Source code for pyqtgraph.graphicsItems.ScatterPlotItem

import itertools
import math
import weakref
from collections import OrderedDict

import numpy as np

from .. import Qt, debug
from .. import functions as fn
from .. import getConfigOption
from ..Point import Point
from ..Qt import QT_LIB, QtCore, QtGui
from .GraphicsObject import GraphicsObject

__all__ = ['ScatterPlotItem', 'SpotItem']

## Build all symbol paths
name_list = ['o', 's', 't', 't1', 't2', 't3', 'd', '+', 'x', 'p', 'h', 'star',
             'arrow_up', 'arrow_right', 'arrow_down', 'arrow_left', 'crosshair']
Symbols = OrderedDict([(name, QtGui.QPainterPath()) for name in name_list])
Symbols['o'].addEllipse(QtCore.QRectF(-0.5, -0.5, 1, 1))
Symbols['s'].addRect(QtCore.QRectF(-0.5, -0.5, 1, 1))

def makeCrosshair(r=0.5, w=1, h=1):
    path = QtGui.QPainterPath()
    rect = QtCore.QRectF(-r, -r, r * 2, r * 2)
    path.moveTo(-w, 0)
    path.lineTo(w, 0)
    path.moveTo(0, -h)
    path.lineTo(0, h)
    return path
Symbols['crosshair'] = makeCrosshair()

coords = {
    't': [(-0.5, -0.5), (0, 0.5), (0.5, -0.5)],
    't1': [(-0.5, 0.5), (0, -0.5), (0.5, 0.5)],
    't2': [(-0.5, -0.5), (-0.5, 0.5), (0.5, 0)],
    't3': [(0.5, 0.5), (0.5, -0.5), (-0.5, 0)],
    'd': [(0., -0.5), (-0.4, 0.), (0, 0.5), (0.4, 0)],
    '+': [
        (-0.5, -0.1), (-0.5, 0.1), (-0.1, 0.1), (-0.1, 0.5),
        (0.1, 0.5), (0.1, 0.1), (0.5, 0.1), (0.5, -0.1),
        (0.1, -0.1), (0.1, -0.5), (-0.1, -0.5), (-0.1, -0.1)
    'p': [(0, -0.5), (-0.4755, -0.1545), (-0.2939, 0.4045),
          (0.2939, 0.4045), (0.4755, -0.1545)],
    'h': [(0.433, 0.25), (0., 0.5), (-0.433, 0.25), (-0.433, -0.25),
          (0, -0.5), (0.433, -0.25)],
    'star': [(0, -0.5), (-0.1123, -0.1545), (-0.4755, -0.1545),
             (-0.1816, 0.059), (-0.2939, 0.4045), (0, 0.1910),
             (0.2939, 0.4045), (0.1816, 0.059), (0.4755, -0.1545),
             (0.1123, -0.1545)],
    'arrow_up': [
        (-0.125, 0.125), (0, 0), (0.125, 0.125),
        (0.05, 0.125), (0.05, 0.5), (-0.05, 0.5), (-0.05, 0.125)
for k, c in coords.items():
    for x,y in c[1:]:
        Symbols[k].lineTo(x, y)
tr = QtGui.QTransform()
Symbols['x'] =['+'])
Symbols['arrow_right'] =['arrow_up'])
Symbols['arrow_down'] =['arrow_right'])
Symbols['arrow_left'] =['arrow_down'])
_DEFAULT_STYLE = {'symbol': None, 'size': -1, 'pen': None, 'brush': None, 'visible': True}

def drawSymbol(painter, symbol, size, pen, brush):
    if symbol is None:
    painter.scale(size, size)
    if isinstance(symbol, str):
        symbol = Symbols[symbol]
    if np.isscalar(symbol):
        symbol = list(Symbols.values())[symbol % len(Symbols)]

def renderSymbol(symbol, size, pen, brush, device=None):
    Render a symbol specification to QImage.
    Symbol may be either a QPainterPath or one of the keys in the Symbols dict.
    If *device* is None, a new QPixmap will be returned. Otherwise,
    the symbol will be rendered into the device specified (See QPainter documentation
    for more information).
    ## Render a spot with the given parameters to a pixmap
    penPxWidth = max(math.ceil(pen.widthF()), 1)
    if device is None:
        device = QtGui.QImage(int(size+penPxWidth), int(size+penPxWidth),
    p = QtGui.QPainter(device)
        p.translate(device.width()*0.5, device.height()*0.5)
        drawSymbol(p, symbol, size, pen, brush)
    return device

def _mkPen(*args, **kwargs):
    Wrapper for fn.mkPen which avoids creating a new QPen object if passed one as its
    sole argument. This is used to avoid unnecessary cache misses in SymbolAtlas which
    uses the QPen object id in its key.
    if len(args) == 1 and isinstance(args[0], QtGui.QPen):
        return args[0]
        return fn.mkPen(*args, **kwargs)

def _mkBrush(*args, **kwargs):
    Wrapper for fn.mkBrush which avoids creating a new QBrush object if passed one as its
    sole argument. This is used to avoid unnecessary cache misses in SymbolAtlas which
    uses the QBrush object id in its key.
    if len(args) == 1 and isinstance(args[0], QtGui.QBrush):
        return args[0]
        return fn.mkBrush(*args, **kwargs)

class PixmapFragments:
    def __init__(self):
        self.use_sip_array = (
            Qt.QT_LIB.startswith('PyQt') and
            hasattr(Qt.sip, 'array') and
                (0x60301 <= QtCore.PYQT_VERSION) or
                (0x50f07 <= QtCore.PYQT_VERSION < 0x60000)

    def alloc(self, size):
        # The C++ native API is:
        #   drawPixmapFragments(const PixmapFragment *fragments, int fragmentCount,
        #                       const QPixmap &pixmap)
        # PySide exposes this API whereas PyQt wraps it to be more Pythonic.
        # In PyQt, a Python list of PixmapFragment instances needs to be provided.
        # This is inefficient because:
        # 1) constructing the Python list involves calling sip.wrapinstance multiple times.
        #    - this is mitigated here by reusing the instance pointers
        # 2) PyQt will anyway deconstruct the Python list and repack the PixmapFragment
        #    instances into a contiguous array, in order to call the underlying C++ native API.
        if self.use_sip_array:
            self.objs = Qt.sip.array(QtGui.QPainter.PixmapFragment, size)
            vp = Qt.sip.voidptr(self.objs, len(self.objs)*10*8)
            self.arr = np.frombuffer(vp, dtype=np.float64).reshape((-1, 10))
            self.arr = np.empty((size, 10), dtype=np.float64)
            if QT_LIB.startswith('PyQt'):
                self.objs = list(map(Qt.sip.wrapinstance,
                    itertools.count(, self.arr.strides[0]),
                    itertools.repeat(QtGui.QPainter.PixmapFragment, self.arr.shape[0])))
                self.objs = Qt.shiboken.wrapInstance(, QtGui.QPainter.PixmapFragment)

    def array(self, size):
        if size != self.arr.shape[0]:
        return self.arr

    def draw(self, painter, pixmap):
        if not len(self.arr):
        if QT_LIB.startswith('PyQt'):
            painter.drawPixmapFragments(self.objs, pixmap)
            painter.drawPixmapFragments(self.objs, len(self.arr), pixmap)

class SymbolAtlas(object):
    Used to efficiently construct a single QPixmap containing all rendered symbols
    for a ScatterPlotItem. This is required for fragment rendering.

    Use example:
        atlas = SymbolAtlas()
        sc1 = atlas[[('o', 5, QPen(..), QBrush(..))]]
        sc2 = atlas[[('t', 10, QPen(..), QBrush(..))]]
        pm = atlas.pixmap

    _idGenerator = itertools.count()

    def __init__(self):
        self._data = np.zeros((0, 0, 4), dtype=np.ubyte)  # numpy array of atlas image
        self._coords = {}
        self._pixmap = None
        self._maxWidth = 0
        self._totalWidth = 0
        self._totalArea = 0
        self._pos = (0, 0)
        self._rowShape = (0, 0)

    def __getitem__(self, styles):
        Given a list of tuples, (symbol, size, pen, brush), return a list of coordinates of
        corresponding symbols within the atlas. Note that these coordinates may change if the atlas is rebuilt.
        keys = self._keys(styles)
        new = {key: style for key, style in zip(keys, styles) if key not in self._coords}

        if new:

        return list(map(self._coords.__getitem__, keys))

    def __len__(self):
        return len(self._coords)

    def pixmap(self):
        if self._pixmap is None:
            self._pixmap = self._createPixmap()
        return self._pixmap

    def maxWidth(self):
        return self._maxWidth

    def rebuild(self, styles=None):
        profiler = debug.Profiler()  # noqa: profiler prints on GC
        if styles is None:
            data = []
            keys = set(self._keys(styles))
            data = list(self._itemData(keys))

        if data:

    def clear(self):

    def diagnostics(self):
        n = len(self)
        w, h, _ = self._data.shape
        a = self._totalArea
        return dict(count=n,
                    area=w * h,
                    area_used=1.0 if n == 0 else a / (w * h),
                    squareness=1.0 if n == 0 else 2 * w * h / (w**2 + h**2))

    def _keys(self, styles):
        def getId(obj):
                return obj._id
            except AttributeError:
                obj._id = next(SymbolAtlas._idGenerator)
                return obj._id

        return [
            (symbol if isinstance(symbol, (str, int)) else getId(symbol), size, getId(pen), getId(brush))
            for symbol, size, pen, brush in styles

    def _itemData(self, keys):
        for key in keys:
            y, x, h, w = self._coords[key]
            yield key, self._data[x:x + w, y:y + h]

    def _extend(self, styles):
        profiler = debug.Profiler()

        images = []
        data = []
        for key, style in styles.items():
            img = renderSymbol(*style)
            arr = fn.ndarray_from_qimage(img)
            images.append(img)  # keep these to delay garbage collection
            data.append((key, arr))


    def _extendFromData(self, data):

        # expand array if necessary
        wNew, hNew = self._minDataShape()
        wOld, hOld, _ = self._data.shape
        if (wNew > wOld) or (hNew > hOld):
            arr = np.zeros((wNew, hNew, 4), dtype=np.ubyte)
            arr[:wOld, :hOld] = self._data
            self._data = arr

        # insert data into array
        for key, arr in data:
            y, x, h, w = self._coords[key]
            self._data[x:x+w, y:y+h] = arr

        self._pixmap = None

    def _pack(self, data):
        # pack each item rectangle as efficiently as possible into a larger, expanding, approximate square
        n = len(self)
        wMax = self._maxWidth
        wSum = self._totalWidth
        aSum = self._totalArea
        x, y = self._pos
        wRow, hRow = self._rowShape

        # update packing statistics
        for _, arr in data:
            w, h, _ = arr.shape
            wMax = max(w, wMax)
            wSum += w
            aSum += w * h
        n += len(data)

        # maybe expand row width for squareness and to accommodate largest width
        wRowEst = int(wSum / (n ** 0.5))
        if wRowEst > 2 * wRow:
            wRow = wRowEst
        wRow = max(wMax, wRow)

        # set coordinates by packing along rows
        # sort by rectangle height first to improve packing density
        for key, arr in sorted(data, key=lambda data: data[1].shape[1]):
            w, h, _ = arr.shape
            if x + w > wRow:
                # move up a row
                x = 0
                y += hRow
                hRow = h
            hRow = max(h, hRow)
            self._coords[key] = (y, x, h, w)
            x += w

        self._maxWidth = wMax
        self._totalWidth = wSum
        self._totalArea = aSum
        self._pos = (x, y)
        self._rowShape = (wRow, hRow)

    def _minDataShape(self):
        x, y = self._pos
        w, h = self._rowShape
        return int(w), int(y + h)

    def _createPixmap(self):
        profiler = debug.Profiler()  # noqa: profiler prints on GC
        if self._data.size == 0:
            pm = QtGui.QPixmap(0, 0)
            img = fn.ndarray_to_qimage(self._data,
            pm = QtGui.QPixmap(img)
        return pm

[docs]class ScatterPlotItem(GraphicsObject): """ 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. 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, ev) Emitted when points are clicked. Sends a list of all the points under the mouse pointer. sigHovered(self, points, ev) Emitted when the item is hovered. Sends a list of all the points under the mouse pointer. ============================ =============================================== """ #sigPointClicked = QtCore.Signal(object, object) sigClicked = QtCore.Signal(object, object, object) sigHovered = QtCore.Signal(object, object, object) sigPlotChanged = QtCore.Signal(object)
[docs] def __init__(self, *args, **kargs): """ Accepts the same arguments as setData() """ profiler = debug.Profiler() GraphicsObject.__init__(self) self.picture = None # QPicture used for rendering when pxmode==False self.fragmentAtlas = SymbolAtlas() dtype = [ ('x', float), ('y', float), ('size', float), ('symbol', object), ('pen', object), ('brush', object), ('visible', bool), ('data', object), ('hovered', bool), ('item', object), ('sourceRect', [ ('x', int), ('y', int), ('w', int), ('h', int) ]) ] = np.empty(0, dtype=dtype) 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 self._pixmapFragments = PixmapFragments() self.opts = { 'pxMode': True, 'useCache': True, ## If useCache is False, symbols are re-drawn on every paint. 'antialias': getConfigOption('antialias'), 'compositionMode': None, 'name': None, 'symbol': 'o', 'size': 7, 'pen': fn.mkPen(getConfigOption('foreground')), 'brush': fn.mkBrush(100, 100, 150), 'hoverable': False, 'tip': 'x: {x:.3g}\ny: {y:.3g}\ndata={data}'.format, } self.opts.update( {'hover' + opt.title(): _DEFAULT_STYLE[opt] for opt in ['symbol', 'size', 'pen', 'brush']} ) profiler() self.setData(*args, **kargs) profiler('setData') #self.setCacheMode(self.DeviceCoordinateCache) # track when the tooltip is cleared so we only clear it once # this allows another item in the VB to set the tooltip self._toolTipCleared = True
[docs] def setData(self, *args, **kargs): """ **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. ====================== =============================================================================================== **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. To ensure effective caching, QPen and QBrush objects should be reused as much as possible. Default is True *symbol* can be one (or a list) of symbols. For a list of supported symbols, see :func:`~ScatterPlotItem.setSymbol`. QPainterPath is also supported 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. *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. *hoverable* If True, sigHovered is emitted with a list of hovered points, a tool tip is shown containing information about them, and an optional separate style for them is used. Default is False. *tip* A string-valued function of a spot's (x, y, data) values. Set to None to prevent a tool tip from being shown. *hoverSymbol* A single symbol to use for hovered spots. Set to None to keep symbol unchanged. Default is None. *hoverSize* A single size to use for hovered spots. Set to -1 to keep size unchanged. Default is -1. *hoverPen* A single pen to use for hovered spots. Set to None to keep pen unchanged. Default is None. *hoverBrush* A single brush to use for hovered spots. Set to None to keep brush unchanged. Default is None. *useCache* (bool) By default, generated point graphics items are cached to improve performance. Setting this to False can improve image quality in certain situations. *antialias* Whether to draw symbols with antialiasing. Note that if pxMode is True, symbols are always rendered with antialiasing (since the rendered symbols can be cached, this incurs very little performance cost) *compositionMode* If specified, this sets the composition mode used when drawing the scatter plot (see QPainter::CompositionMode in the Qt documentation). *name* The name of this item. Names are used for automatically generating LegendItem entries and by some exporters. ====================== =============================================================================================== """ oldData = ## this causes cached pixmaps to be preserved while new data is registered. self.clear() ## clear out all old data self.addPoints(*args, **kargs)
[docs] def addPoints(self, *args, **kargs): """ Add new points to the scatter plot. Arguments are the same as setData() """ ## 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.') ## 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 ## 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']) else: kargs['x'] = [] kargs['y'] = [] numPts = 0 ## Clear current SpotItems since the data references they contain will no longer be current['item'][...] = None ## Extend record array oldData = = np.empty(len(oldData)+numPts, ## note that np.empty initializes object fields to None and string fields to ''[:len(oldData)] = oldData #for i in range(len(oldData)): #oldData[i]['item']._data =[i] ## Make sure items have proper reference to new array newData =[len(oldData):] newData['size'] = -1 ## indicates to use default size newData['visible'] = True if 'spots' in kargs: spots = kargs['spots'] for i in range(len(spots)): spot = spots[i] for k in spot: if k == 'pos': pos = spot[k] if isinstance(pos, QtCore.QPointF): x,y = pos.x(), pos.y() else: x,y = pos[0], pos[1] newData[i]['x'] = x newData[i]['y'] = y elif k == 'pen': newData[i][k] = _mkPen(spot[k]) elif k == 'brush': newData[i][k] = _mkBrush(spot[k]) elif k in ['x', 'y', 'size', 'symbol', 'data']: newData[i][k] = spot[k] else: raise Exception("Unknown spot parameter: %s" % k) elif 'y' in kargs: newData['x'] = kargs['x'] newData['y'] = kargs['y'] if 'name' in kargs: self.opts['name'] = kargs['name'] if 'pxMode' in kargs: self.setPxMode(kargs['pxMode']) if 'antialias' in kargs: self.opts['antialias'] = kargs['antialias'] if 'hoverable' in kargs: self.opts['hoverable'] = bool(kargs['hoverable']) if 'tip' in kargs: self.opts['tip'] = kargs['tip'] if 'useCache' in kargs: self.opts['useCache'] = kargs['useCache'] ## Set any extra parameters provided in keyword arguments for k in ['pen', 'brush', 'symbol', 'size']: if k in kargs: setMethod = getattr(self, 'set' + k[0].upper() + k[1:]) setMethod(kargs[k], update=False, dataSet=newData, mask=kargs.get('mask', None)) kh = 'hover' + k.title() if kh in kargs: vh = kargs[kh] if k == 'pen': vh = _mkPen(vh) elif k == 'brush': vh = _mkBrush(vh) self.opts[kh] = vh if 'data' in kargs: self.setPointData(kargs['data'], dataSet=newData) self.prepareGeometryChange() self.informViewBoundsChanged() self.bounds = [None, None] self.invalidate() self.updateSpots(newData) self.sigPlotChanged.emit(self)
def invalidate(self): ## clear any cached drawing state self.picture = None self.update() def getData(self): return['x'],['y'] def implements(self, interface=None): ints = ['plotData'] if interface is None: return ints return interface in ints def name(self): return self.opts.get('name', None)
[docs] def setPen(self, *args, **kargs): """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', if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)): pens = args[0] if 'mask' in kargs and kargs['mask'] is not None: pens = pens[kargs['mask']] if len(pens) != len(dataSet): raise Exception("Number of pens does not match number of points (%d != %d)" % (len(pens), len(dataSet))) dataSet['pen'] = list(map(_mkPen, pens)) else: self.opts['pen'] = _mkPen(*args, **kargs) dataSet['sourceRect'] = 0 if update: self.updateSpots(dataSet)
[docs] def setBrush(self, *args, **kargs): """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', if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)): brushes = args[0] if 'mask' in kargs and kargs['mask'] is not None: brushes = brushes[kargs['mask']] if len(brushes) != len(dataSet): raise Exception("Number of brushes does not match number of points (%d != %d)" % (len(brushes), len(dataSet))) dataSet['brush'] = list(map(_mkBrush, brushes)) else: self.opts['brush'] = _mkBrush(*args, **kargs) dataSet['sourceRect'] = 0 if update: self.updateSpots(dataSet)
