def rotateIndices2DNew(shape, rot, orig=None, dtype=N.float64):
"""
shape: 2D
rot: anti-clockwise
orig: (y, x)
return: yi, xi
"""
# FIX ME Rot is something wrong!! 081027
shape = N.asarray(shape, N.int)
if orig is None:
y, x = shape / 2.
else:
y, x = orig
print(y, x)
if not rot:
yi, xi = N.indices(shape, dtype=N.float64)
yi -= y - 0.5 # remove pix center
xi -= x - 0.5
return yi, xi
# twice as large window
# mo = N.abs(N.mod(shape, 2) + [-1,-1])
s2 = shape * 2 #+ mo # always odd for even shape, even for odd shape
yi, xi = N.indices(s2, dtype=N.float32)
mm = N.ceil(shape / 2.) #(s2 -1 - shape)//2 # offset always int
yi -= mm[0]
xi -= mm[1]
pxc = imgGeo.RotateXY((0.5, 0.5), rot) # remove pix center
yi += pxc[0]
xi += pxc[1]
y0, x0 = shape / 2. #N.ceil(shape / 2) # img center
yc = y0 - y # delta rotation center
xc = x0 - x
yi = U.trans2d(yi, None, (xc, yc, rot, 1, 0, 1))
xi = U.trans2d(xi, None, (xc, yc, rot, 1, 0, 1))
yi = U.trans2d(yi, None, (-xc, -yc, 0, 1, 0, 1))
xi = U.trans2d(xi, None, (-xc, -yc, 0, 1, 0, 1))
yi = yi.astype(dtype)
xi = xi.astype(dtype)
yi -= y
xi -= x
yi = imgFilters.cutOutCenter(yi, shape)
xi = imgFilters.cutOutCenter(xi, shape)
return yi, xi
def rotateIndices2DNew(shape, rot, orig=None, dtype=N.float64):
"""
shape: 2D
rot: anti-clockwise
orig: (y, x)
return: yi, xi
"""
# FIX ME Rot is something wrong!! 081027
shape = N.asarray(shape, N.int)
if orig is None:
y, x = shape / 2.
else:
y, x = orig
print(y,x)
if not rot:
yi,xi = N.indices(shape, dtype=N.float64)
yi -= y - 0.5 # remove pix center
xi -= x - 0.5
return yi,xi
# twice as large window
# mo = N.abs(N.mod(shape, 2) + [-1,-1])
s2 = shape * 2 #+ mo # always odd for even shape, even for odd shape
yi, xi = N.indices(s2, dtype=N.float32)
mm = N.ceil(shape / 2.)#(s2 -1 - shape)//2 # offset always int
yi -= mm[0]
xi -= mm[1]
pxc = imgGeo.RotateXY((0.5,0.5), rot) # remove pix center
yi += pxc[0]
xi += pxc[1]
y0, x0 = shape / 2. #N.ceil(shape / 2) # img center
yc = y0 - y # delta rotation center
xc = x0 - x
yi = U.trans2d(yi, None, (xc,yc,rot,1,0,1))
xi = U.trans2d(xi, None, (xc,yc,rot,1,0,1))
yi = U.trans2d(yi, None, (-xc,-yc,0,1,0,1))
xi = U.trans2d(xi, None, (-xc,-yc,0,1,0,1))
yi = yi.astype(dtype)
xi = xi.astype(dtype)
yi -= y
xi -= x
yi = imgFilters.cutOutCenter(yi, shape)
xi = imgFilters.cutOutCenter(xi, shape)
return yi, xi
def _doBilinear2D(a2d, tyx=(0,0), r=0, mag=1, anismag=1, dyx=(0,0), mr=0, b2d=None):
if b2d is None:
b2d = N.empty_like(a2d)
else:
b2d = N.ascontiguousarray(b2d)
a2d = a2d.copy() # otherwise, the following code will mess up the input
if N.any(dyx[-2:]) or mr:
temp = b2d
target = a2d
U.trans2d(target, temp, (dyx[-1], dyx[-2], mr, 1, 0, 1))
