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)
+    
+    
     

GradientWidgetTest.py

@@ -1,26 +0,0 @@
-# -*- 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
     

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

@@ -0,0 +1,38 @@
+# -*- 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

@@ -0,0 +1,32 @@
+# -*- 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)
+
+

graphicsItems.py

@@ -11,7 +11,8 @@ Provides ImageItem, PlotCurveItem, and ViewBox, amongst others.
 from PyQt4 import QtGui, QtCore
 from ObjectWorkaround import *
 #tryWorkaround(QtCore, QtGui)
-from numpy import *
+#from numpy import *
+import numpy as np
 try:
     import scipy.weave as weave
     from scipy.weave import converters
@@ -171,10 +172,14 @@ class GraphicsObject(QGraphicsObject):
         
         
 
-class ImageItem(QtGui.QGraphicsPixmapItem):
-    useWeave = True
+class ImageItem(QtGui.QGraphicsPixmapItem, QObjectWorkaround):
+    if 'linux' not in sys.platform:  ## disable weave optimization on linux--broken there.
+        useWeave = True
+    else:
+        useWeave = False
     
     def __init__(self, image=None, copy=True, parent=None, *args):
+        QObjectWorkaround.__init__(self)
         self.qimage = QtGui.QImage()
         self.pixmap = None
         #self.useWeave = True
@@ -183,6 +188,8 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
         self.alpha = 1.0
         self.image = None
         self.clipLevel = None
+        self.drawKernel = None
+        
         QtGui.QGraphicsPixmapItem.__init__(self, parent, *args)
         #self.pixmapItem = QtGui.QGraphicsPixmapItem(self)
         if image is not None:
@@ -222,6 +229,9 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
         if black is not None:
             self.blackLevel = black  
         self.updateImage()
+        
+    def getLevels(self):
+        return self.whiteLevel, self.blackLevel
 
     def updateImage(self, image=None, copy=True, autoRange=False, clipMask=None, white=None, black=None):
         axh = {'x': 0, 'y': 1, 'c': 2}
@@ -231,11 +241,12 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
         if black is not None:
             self.blackLevel = black  
         
-        
+        gotNewData = False
         if image is None:
             if self.image is None:
                 return
         else:
+            gotNewData = True
             if copy:
                 self.image = image.copy()
             else:
@@ -261,9 +272,9 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
         try:
             if not ImageItem.useWeave:
                 raise Exception('Skipping weave compile')
-            sim = ascontiguousarray(self.image)
+            sim = np.ascontiguousarray(self.image)
             sim.shape = sim.size
-            im = zeros(sim.shape, dtype=ubyte)
+            im = np.empty(sim.shape, dtype=np.ubyte)
             n = im.size
             
             code = """
@@ -287,15 +298,15 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
                 #print "=============================================================================="
                 print "Weave compile failed, falling back to slower version."
             self.image.shape = shape
-            im = ((self.image - black) * scale).clip(0.,255.).astype(ubyte)
+            im = ((self.image - black) * scale).clip(0.,255.).astype(np.ubyte)
                 
 
         try:
-            im1 = empty((im.shape[axh['y']], im.shape[axh['x']], 4), dtype=ubyte)
+            im1 = np.empty((im.shape[axh['y']], im.shape[axh['x']], 4), dtype=np.ubyte)
         except:
             print im.shape, axh
             raise
-        alpha = clip(int(255 * self.alpha), 0, 255)
+        alpha = np.clip(int(255 * self.alpha), 0, 255)
         # Fill image 
         if im.ndim == 2:
             im2 = im.transpose(axh['y'], axh['x'])
@@ -303,7 +314,7 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
             im1[..., 1] = im2
             im1[..., 2] = im2
             im1[..., 3] = alpha
-        elif im.ndim == 3:
+        elif im.ndim == 3: #color image
             im2 = im.transpose(axh['y'], axh['x'], axh['c'])
             
             for i in range(0, im.shape[axh['c']]):
@@ -335,10 +346,43 @@ class ImageItem(QtGui.QGraphicsPixmapItem):
         self.setPixmap(self.pixmap)
         self.update()
         
+        if gotNewData:
+            self.emit(QtCore.SIGNAL('imageChanged'))
+        
     def getPixmap(self):
         return self.pixmap.copy()
 
+    def getHistogram(self, bins=500, step=3):
+        """returns an x and y arrays containing the histogram values for the current image.
+        The step argument causes pixels to be skipped when computing the histogram to save time."""
+        stepData = self.image[::step, ::step]
+        hist = np.histogram(stepData, bins=bins)
+        return hist[1][:-1], hist[0]
         