[docs] def setSymbol(self, symbol, update=True, dataSet=None, mask=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. **Supported symbols:** * 'o' circle (default) * 's' square * 't' triangle * 'd' diamond * '+' plus * 't1' triangle pointing upwards * 't2' triangle pointing right side * 't3' triangle pointing left side * 'p' pentagon * 'h' hexagon * 'star' * 'x' cross * 'arrow_up' * 'arrow_right' * 'arrow_down' * 'arrow_left' * 'crosshair' * any QPainterPath to specify custom symbol shapes. """ if dataSet is None: dataSet = if isinstance(symbol, np.ndarray) or isinstance(symbol, list): symbols = symbol if mask is not None: symbols = symbols[mask] 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 else: self.opts['symbol'] = symbol self._spotPixmap = None dataSet['sourceRect'] = 0 if update: self.updateSpots(dataSet)
[docs] def setSize(self, size, update=True, dataSet=None, mask=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 = if isinstance(size, np.ndarray) or isinstance(size, list): sizes = size if mask is not None: sizes = sizes[mask] 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 else: self.opts['size'] = size self._spotPixmap = None dataSet['sourceRect'] = 0 if update: self.updateSpots(dataSet)
[docs] def setPointsVisible(self, visible, update=True, dataSet=None, mask=None): """Set whether or not each spot is visible. If a list or array is provided, then the visibility for each spot will be set separately. Otherwise, the argument will be used for all spots.""" if dataSet is None: dataSet = if isinstance(visible, np.ndarray) or isinstance(visible, list): visibilities = visible if mask is not None: visibilities = visibilities[mask] if len(visibilities) != len(dataSet): raise Exception("Number of visibilities does not match number of points (%d != %d)" % (len(visibilities), len(dataSet))) dataSet['visible'] = visibilities else: dataSet['visible'] = visible dataSet['sourceRect'] = 0 if update: self.updateSpots(dataSet)
def setPointData(self, data, dataSet=None, mask=None): if dataSet is None: dataSet = if isinstance(data, np.ndarray) or isinstance(data, list): if mask is not None: data = data[mask] if len(data) != len(dataSet): raise Exception("Length of meta data does not match number of points (%d != %d)" % (len(data), len(dataSet))) ## 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 (data.dtype.fields is not None)and len(data.dtype.fields) > 1: for i, rec in enumerate(data): dataSet['data'][i] = rec else: dataSet['data'] = data def setPxMode(self, mode): if self.opts['pxMode'] == mode: return self.opts['pxMode'] = mode self.invalidate() def updateSpots(self, dataSet=None): profiler = debug.Profiler() # noqa: profiler prints on GC if dataSet is None: dataSet = invalidate = False if self.opts['pxMode'] and self.opts['useCache']: mask = dataSet['sourceRect']['w'] == 0 if np.any(mask): invalidate = True coords = self.fragmentAtlas[ list(zip(*self._style(['symbol', 'size', 'pen', 'brush'], data=dataSet, idx=mask))) ] dataSet['sourceRect'][mask] = coords self._maybeRebuildAtlas() else: invalidate = True self._updateMaxSpotSizes(data=dataSet) if invalidate: self.invalidate() def _maybeRebuildAtlas(self, threshold=4, minlen=1000): n = len(self.fragmentAtlas) if (n > minlen) and (n > threshold * len( self.fragmentAtlas.rebuild( list(zip(*self._style(['symbol', 'size', 'pen', 'brush']))) )['sourceRect'] = 0 self.updateSpots() def _style(self, opts, data=None, idx=None, scale=None): if data is None: data = if idx is None: idx = np.s_[:] for opt in opts: col = data[opt][idx] if col.base is not None: col = col.copy() if self.opts['hoverable']: val = self.opts['hover' + opt.title()] if val != _DEFAULT_STYLE[opt]: col[data['hovered'][idx]] = val col[np.equal(col, _DEFAULT_STYLE[opt])] = self.opts[opt] if opt == 'size' and scale is not None: col *= scale yield col def _updateMaxSpotSizes(self, **kwargs): if self.opts['pxMode'] and self.opts['useCache']: w, pw = 0, self.fragmentAtlas.maxWidth else: w, pw = max(itertools.chain([(self._maxSpotWidth, self._maxSpotPxWidth)], self._measureSpotSizes(**kwargs))) self._maxSpotWidth = w self._maxSpotPxWidth = pw self.bounds = [None, None] def _measureSpotSizes(self, **kwargs): """Generate pairs (width, pxWidth) for spots in data""" styles = zip(*self._style(['size', 'pen'], **kwargs)) if self.opts['pxMode']: for size, pen in styles: yield 0, size + pen.widthF() else: for size, pen in styles: if pen.isCosmetic(): yield size, pen.widthF() else: yield size + pen.widthF(), 0
[docs] def clear(self): """Remove all spots from the scatter plot""" #self.clearItems() self._maxSpotWidth = 0 self._maxSpotPxWidth = 0 = np.empty(0, self.bounds = [None, None] self.invalidate()
def dataBounds(self, ax, frac=1.0, orthoRange=None): if frac >= 1.0 and orthoRange is None and self.bounds[ax] is not None: return self.bounds[ax] #self.prepareGeometryChange() if is None or len( == 0: return (None, None) if ax == 0: d =['x'] d2 =['y'] elif ax == 1: d =['y'] d2 =['x'] else: raise ValueError("Invalid axis value") if orthoRange is not None: mask = (d2 >= orthoRange[0]) * (d2 <= orthoRange[1]) d = d[mask] if d.size == 0: return (None, None) if frac >= 1.0: self.bounds[ax] = (np.nanmin(d) - self._maxSpotWidth*0.7072, np.nanmax(d) + self._maxSpotWidth*0.7072) return self.bounds[ax] elif frac <= 0.0: raise Exception("Value for parameter 'frac' must be > 0. (got %s)" % str(frac)) else: mask = np.isfinite(d) d = d[mask] return np.percentile(d, [50 * (1 - frac), 50 * (1 + frac)]) def pixelPadding(self): return self._maxSpotPxWidth*0.7072 def boundingRect(self): (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 px = py = 0.0 pxPad = self.pixelPadding() if pxPad > 0: # determine length of pixel in local x, y directions px, py = self.pixelVectors() try: px = 0 if px is None else px.length() except OverflowError: px = 0 try: py = 0 if py is None else py.length() except OverflowError: py = 0 # return bounds expanded by pixel size px *= pxPad py *= pxPad return QtCore.QRectF(xmn-px, ymn-py, (2*px)+xmx-xmn, (2*py)+ymx-ymn) def viewTransformChanged(self): self.prepareGeometryChange() GraphicsObject.viewTransformChanged(self) self.bounds = [None, None] def setExportMode(self, *args, **kwds): GraphicsObject.setExportMode(self, *args, **kwds) self.invalidate() @debug.warnOnException ## raising an exception here causes crash def paint(self, p, *args): profiler = debug.Profiler() cmode = self.opts.get('compositionMode', None) if cmode is not None: p.setCompositionMode(cmode) #p.setPen(fn.mkPen('r')) #p.drawRect(self.boundingRect()) if self._exportOpts is not False: aa = self._exportOpts.get('antialias', True) scale = self._exportOpts.get('resolutionScale', 1.0) ## exporting to image; pixel resolution may have changed else: aa = self.opts['antialias'] scale = 1.0 if self.opts['pxMode'] is True: # Cull points that are outside view viewMask = self._maskAt(self.viewRect()) # Map points using painter's world transform so they are drawn with pixel-valued sizes pts = np.vstack([['x'],['y']]) pts = fn.transformCoordinates(p.transform(), pts) pts = fn.clip_array(pts, -2 ** 30, 2 ** 30) # prevent Qt segmentation fault. p.resetTransform() if self.opts['useCache'] and self._exportOpts is False: # Draw symbols from pre-rendered atlas # x, y is the center of the target rect xy = pts[:, viewMask].T sr =['sourceRect'][viewMask] frags = self._pixmapFragments.array(sr.size) frags[:, 0:2] = xy frags[:, 2:6] = np.frombuffer(sr, dtype=int).reshape((-1, 4)) # sx, sy, sw, sh frags[:, 6:10] = [1.0, 1.0, 0.0, 1.0] # scaleX, scaleY, rotation, opacity profiler('prep') self._pixmapFragments.draw(p, self.fragmentAtlas.pixmap) profiler('draw') else: # render each symbol individually p.setRenderHint(p.RenderHint.Antialiasing, aa) for pt, style in zip( pts[:, viewMask].T, zip(*(self._style(['symbol', 'size', 'pen', 'brush'], idx=viewMask, scale=scale))) ): p.resetTransform() p.translate(*pt) drawSymbol(p, *style) else: if self.picture is None: self.picture = QtGui.QPicture() p2 = QtGui.QPainter(self.picture) for x, y, style in zip(['x'],['y'], zip(*self._style(['symbol', 'size', 'pen', 