else:
temp = a2d
target = b2d
# rot mag first to make consistent with affine
magaxis = 1 # only this axis works
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
# then translate
tyx2 = N.array(tyx) # copy
tyx2[-2:] -= dyx[-2:]
if N.any(tyx2[-2:]) or mr:
U.trans2d(target, temp, (tyx2[-1], tyx2[-2], -mr, 1, 0, 1))
else:
temp[:] = target[:]
#a[z] = temp[:]
return temp
def _doBilinear2D(a2d, tyx=(0,0), r=0, mag=1, anismag=1, dyx=(0,0), mr=0, b2d=None):
if b2d is None:
b2d = N.empty_like(a2d)
else:
b2d = N.ascontiguousarray(b2d)
a2d = a2d.copy() # otherwise, the following code will mess up the input
if N.any(dyx[-2:]) or mr:
temp = b2d
target = a2d
U.trans2d(target, temp, (dyx[-1], dyx[-2], mr, 1, 0, 1))
else:
temp = a2d
target = b2d
# rot mag first to make consistent with affine
magaxis = 1 # only this axis works
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
# then translate
tyx2 = N.array(tyx) # copy
tyx2[-2:] -= dyx[-2:]
if N.any(tyx2[-2:]) or mr:
U.trans2d(target, temp, (tyx2[-1], tyx2[-2], -mr, 1, 0, 1))
else:
temp[:] = target[:]
#a[z] = temp[:]
return temp
def trans3D_bilinear(a,
tzyx=(0, 0, 0),
r=0,
mag=1,
dzyx=(0, 0, 0),
b=None,
rzy=0,
**kwds):
"""
magyx: scalar or [y,x] or [y,x, direction in degrees]
"""
a = a.copy()
ndim = a.ndim
if ndim == 2:
a = a.reshape((1, ) + a.shape)
try:
if len(magyx) == 3:
mr = magyx[-1]
magyx = magyx[:2]
else:
mr = 0
except:
mr = 0
if b is None:
b2d = N.empty_like(a[0])
dzyx = N.asarray(dzyx)
tzyx = N.asarray(tzyx)
tzyx[-2:] += dzyx[-2:]
magaxis = 1 # only this axis works
magz = 1
try:
if len(mag) == 3:
magz, magy, magx = mag
elif len(mag) == 2:
magy, magx = mag
else:
magy = magx = mag[0]
except:
magy = magx = mag
mag = magy
anismag = magx / magy
for z, a2d in enumerate(a):
if N.any(dzyx[-2:]) or mr:
temp = N.ascontiguousarray(b2d)
target = N.ascontiguousarray(a2d)
#U.trans2d(target, temp, (-dyx[1], -dyx[0], -mr, 1, 0, 1))
U.trans2d(target, temp, (-dzyx[-1], -dzyx[-2], -mr, 1, 0, 1))
else:
temp = N.ascontiguousarray(a2d)
target = N.ascontiguousarray(b2d)
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
#if rzx: # is this correct?? havn't tried yet
# target = U.nd.rotate(target, rzx, axes=(0,2), order=1, prefilter=False)
if N.any(tzyx[-2:]) or mr: #N.any(dyx) or mr:
#U.trans2d(target, temp, (dyx[1], dyx[0], mr, 1, 0, 1))
U.trans2d(target, temp, (tzyx[-1], tzyx[-2], mr, 1, 0, 1))
else:
temp[:] = target[:]
a[z] = temp[:]
if ndim == 2:
a = a[0]
elif ndim == 3 and (magz != 1 or tzyx[-3]):
at = a.T # zyx -> xyz
mag = 1 #magz
anismag = magz #magy / magz
canvas = N.empty_like(at)
target = b2d.T
for x, a2d in enumerate(at):
if dzyx[-3]:
U.trans2d(a2d, target, (0, -dyzx[-3], 0, 1, 1, 1))
else:
target = a2d
canvas[x] = U.trans2d(target, None,
(tzyx[-3], 0, rzy, mag, magaxis, anismag))
#canvas = canvas.T
a = canvas.T
return a
def rotateIndicesND(slicelist, dtype=N.float64, rot=0, mode=2):
"""
slicelist: even shape works much better than odd shape
rot: counter-clockwise, xy-plane
mode: testing different ways of doing, (1 or 2 and the same result)
return inds, LD
"""
global INDS_DIC
shape = []
LD = []
for sl in slicelist:
if isinstance(sl, slice):
shape.append(sl.stop - sl.start)
LD.append(sl.start)
shapeTuple = tuple(shape + [rot])
if shapeTuple in INDS_DIC:
inds = INDS_DIC[shapeTuple]
else:
shape = N.array(shape)
ndim = len(shape)
odd_even = shape % 2
s2 = N.ceil(shape * (2**0.5))
if mode == 1: # everything is even
s2 = N.where(s2 % 2, s2 + 1, s2)
elif mode == 2: # even & even or odd & odd
for d, s in enumerate(shape):
if (s % 2 and not s2[d] % 2) or (not s % 2 and s2[d] % 2):
s2[d] += 1
cent = s2 / 2.
dif = (s2 - shape) / 2.
dm = dif % 1
# print s2, cent, dif, dm
slc = [Ellipsis] + [
slice(int(d),
int(d) + shape[i]) for i, d in enumerate(dif)
]
# This slice is float which shift array when cutting out!!
s2 = tuple([int(ss)
for ss in s2]) # numpy array cannot use used for slice
inds = N.indices(s2, N.float32)
ind_shape = inds.shape
nz = N.product(ind_shape[:-2])
nsec = nz / float(ndim)
if ndim > 2:
inds = N.reshape(inds, (nz, ) + ind_shape[-2:])
irs = N.empty_like(inds)
for d, ind in enumerate(inds):
idx = int(d // nsec)
c = cent[idx]
if rot and inds.ndim > 2:
U.trans2d(ind - c, irs[d], (0, 0, rot, 1, 0, 1))
irs[d] += c - dif[idx]
else:
irs[d] = ind - dif[idx]
if len(ind_shape) > 2:
irs = N.reshape(irs, ind_shape)
irs = irs[slc]
if mode == 1 and N.sometrue(dm):
inds = N.empty_like(irs)
# print 'translate', dm
for d, ind in enumerate(irs):
U.trans2d(ind, inds[d], (-dm[1], -dm[0], 0, 1, 0, 1))
else:
inds = irs
INDS_DIC[shapeTuple] = inds
r_inds = N.empty_like(inds)
for d, ld in enumerate(LD):
r_inds[d] = inds[d] + ld
return r_inds, LD
def trans3D_bilinear(a, tzyx=(0,0,0), r=0, mag=1, dzyx=(0,0,0), b=None, rzy=0, **kwds):
"""
magyx: scalar or [y,x] or [y,x, direction in degrees]
"""
a = a.copy()
ndim = a.ndim
if ndim == 2:
a = a.reshape((1,)+a.shape)
try:
if len(magyx) == 3:
mr = magyx[-1]
magyx = magyx[:2]
else:
mr = 0
except:
mr = 0
if b is None:
b2d = N.empty_like(a[0])
dzyx = N.asarray(dzyx)
tzyx = N.asarray(tzyx)
tzyx[-2:] += dzyx[-2:]
magaxis = 1 # only this axis works
magz = 1
try:
if len(mag) == 3:
magz, magy, magx = mag
elif len(mag) == 2:
magy, magx = mag
else:
magy = magx = mag[0]
except:
magy = magx = mag
mag = magy
anismag = magx / magy