+    def mousePressEvent(self, ev):
+        if self.drawKernel is not None and ev.button() == QtCore.Qt.LeftButton:
+            self.drawAt(ev.pos())
+            ev.accept()
+        else:
+            ev.ignore()
+        
+    def mouseMoveEvent(self, ev):
+        #print "mouse move", ev.pos()
+        if self.drawKernel is not None:
+            self.drawAt(ev.pos())
+    
+    def mouseReleaseEvent(self, ev):
+        pass
+    
+    def drawAt(self, pos):
+        self.image[int(pos.x()), int(pos.y())] += 1
+        self.updateImage()
+        
+    def setDrawKernel(self, kernel=None):
+        self.drawKernel = kernel
+    
+    
+
 
 class PlotCurveItem(GraphicsObject):
     """Class representing a single plot curve."""
@@ -376,9 +420,13 @@ class PlotCurveItem(GraphicsObject):
         if self.xData is None:
             return (None, None)
         if self.xDisp is None:
-            nanMask = isnan(self.xData) | isnan(self.yData)
-            x = self.xData[~nanMask]
-            y = self.yData[~nanMask]
+            nanMask = np.isnan(self.xData) | np.isnan(self.yData)
+            if any(nanMask):
+                x = self.xData[~nanMask]
+                y = self.yData[~nanMask]
+            else:
+                x = self.xData
+                y = self.yData
             ds = self.opts['downsample']
             if ds > 1:
                 x = x[::ds]
@@ -387,11 +435,11 @@ class PlotCurveItem(GraphicsObject):
                 f = fft(y) / len(y)
                 y = abs(f[1:len(f)/2])
                 dt = x[-1] - x[0]
-                x = linspace(0, 0.5*len(x)/dt, len(y))
+                x = np.linspace(0, 0.5*len(x)/dt, len(y))
             if self.opts['logMode'][0]:
-                x = log10(x)
+                x = np.log10(x)
             if self.opts['logMode'][1]:
-                y = log10(y)
+                y = np.log10(y)
             self.xDisp = x
             self.yDisp = y
         #print self.yDisp.shape, self.yDisp.min(), self.yDisp.max()
@@ -494,10 +542,10 @@ class PlotCurveItem(GraphicsObject):
         
     def updateData(self, data, x=None, copy=False):
         if isinstance(data, list):
-            data = array(data)
+            data = np.array(data)
         if isinstance(x, list):
-            x = array(x)
-        if not isinstance(data, ndarray) or data.ndim > 2:
+            x = np.array(x)
+        if not isinstance(data, np.ndarray) or data.ndim > 2:
             raise Exception("Plot data must be 1 or 2D ndarray (data shape is %s)" % str(data.shape))
         if data.ndim == 2:  ### If data is 2D array, then assume x and y values are in first two columns or rows.
             if x is not None:
@@ -542,9 +590,9 @@ class PlotCurveItem(GraphicsObject):
         ## Create all vertices in path. The method used below creates a binary format so that all 
         ## vertices can be read in at once. This binary format may change in future versions of Qt, 
         ## so the original (slower) method is left here for emergencies:
-        #self.path.moveTo(x[0], y[0])
+        #path.moveTo(x[0], y[0])
         #for i in range(1, y.shape[0]):
-            #self.path.lineTo(x[i], y[i])
+        #    path.lineTo(x[i], y[i])
             
         ## Speed this up using >> operator
         ## Format is:
@@ -558,7 +606,7 @@ class PlotCurveItem(GraphicsObject):
         #
         n = x.shape[0]
         # create empty array, pad with extra space on either end
-        arr = empty(n+2, dtype=[('x', '>f8'), ('y', '>f8'), ('c', '>i4')])
+        arr = np.empty(n+2, dtype=[('x', '>f8'), ('y', '>f8'), ('c', '>i4')])
         # write first two integers
         arr.data[12:20] = struct.pack('>ii', n, 0)
         # Fill array with vertex values
@@ -643,7 +691,113 @@ class PlotCurveItem(GraphicsObject):
         self.path = None
         #del self.xData, self.yData, self.xDisp, self.yDisp, self.path
         
+
+class ScatterPlotItem(QtGui.QGraphicsItem):
+    def __init__(self, spots=None, pxMode=True, pen=None, brush=None, size=5):
+        QtGui.QGraphicsItem.__init__(self)
+        self.spots = []
+        self.range = [[0,0], [0,0]]
         
