ScatterPlotItem.py 24.9 KB
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from pyqtgraph.Qt import QtGui, QtCore
from pyqtgraph.Point import Point
import pyqtgraph.functions as fn
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from .GraphicsItem import GraphicsItem
from .GraphicsObject import GraphicsObject
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import numpy as np
import scipy.stats
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import weakref
import pyqtgraph.debug as debug
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from pyqtgraph.pgcollections import OrderedDict
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#import pyqtgraph as pg 
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__all__ = ['ScatterPlotItem', 'SpotItem']
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## Build all symbol paths
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Symbols = OrderedDict([(name, QtGui.QPainterPath()) for name in ['o', 's', 't', 'd', '+']])
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Symbols['o'].addEllipse(QtCore.QRectF(-0.5, -0.5, 1, 1))
Symbols['s'].addRect(QtCore.QRectF(-0.5, -0.5, 1, 1))
coords = {
    't': [(-0.5, -0.5), (0, 0.5), (0.5, -0.5)],
    'd': [(0., -0.5), (-0.4, 0.), (0, 0.5), (0.4, 0)],
    '+': [
        (-0.5, -0.05), (-0.5, 0.05), (-0.05, 0.05), (-0.05, 0.5),
        (0.05, 0.5), (0.05, 0.05), (0.5, 0.05), (0.5, -0.05), 
        (0.05, -0.05), (0.05, -0.5), (-0.05, -0.5), (-0.05, -0.05)
    ],
}
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for k, c in coords.items():
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    Symbols[k].moveTo(*c[0])
    for x,y in c[1:]:
        Symbols[k].lineTo(x, y)
    Symbols[k].closeSubpath()


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def makeSymbolPixmap(size, pen, brush, symbol):
    ## Render a spot with the given parameters to a pixmap
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    penPxWidth = max(np.ceil(pen.width()), 1)
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    image = QtGui.QImage(int(size+penPxWidth), int(size+penPxWidth), QtGui.QImage.Format_ARGB32_Premultiplied)
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    image.fill(0)
    p = QtGui.QPainter(image)
    p.setRenderHint(p.Antialiasing)
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    p.translate(image.width()*0.5, image.height()*0.5)
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    p.scale(size, size)
    p.setPen(pen)
    p.setBrush(brush)
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    if isinstance(symbol, basestring):
        symbol = Symbols[symbol]
    p.drawPath(symbol)
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    p.end()
    return QtGui.QPixmap(image)


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class ScatterPlotItem(GraphicsObject):
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    """
    Displays a set of x/y points. Instances of this class are created
    automatically as part of PlotDataItem; these rarely need to be instantiated
    directly.
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    The size, shape, pen, and fill brush may be set for each point individually 
    or for all points. 
    
    
    ========================  ===============================================
    **Signals:**
    sigPlotChanged(self)      Emitted when the data being plotted has changed
    sigClicked(self, points)  Emitted when the curve is clicked. Sends a list
                              of all the points under the mouse pointer.
    ========================  ===============================================
    
    """
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    #sigPointClicked = QtCore.Signal(object, object)
    sigClicked = QtCore.Signal(object, object)  ## self, points
    sigPlotChanged = QtCore.Signal(object)
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    def __init__(self, *args, **kargs):
        """
        Accepts the same arguments as setData()
        """
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        prof = debug.Profiler('ScatterPlotItem.__init__', disabled=True)
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        GraphicsObject.__init__(self)
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        self.setFlag(self.ItemHasNoContents, True)
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        self.data = np.empty(0, dtype=[('x', float), ('y', float), ('size', float), ('symbol', object), ('pen', object), ('brush', object), ('item', object), ('data', object)])
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        self.bounds = [None, None]  ## caches data bounds
        self._maxSpotWidth = 0      ## maximum size of the scale-variant portion of all spots
        self._maxSpotPxWidth = 0    ## maximum size of the scale-invariant portion of all spots
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        self._spotPixmap = None
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        self.opts = {'pxMode': True}
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        self.setPen(200,200,200, update=False)
        self.setBrush(100,100,150, update=False)
        self.setSymbol('o', update=False)
        self.setSize(7, update=False)
        prof.mark('1')
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        self.setData(*args, **kargs)
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        prof.mark('setData')
        prof.finish()
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    def setData(self, *args, **kargs):
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        """
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        **Ordered Arguments:**
        
        * If there is only one unnamed argument, it will be interpreted like the 'spots' argument.
        * If there are two unnamed arguments, they will be interpreted as sequences of x and y values.
        