'brush'], scale=scale)) ): p2.resetTransform() p2.translate(x, y) drawSymbol(p2, *style) p2.end() p.setRenderHint(p.RenderHint.Antialiasing, aa) def points(self): m = np.equal(['item'], None) for i in np.argwhere(m)[:, 0]: rec =[i] if rec['item'] is None: rec['item'] = SpotItem(rec, self, i) return['item'] def pointsAt(self, pos): return self.points()[self._maskAt(pos)][::-1] def _maskAt(self, obj): """ Return a boolean mask indicating all points that overlap obj, a QPointF or QRectF. """ if isinstance(obj, QtCore.QPointF): l = r = obj.x() t = b = obj.y() elif isinstance(obj, QtCore.QRectF): l = obj.left() r = obj.right() t = b = obj.bottom() else: raise TypeError if self.opts['pxMode'] and self.opts['useCache']: w =['sourceRect']['w'] h =['sourceRect']['h'] else: s, = self._style(['size']) w = h = s w = w / 2 h = h / 2 if self.opts['pxMode']: # determine length of pixel in local x, y directions px, py = self.pixelVectors() try: px = 0 if px is None else px.length() except OverflowError: px = 0 try: py = 0 if py is None else py.length() except OverflowError: py = 0 w *= px h *= py return (['visible'] & (['x'] + w > l) & (['x'] - w < r) & (['y'] + h > t) & (['y'] - h < b)) def mouseClickEvent(self, ev): if ev.button() == QtCore.Qt.MouseButton.LeftButton: pts = self.pointsAt(ev.pos()) if len(pts) > 0: self.ptsClicked = pts ev.accept() self.sigClicked.emit(self, self.ptsClicked, ev) else: #print "no spots" ev.ignore() else: ev.ignore() def hoverEvent(self, ev): if self.opts['hoverable']: old =['hovered'] if ev.exit: new = np.zeros_like(['hovered']) else: new = self._maskAt(ev.pos()) if self._hasHoverStyle():['sourceRect'][old ^ new] = 0['hovered'] = new self.updateSpots() points = self.points()[new][::-1] # Show information about hovered points in a tool tip vb = self.getViewBox() if vb is not None and self.opts['tip'] is not None: if len(points) > 0: cutoff = 3 tip = [self.opts['tip'](x=pt.pos().x(), y=pt.pos().y(), for pt in points[:cutoff]] if len(points) > cutoff: tip.append('({} others...)'.format(len(points) - cutoff)) vb.setToolTip('\n\n'.join(tip)) self._toolTipCleared = False elif not self._toolTipCleared: vb.setToolTip("") self._toolTipCleared = True self.sigHovered.emit(self, points, ev) def _hasHoverStyle(self): return any(self.opts['hover' + opt.title()] != _DEFAULT_STYLE[opt] for opt in ['symbol', 'size', 'pen', 'brush'])
class SpotItem(object): """ 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. """ def __init__(self, data, plot, index): self._data = data self._index = index # SpotItems are kept in["items"] numpy object array which # does not support cyclic garbage collection (numpy issue 6581). # Keeping a strong ref to plot here would leak the cycle self.__plot_ref = weakref.ref(plot) @property def _plot(self): return self.__plot_ref() def data(self): """Return the user data associated with this spot.""" return self._data['data'] def index(self): """Return the index of this point as given in the scatter plot data.""" return self._index 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 pos(self): return Point(self._data['x'], self._data['y']) def viewPos(self): return self._plot.mapToView(self.pos()) 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'] if symbol is None: symbol = self._plot.opts['symbol'] try: n = int(symbol) symbol = list(Symbols.keys())[n % len(Symbols)] except: pass 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""" self._data['pen'] = _mkPen(*args, **kargs) 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""" self._data['brush'] = _mkBrush(*args, **kargs) 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 isVisible(self): return self._data['visible'] def setVisible(self, visible): """Set whether or not this spot is visible.""" self._data['visible'] = visible self.updateItem() def setData(self, data): """Set the user-data associated with this spot""" self._data['data'] = data def updateItem(self): self._data['sourceRect'] = (0, 0, 0, 0) # numpy <=1.13.1 won't let us set this with a single zero self._plot.updateSpots(self._data.reshape(1))