidget import *
+from pyqtgraph.graphicsItems import *
+
+
+app = QtGui.QApplication([])
+mw = QtGui.QMainWindow()
+cw = PlotWidget()
+mw.setCentralWidget(cw)
+mw.show()
+
+
+#s1 = SpotItem(5, pxMode=True, brush=QtGui.QBrush(QtGui.QColor(0, 0, 200)), pen=QtGui.QPen(QtGui.QColor(100,100,100)))
+#s1.setPos(1, 0)
+#s2 = SpotItem(.1, pxMode=False, brush=QtGui.QBrush(QtGui.QColor(0, 200, 0)), pen=QtGui.QPen(QtGui.QColor(100,100,100)))
+#s2.setPos(0, 1)
+#cw.addItem(s1)
+#cw.addItem(s2)
+
+import numpy as np
+s1 = ScatterPlotItem(size=10, pen=QtGui.QPen(QtCore.Qt.NoPen), brush=QtGui.QBrush(QtGui.QColor(255, 255, 255, 20)))
+pos = np.random.normal(size=(2,3000))
+spots = [{'pos': pos[:,i]} for i in range(3000)]
+s1.addPoints(spots)
+
+cw.addDataItem(s1)
+
+

widgets.py

@@ -10,7 +10,8 @@ of array data from ImageItems.
 """
 
 from PyQt4 import QtCore, QtGui, QtOpenGL, QtSvg
-from numpy import array, arccos, dot, pi, zeros, vstack, ubyte, fromfunction, ceil, floor, arctan2
+#from numpy import array, arccos, dot, pi, zeros, vstack, ubyte, fromfunction, ceil, floor, arctan2
+import numpy as np
 from numpy.linalg import norm
 import scipy.ndimage as ndimage
 from Point import *
@@ -50,7 +51,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         self.state = {'pos': pos, 'size': size, 'angle': angle}
         self.lastState = None
         self.setPos(pos)
-        self.rotate(-angle * 180. / pi)
+        self.rotate(-angle * 180. / np.pi)
         self.setZValue(10)
         
         self.handleSize = 5
@@ -62,7 +63,15 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         self.rotateSnap = rotateSnap
         self.scaleSnap = scaleSnap
         self.setFlag(self.ItemIsSelectable, True)
-        
+    
+    def getState(self):
+        return self.state.copy()
+    
+    def setState(self, state):
+        self.setPos(state['pos'], update=False)
+        self.setSize(state['size'], update=False)
+        self.setAngle(state['angle'])
+    
     def setZValue(self, z):
         QtGui.QGraphicsItem.setZValue(self, z)
         for h in self.handles:
@@ -79,10 +88,12 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         self.update()
         
     def setPos(self, pos, update=True):
+        #print "setPos() called."
         pos = Point(pos)
         self.state['pos'] = pos
         QtGui.QGraphicsItem.setPos(self, pos)
         if update: