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Merge pull request #1796 from j9ac9k/test-polyline

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If arrayToQPath uses connect=all, use a different construction for QPainterPath
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Ogi Moore 2021-06-04 21:33:45 -07:00 committed by GitHub
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5 changed files with 276 additions and 90 deletions
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2
examples/MultiPlotSpeedTest.py
View File

@ -45,7 +45,7 @@ def update():
count += 1
for i in range(nPlots):
curves[i].setData(data[(ptr+i)%data.shape[0]])
curves[i].setData(data[(ptr+i)%data.shape[0]], skipFiniteCheck=True)
ptr += nPlots
now = time()

239
pyqtgraph/functions.py
View File

@ -1690,69 +1690,92 @@ def downsample(data, n, axis=0, xvals='subsample'):
return MetaArray(d2, info=info)
def arrayToQPath(x, y, connect='all'):
"""Convert an array of x,y coordinats to QPainterPath as efficiently as possible.
The *connect* argument may be 'all', indicating that each point should be
connected to the next; 'pairs', indicating that each pair of points
should be connected, or an array of int32 values (0 or 1) indicating
def arrayToQPath(x, y, connect='all', finiteCheck=True):
"""
Convert an array of x,y coordinates to QPainterPath as efficiently as
possible. The *connect* argument may be 'all', indicating that each point
should be connected to the next; 'pairs', indicating that each pair of
points should be connected, or an array of int32 values (0 or 1) indicating
connections.
Parameters
----------
x : (N,) ndarray
x-values to be plotted
y : (N,) ndarray
y-values to be plotted, must be same length as `x`
connect : {'all', 'pairs', 'finite', (N,) ndarray}, optional
Argument detailing how to connect the points in the path. `all` will
have sequential points being connected. `pairs` generates lines
between every other point. `finite` only connects points that are
finite. If an ndarray is passed, containing int32 values of 0 or 1,
only values with 1 will connect to the previous point. Def
finiteCheck : bool, default Ture
When false, the check for finite values will be skipped, which can
improve performance. If finite values are present in `x` or `y`,
an empty QPainterPath will be generated.
Returns
-------
QPainterPath
QPainterPath object to be drawn
Raises
------
ValueError
Raised when the connect argument has an invalid value placed within.
Notes
-----
A QPainterPath is generated through one of two ways. When the connect
parameter is 'all', a QPolygonF object is created, and
``QPainterPath.addPolygon()`` is called. For other connect parameters
a ``QDataStream`` object is created and the QDataStream >> QPainterPath
operator is used to pass the data. The memory format is as follows
numVerts(i4)
0(i4) x(f8) y(f8) <-- 0 means this vertex does not connect
1(i4) x(f8) y(f8) <-- 1 means this vertex connects to the previous vertex
...
cStart(i4) fillRule(i4)
see: https://github.com/qt/qtbase/blob/dev/src/gui/painting/qpainterpath.cpp
All values are big endian--pack using struct.pack('>d') or struct.pack('>i')
This binary format may change in future versions of Qt
"""
## Create all vertices in path. The method used below creates a binary format so that all
## vertices can be read in at once. This binary format may change in future versions of Qt,
## so the original (slower) method is left here for emergencies:
#path.moveTo(x[0], y[0])
#if connect == 'all':
#for i in range(1, y.shape[0]):
#path.lineTo(x[i], y[i])
#elif connect == 'pairs':
#for i in range(1, y.shape[0]):
#if i%2 == 0:
#path.lineTo(x[i], y[i])
#else:
#path.moveTo(x[i], y[i])
#elif isinstance(connect, np.ndarray):
#for i in range(1, y.shape[0]):
#if connect[i] == 1:
#path.lineTo(x[i], y[i])
#else:
#path.moveTo(x[i], y[i])
#else:
#raise Exception('connect argument must be "all", "pairs", or array')
## Speed this up using >> operator
## Format is:
## numVerts(i4)
## 0(i4) x(f8) y(f8) <-- 0 means this vertex does not connect
## 1(i4) x(f8) y(f8) <-- 1 means this vertex connects to the previous vertex
## ...
## cStart(i4) fillRule(i4)
##
## see: https://github.com/qt/qtbase/blob/dev/src/gui/painting/qpainterpath.cpp
## All values are big endian--pack using struct.pack('>d') or struct.pack('>i')
path = QtGui.QPainterPath()
n = x.shape[0]
# create empty array, pad with extra space on either end
arr = np.empty(n+2, dtype=[('c', '>i4'), ('x', '>f8'), ('y', '>f8')])
connect_array = None
if isinstance(connect, np.ndarray):
# make connect argument contain only str type
connect_array, connect = connect, 'array'
# write first two integers
byteview = arr.view(dtype=np.ubyte)
byteview[:16] = 0
byteview.data[16:20] = struct.pack('>i', n)
use_qpolygonf = connect == 'all'
if use_qpolygonf:
backstore = create_qpolygonf(n)
arr = np.frombuffer(ndarray_from_qpolygonf(backstore), dtype=[('x', 'f8'), ('y', 'f8')])
else:
backstore = bytearray(4 + n*20 + 8)
arr = np.frombuffer(backstore, dtype=[('c', '>i4'), ('x', '>f8'), ('y', '>f8')],
count=n, offset=4)
struct.pack_into('>i', backstore, 0, n)
# cStart, fillRule (Qt.OddEvenFill)
struct.pack_into('>ii', backstore, 4+n*20, 0, 0)
# Fill array with vertex values
arr[1:-1]['x'] = x
arr[1:-1]['y'] = y
arr['x'] = x
arr['y'] = y
# inf/nans completely prevent the plot from being displayed starting on
# Qt version 5.12.3; these must now be manually cleaned out.
# the presence of inf/nans result in an empty QPainterPath being generated
# this behavior started in Qt 5.12.3 and was introduced in this commit
# https://github.com/qt/qtbase/commit/c04bd30de072793faee5166cff866a4c4e0a9dd7
# We therefore replace non-finite values
isfinite = None
qtver = [int(x) for x in QtVersion.split('.')]
if qtver >= [5, 12, 3]:
if finiteCheck:
isfinite = np.isfinite(x) & np.isfinite(y)
if not np.all(isfinite):
# credit: Divakar https://stackoverflow.com/a/41191127/643629
@ -1764,51 +1787,103 @@ def arrayToQPath(x, y, connect='all'):
if first < len(x):
# Replace all non-finite entries from beginning of arr with the first finite one
idx[:first] = first
arr[1:-1] = arr[1:-1][idx]
arr[:] = arr[:][idx]
# decide which points are connected by lines
if eq(connect, 'all'):
arr[1:-1]['c'] = 1
elif eq(connect, 'pairs'):
arr[1:-1]['c'][::2] = 0
arr[1:-1]['c'][1::2] = 1 # connect every 2nd point to every 1st one
elif eq(connect, 'finite'):
if connect == 'all':
path.addPolygon(backstore)
return path
elif connect == 'pairs':
arr['c'][::2] = 0
arr['c'][1::2] = 1 # connect every 2nd point to every 1st one
elif connect == 'finite':
# Let's call a point with either x or y being nan is an invalid point.
# A point will anyway not connect to an invalid point regardless of the
# 'c' value of the invalid point. Therefore, we should set 'c' to 0 for
# the next point of an invalid point.
if isfinite is None:
isfinite = np.isfinite(x) & np.isfinite(y)
arr[2:]['c'] = isfinite
elif isinstance(connect, np.ndarray):
arr[2:-1]['c'] = connect[:-1]
arr[1:]['c'] = isfinite[:-1]
elif connect == 'array':
arr[1:]['c'] = connect_array[:-1]
else:
raise Exception('connect argument must be "all", "pairs", "finite", or array')
raise ValueError('connect argument must be "all", "pairs", "finite", or array')
arr[1]['c'] = 0 # the first vertex has no previous vertex to connect
byteview.data[-20:-16] = struct.pack('>i', 0) # cStart
byteview.data[-16:-12] = struct.pack('>i', 0) # fillRule (Qt.OddEvenFill)
# create datastream object and stream into path
## Avoiding this method because QByteArray(str) leaks memory in PySide
#buf = QtCore.QByteArray(arr.data[12:lastInd+4]) # I think one unnecessary copy happens here
path.strn = byteview.data[16:-12] # make sure data doesn't run away
try:
buf = QtCore.QByteArray.fromRawData(path.strn)
except TypeError:
buf = QtCore.QByteArray(bytes(path.strn))
except AttributeError:
# PyQt6 raises AttributeError
buf = QtCore.QByteArray(path.strn, path.strn.nbytes)
arr[0]['c'] = 0 # the first vertex has no previous vertex to connect
# create QDataStream object and stream into QPainterPath
path.strn = backstore
if QT_LIB == "PyQt6" and QtCore.PYQT_VERSION < 0x60101:
# due to issue detailed here:
# https://www.riverbankcomputing.com/pipermail/pyqt/2021-May/043942.html
buf = QtCore.QByteArray(path.strn, len(path.strn))
else:
buf = QtCore.QByteArray(path.strn)
ds = QtCore.QDataStream(buf)
ds >> path
return path
def ndarray_from_qpolygonf(polyline):
nbytes = 2 * len(polyline) * 8
if QT_LIB == "PySide2":
buffer = Qt.shiboken2.VoidPtr(polyline.data(), nbytes, True)
elif QT_LIB == "PySide6":
buffer = Qt.shiboken6.VoidPtr(polyline.data(), nbytes, True)
else:
buffer = polyline.data()
buffer.setsize(nbytes)
memory = np.frombuffer(buffer, np.double).reshape((-1, 2))
return memory
def create_qpolygonf(size):
if QtVersion.startswith("5"):
polyline = QtGui.QPolygonF(size)
else:
polyline = QtGui.QPolygonF()
if QT_LIB == "PySide6":
polyline.resize(size)
else:
polyline.fill(QtCore.QPointF(), size)
return polyline
def arrayToQPolygonF(x, y):
"""
Utility function to convert two 1D-NumPy arrays representing curve data
(X-axis, Y-axis data) into a single open polygon (QtGui.PolygonF) object.
Thanks to PythonQwt for making this code available
License/copyright: MIT License © Pierre Raybaut 2020.
Parameters
----------
x : np.array
x-axis coordinates for data to be plotted, must have have ndim of 1
y : np.array
y-axis coordinates for data to be plotted, must have ndim of 1 and
be the same length as x
Returns
-------
QPolygonF
Open QPolygonF object that represents the path looking to be plotted
Raises
------
ValueError
When xdata or ydata does not meet the required criteria
"""
if not (
x.size == y.size == x.shape[0] == y.shape[0]
):
raise ValueError("Arguments must be 1D and the same size")
size = x.size
polyline = create_qpolygonf(size)
memory = ndarray_from_qpolygonf(polyline)
memory[:, 0] = x
memory[:, 1] = y
return polyline
#def isosurface(data, level):
#"""
#Generate isosurface from volumetric data using marching tetrahedra algorithm.

