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Merge pull request #1965 from pijyoi/qpath_chunks

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perform arrayToQPath in chunks
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Ogi Moore 2021-08-13 10:37:14 -07:00 committed by GitHub
commit e752336b55
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2 changed files with 226 additions and 98 deletions
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30
benchmarks/arrayToQPath.py Normal file
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@ -0,0 +1,30 @@
import numpy as np
import pyqtgraph as pg
rng = np.random.default_rng(12345)
class _TimeSuite:
params = ([10_000, 100_000, 1_000_000], ['all', 'finite', 'pairs', 'array'])
def setup(self, nelems, connect):
self.xdata = np.arange(nelems, dtype=np.float64)
self.ydata = rng.standard_normal(nelems, dtype=np.float64)
if connect == 'array':
self.connect_array = np.ones(nelems, dtype=bool)
if self.have_nonfinite:
self.ydata[::5000] = np.nan
def time_test(self, nelems, connect):
if connect == 'array':
connect = self.connect_array
pg.arrayToQPath(self.xdata, self.ydata, connect=connect)
class TimeSuiteAllFinite(_TimeSuite):
def __init__(self):
super().__init__()
self.have_nonfinite = False
class TimeSuiteWithNonFinite(_TimeSuite):
def __init__(self):
super().__init__()
self.have_nonfinite = True

276
pyqtgraph/functions.py
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@ -1870,6 +1870,156 @@ def downsample(data, n, axis=0, xvals='subsample'):
return MetaArray(d2, info=info)
def _compute_backfill_indices(isfinite):
# 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
# credit: Divakar https://stackoverflow.com/a/41191127/643629
mask = ~isfinite
idx = np.arange(len(isfinite))
idx[mask] = -1
np.maximum.accumulate(idx, out=idx)
first = np.searchsorted(idx, 0)
if first < len(isfinite):
# Replace all non-finite entries from beginning of arr with the first finite one
idx[:first] = first
return idx
else:
return None
def _arrayToQPath_all(x, y, finiteCheck):
n = x.shape[0]
if n == 0:
return QtGui.QPainterPath()
backfill_idx = None
if finiteCheck:
isfinite = np.isfinite(x) & np.isfinite(y)
if not np.all(isfinite):
backfill_idx = _compute_backfill_indices(isfinite)
chunksize = 10000
numchunks = (n + chunksize - 1) // chunksize
minchunks = 3
if numchunks < minchunks:
# too few chunks, batching would be a pessimization
poly = create_qpolygonf(n)
arr = ndarray_from_qpolygonf(poly)
if backfill_idx is None:
arr[:, 0] = x
arr[:, 1] = y
else:
arr[:, 0] = x[backfill_idx]
arr[:, 1] = y[backfill_idx]
path = QtGui.QPainterPath()
if hasattr(path, 'reserve'): # Qt 5.13
path.reserve(n)
path.addPolygon(poly)
return path
# at this point, we have numchunks >= minchunks
path = QtGui.QPainterPath()
if hasattr(path, 'reserve'): # Qt 5.13
path.reserve(n)
subpoly = QtGui.QPolygonF()
subpath = None
for idx in range(numchunks):
sl = slice(idx*chunksize, min((idx+1)*chunksize, n))
currsize = sl.stop - sl.start
if currsize != subpoly.size():
if hasattr(subpoly, 'resize'):
subpoly.resize(currsize)
else:
subpoly.fill(QtCore.QPointF(), currsize)
subarr = ndarray_from_qpolygonf(subpoly)
if backfill_idx is None:
subarr[:, 0] = x[sl]
subarr[:, 1] = y[sl]
else:
bfv = backfill_idx[sl] # view
subarr[:, 0] = x[bfv]
subarr[:, 1] = y[bfv]
if subpath is None:
subpath = QtGui.QPainterPath()
subpath.addPolygon(subpoly)
path.connectPath(subpath)
if hasattr(subpath, 'clear'): # Qt 5.13
subpath.clear()
else:
subpath = None
return path
def _arrayToQPath_finite(x, y, isfinite=None):
n = x.shape[0]
if n == 0:
return QtGui.QPainterPath()
if isfinite is None:
isfinite = np.isfinite(x) & np.isfinite(y)
path = QtGui.QPainterPath()
if hasattr(path, 'reserve'): # Qt 5.13
path.reserve(n)
sidx = np.nonzero(~isfinite)[0] + 1
# note: the chunks are views
xchunks = np.split(x, sidx)
ychunks = np.split(y, sidx)
chunks = list(zip(xchunks, ychunks))
# create a single polygon able to hold the largest chunk
maxlen = max(len(chunk) for chunk in xchunks)
subpoly = create_qpolygonf(maxlen)
subarr = ndarray_from_qpolygonf(subpoly)
# resize and fill do not change the capacity
if hasattr(subpoly, 'resize'):
subpoly_resize = subpoly.resize
else:
# PyQt will be less efficient
subpoly_resize = lambda n, v=QtCore.QPointF() : subpoly.fill(v, n)
# notes:
# - we backfill the non-finite in order to get the same image as the
# old codepath on the CI. somehow P1--P2 gets rendered differently
# from P1--P2--P2
# - we do not generate MoveTo(s) that are not followed by a LineTo,
# thus the QPainterPath can be different from the old codepath's
# all chunks except the last chunk have a trailing non-finite
for xchunk, ychunk in chunks[:-1]:
lc = len(xchunk)
if lc <= 1:
# len 1 means we have a string of non-finite
continue
subpoly_resize(lc)
subarr[:lc, 0] = xchunk
subarr[:lc, 1] = ychunk
subarr[lc-1] = subarr[lc-2] # fill non-finite with its neighbour
path.addPolygon(subpoly)
# handle last chunk, which is either all-finite or empty
for xchunk, ychunk in chunks[-1:]:
lc = len(xchunk)
if lc <= 1:
# can't draw a line with just 1 point
continue
subpoly_resize(lc)
subarr[:lc, 0] = xchunk
subarr[:lc, 1] = ychunk
path.addPolygon(subpoly)
return path
def arrayToQPath(x, y, connect='all', finiteCheck=True):
"""
Convert an array of x,y coordinates to QPainterPath as efficiently as
@ -1925,38 +2075,42 @@ def arrayToQPath(x, y, connect='all', finiteCheck=True):
This binary format may change in future versions of Qt
"""
path = QtGui.QPainterPath()
n = x.shape[0]
if n == 0:
return path
return QtGui.QPainterPath()
connect_array = None
if isinstance(connect, np.ndarray):
# make connect argument contain only str type
connect_array, connect = connect, 'array'
use_qpolygonf = connect == 'all'
isfinite = None
if connect == 'finite':
isfinite = np.isfinite(x) & np.isfinite(y)
if not finiteCheck:
# if user specified to skip finite check, then that forces use_qpolygonf
use_qpolygonf = True
else:
# if user specified to skip finite check, then we skip the heuristic
return _arrayToQPath_finite(x, y)
# otherwise use a heuristic
# if non-finite aren't that many, then use_qpolyponf
isfinite = np.isfinite(x) & np.isfinite(y)
nonfinite_cnt = n - np.sum(isfinite)
if nonfinite_cnt / n < 2 / 100:
use_qpolygonf = True
finiteCheck = False
if nonfinite_cnt == 0:
all_isfinite = nonfinite_cnt == 0
if all_isfinite:
# delegate to connect='all'
connect = 'all'
if use_qpolygonf:
backstore = create_qpolygonf(n)
arr = np.frombuffer(ndarray_from_qpolygonf(backstore), dtype=[('x', 'f8'), ('y', 'f8')])
finiteCheck = False
elif nonfinite_cnt / n < 2 / 100:
return _arrayToQPath_finite(x, y, isfinite)
else:
# delegate to connect=ndarray
# finiteCheck=True, all_isfinite=False
connect = 'array'