+        if brush is None:
+            brush = QtGui.QBrush(QtGui.QColor(100, 100, 150))
+        self.brush = brush
+        
+        if pen is None:
+            pen = QtGui.QPen(QtGui.QColor(200, 200, 200))
+        self.pen = pen
+        
+        self.size = size
+        
+        self.pxMode = pxMode
+        if spots is not None:
+            self.setPoints(spots)
+            
+    def setPxMode(self, mode):
+        self.pxMode = mode
+            
+    def clear(self):
+        for i in self.spots:
+            i.setParentItem(None)
+            s = i.scene()
+            if s is not None:
+                s.removeItem(i)
+        self.spots = []
+        
+
+    def getRange(self, ax, percent):
+        return self.range[ax]
+        
+    def setPoints(self, spots):
+        self.clear()
+        self.range = [[0,0],[0,0]]
+        self.addPoints(spots)
+
+    def addPoints(self, spots):
+        xmn = ymn = xmx = ymx = None
+        for s in spots:
+            pos = Point(s['pos'])
+            size = s.get('size', self.size)
+            brush = s.get('brush', self.brush)
+            pen = s.get('pen', self.pen)
+            pen.setCosmetic(True)
+            item = self.mkSpot(pos, size, self.pxMode, brush, pen)
+            self.spots.append(item)
+            if xmn is None:
+                xmn = pos[0]-size
+                xmx = pos[0]+size
+                ymn = pos[1]-size
+                ymx = pos[1]+size
+            else:
+                xmn = min(xmn, pos[0]-size)
+                xmx = max(xmx, pos[0]+size)
+                ymn = min(ymn, pos[1]-size)
+                ymx = max(ymx, pos[1]+size)
+        self.range = [[xmn, xmx], [ymn, ymx]]
+                
+
+    def mkSpot(self, pos, size, pxMode, brush, pen):
+        item = SpotItem(size, pxMode, brush, pen)
+        item.setParentItem(self)
+        item.setPos(pos)
+        return item
+        
+    def boundingRect(self):
+        ((xmn, xmx), (ymn, ymx)) = self.range
+        
+        return QtCore.QRectF(xmn, ymn, xmx-xmn, ymx-ymn)
+        
+    def paint(self, p, *args):
+        pass
+
+
+
+class SpotItem(QtGui.QGraphicsItem):
+    def __init__(self, size, pxMode, brush, pen):
+        QtGui.QGraphicsItem.__init__(self)
+        if pxMode:
+            self.setFlags(self.flags() | self.ItemIgnoresTransformations)
+            #self.setCacheMode(self.DeviceCoordinateCache)  ## causes crash on linux
+        self.pen = pen
+        self.brush = brush
+        self.path = QtGui.QPainterPath()
+        s2 = size/2.
+        self.path.addEllipse(QtCore.QRectF(-s2, -s2, size, size))
+        
+    def boundingRect(self):
+        return self.path.boundingRect()
+        
+    def shape(self):
+        return self.path
+        
+    def paint(self, p, *opts):
+        p.setPen(self.pen)
+        p.setBrush(self.brush)
+        p.drawPath(self.path)
+        
+        
+        
+        
+
 class ROIPlotItem(PlotCurveItem):
     def __init__(self, roi, data, img, axes=(0,1), xVals=None, color=None):
         self.roi = roi
@@ -978,7 +1132,7 @@ class ScaleItem(QtGui.QGraphicsWidget):
             self.update()
         
     def setRange(self, mn, mx):
-        if mn in [nan, inf, -inf] or mx in [nan, inf, -inf]:
+        if mn in [np.nan, np.inf, -np.inf] or mx in [np.nan, np.inf, -np.inf]:
             raise Exception("Not setting range to [%s, %s]" % (str(mn), str(mx)))
         self.range = [mn, mx]
         if self.autoScale:
@@ -1049,7 +1203,7 @@ class ScaleItem(QtGui.QGraphicsWidget):
         if dif == 0.0:
             return
         #print "dif:", dif
-        pw = 10 ** (floor(log10(dif))-1)
+        pw = 10 ** (np.floor(np.log10(dif))-1)
         for i in range(len(intervals)):
             i1 = i
             if dif / (pw*intervals[i]) < 10:
@@ -1075,7 +1229,7 @@ class ScaleItem(QtGui.QGraphicsWidget):
             sp = pw*intervals[i]
             
             ## determine starting tick
-            start = ceil(self.range[0] / sp) * sp
+            start = np.ceil(self.range[0] / sp) * sp
             
             ## determine number of ticks
             num = int(dif / sp) + 1
@@ -1085,7 +1239,7 @@ class ScaleItem(QtGui.QGraphicsWidget):
             
             ## Number of decimal places to print
             maxVal = max(abs(start), abs(last))
-            places = max(0, 1-int(log10(sp*self.scale)))
+            places = max(0, 1-int(np.log10(sp*self.scale)))
         
             ## length of tick
             h = min(self.tickLength, (self.tickLength*3 / num) - 1.)
@@ -1292,11 +1446,11 @@ class ViewBox(QtGui.QGraphicsWidget):
         yd = pr[1][1] - pr[1][0]
         if xd == 0 or yd == 0:
             print "Warning: 0 range in view:", xd, yd
-            return array([1,1])
+            return np.array([1,1])
         