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        ====================== ===============================================================================================
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        **Keyword Arguments:**
        *spots*                Optional list of dicts. Each dict specifies parameters for a single spot:
                               {'pos': (x,y), 'size', 'pen', 'brush', 'symbol'}. This is just an alternate method
                               of passing in data for the corresponding arguments.
        *x*,*y*                1D arrays of x,y values.
        *pos*                  2D structure of x,y pairs (such as Nx2 array or list of tuples)
        *pxMode*               If True, spots are always the same size regardless of scaling, and size is given in px.
                               Otherwise, size is in scene coordinates and the spots scale with the view.
                               Default is True
        *symbol*               can be one (or a list) of:
                               * 'o'  circle (default)
                               * 's'  square
                               * 't'  triangle
                               * 'd'  diamond
                               * '+'  plus
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                               * any QPainterPath to specify custom symbol shapes. To properly obey the position and size,
                               custom symbols should be centered at (0,0) and width and height of 1.0. Note that it is also
                               possible to 'install' custom shapes by setting ScatterPlotItem.Symbols[key] = shape.
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        *pen*                  The pen (or list of pens) to use for drawing spot outlines.
        *brush*                The brush (or list of brushes) to use for filling spots.
        *size*                 The size (or list of sizes) of spots. If *pxMode* is True, this value is in pixels. Otherwise,
                               it is in the item's local coordinate system.
        *data*                 a list of python objects used to uniquely identify each spot.
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        *identical*            *Deprecated*. This functionality is handled automatically now.
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        ====================== ===============================================================================================
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        """
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        self.clear()  ## clear out all old data
        self.addPoints(*args, **kargs)
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    def addPoints(self, *args, **kargs):
        """
        Add new points to the scatter plot. 
        Arguments are the same as setData()
        """
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        ## deal with non-keyword arguments
        if len(args) == 1:
            kargs['spots'] = args[0]
        elif len(args) == 2:
            kargs['x'] = args[0]
            kargs['y'] = args[1]
        elif len(args) > 2:
            raise Exception('Only accepts up to two non-keyword arguments.')
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        ## convert 'pos' argument to 'x' and 'y'
        if 'pos' in kargs:
            pos = kargs['pos']
            if isinstance(pos, np.ndarray):
                kargs['x'] = pos[:,0]
                kargs['y'] = pos[:,1]
            else:
                x = []
                y = []
                for p in pos:
                    if isinstance(p, QtCore.QPointF):
                        x.append(p.x())
                        y.append(p.y())
                    else:
                        x.append(p[0])
                        y.append(p[1])
                kargs['x'] = x
                kargs['y'] = y
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        ## determine how many spots we have
        if 'spots' in kargs:
            numPts = len(kargs['spots'])
        elif 'y' in kargs and kargs['y'] is not None:
            numPts = len(kargs['y'])
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        else:
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            kargs['x'] = []
            kargs['y'] = []
            numPts = 0
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        ## Extend record array
        oldData = self.data
        self.data = np.empty(len(oldData)+numPts, dtype=self.data.dtype)
        ## note that np.empty initializes object fields to None and string fields to ''
        
        self.data[:len(oldData)] = oldData
        for i in range(len(oldData)):
            oldData[i]['item']._data = self.data[i]  ## Make sure items have proper reference to new array
            
        newData = self.data[len(oldData):]
        newData['size'] = -1  ## indicates to use default size
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        if 'spots' in kargs:
            spots = kargs['spots']
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            for i in range(len(spots)):
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                spot = spots[i]
                for k in spot:
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                    #if k == 'pen':
                        #newData[k] = fn.mkPen(spot[k])
                    #elif k == 'brush':
                        #newData[k] = fn.mkBrush(spot[k])
                    if k == 'pos':
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                        pos = spot[k]
                        if isinstance(pos, QtCore.QPointF):
                            x,y = pos.x(), pos.y()
                        else:
                            x,y = pos[0], pos[1]
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                        newData[i]['x'] = x
                        newData[i]['y'] = y
                    elif k in ['x', 'y', 'size', 'symbol', 'pen', 'brush', 'data']:
                        newData[i][k] = spot[k]
                    #elif k == 'data':
                        #self.pointData[i] = spot[k]
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                    else:
                        raise Exception("Unknown spot parameter: %s" % k)
        elif 'y' in kargs:
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            newData['x'] = kargs['x']
            newData['y'] = kargs['y']
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        if 'pxMode' in kargs:
            self.setPxMode(kargs['pxMode'], update=False)
            
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        ## Set any extra parameters provided in keyword arguments
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        for k in ['pen', 'brush', 'symbol', 'size']:
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            if k in kargs:
                setMethod = getattr(self, 'set' + k[0].upper() + k[1:])
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                setMethod(kargs[k], update=False, dataSet=newData)
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        if 'data' in kargs:
            self.setPointData(kargs['data'], dataSet=newData)
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        #self.updateSpots()
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        self.prepareGeometryChange()
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        self.bounds = [None, None]
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        self.generateSpotItems()
        self.sigPlotChanged.emit(self)
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    def getData(self):
        return self.data['x'], self.data['y']
    
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    def setPoints(self, *args, **kargs):
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        ##Deprecated; use setData
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        return self.setData(*args, **kargs)
        
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    def implements(self, interface=None):
        ints = ['plotData']
        if interface is None:
            return ints
        return interface in ints
    
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    def setPen(self, *args, **kargs):
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        """Set the pen(s) used to draw the outline around each spot. 
        If a list or array is provided, then the pen for each spot will be set separately.
        Otherwise, the arguments are passed to pg.mkPen and used as the default pen for 
        all spots which do not have a pen explicitly set."""
        update = kargs.pop('update', True)
        dataSet = kargs.pop('dataSet', self.data)
        
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        if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)):
            pens = args[0]
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            if len(pens) != len(dataSet):
                raise Exception("Number of pens does not match number of points (%d != %d)" % (len(pens), len(dataSet)))
            dataSet['pen'] = pens
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        else:
            self.opts['pen'] = fn.mkPen(*args, **kargs)
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            self._spotPixmap = None
        
        if update:
            self.updateSpots(dataSet)
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    def setBrush(self, *args, **kargs):
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        """Set the brush(es) used to fill the interior of each spot. 
        If a list or array is provided, then the brush for each spot will be set separately.
        Otherwise, the arguments are passed to pg.mkBrush and used as the default brush for 
        all spots which do not have a brush explicitly set."""
        update = kargs.pop('update', True)
        dataSet = kargs.pop('dataSet', self.data)
            
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        if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)):
            brushes = args[0]
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            if len(brushes) != len(dataSet):
                raise Exception("Number of brushes does not match number of points (%d != %d)" % (len(brushes), len(dataSet)))
            #for i in xrange(len(brushes)):
                #self.data[i]['brush'] = fn.mkBrush(brushes[i], **kargs)
            dataSet['brush'] = brushes
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        else:
            self.opts['brush'] = fn.mkBrush(*args, **kargs)
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            self._spotPixmap = None
        
        if update:
            self.updateSpots(dataSet)
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    def setSymbol(self, symbol, update=True, dataSet=None):
        """Set the symbol(s) used to draw each spot. 
        If a list or array is provided, then the symbol for each spot will be set separately.
        Otherwise, the argument will be used as the default symbol for 
        all spots which do not have a symbol explicitly set."""
        if dataSet is None:
            dataSet = self.data
            
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        if isinstance(symbol, np.ndarray) or isinstance(symbol, list):
            symbols = symbol
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            if len(symbols) != len(dataSet):
                raise Exception("Number of symbols does not match number of points (%d != %d)" % (len(symbols), len(dataSet)))
            dataSet['symbol'] = symbols
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        else:
            self.opts['symbol'] = symbol
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            self._spotPixmap = None
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        if update:
            self.updateSpots(dataSet)
    
    def setSize(self, size, update=True, dataSet=None):
        """Set the size(s) used to draw each spot. 
        If a list or array is provided, then the size for each spot will be set separately.
        Otherwise, the argument will be used as the default size for 
        all spots which do not have a size explicitly set."""
        if dataSet is None:
            dataSet = self.data
            
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        if isinstance(size, np.ndarray) or isinstance(size, list):
            sizes = size
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            if len(sizes) != len(dataSet):
                raise Exception("Number of sizes does not match number of points (%d != %d)" % (len(sizes), len(dataSet)))
            dataSet['size'] = sizes
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        else:
            self.opts['size'] = size
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            self._spotPixmap = None
            
        if update:
            self.updateSpots(dataSet)
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    def setPointData(self, data, dataSet=None):
        if dataSet is None:
            dataSet = self.data
            
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        if isinstance(data, np.ndarray) or isinstance(data, list):
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            if len(data) != len(dataSet):
                raise Exception("Length of meta data does not match number of points (%d != %d)" % (len(data), len(dataSet)))
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        ## Bug: If data is a numpy record array, then items from that array must be copied to dataSet one at a time.
        ## (otherwise they are converted to tuples and thus lose their field names.
        if isinstance(data, np.ndarray) and len(data.dtype.fields) > 1:
            for i, rec in enumerate(data):
                dataSet['data'][i] = rec
        else:
            dataSet['data'] = data
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    def setPxMode(self, mode, update=True):
        if self.opts['pxMode'] == mode:
            return
            
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        self.opts['pxMode'] = mode
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        self.clearItems()
        if update:
            self.generateSpotItems()
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    def updateSpots(self, dataSet=None):
        if dataSet is None:
            dataSet = self.data
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        self._maxSpotWidth = 0
        self._maxSpotPxWidth = 0
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        for spot in dataSet['item']:
            spot.updateItem()
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        self.measureSpotSizes(dataSet)

    def measureSpotSizes(self, dataSet):
        for spot in dataSet['item']:
            ## keep track of the maximum spot size and pixel size
            width = 0
            pxWidth = 0
            pen = spot.pen()
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            if self.opts['pxMode']:
                pxWidth = spot.size() + pen.width()
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            else:
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                width = spot.size()
                if pen.isCosmetic():
                    pxWidth += pen.width()
                else:
                    width += pen.width()
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            self._maxSpotWidth = max(self._maxSpotWidth, width)
            self._maxSpotPxWidth = max(self._maxSpotPxWidth, pxWidth)
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        self.bounds = [None, None]
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    def clear(self):
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        """Remove all spots from the scatter plot"""
        self.clearItems()
        self.data = np.empty(0, dtype=self.data.dtype)
        self.bounds = [None, None]

    def clearItems(self):
        for i in self.data['item']:
            if i is None:
                continue
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            i.setParentItem(None)
            s = i.scene()
            if s is not None:
                s.removeItem(i)
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        self.data['item'] = None
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    def dataBounds(self, ax, frac=1.0, orthoRange=None):
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        if frac >= 1.0 and self.bounds[ax] is not None:
            return self.bounds[ax]
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        #self.prepareGeometryChange()
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        if self.data is None or len(self.data) == 0:
            return (None, None)
        
        if ax == 0:
            d = self.data['x']
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            d2 = self.data['y']
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        elif ax == 1:
            d = self.data['y']
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            d2 = self.data['x']
        
        if orthoRange is not None:
            mask = (d2 >= orthoRange[0]) * (d2 <= orthoRange[1])
            d = d[mask]
            d2 = d2[mask]
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        if frac >= 1.0:
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            ## increase size of bounds based on spot size and pen width
            px = self.pixelLength(Point(1, 0) if ax == 0 else Point(0, 1))  ## determine length of pixel along this axis
            if px is None:
                px = 0
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            minIndex = np.argmin(d)
            maxIndex = np.argmax(d)
            minVal = d[minIndex]
            maxVal = d[maxIndex]
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            spotSize = 0.5 * (self._maxSpotWidth + px * self._maxSpotPxWidth)
            self.bounds[ax] = (minVal-spotSize, maxVal+spotSize)
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            return self.bounds[ax]
        elif frac <= 0.0:
            raise Exception("Value for parameter 'frac' must be > 0. (got %s)" % str(frac))
        else:
            return (scipy.stats.scoreatpercentile(d, 50 - (frac * 50)), scipy.stats.scoreatpercentile(d, 50 + (frac * 50)))
            
            

    
    
    
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    def generateSpotItems(self):
        if self.opts['pxMode']:
            for rec in self.data:
                if rec['item'] is None:
                    rec['item'] = PixmapSpotItem(rec, self)
        else:
            for rec in self.data:
                if rec['item'] is None:
                    rec['item'] = PathSpotItem(rec, self)
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        self.measureSpotSizes(self.data)
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        self.sigPlotChanged.emit(self)
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    def defaultSpotPixmap(self):
        ## Return the default spot pixmap
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        if self._spotPixmap is None:
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            self._spotPixmap = makeSymbolPixmap(size=self.opts['size'], brush=self.opts['brush'], pen=self.opts['pen'], symbol=self.opts['symbol'])
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        return self._spotPixmap

    def boundingRect(self):
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        (xmn, xmx) = self.dataBounds(ax=0)
        (ymn, ymx) = self.dataBounds(ax=1)
        if xmn is None or xmx is None:
            xmn = 0
            xmx = 0
        if ymn is None or ymx is None:
            ymn = 0
            ymx = 0
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        return QtCore.QRectF(xmn, ymn, xmx-xmn, ymx-ymn)
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    def viewRangeChanged(self):
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        self.prepareGeometryChange()
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        GraphicsObject.viewRangeChanged(self)
        self.bounds = [None, None]
        
    def paint(self, p, *args):
        ## NOTE: self.paint is disabled by this line in __init__:
        ## self.setFlag(self.ItemHasNoContents, True)
        p.setPen(fn.mkPen('r'))
        p.drawRect(self.boundingRect())

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    def points(self):
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        return self.data['item']
        
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    def pointsAt(self, pos):
        x = pos.x()
        y = pos.y()
        pw = self.pixelWidth()
        ph = self.pixelHeight()
        pts = []
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        for s in self.points():
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            sp = s.pos()
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            ss = s.size()
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            sx = sp.x()
            sy = sp.y()
            s2x = s2y = ss * 0.5
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            if self.opts['pxMode']:
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                s2x *= pw
                s2y *= ph
            if x > sx-s2x and x < sx+s2x and y > sy-s2y and y < sy+s2y:
                pts.append(s)
                #print "HIT:", x, y, sx, sy, s2x, s2y
            #else:
                #print "No hit:", (x, y), (sx, sy)
                #print "       ", (sx-s2x, sy-s2y), (sx+s2x, sy+s2y)
        pts.sort(lambda a,b: cmp(b.zValue(), a.zValue()))
        return pts
            

    def mouseClickEvent(self, ev):
        if ev.button() == QtCore.Qt.LeftButton:
            pts = self.pointsAt(ev.pos())
            if len(pts) > 0:
                self.ptsClicked = pts
                self.sigClicked.emit(self, self.ptsClicked)
                ev.accept()
            else:
                #print "no spots"
                ev.ignore()
        else:
            ev.ignore()