19
pyqtgraph/graphicsItems/PlotCurveItem.py
View File

@ -65,6 +65,7 @@ class PlotCurveItem(GraphicsObject):
'connect': 'all',
'mouseWidth': 8, # width of shape responding to mouse click
'compositionMode': None,
'skipFiniteCheck': True
}
if 'pen' not in kargs:
self.opts['pen'] = fn.mkPen('w')
@ -336,6 +337,11 @@ class PlotCurveItem(GraphicsObject):
connectivity, specify an array of boolean values.
compositionMode See :func:`setCompositionMode
<pyqtgraph.PlotCurveItem.setCompositionMode>`.
skipFiniteCheck Optimization parameter that can speed up plot time by
telling the painter to not check and compensate for NaN
values. If set to True, and NaN values exist, the data
may not be displayed or your plot will take a
significant performance hit. Defaults to False.
=============== ========================================================
If non-keyword arguments are used, they will be interpreted as
@ -373,6 +379,7 @@ class PlotCurveItem(GraphicsObject):
if data.dtype.kind == 'c':
raise Exception("Can not plot complex data types.")
profiler("data checks")
#self.setCacheMode(QtGui.QGraphicsItem.NoCache) ## Disabling and re-enabling the cache works around a bug in Qt 4.6 causing the cached results to display incorrectly
@ -421,6 +428,8 @@ class PlotCurveItem(GraphicsObject):
if 'antialias' in kargs:
self.opts['antialias'] = kargs['antialias']
self.opts['skipFiniteCheck'] = kargs.get('skipFiniteCheck', False)
profiler('set')
self.update()
profiler('update')
@ -458,10 +467,12 @@ class PlotCurveItem(GraphicsObject):
y[0] = self.opts['fillLevel']
y[-1] = self.opts['fillLevel']
path = fn.arrayToQPath(x, y, connect=self.opts['connect'])
return path
return fn.arrayToQPath(
x,
y,
connect=self.opts['connect'],
finiteCheck=not self.opts['skipFiniteCheck']
)
def getPath(self):
if self.path is None:

29
pyqtgraph/graphicsItems/PlotDataItem.py
View File

@ -140,6 +140,11 @@ class PlotDataItem(GraphicsObject):
at any time.
dynamicRangeLimit (float or None) Limit off-screen positions of data points at large
magnification to avoids display errors. Disabled if None.
skipFiniteCheck (bool) Optimization parameter that can speed up plot time by
telling the painter to not check and compensate for NaN
values. If set to True, and NaN values exist, the data
may not be displayed or your plot will take a
significant performance hit. Defaults to False.
identical *deprecated*
================= =====================================================================
@ -210,7 +215,7 @@ class PlotDataItem(GraphicsObject):
'clipToView': False,
'dynamicRangeLimit': 1e6,
'dynamicRangeHyst': 3.0,
'skipFiniteCheck': False,
'data': None,
}
self.setCurveClickable(kargs.get('clickable', False))
@ -605,11 +610,29 @@ class PlotDataItem(GraphicsObject):
scatterArgs = {}
if styleUpdate: # repeat style arguments only when changed
for k,v in [('pen','pen'), ('shadowPen','shadowPen'), ('fillLevel','fillLevel'), ('fillOutline', 'fillOutline'), ('fillBrush', 'brush'), ('antialias', 'antialias'), ('connect', 'connect'), ('stepMode', 'stepMode')]:
for k, v in [
('pen','pen'),
('shadowPen','shadowPen'),
('fillLevel','fillLevel'),
('fillOutline', 'fillOutline'),
('fillBrush', 'brush'),
('antialias', 'antialias'),
('connect', 'connect'),
('stepMode', 'stepMode'),
('skipFiniteCheck', 'skipFiniteCheck')
]:
if k in self.opts:
curveArgs[v] = self.opts[k]
for k,v in [('symbolPen','pen'), ('symbolBrush','brush'), ('symbol','symbol'), ('symbolSize', 'size'), ('data', 'data'), ('pxMode', 'pxMode'), ('antialias', 'antialias')]:
for k, v in [
('symbolPen','pen'),
('symbolBrush','brush'),
('symbol','symbol'),
('symbolSize', 'size'),
('data', 'data'),
('pxMode', 'pxMode'),
('antialias', 'antialias')
]:
if k in self.opts:
scatterArgs[v] = self.opts[k]

77
tests/test_functions.py
View File

@ -1,6 +1,8 @@
# -*- coding: utf-8 -*-
from collections import OrderedDict
from copy import deepcopy
from contextlib import suppress
from pyqtgraph.functions import arrayToQPath, eq
import numpy as np
import pytest
@ -245,3 +247,78 @@ def test_siParse(s, suffix, expected):
else:
with pytest.raises(expected):
pg.siParse(s, suffix=suffix)
MoveToElement = pg.QtGui.QPainterPath.ElementType.MoveToElement
LineToElement = pg.QtGui.QPainterPath.ElementType.LineToElement
@pytest.mark.parametrize(
"xs, ys, connect, expected", [
(
np.arange(6), np.arange(0, -6, step=-1), 'all', (
(MoveToElement, 0.0, 0.0),
(LineToElement, 1.0, -1.0),
(LineToElement, 2.0, -2.0),
(LineToElement, 3.0, -3.0),
(LineToElement, 4.0, -4.0),
(LineToElement, 5.0, -5.0),
)
),
(
np.arange(6), np.arange(0, -6, step=-1), 'pairs', (
(MoveToElement, 0.0, 0.0),
(LineToElement, 1.0, -1.0),
(MoveToElement, 2.0, -2.0),
(LineToElement, 3.0, -3.0),
(MoveToElement, 4.0, -4.0),
(LineToElement, 5.0, -5.0),
)
),
(
np.arange(5), np.arange(0, -5, step=-1), 'pairs', (
(MoveToElement, 0.0, 0.0),
(LineToElement, 1.0, -1.0),
(MoveToElement, 2.0, -2.0),
(LineToElement, 3.0, -3.0),
(MoveToElement, 4.0, -4.0)
)
),
(
np.arange(5), np.array([0, -1, np.NaN, -3, -4]), 'finite', (
(MoveToElement, 0.0, 0.0),
(LineToElement, 1.0, -1.0),
(LineToElement, 1.0, -1.0),
(MoveToElement, 3.0, -3.0),
(LineToElement, 4.0, -4.0)
)
),
(
np.array([0, 1, np.NaN, 3, 4]), np.arange(0, -5, step=-1), 'finite', (
(MoveToElement, 0.0, 0.0),
(LineToElement, 1.0, -1.0),
(LineToElement, 1.0, -1.0),
(MoveToElement, 3.0, -3.0),
(LineToElement, 4.0, -4.0)
)
),
(
np.arange(5), np.arange(0, -5, step=-1), np.array([0, 1, 0, 1, 0]), (
(MoveToElement, 0.0, 0.0),
(MoveToElement, 1.0, -1.0),
(LineToElement, 2.0, -2.0),
(MoveToElement, 3.0, -3.0),
(LineToElement, 4.0, -4.0)
)
)
]
)
def test_arrayToQPath(xs, ys, connect, expected):
path = arrayToQPath(xs, ys, connect=connect)
for i in range(path.elementCount()):
with suppress(NameError):
# nan elements add two line-segments, for simplicity of test config
# we can ignore the second segment
if (eq(element.x, np.nan) or eq(element.y, np.nan)):
continue
element = path.elementAt(i)
assert eq(expected[i], (element.type, element.x, element.y))