def testsmall(self):
''' sse / avx issue for tiny? '''
# print("testsmall, fixme, segfault/infinite loop so no CI")
im = np.array([[0, 0, 0, 0, 0], [0, 2, 0, 0, 0], [0, 1, 1, 0, 0],
[0, 0, 0, 0, 0]], np.float32)
la = np.empty(im.shape, 'i')
wk = np.empty(im.shape, 'b')
localmaxlabel(im, la, wk)
self.assertEqual(la[1, 1], 1)
def testbug(self):
''' case caught with image from Mariana Mar Lucas,
caused a segfault'''
im = np.array([[0, 0, 0, 0, 0, 0, 0, 0], [0, 2, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0]],
np.float32)
la = np.empty(im.shape, 'i')
wk = np.empty(im.shape, 'b')
localmaxlabel(im, la, wk)
self.assertEqual(la[1, 1], 1)
def test3(self):
# print("in test 2")
im = make_test_image(N=2048)
l1 = np.zeros(im.shape, np.int32)
l2 = np.zeros(im.shape, np.int32)
l3 = np.zeros(im.shape, np.int32)
wk = np.zeros(im.shape, np.int8)
start = time.time()
for i in range(10):
npks = localmaxlabel(im, l1, wk)
end = time.time()
npks = localmaxlabel(im, l1, wk, 10)
ctime = (end - start) * 100.
start = time.time()
for i in range(10):
npks = localmaxlabel(im, l2, wk, 1)
end = time.time()
npks = localmaxlabel(im, l2, wk, 11)
stime = (end - start) * 100.
start = time.time()
for i in range(10):
npks = localmaxlabel(im, l3, wk, 2)
end = time.time()
npks = localmaxlabel(im, l3, wk, 12)
atime = (end - start) * 100.
if not (l2 == l3).all():
import pylab as pl
pl.imshow(l2)
pl.imshow(l3)
pl.show()
self.assertEqual((l2 == l3).all(), True)
self.assertEqual((l1 == l3).all(), True)
print("Timing 2048 c %.3f ms, sse %.3f, avx %.3f" %
(ctime, stime, atime))
def test1( self):
im = make_test_image()
start = time.time()
l1 = localmax(im)
end = time.time()
pytime = (end-start)*1000.
l2 = np.zeros(im.shape,np.int32)
wk = np.zeros(im.shape,np.int8)
start = time.time()
npks = localmaxlabel(im, l2 , wk )
end=time.time()
ctime = (end-start)*1000.
self.assertEqual( (l2==l1).all(), True )
print("Timing python %.3f ms, c %.3f ms"%(pytime,ctime))
def test3(self):
# print("in test 2")
im = make_test_image(N=2048)
l0 = np.zeros(im.shape, np.int32)
l1 = np.zeros(im.shape, np.int32)
wp = np.zeros(im.shape, np.int32)
wk = np.zeros(im.shape, np.int8)
N = 4
if GOTNUMBA:
npks = localmax(im, l0, wp)
start = timer()
for i in range(N):
npks = localmax(im, l0, wp)
end = timer()
ptime = (end - start) * 1000. / N
else:
ptime = np.nan
npks = localmaxlabel(im, l1, wk)
start = timer()
for i in range(N):
npks = localmaxlabel(im, l1, wk)
end = timer()
ctime = (end - start) * 1000. / N
print("Timing 2048 numba %.3f ms c %.3f ms" % (ptime, ctime))
def demo():
import pylab as pl
im = make_test_image()
l1 = localmax(im)
l2 = np.zeros(im.shape, np.int32)
wk = np.zeros(im.shape, np.int8)
npks = localmaxlabel(im, l2, wk, cpu=0)
ax1 = pl.subplot(2, 2, 1)
pl.imshow(im)
pl.xlim(0, im.shape[0])
pl.ylim(0, im.shape[1])
ax1 = pl.subplot(2, 2, 2, sharex=ax1, sharey=ax1)
pl.imshow((l1 * 13.0) % 37)
pl.xlim(0, im.shape[0])
pl.ylim(0, im.shape[1])
ax1 = pl.subplot(2, 2, 3, sharex=ax1, sharey=ax1)
pl.imshow((l2 * 13.0) % 37)
pl.xlim(0, im.shape[0])
pl.ylim(0, im.shape[1])
pl.show()
def test1(self):
im = self.im
if self.dopy:
l1 = np.zeros(im.shape, np.int32)
wp = np.zeros(im.shape, np.int32)
start = timer()
localmax(im, l1, wp)
end = timer()
pytime = (end - start) * 1000.
l = [
l1,
]
wk = [
0,
]
times = [
pytime,
]
names = [
"python",
]
for cpu, name in [(0, "ansi"), (1, "sse2"), (2, "avx2")]:
li = np.zeros(im.shape, np.int32)
wi = np.zeros(im.shape, np.int8)
start = timer()
# print("cpu",cpu)
npks = localmaxlabel(im.copy(), li, wi, cpu=cpu)
end = timer()
ctime = (end - start) * 1000.
l.append(li)
times.append(ctime)
names.append(name)
lref = l[0]
print("Timing", end=" ")
for i in range(len(names)):
print("%s %.3f ms" % (names[i], times[i]), end=" ")
print()
for li in l[1:]:
self.assertTrue((lref == l1).all())
def bench(int_im):
im = int_im
float_im = int_im.astype(np.float32)
labelc = np.zeros(im.shape, np.int32)
labelm = np.zeros(im.shape, np.int32)
work = np.zeros(im.shape, np.int8)
end0 = time.time()
nc = cImageD11.connectedpixels(float_im, labelc, 1000)
end1 = time.time()
rc = cImageD11.blobproperties(float_im, labelc, nc, 0)
cImageD11.blob_moments(rc)
end2 = time.time()
print("cptime", nc,
"%.3f %.3f" % ((end1 - end0) * 1000, (end2 - end1) * 1000))
wfloatim = np.where(float_im > 1000, float_im, 0)
#import scipy.ndimage as ndi
#wfloatim= (float_im - ndi.gaussian_filter( float_im , 32)).clip(0,1e9)
end0 = time.time()
nw = cImageD11.localmaxlabel(wfloatim, labelm, work)
end1 = time.time()
rw = cImageD11.blobproperties(wfloatim, labelm, nw, 0)
cImageD11.blob_moments(rw)
end2 = time.time()
print("lmtime", nw,
"%.3f %.3f" % ((end1 - end0) * 1000, (end2 - end1) * 1000))
if 0:
pks = np.array(pks).T
import pylab as pl
pl.imshow(pl.log(float_im),
origin='lower',
interpolation='nearest',
aspect='auto')
pl.plot(pks[1], pks[0], "r+", label="ideal")
pl.plot(rc[:, cImageD11.f_raw],
rc[:, cImageD11.s_raw],
"wx",
label="connect")
pl.plot(rw[:, cImageD11.f_raw],
rw[:, cImageD11.s_raw],
"ko",
label="watershed",
markerfacecolor='None')
pl.legend()
pl.figure()
dci = [
np.sqrt(np.min((pks[1] - x)**2 + (pks[0] - y)**2))
for x, y in zip(rc[:, cImageD11.f_raw], rc[:, cImageD11.s_raw])
]
pl.subplot(121)
pl.plot(rc[:, cImageD11.s_raw], dci, '.', label="sconnected")
pl.plot(rc[:, cImageD11.f_raw], dci, '.', label="fconnected")
dwi = [
np.sqrt(np.min((pks[1] - x)**2 + (pks[0] - y)**2))
for x, y in zip(rw[:, cImageD11.f_raw], rw[:, cImageD11.s_raw])
]
pl.subplot(122)
pl.plot(rw[:, cImageD11.s_raw], dwi, '.', label="slocalmax")
pl.plot(rw[:, cImageD11.f_raw], dwi, '.', label="flocalmax")
pl.legend()
pl.show()
float_im=int_im.astype(np.float32)
labelc = np.zeros( im.shape, np.int32 )
labelm = np.zeros( im.shape, np.int32 )
work = np.zeros( im.shape, np.int8 )
end0 = time.time()
nc = cImageD11.connectedpixels( float_im, labelc, 1000 )
end1 = time.time()
rc = cImageD11.blobproperties( float_im, labelc, nc, 0 )
cImageD11.blob_moments(rc)
end2 = time.time()
print(nc,"%.3f %.3f"%((end1-end0)*1000,(end2-end1)*1000))
wfloatim = np.where( float_im > 1000, float_im, float_im)
end0 = time.time()
nw = cImageD11.localmaxlabel( wfloatim, labelm, work )
end1 = time.time()
rw = cImageD11.blobproperties( wfloatim, labelm, nw, 0 )
cImageD11.blob_moments(rw)
end2 = time.time()
print(nw,"%.3f %.3f"%((end1-end0)*1000,(end2-end1)*1000))
if 0:
pks=np.array(pks).T
import pylab as pl
pl.imshow( pl.log(float_im), origin='lower',
interpolation='nearest', aspect='auto')
pl.plot( pks[1], pks[0],"+",label="ideal" )
pl.plot( rc[:,cImageD11.f_raw],rc[:,cImageD11.s_raw],"x",
label="connect")
pl.plot( rw[:,cImageD11.f_raw],rw[:,cImageD11.s_raw],"o",
label="watershed",
[0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0]],
np.float32)
la = np.empty(im.shape, 'i')
wk = np.empty(im.shape, 'b')
localmaxlabel(im, la, wk, cpu)
self.assertEqual(la[1, 1], 1)
def testsmall(self):
''' sse / avx issue for tiny? '''
# print("testsmall, fixme, segfault/infinite loop so no CI")
for cpu in [0, 1, 2]: #11,12]:
im = np.array([[0, 0, 0, 0, 0], [0, 2, 0, 0, 0], [0, 1, 1, 0, 0],
[0, 0, 0, 0, 0]], np.float32)
la = np.empty(im.shape, 'i')
wk = np.empty(im.shape, 'b')
localmaxlabel(im, la, wk, cpu)
self.assertEqual(la[1, 1], 1)
if __name__ == "__main__":
import sys
if len(sys.argv) > 1:
demo()
unittest.main()
else:
im = make_test_image(256)
l2 = np.zeros(im.shape, 'i')
wk = np.zeros(im.shape, np.uint8)
npks = localmaxlabel(im, l2, wk)