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class SpotItem(GraphicsItem):
    """
    Class referring to individual spots in a scatter plot.
    These can be retrieved by calling ScatterPlotItem.points() or 
    by connecting to the ScatterPlotItem's click signals.
    """
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    def __init__(self, data, plot):
        GraphicsItem.__init__(self, register=False)
        self._data = data
        self._plot = plot
        #self._viewBox = None
        #self._viewWidget = None
        self.setParentItem(plot)
        self.setPos(QtCore.QPointF(data['x'], data['y']))
        self.updateItem()
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    def data(self):
        """Return the user data associated with this spot."""
        return self._data['data']
    
    def size(self):
        """Return the size of this spot. 
        If the spot has no explicit size set, then return the ScatterPlotItem's default size instead."""
        if self._data['size'] == -1:
            return self._plot.opts['size']
        else:
            return self._data['size']
    
    def setSize(self, size):
        """Set the size of this spot. 
        If the size is set to -1, then the ScatterPlotItem's default size 
        will be used instead."""
        self._data['size'] = size
        self.updateItem()
    
    def symbol(self):
        """Return the symbol of this spot. 
        If the spot has no explicit symbol set, then return the ScatterPlotItem's default symbol instead.
        """
        symbol = self._data['symbol']
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        if symbol is None:
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            symbol = self._plot.opts['symbol']
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        try:
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            n = int(symbol)
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            symbol = list(Symbols.keys())[n % len(Symbols)]
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        except:
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            pass
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        return symbol
    
    def setSymbol(self, symbol):
        """Set the symbol for this spot.
        If the symbol is set to '', then the ScatterPlotItem's default symbol will be used instead."""
        self._data['symbol'] = symbol
        self.updateItem()

    def pen(self):
        pen = self._data['pen']
        if pen is None:
            pen = self._plot.opts['pen']
        return fn.mkPen(pen)
    
    def setPen(self, *args, **kargs):
        """Set the outline pen for this spot"""
        pen = fn.mkPen(*args, **kargs)
        self._data['pen'] = pen
        self.updateItem()
    
    def resetPen(self):
        """Remove the pen set for this spot; the scatter plot's default pen will be used instead."""
        self._data['pen'] = None  ## Note this is NOT the same as calling setPen(None)
        self.updateItem()
    
    def brush(self):
        brush = self._data['brush']
        if brush is None:
            brush = self._plot.opts['brush']
        return fn.mkBrush(brush)
    
    def setBrush(self, *args, **kargs):
        """Set the fill brush for this spot"""
        brush = fn.mkBrush(*args, **kargs)
        self._data['brush'] = brush
        self.updateItem()
    
    def resetBrush(self):
        """Remove the brush set for this spot; the scatter plot's default brush will be used instead."""
        self._data['brush'] = None  ## Note this is NOT the same as calling setBrush(None)
        self.updateItem()
    
    def setData(self, data):
        """Set the user-data associated with this spot"""
        self._data['data'] = data


class PixmapSpotItem(SpotItem, QtGui.QGraphicsPixmapItem):
    def __init__(self, data, plot):
        QtGui.QGraphicsPixmapItem.__init__(self)
        self.setFlags(self.flags() | self.ItemIgnoresTransformations)
        SpotItem.__init__(self, data, plot)
    
    def setPixmap(self, pixmap):
        QtGui.QGraphicsPixmapItem.setPixmap(self, pixmap)
        self.setOffset(-pixmap.width()/2.+0.5, -pixmap.height()/2.)
    
    def updateItem(self):
        symbolOpts = (self._data['pen'], self._data['brush'], self._data['size'], self._data['symbol'])
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        ## If all symbol options are default, use default pixmap
        if symbolOpts == (None, None, -1, ''):
            pixmap = self._plot.defaultSpotPixmap()
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        else:
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            pixmap = makeSymbolPixmap(size=self.size(), pen=self.pen(), brush=self.brush(), symbol=self.symbol())
        self.setPixmap(pixmap)
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class PathSpotItem(SpotItem, QtGui.QGraphicsPathItem):
    def __init__(self, data, plot):
        QtGui.QGraphicsPathItem.__init__(self)
        SpotItem.__init__(self, data, plot)
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    def updateItem(self):
        QtGui.QGraphicsPathItem.setPath(self, Symbols[self.symbol()])
        QtGui.QGraphicsPathItem.setPen(self, self.pen())
        QtGui.QGraphicsPathItem.setBrush(self, self.brush())
        size = self.size()
        self.resetTransform()
        self.scale(size, size)