         #cs = self.canvas().size()
         cs = self.boundingRect()
-        scale = array([cs.width() / xd, cs.height() / yd])
+        scale = np.array([cs.width() / xd, cs.height() / yd])
         #print "view scale:", scale
         return scale
 
@@ -1324,7 +1478,7 @@ class ViewBox(QtGui.QGraphicsWidget):
         #print self.range
         
     def translateBy(self, t, viewCoords=False):
-        t = t.astype(float)
+        t = t.astype(np.float)
         #print "translate:", t, self.viewScale()
         if viewCoords:  ## scale from pixels
             t /= self.viewScale()
@@ -1339,25 +1493,25 @@ class ViewBox(QtGui.QGraphicsWidget):
         
         
     def mouseMoveEvent(self, ev):
-        pos = array([ev.pos().x(), ev.pos().y()])
+        pos = np.array([ev.pos().x(), ev.pos().y()])
         dif = pos - self.mousePos
         dif *= -1
         self.mousePos = pos
         
         ## Ignore axes if mouse is disabled
-        mask = array(self.mouseEnabled, dtype=float)
+        mask = np.array(self.mouseEnabled, dtype=np.float)
         
         ## Scale or translate based on mouse button
         if ev.buttons() & QtCore.Qt.LeftButton:
             if not self.yInverted:
-                mask *= array([1, -1])
+                mask *= np.array([1, -1])
             tr = dif*mask
             self.translateBy(tr, viewCoords=True)
             self.emit(QtCore.SIGNAL('rangeChangedManually'), self.mouseEnabled)
             ev.accept()
         elif ev.buttons() & QtCore.Qt.RightButton:
             dif = ev.screenPos() - ev.lastScreenPos()
-            dif = array([dif.x(), dif.y()])
+            dif = np.array([dif.x(), dif.y()])
             dif[0] *= -1
             s = ((mask * 0.02) + 1) ** dif
             #print mask, dif, s
@@ -1369,12 +1523,12 @@ class ViewBox(QtGui.QGraphicsWidget):
             ev.ignore()
         
     def mousePressEvent(self, ev):
-        self.mousePos = array([ev.pos().x(), ev.pos().y()])
+        self.mousePos = np.array([ev.pos().x(), ev.pos().y()])
         self.pressPos = self.mousePos.copy()
         ev.accept()
         
     def mouseReleaseEvent(self, ev):
-        pos = array([ev.pos().x(), ev.pos().y()])
+        pos = np.array([ev.pos().x(), ev.pos().y()])
         #if sum(abs(self.pressPos - pos)) < 3:  ## Detect click
             #if ev.button() == QtCore.Qt.RightButton:
                 #self.ctrlMenu.popup(self.mapToGlobal(ev.pos()))
@@ -1396,7 +1550,7 @@ class ViewBox(QtGui.QGraphicsWidget):
             min -= dy*0.5
             max += dy*0.5
             #raise Exception("Tried to set range with 0 width.")
-        if any(isnan([min, max])) or any(isinf([min, max])):
+        if any(np.isnan([min, max])) or any(np.isinf([min, max])):
             raise Exception("Not setting range [%s, %s]" % (str(min), str(max)))
             
         padding = (max-min) * padding
@@ -1422,7 +1576,7 @@ class ViewBox(QtGui.QGraphicsWidget):
             max += dx*0.5
             #print "Warning: Tried to set range with 0 width."
             #raise Exception("Tried to set range with 0 width.")
-        if any(isnan([min, max])) or any(isinf([min, max])):
+        if any(np.isnan([min, max])) or any(np.isinf([min, max])):
             raise Exception("Not setting range [%s, %s]" % (str(min), str(max)))
         padding = (max-min) * padding
         min -= padding
@@ -1474,6 +1628,7 @@ class InfiniteLine(GraphicsObject):
         if movable:
             self.setAcceptHoverEvents(True)
             
+        self.hasMoved = False
 
         
         if pen is None:
@@ -1585,13 +1740,13 @@ class InfiniteLine(GraphicsObject):
         #print 'before', self.bounds
         
         if self.angle > 45:
-            m = tan((90-self.angle) * pi / 180.)
+            m = np.tan((90-self.angle) * np.pi / 180.)
             y2 = vr.bottom()
             y1 = vr.top()
             x1 = self.p[0] + (y1 - self.p[1]) * m
             x2 = self.p[0] + (y2 - self.p[1]) * m
         else:
-            m = tan(self.angle * pi / 180.)
+            m = np.tan(self.angle * np.pi / 180.)
             x1 = vr.left()
             x2 = vr.right()
             y2 = self.p[1] + (x1 - self.p[0]) * m
@@ -1650,12 +1805,18 @@ class InfiniteLine(GraphicsObject):
     def mouseMoveEvent(self, ev):
         self.setPos(self.mapToParent(ev.pos()) - self.pressDelta)
         self.emit(QtCore.SIGNAL('dragged'), self)
- 
+        self.hasMoved = True
+
+    def mouseReleaseEvent(self, ev):
+        if self.hasMoved and ev.button() == QtCore.Qt.LeftButton:
+            self.hasMoved = False
+            self.emit(QtCore.SIGNAL('positionChangeFinished'), self)
+            
 
 
 class LinearRegionItem(GraphicsObject):
     """Used for marking a horizontal or vertical region in plots."""
-    def __init__(self, view, orientation="horizontal", vals=[0,1], brush=None, movable=True, bounds=None):
+    def __init__(self, view, orientation="vertical", vals=[0,1], brush=None, movable=True, bounds=None):
         GraphicsObject.__init__(self)
         self.orientation = orientation
         if hasattr(self, "ItemHasNoContents"):  
@@ -1680,6 +1841,7 @@ class LinearRegionItem(GraphicsObject):
         
         for l in self.lines:
             l.setParentItem(self)
+            l.connect(QtCore.SIGNAL('positionChangeFinished'), self.lineMoveFinished)
             l.connect(QtCore.SIGNAL('positionChanged'), self.lineMoved)
             
         if brush is None:
@@ -1698,12 +1860,16 @@ class LinearRegionItem(GraphicsObject):
         self.updateBounds()
         self.emit(QtCore.SIGNAL('regionChanged'), self)
             
+    def lineMoveFinished(self):
+        self.emit(QtCore.SIGNAL('regionChangeFinished'), self)
+        
+            
     def updateBounds(self):
         vb = self.view().viewRect()
         vals = [self.lines[0].value(), self.lines[1].value()]
         if self.orientation[0] == 'h':
-            vb.setTop(max(vals))
-            vb.setBottom(min(vals))
+            vb.setTop(min(vals))
+            vb.setBottom(max(vals))
         else:
             vb.setLeft(min(vals))
             vb.setRight(max(vals))
@@ -1713,14 +1879,19 @@ class LinearRegionItem(GraphicsObject):
         
     def mousePressEvent(self, ev):
         for l in self.lines:
-            l.mousePressEvent(ev)
+            l.mousePressEvent(ev)  ## pass event to both lines so they move together
         #if self.movable and ev.button() == QtCore.Qt.LeftButton:
             #ev.accept()
             #self.pressDelta = self.mapToParent(ev.pos()) - QtCore.QPointF(*self.p)
         #else:
             #ev.ignore()
             
+    def mouseReleaseEvent(self, ev):
+        for l in self.lines:
+            l.mouseReleaseEvent(ev)
+            
     def mouseMoveEvent(self, ev):
+        #print "move", ev.pos()
         self.lines[0].blockSignals(True)  # only want to update once
         for l in self.lines:
             l.mouseMoveEvent(ev)
@@ -1858,8 +2029,10 @@ class GridItem(UIGraphicsItem):
         self.picture = None
         
         
-    def viewChangedEvent(self, newRect, oldRect):
+    def viewChangedEvent(self):
         self.picture = None
+        UIGraphicsItem.viewChangedEvent(self)
+        #self.update()
         
     def paint(self, p, opt, widget):
         #p.setPen(QtGui.QPen(QtGui.QColor(100, 100, 100)))
@@ -1883,8 +2056,8 @@ class GridItem(UIGraphicsItem):
         unit = self.unitRect()
         dim = [vr.width(), vr.height()]
         lvr = self.boundingRect()
-        ul = array([lvr.left(), lvr.top()])
-        br = array([lvr.right(), lvr.bottom()])
+        ul = np.array([lvr.left(), lvr.top()])
+        br = np.array([lvr.right(), lvr.bottom()])
         
         texts = []
         
@@ -1897,22 +2070,22 @@ class GridItem(UIGraphicsItem):
             
             dist = br-ul
             nlTarget = 10.**i
-            d = 10. ** floor(log10(abs(dist/nlTarget))+0.5)
-            ul1 = floor(ul / d) * d
-            br1 = ceil(br / d) * d
+            d = 10. ** np.floor(np.log10(abs(dist/nlTarget))+0.5)
+            ul1 = np.floor(ul / d) * d
+            br1 = np.ceil(br / d) * d
             dist = br1-ul1
             nl = (dist / d) + 0.5
             for ax in range(0,2):  ## Draw grid for both axes
                 ppl = dim[ax] / nl[ax]
-                c = clip(3.*(ppl-3), 0., 30.)
+                c = np.clip(3.*(ppl-3), 0., 30.)
                 linePen = QtGui.QPen(QtGui.QColor(255, 255, 255, c)) 
                 textPen = QtGui.QPen(QtGui.QColor(255, 255, 255, c*2)) 
                 