connect_array = isfinite
if connect == 'all':
return _arrayToQPath_all(x, y, finiteCheck)
backstore = QtCore.QByteArray()
backstore.resize(4 + n*20 + 8) # contents uninitialized
backstore.replace(0, 4, struct.pack('>i', n))
@ -1965,95 +2119,39 @@ def arrayToQPath(x, y, connect='all', finiteCheck=True):
arr = np.frombuffer(backstore, dtype=[('c', '>i4'), ('x', '>f8'), ('y', '>f8')],
count=n, offset=4)
# Fill array with vertex values
arr['x'] = x
arr['y'] = y
# 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
backfill_idx = None
if finiteCheck:
if isfinite is None:
isfinite = np.isfinite(x) & np.isfinite(y)
if not np.all(isfinite):
# credit: Divakar https://stackoverflow.com/a/41191127/643629
mask = ~isfinite
idx = np.arange(len(x))
idx[mask] = -1
np.maximum.accumulate(idx, out=idx)
first = np.searchsorted(idx, 0)
if first < len(x):
# Replace all non-finite entries from beginning of arr with the first finite one
idx[:first] = first
arr[:] = arr[:][idx]
all_isfinite = np.all(isfinite)
if not all_isfinite:
backfill_idx = _compute_backfill_indices(isfinite)
if backfill_idx is None:
arr['x'] = x
arr['y'] = y
else:
arr['x'] = x[backfill_idx]
arr['y'] = y[backfill_idx]
# decide which points are connected by lines
if connect == 'all':
path.addPolygon(backstore)
return path
elif connect == 'pairs':
if connect == 'pairs':
arr['c'][0::2] = 0
arr['c'][1::2] = 1 # connect every 2nd point to every 1st one
elif connect == 'finite':
elif connect == 'array':
# 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 not use_qpolygonf:
arr['c'][:1] = 0 # the first vertex has no previous vertex to connect
arr['c'][1:] = isfinite[:-1]
else:
sidx = np.nonzero(~isfinite)[0] + 1
chunks = np.split(arr, sidx) # note: the chunks are views
# create a single polygon able to hold the largest chunk
maxlen = max(len(chunk) for chunk in chunks)
subpoly = create_qpolygonf(maxlen)
subarr = np.frombuffer(ndarray_from_qpolygonf(subpoly), dtype=arr.dtype)
# resize and fill do not change the capacity
if hasattr(subpoly, 'resize'):
subpoly_resize = subpoly.resize
else:
# PyQt will be less efficient
subpoly_resize = lambda n, v=QtCore.QPointF() : subpoly.fill(v, n)
# notes:
# - we backfill the non-finite in order to get the same image as the
# old codepath on the CI. somehow P1--P2 gets rendered differently
# from P1--P2--P2
# - we do not generate MoveTo(s) that are not followed by a LineTo,
# thus the QPainterPath can be different from the old codepath's
# all chunks except the last chunk have a trailing non-finite
for chunk in chunks[:-1]:
lc = len(chunk)
if lc <= 1:
# len 1 means we have a string of non-finite
continue
subpoly_resize(lc)
subarr[:lc] = chunk
subarr[lc-1] = subarr[lc-2] # fill non-finite with its neighbour
path.addPolygon(subpoly)
# handle last chunk, which is either all-finite or empty
for chunk in chunks[-1:]:
lc = len(chunk)
if lc <= 1:
# can't draw a line with just 1 point
continue
subpoly_resize(lc)
subarr[:lc] = chunk
path.addPolygon(subpoly)
return path
elif connect == 'array':
arr['c'][:1] = 0 # the first vertex has no previous vertex to connect
arr['c'][1:] = connect_array[:-1]
else:
raise ValueError('connect argument must be "all", "pairs", "finite", or array')
path = QtGui.QPainterPath()
if hasattr(path, 'reserve'): # Qt 5.13
path.reserve(n)
ds = QtCore.QDataStream(backstore)
ds >> path
return path