929 lines
36 KiB
Python
929 lines
36 KiB
Python
from pyqtgraph.Qt import QtGui, QtCore, USE_PYSIDE
|
|
from pyqtgraph.Point import Point
|
|
import pyqtgraph.functions as fn
|
|
from .GraphicsItem import GraphicsItem
|
|
from .GraphicsObject import GraphicsObject
|
|
import numpy as np
|
|
import scipy.stats
|
|
import weakref
|
|
import pyqtgraph.debug as debug
|
|
from pyqtgraph.pgcollections import OrderedDict
|
|
import pyqtgraph as pg
|
|
#import pyqtgraph as pg
|
|
|
|
__all__ = ['ScatterPlotItem', 'SpotItem']
|
|
|
|
|
|
## Build all symbol paths
|
|
Symbols = OrderedDict([(name, QtGui.QPainterPath()) for name in ['o', 's', 't', 'd', '+']])
|
|
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)
|
|
],
|
|
}
|
|
for k, c in coords.items():
|
|
Symbols[k].moveTo(*c[0])
|
|
for x,y in c[1:]:
|
|
Symbols[k].lineTo(x, y)
|
|
Symbols[k].closeSubpath()
|
|
|
|
|
|
def drawSymbol(painter, symbol, size, pen, brush):
|
|
painter.scale(size, size)
|
|
painter.setPen(pen)
|
|
painter.setBrush(brush)
|
|
if isinstance(symbol, basestring):
|
|
symbol = Symbols[symbol]
|
|
if np.isscalar(symbol):
|
|
symbol = list(Symbols.values())[symbol % len(Symbols)]
|
|
painter.drawPath(symbol)
|
|
|
|
|
|
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).
|
|
"""
|
|
## see if this pixmap is already cached
|
|
#global SymbolPixmapCache
|
|
#key = (symbol, size, fn.colorTuple(pen.color()), pen.width(), pen.style(), fn.colorTuple(brush.color()))
|
|
#if key in SymbolPixmapCache:
|
|
#return SymbolPixmapCache[key]
|
|
|
|
## Render a spot with the given parameters to a pixmap
|
|
penPxWidth = max(np.ceil(pen.widthF()), 1)
|
|
image = QtGui.QImage(int(size+penPxWidth), int(size+penPxWidth), QtGui.QImage.Format_ARGB32)
|
|
image.fill(0)
|
|
p = QtGui.QPainter(image)
|
|
p.setRenderHint(p.Antialiasing)
|
|
p.translate(image.width()*0.5, image.height()*0.5)
|
|
drawSymbol(p, symbol, size, pen, brush)
|
|
p.end()
|
|
return image
|
|
#pixmap = QtGui.QPixmap(image)
|
|
#SymbolPixmapCache[key] = pixmap
|
|
#return pixmap
|
|
|
|
def makeSymbolPixmap(size, pen, brush, symbol):
|
|
## deprecated
|
|
img = renderSymbol(symbol, size, pen, brush)
|
|
return QtGui.QPixmap(img)
|
|
|
|
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.getSymbolCoords('o', 5, QPen(..), QBrush(..))
|
|
sc2 = atlas.getSymbolCoords('t', 10, QPen(..), QBrush(..))
|
|
pm = atlas.getAtlas()
|
|
|
|
"""
|
|
class SymbolCoords(list): ## needed because lists are not allowed in weak references.
|
|
pass
|
|
|
|
def __init__(self):
|
|
# symbol key : [x, y, w, h] atlas coordinates
|
|
# note that the coordinate list will always be the same list object as
|
|
# long as the symbol is in the atlas, but the coordinates may
|
|
# change if the atlas is rebuilt.
|
|
# weak value; if all external refs to this list disappear,
|
|
# the symbol will be forgotten.
|
|
self.symbolMap = weakref.WeakValueDictionary()
|
|
|
|
self.atlasData = None # numpy array of atlas image
|
|
self.atlas = None # atlas as QPixmap
|
|
self.atlasValid = False
|
|
|
|
def getSymbolCoords(self, opts):
|
|
"""
|
|
Given a list of spot records, return an object representing the coordinates of that symbol within the atlas
|
|
"""
|
|
coords = np.empty(len(opts), dtype=object)
|
|
for i, rec in enumerate(opts):
|
|
symbol, size, pen, brush = rec['symbol'], rec['size'], rec['pen'], rec['brush']
|
|
pen = fn.mkPen(pen) if not isinstance(pen, QtGui.QPen) else pen
|
|
brush = fn.mkBrush(brush) if not isinstance(pen, QtGui.QBrush) else brush
|
|
key = (symbol, size, fn.colorTuple(pen.color()), pen.widthF(), pen.style(), fn.colorTuple(brush.color()))
|
|
if key not in self.symbolMap:
|
|
newCoords = SymbolAtlas.SymbolCoords()
|
|
self.symbolMap[key] = newCoords
|
|
self.atlasValid = False
|
|
#try:
|
|
#self.addToAtlas(key) ## squeeze this into the atlas if there is room
|
|
#except:
|
|
#self.buildAtlas() ## otherwise, we need to rebuild
|
|
|
|
coords[i] = self.symbolMap[key]
|
|
return coords
|
|
|
|
def buildAtlas(self):
|
|
# get rendered array for all symbols, keep track of avg/max width
|
|
rendered = {}
|
|
avgWidth = 0.0
|
|
maxWidth = 0
|
|
images = []
|
|
for key, coords in self.symbolMap.items():
|
|
if len(coords) == 0:
|
|
pen = fn.mkPen(color=key[2], width=key[3], style=key[4])
|
|
brush = fn.mkBrush(color=key[5])
|
|
img = renderSymbol(key[0], key[1], pen, brush)
|
|
images.append(img) ## we only need this to prevent the images being garbage collected immediately
|
|
arr = fn.imageToArray(img, copy=False, transpose=False)
|
|
else:
|
|
(x,y,w,h) = self.symbolMap[key]
|
|
arr = self.atlasData[x:x+w, y:y+w]
|
|
rendered[key] = arr
|
|
w = arr.shape[0]
|
|
avgWidth += w
|
|
maxWidth = max(maxWidth, w)
|
|
|
|
nSymbols = len(rendered)
|
|
if nSymbols > 0:
|
|
avgWidth /= nSymbols
|
|
width = max(maxWidth, avgWidth * (nSymbols**0.5))
|
|
else:
|
|
avgWidth = 0
|
|
width = 0
|
|
|
|
# sort symbols by height
|
|
symbols = sorted(rendered.keys(), key=lambda x: rendered[x].shape[1], reverse=True)
|
|
|
|
self.atlasRows = []
|
|
|
|
x = width
|
|
y = 0
|
|
rowheight = 0
|
|
for key in symbols:
|
|
arr = rendered[key]
|
|
w,h = arr.shape[:2]
|
|
if x+w > width:
|
|
y += rowheight
|
|
x = 0
|
|
rowheight = h
|
|
self.atlasRows.append([y, rowheight, 0])
|
|
self.symbolMap[key][:] = x, y, w, h
|
|
x += w
|
|
self.atlasRows[-1][2] = x
|
|
height = y + rowheight
|
|
|
|
self.atlasData = np.zeros((width, height, 4), dtype=np.ubyte)
|
|
for key in symbols:
|
|
x, y, w, h = self.symbolMap[key]
|
|
self.atlasData[x:x+w, y:y+h] = rendered[key]
|
|
self.atlas = None
|
|
self.atlasValid = True
|
|
|
|
def getAtlas(self):
|
|
if not self.atlasValid:
|
|
self.buildAtlas()
|
|
if self.atlas is None:
|
|
if len(self.atlasData) == 0:
|
|
return QtGui.QPixmap(0,0)
|
|
img = fn.makeQImage(self.atlasData, copy=False, transpose=False)
|
|
self.atlas = QtGui.QPixmap(img)
|
|
return self.atlas
|
|
|
|
|
|
|
|
|
|
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) Emitted when the curve is clicked. Sends a list
|
|
of all the points under the mouse pointer.
|
|
======================== ===============================================
|
|
|
|
"""
|
|
#sigPointClicked = QtCore.Signal(object, object)
|
|
sigClicked = QtCore.Signal(object, object) ## self, points
|
|
sigPlotChanged = QtCore.Signal(object)
|
|
def __init__(self, *args, **kargs):
|
|
"""
|
|
Accepts the same arguments as setData()
|
|
"""
|
|
prof = debug.Profiler('ScatterPlotItem.__init__', disabled=True)
|
|
GraphicsObject.__init__(self)
|
|
|
|
self.picture = None # QPicture used for rendering when pxmode==False
|
|
self.fragments = None # fragment specification for pxmode; updated every time the view changes.
|
|
self.fragmentAtlas = SymbolAtlas()
|
|
|
|
self.data = np.empty(0, dtype=[('x', float), ('y', float), ('size', float), ('symbol', object), ('pen', object), ('brush', object), ('data', object), ('fragCoords', object), ('item', object)])
|
|
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.opts = {
|
|
'pxMode': True,
|
|
'useCache': True, ## If useCache is False, symbols are re-drawn on every paint.
|
|
'antialias': pg.getConfigOption('antialias'),
|
|
}
|
|
|
|
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')
|
|
self.setData(*args, **kargs)
|
|
prof.mark('setData')
|
|
prof.finish()
|
|
|
|
#self.setCacheMode(self.DeviceCoordinateCache)
|
|
|
|
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.
|
|
Default is True
|
|
*symbol* can be one (or a list) of:
|
|
* 'o' circle (default)
|
|
* 's' square
|
|
* 't' triangle
|
|
* 'd' diamond
|
|
* '+' plus
|
|
* 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.
|
|
*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.
|
|
*identical* *Deprecated*. This functionality is handled automatically now.
|
|
*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)
|
|
====================== ===============================================================================================
|
|
"""
|
|
oldData = self.data ## this causes cached pixmaps to be preserved while new data is registered.
|
|
self.clear() ## clear out all old data
|
|
self.addPoints(*args, **kargs)
|
|
|
|
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
|
|
|
|
## 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
|
|
|
|
if 'spots' in kargs:
|
|
spots = kargs['spots']
|
|
for i in range(len(spots)):
|
|
spot = spots[i]
|
|
for k in spot:
|
|
#if k == 'pen':
|
|
#newData[k] = fn.mkPen(spot[k])
|
|
#elif k == 'brush':
|
|
#newData[k] = fn.mkBrush(spot[k])
|
|
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 in ['x', 'y', 'size', 'symbol', 'pen', 'brush', 'data']:
|
|
newData[i][k] = spot[k]
|
|
#elif k == 'data':
|
|
#self.pointData[i] = spot[k]
|
|
else:
|
|
raise Exception("Unknown spot parameter: %s" % k)
|
|
elif 'y' in kargs:
|
|
newData['x'] = kargs['x']
|
|
newData['y'] = kargs['y']
|
|
|
|
if 'pxMode' in kargs:
|
|
self.setPxMode(kargs['pxMode'])
|
|
if 'antialias' in kargs:
|
|
self.opts['antialias'] = kargs['antialias']
|
|
|
|
## 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))
|
|
|
|
if 'data' in kargs:
|
|
self.setPointData(kargs['data'], dataSet=newData)
|
|
|
|
self.prepareGeometryChange()
|
|
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.fragments = None
|
|
self.update()
|
|
|
|
def getData(self):
|
|
return self.data['x'], self.data['y']
|
|
|
|
|
|
def setPoints(self, *args, **kargs):
|
|
##Deprecated; use setData
|
|
return self.setData(*args, **kargs)
|
|
|
|
def implements(self, interface=None):
|
|
ints = ['plotData']
|
|
if interface is None:
|
|
return ints
|
|
return interface in ints
|
|
|
|
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', self.data)
|
|
|
|
if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)):
|
|
pens = args[0]
|
|
if 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'] = pens
|
|
else:
|
|
self.opts['pen'] = fn.mkPen(*args, **kargs)
|
|
|
|
dataSet['fragCoords'] = None
|
|
if update:
|
|
self.updateSpots(dataSet)
|
|
|
|
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', self.data)
|
|
|
|
if len(args) == 1 and (isinstance(args[0], np.ndarray) or isinstance(args[0], list)):
|
|
brushes = args[0]
|
|
if 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)))
|
|
#for i in xrange(len(brushes)):
|
|
#self.data[i]['brush'] = fn.mkBrush(brushes[i], **kargs)
|
|
dataSet['brush'] = brushes
|
|
else:
|
|
self.opts['brush'] = fn.mkBrush(*args, **kargs)
|
|
#self._spotPixmap = None
|
|
|
|
dataSet['fragCoords'] = None
|
|
if update:
|
|
self.updateSpots(dataSet)
|
|
|
|
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."""
|
|
if dataSet is None:
|
|
dataSet = self.data
|
|
|
|
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['fragCoords'] = None
|
|
if update:
|
|
self.updateSpots(dataSet)
|
|
|
|
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 = self.data
|
|
|
|
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['fragCoords'] = None
|
|
if update:
|
|
self.updateSpots(dataSet)
|
|
|
|
def setPointData(self, data, dataSet=None, mask=None):
|
|
if dataSet is None:
|
|
dataSet = self.data
|
|
|
|
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 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):
|
|
if dataSet is None:
|
|
dataSet = self.data
|
|
self._maxSpotWidth = 0
|
|
self._maxSpotPxWidth = 0
|
|
invalidate = False
|
|
self.measureSpotSizes(dataSet)
|
|
if self.opts['pxMode']:
|
|
mask = np.equal(dataSet['fragCoords'], None)
|
|
if np.any(mask):
|
|
invalidate = True
|
|
opts = self.getSpotOpts(dataSet[mask])
|
|
coords = self.fragmentAtlas.getSymbolCoords(opts)
|
|
dataSet['fragCoords'][mask] = coords
|
|
|
|
#for rec in dataSet:
|
|
#if rec['fragCoords'] is None:
|
|
#invalidate = True
|
|
#rec['fragCoords'] = self.fragmentAtlas.getSymbolCoords(*self.getSpotOpts(rec))
|
|
if invalidate:
|
|
self.invalidate()
|
|
|
|
def getSpotOpts(self, recs, scale=1.0):
|
|
if recs.ndim == 0:
|
|
rec = recs
|
|
symbol = rec['symbol']
|
|
if symbol is None:
|
|
symbol = self.opts['symbol']
|
|
size = rec['size']
|
|
if size < 0:
|
|
size = self.opts['size']
|
|
pen = rec['pen']
|
|
if pen is None:
|
|
pen = self.opts['pen']
|
|
brush = rec['brush']
|
|
if brush is None:
|
|
brush = self.opts['brush']
|
|
return (symbol, size*scale, fn.mkPen(pen), fn.mkBrush(brush))
|
|
else:
|
|
recs = recs.copy()
|
|
recs['symbol'][np.equal(recs['symbol'], None)] = self.opts['symbol']
|
|
recs['size'][np.equal(recs['size'], -1)] = self.opts['size']
|
|
recs['size'] *= scale
|
|
recs['pen'][np.equal(recs['pen'], None)] = fn.mkPen(self.opts['pen'])
|
|
recs['brush'][np.equal(recs['brush'], None)] = fn.mkBrush(self.opts['brush'])
|
|
return recs
|
|
|
|
|
|
|
|
def measureSpotSizes(self, dataSet):
|
|
for rec in dataSet:
|
|
## keep track of the maximum spot size and pixel size
|
|
symbol, size, pen, brush = self.getSpotOpts(rec)
|
|
width = 0
|
|
pxWidth = 0
|
|
if self.opts['pxMode']:
|
|
pxWidth = size + pen.widthF()
|
|
else:
|
|
width = size
|
|
if pen.isCosmetic():
|
|
pxWidth += pen.widthF()
|
|
else:
|
|
width += pen.widthF()
|
|
self._maxSpotWidth = max(self._maxSpotWidth, width)
|
|
self._maxSpotPxWidth = max(self._maxSpotPxWidth, pxWidth)
|
|
self.bounds = [None, None]
|
|
|
|
|
|
def clear(self):
|
|
"""Remove all spots from the scatter plot"""
|
|
#self.clearItems()
|
|
self.data = np.empty(0, dtype=self.data.dtype)
|
|
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 self.data is None or len(self.data) == 0:
|
|
return (None, None)
|
|
|
|
if ax == 0:
|
|
d = self.data['x']
|
|
d2 = self.data['y']
|
|
elif ax == 1:
|
|
d = self.data['y']
|
|
d2 = self.data['x']
|
|
|
|
if orthoRange is not None:
|
|
mask = (d2 >= orthoRange[0]) * (d2 <= orthoRange[1])
|
|
d = d[mask]
|
|
d2 = d2[mask]
|
|
|
|
if frac >= 1.0:
|
|
self.bounds[ax] = (d.min() - self._maxSpotWidth*0.7072, d.max() + 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:
|
|
return (scipy.stats.scoreatpercentile(d, 50 - (frac * 50)), scipy.stats.scoreatpercentile(d, 50 + (frac * 50)))
|
|
|
|
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()
|
|
px = 0 if px is None else px.length()
|
|
py = 0 if py is None else py.length()
|
|
|
|
# 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]
|
|
self.fragments = None
|
|
|
|
def generateFragments(self):
|
|
tr = self.deviceTransform()
|
|
if tr is None:
|
|
return
|
|
pts = np.empty((2,len(self.data['x'])))
|
|
pts[0] = self.data['x']
|
|
pts[1] = self.data['y']
|
|
pts = fn.transformCoordinates(tr, pts)
|
|
self.fragments = []
|
|
pts = np.clip(pts, -2**31, 2**31) ## prevent Qt segmentation fault.
|
|
## Still won't be able to render correctly, though.
|
|
for i in xrange(len(self.data)):
|
|
rec = self.data[i]
|
|
pos = QtCore.QPointF(pts[0,i], pts[1,i])
|
|
x,y,w,h = rec['fragCoords']
|
|
if abs(w) > 10000 or abs(h) > 10000:
|
|
print self.data
|
|
raise Exception("fragment corrupt")
|
|
rect = QtCore.QRectF(y, x, h, w)
|
|
self.fragments.append(QtGui.QPainter.PixmapFragment.create(pos, rect))
|
|
|
|
def setExportMode(self, *args, **kwds):
|
|
GraphicsObject.setExportMode(self, *args, **kwds)
|
|
self.invalidate()
|
|
|
|
def paint(self, p, *args):
|
|
|
|
#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:
|
|
atlas = self.fragmentAtlas.getAtlas()
|
|
#arr = fn.imageToArray(atlas.toImage(), copy=True)
|
|
#if hasattr(self, 'lastAtlas'):
|
|
#if np.any(self.lastAtlas != arr):
|
|
#print "Atlas changed:", arr
|
|
#self.lastAtlas = arr
|
|
|
|
if self.fragments is None:
|
|
self.updateSpots()
|
|
self.generateFragments()
|
|
|
|
p.resetTransform()
|
|
|
|
if not USE_PYSIDE and self.opts['useCache'] and self._exportOpts is False:
|
|
p.drawPixmapFragments(self.fragments, atlas)
|
|
else:
|
|
p.setRenderHint(p.Antialiasing, aa)
|
|
|
|
for i in range(len(self.data)):
|
|
rec = self.data[i]
|
|
frag = self.fragments[i]
|
|
p.resetTransform()
|
|
p.translate(frag.x, frag.y)
|
|
drawSymbol(p, *self.getSpotOpts(rec, scale))
|
|
else:
|
|
if self.picture is None:
|
|
self.picture = QtGui.QPicture()
|
|
p2 = QtGui.QPainter(self.picture)
|
|
for rec in self.data:
|
|
if scale != 1.0:
|
|
rec = rec.copy()
|
|
rec['size'] *= scale
|
|
p2.resetTransform()
|
|
p2.translate(rec['x'], rec['y'])
|
|
drawSymbol(p2, *self.getSpotOpts(rec, scale))
|
|
p2.end()
|
|
|
|
self.picture.play(p)
|
|
|
|
def points(self):
|
|
for rec in self.data:
|
|
if rec['item'] is None:
|
|
rec['item'] = SpotItem(rec, self)
|
|
return self.data['item']
|
|
|
|
def pointsAt(self, pos):
|
|
x = pos.x()
|
|
y = pos.y()
|
|
pw = self.pixelWidth()
|
|
ph = self.pixelHeight()
|
|
pts = []
|
|
for s in self.points():
|
|
sp = s.pos()
|
|
ss = s.size()
|
|
sx = sp.x()
|
|
sy = sp.y()
|
|
s2x = s2y = ss * 0.5
|
|
if self.opts['pxMode']:
|
|
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[::-1]
|
|
|
|
|
|
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()
|
|
|
|
|
|
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):
|
|
#GraphicsItem.__init__(self, register=False)
|
|
self._data = data
|
|
self._plot = plot
|
|
#self.setParentItem(plot)
|
|
#self.setPos(QtCore.QPointF(data['x'], data['y']))
|
|
#self.updateItem()
|
|
|
|
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 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"""
|
|
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
|
|
|
|
def updateItem(self):
|
|
self._data['fragCoords'] = None
|
|
self._plot.updateSpots(self._data.reshape(1))
|
|
self._plot.invalidate()
|
|
|
|
#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'])
|
|
|
|
### If all symbol options are default, use default pixmap
|
|
#if symbolOpts == (None, None, -1, ''):
|
|
#pixmap = self._plot.defaultSpotPixmap()
|
|
#else:
|
|
#pixmap = makeSymbolPixmap(size=self.size(), pen=self.pen(), brush=self.brush(), symbol=self.symbol())
|
|
#self.setPixmap(pixmap)
|
|
|
|
|
|
#class PathSpotItem(SpotItem, QtGui.QGraphicsPathItem):
|
|
#def __init__(self, data, plot):
|
|
#QtGui.QGraphicsPathItem.__init__(self)
|
|
#SpotItem.__init__(self, data, plot)
|
|
|
|
#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)
|