                 bx = (ax+1) % 2
                 for x in range(0, int(nl[ax])):
                     p.setPen(linePen)
-                    p1 = array([0.,0.])
-                    p2 = array([0.,0.])
+                    p1 = np.array([0.,0.])
+                    p2 = np.array([0.,0.])
                     p1[ax] = ul1[ax] + x * d[ax]
                     p2[ax] = p1[ax]
                     p1[bx] = ul[bx]
@@ -1969,7 +2142,7 @@ class ScaleBar(UIGraphicsItem):
         p.scale(rect.width(), rect.height())
         p.drawRect(0, 0, 1, 1)
         
-        alpha = clip(((self.size/unit.width()) - 40.) * 255. / 80., 0, 255)
+        alpha = np.clip(((self.size/unit.width()) - 40.) * 255. / 80., 0, 255)
         p.setPen(QtGui.QPen(QtGui.QColor(0, 0, 0, alpha)))
         for i in range(1, 10):
             #x2 = x + (x1-x) * 0.1 * i

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:
+            self.updateHandles()
             self.handleChange()
         
     def setSize(self, size, update=True):
@@ -93,35 +104,45 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
             self.updateHandles()
             self.handleChange()
         
-    def addTranslateHandle(self, pos, axes=None, item=None):
+    def setAngle(self, angle, update=True):
+        self.state['angle'] = angle
+        tr = QtGui.QTransform()
+        tr.rotate(-angle * 180 / np.pi)
+        self.setTransform(tr)
+        if update:
+            self.updateHandles()
+            self.handleChange()
+        
+        
+    def addTranslateHandle(self, pos, axes=None, item=None, name=None):
         pos = Point(pos)
-        return self.addHandle({'type': 't', 'pos': pos, 'item': item})
+        return self.addHandle({'name': name, 'type': 't', 'pos': pos, 'item': item})
     
-    def addFreeHandle(self, pos, axes=None, item=None):
+    def addFreeHandle(self, pos, axes=None, item=None, name=None):
         pos = Point(pos)
-        return self.addHandle({'type': 'f', 'pos': pos, 'item': item})
+        return self.addHandle({'name': name, 'type': 'f', 'pos': pos, 'item': item})
     
-    def addScaleHandle(self, pos, center, axes=None, item=None):
+    def addScaleHandle(self, pos, center, axes=None, item=None, name=None):
         pos = Point(pos)
         center = Point(center)
-        info = {'type': 's', 'center': center, 'pos': pos, 'item': item}
+        info = {'name': name, 'type': 's', 'center': center, 'pos': pos, 'item': item}
         if pos.x() == center.x():
             info['xoff'] = True
         if pos.y() == center.y():
             info['yoff'] = True
         return self.addHandle(info)
     
-    def addRotateHandle(self, pos, center, item=None):
+    def addRotateHandle(self, pos, center, item=None, name=None):
         pos = Point(pos)
         center = Point(center)
-        return self.addHandle({'type': 'r', 'center': center, 'pos': pos, 'item': item})
+        return self.addHandle({'name': name, 'type': 'r', 'center': center, 'pos': pos, 'item': item})
     
-    def addScaleRotateHandle(self, pos, center, item=None):
+    def addScaleRotateHandle(self, pos, center, item=None, name=None):
         pos = Point(pos)
         center = Point(center)
         if pos[0] != center[0] and pos[1] != center[1]:
             raise Exception("Scale/rotate handles must have either the same x or y coordinate as their center point.")
-        return self.addHandle({'type': 'sr', 'center': center, 'pos': pos, 'item': item})
+        return self.addHandle({'name': name, 'type': 'sr', 'center': center, 'pos': pos, 'item': item})
     
     def addHandle(self, info):
         if not info.has_key('item') or info['item'] is None:
@@ -144,6 +165,26 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         #else:
             #h.hide()
         return h
+    
+    def getLocalHandlePositions(self, index=None):
+        """Returns the position of a handle in ROI coordinates"""
+        if index == None:
+            positions = []
+            for h in self.handles:
+                positions.append((h['name'], h['pos']))
+            return positions
+        else:
+            return (self.handles[index]['name'], self.handles[index]['pos'])
+            
+    def getSceneHandlePositions(self, index = None):
+        if index == None:
+            positions = []
+            for h in self.handles:
+                positions.append((h['name'], h['item'].scenePos()))
+            return positions
+        else:
+            return (self.handles[index]['name'], self.handles[index]['item'].scenePos())
+        
         
     def mapSceneToParent(self, pt):
         return self.mapToParent(self.mapFromScene(pt))
@@ -220,7 +261,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         
         
     def movePoint(self, pt, pos, modifiers=QtCore.Qt.KeyboardModifier()):
-        #print "movePoint", pos
+        #print "movePoint() called."
         newState = self.stateCopy()
         h = self.handles[pt]
         #p0 = self.mapToScene(h['item'].pos())
@@ -248,6 +289,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         
         elif h['type'] == 'f':
             h['item'].setPos(self.mapFromScene(pos))
+            self.emit(QtCore.SIGNAL('regionChanged'), self)
             
         elif h['type'] == 's':
             #c = h['center']
@@ -312,11 +354,11 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
             if ang is None:
                 return
             if self.rotateSnap or (modifiers & QtCore.Qt.ControlModifier):
-                ang = round(ang / (pi/12.)) * (pi/12.)
+                ang = round(ang / (np.pi/12.)) * (np.pi/12.)
             
             
             tr = QtGui.QTransform()
-            tr.rotate(-ang * 180. / pi)
+            tr.rotate(-ang * 180. / np.pi)
             
             cc = self.mapToParent(cs) - (tr.map(cs) + self.state['pos'])
             newState['angle'] = ang
@@ -347,7 +389,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
             if ang is None:
                 return
             if self.rotateSnap or (modifiers & QtCore.Qt.ControlModifier):
-                ang = round(ang / (pi/12.)) * (pi/12.)
+                ang = round(ang / (np.pi/12.)) * (np.pi/12.)
             
             hs = abs(h['pos'][scaleAxis] - c[scaleAxis])
             newState['size'][scaleAxis] = lp1.length() / hs
@@ -358,7 +400,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
                 
             c1 = c * newState['size']
             tr = QtGui.QTransform()
-            tr.rotate(-ang * 180. / pi)
+            tr.rotate(-ang * 180. / np.pi)
             
             cc = self.mapToParent(cs) - (tr.map(c1) + self.state['pos'])
             newState['angle'] = ang
@@ -377,16 +419,21 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         self.handleChange()
     
     def handleChange(self):
+        #print "handleChange() called."
         changed = False
+        #print "self.lastState:", self.lastState
         if self.lastState is None:
             changed = True
         else:
             for k in self.state.keys():
+                #print k, self.state[k], self.lastState[k]
                 if self.state[k] != self.lastState[k]:
                     #print "state %s has changed; emit signal" % k
                     changed = True
         self.lastState = self.stateCopy()
+        #print "changed =", changed
         if changed:
+            #print "handle changed."
             self.update()
             self.emit(QtCore.SIGNAL('regionChanged'), self)
             
@@ -442,7 +489,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
     def stateRect(self, state):
         r = QtCore.QRectF(0, 0, state['size'][0], state['size'][1])
         tr = QtGui.QTransform()
-        tr.rotate(-state['angle'] * 180 / pi)
+        tr.rotate(-state['angle'] * 180 / np.pi)
         r = tr.mapRect(r)
         return r.adjusted(state['pos'][0], state['pos'][1], state['pos'][0], state['pos'][1])
     
@@ -533,10 +580,10 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         
         ## Rotate array
         if abs(self.state['angle']) > 1e-5:
-            arr2 = ndimage.rotate(arr1, self.state['angle'] * 180 / pi, order=1)
+            arr2 = ndimage.rotate(arr1, self.state['angle'] * 180 / np.pi, order=1)
             
             ## update data transforms to reflect this rotation
-            rot = QtGui.QTransform().rotate(self.state['angle'] * 180 / pi)
+            rot = QtGui.QTransform().rotate(self.state['angle'] * 180 / np.pi)
             roiDataTransform *= rot
             
             ## The rotation also causes a shift which must be accounted for:
@@ -557,7 +604,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         shift = (int(roiBounds.left()) - roiBounds.left(), int(roiBounds.bottom()) - roiBounds.bottom())
         if abs(shift[0]) > 1e-6 or abs(shift[1]) > 1e-6:
             # 3. pad array with 0s before shifting
-            arr2a = zeros((arr2.shape[0]+2, arr2.shape[1]+2) + arr2.shape[2:], dtype=arr2.dtype)
+            arr2a = np.zeros((arr2.shape[0]+2, arr2.shape[1]+2) + arr2.shape[2:], dtype=arr2.dtype)
             arr2a[1:-1, 1:-1] = arr2
             
             # 4. shift array and udpate transforms
@@ -588,7 +635,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         arr4 = arr3[bounds[0][0]:bounds[0][1], bounds[1][0]:bounds[1][1]]
 
         ### Create zero array in size of ROI
-        arr5 = zeros((roiBounds.width(), roiBounds.height()) + arr4.shape[2:], dtype=arr4.dtype)
+        arr5 = np.zeros((roiBounds.width(), roiBounds.height()) + arr4.shape[2:], dtype=arr4.dtype)
         
         ## Fill array with ROI data
         orig = Point(dataBounds.topLeft() - roiBounds.topLeft())
@@ -597,7 +644,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         
         
         ## figure out the reverse transpose order
-        tr2 = array(tr1)
+        tr2 = np.array(tr1)
         for i in range(0, len(tr2)):
             tr2[tr1[i]] = i
         tr2 = tuple(tr2)
@@ -605,7 +652,7 @@ class ROI(QtGui.QGraphicsItem, QObjectWorkaround):
         ## Untranspose array before returning
         return arr5.transpose(tr2)
 
-
+    
 
 
 
@@ -627,10 +674,10 @@ class Handle(QtGui.QGraphicsItem):
         self.pen.setCosmetic(True)
         if typ == 't':
             self.sides = 4
-            self.startAng = pi/4
+            self.startAng = np.pi/4
         elif typ == 'f':
             self.sides = 4
-            self.startAng = pi/4
+            self.startAng = np.pi/4
         elif typ == 's':
             self.sides = 4
             self.startAng = 0
@@ -642,7 +689,7 @@ class Handle(QtGui.QGraphicsItem):
             self.startAng = 0
         else:
             self.sides = 4
-            self.startAng = pi/4
+            self.startAng = np.pi/4
             
     def connectROI(self, roi, i):
         self.roi.append((roi, i))
@@ -684,7 +731,7 @@ class Handle(QtGui.QGraphicsItem):
         m = self.sceneTransform()
         #mi = m.inverted()[0]
         v = m.map(QtCore.QPointF(1, 0)) - m.map(QtCore.QPointF(0, 0))
-        va = arctan2(v.y(), v.x())
+        va = np.arctan2(v.y(), v.x())
         
         ## Determine length of unit vector in painter's coords
         #size = mi.map(Point(self.radius, self.radius)) - mi.map(Point(0, 0))
@@ -698,7 +745,7 @@ class Handle(QtGui.QGraphicsItem):
         p.setRenderHints(p.Antialiasing, True)
         p.setPen(self.pen)
         ang = self.startAng + va
-        dt = 2*pi / self.sides
+        dt = 2*np.pi / self.sides
         for i in range(0, self.sides):
             x1 = size * cos(ang)
             y1 = size * sin(ang)
@@ -751,7 +798,7 @@ class LineROI(ROI):
         c = Point(-width/2. * sin(ang), -width/2. * cos(ang))
         pos1 = pos1 + c
         
-        ROI.__init__(self, pos1, size=Point(l, width), angle=ang*180/pi, **args)
+        ROI.__init__(self, pos1, size=Point(l, width), angle=ang*180/np.pi, **args)
         self.addScaleRotateHandle([0, 0.5], [1, 0.5])
         self.addScaleRotateHandle([1, 0.5], [0, 0.5])
         self.addScaleHandle([0.5, 1], [0.5, 0.5])
@@ -816,7 +863,7 @@ class MultiLineROI(QtGui.QGraphicsItem, QObjectWorkaround):
             rgns.append(rgn)
             #print l.state['size']
         #print [(r.shape) for r in rgns]
-        return vstack(rgns)
+        return np.vstack(rgns)
         
         
 class EllipseROI(ROI):
@@ -843,7 +890,7 @@ class EllipseROI(ROI):
         w = arr.shape[0]
         h = arr.shape[1]
         ## generate an ellipsoidal mask
-        mask = fromfunction(lambda x,y: (((x+0.5)/(w/2.)-1)**2+ ((y+0.5)/(h/2.)-1)**2)**0.5 < 1, (w, h))
+        mask = np.fromfunction(lambda x,y: (((x+0.5)/(w/2.)-1)**2+ ((y+0.5)/(h/2.)-1)**2)**0.5 < 1, (w, h))
     
         return arr * mask
     
@@ -861,11 +908,17 @@ class CircleROI(EllipseROI):
         self.addScaleHandle([0.5*2.**-0.5 + 0.5, 0.5*2.**-0.5 + 0.5], [0.5, 0.5])
         
 class PolygonROI(ROI):
-    def __init__(self, positions, **args):
-        ROI.__init__(self, [0,0], [100,100], **args)
+    def __init__(self, positions, pos=None, **args):
+        if pos is None:
+            pos = [0,0]
+        ROI.__init__(self, pos, [1,1], **args)
+        #ROI.__init__(self, positions[0])
         for p in positions:
             self.addFreeHandle(p)
             
+    def listPoints(self):
+        return [p['item'].pos() for p in self.handles]
+            
     def movePoint(self, *args, **kargs):
         ROI.movePoint(self, *args, **kargs)
         self.prepareGeometryChange()