for z, a2d in enumerate(a):
if N.any(dzyx[-2:]) or mr:
temp = N.ascontiguousarray(b2d)
target = N.ascontiguousarray(a2d)
#U.trans2d(target, temp, (-dyx[1], -dyx[0], -mr, 1, 0, 1))
U.trans2d(target, temp, (-dzyx[-1], -dzyx[-2], -mr, 1, 0, 1))
else:
temp = N.ascontiguousarray(a2d)
target = N.ascontiguousarray(b2d)
if r or mag != 1 or anismag != 1:
U.trans2d(temp, target, (0, 0, r, mag, magaxis, anismag))
else:
target[:] = temp[:]
#if rzx: # is this correct?? havn't tried yet
# target = U.nd.rotate(target, rzx, axes=(0,2), order=1, prefilter=False)
if N.any(tzyx[-2:]) or mr:#N.any(dyx) or mr:
#U.trans2d(target, temp, (dyx[1], dyx[0], mr, 1, 0, 1))
U.trans2d(target, temp, (tzyx[-1], tzyx[-2], mr, 1, 0, 1))
else:
temp[:] = target[:]
a[z] = temp[:]
if ndim == 2:
a = a[0]
elif ndim == 3 and (magz != 1 or tzyx[-3]):
at = a.T # zyx -> xyz
mag = 1#magz
anismag = magz #magy / magz
canvas = N.empty_like(at)
target = b2d.T
for x, a2d in enumerate(at):
if dzyx[-3]:
U.trans2d(a2d, target, (0, -dyzx[-3], 0, 1, 1, 1))
else:
target = a2d
canvas[x] = U.trans2d(target, None, (tzyx[-3], 0, rzy, mag, magaxis, anismag))
#canvas = canvas.T
a = canvas.T
return a
def rotateIndicesND(slicelist, dtype=N.float64, rot=0, mode=2):
"""
slicelist: even shape works much better than odd shape
rot: counter-clockwise, xy-plane
mode: testing different ways of doing, (1 or 2 and the same result)
return inds, LD
"""
global INDS_DIC
shape = []
LD = []
for sl in slicelist:
if isinstance(sl, slice):
shape.append(sl.stop - sl.start)
LD.append(sl.start)
shapeTuple = tuple(shape+[rot])
if shapeTuple in INDS_DIC:
inds = INDS_DIC[shapeTuple]
else:
shape = N.array(shape)
ndim = len(shape)
odd_even = shape % 2
s2 = N.ceil(shape * (2**0.5))
if mode == 1: # everything is even
s2 = N.where(s2 % 2, s2 + 1, s2)
elif mode == 2: # even & even or odd & odd
for d, s in enumerate(shape):
if (s % 2 and not s2[d] % 2) or (not s % 2 and s2[d] % 2):
s2[d] += 1
cent = s2 / 2.
dif = (s2 - shape) / 2.
dm = dif % 1
# print s2, cent, dif, dm
slc = [Ellipsis] + [slice(int(d), int(d)+shape[i]) for i, d in enumerate(dif)]
# This slice is float which shift array when cutting out!!
s2 = tuple([int(ss) for ss in s2]) # numpy array cannot use used for slice
inds = N.indices(s2, N.float32)
ind_shape = inds.shape
nz = N.product(ind_shape[:-2])
nsec = nz / float(ndim)
if ndim > 2:
inds = N.reshape(inds, (nz,)+ind_shape[-2:])
irs = N.empty_like(inds)
for d, ind in enumerate(inds):
idx = int(d//nsec)
c = cent[idx]
if rot and inds.ndim > 2:
U.trans2d(ind - c, irs[d], (0,0,rot,1,0,1))
irs[d] += c - dif[idx]
else:
irs[d] = ind - dif[idx]
if len(ind_shape) > 2:
irs = N.reshape(irs, ind_shape)
irs = irs[slc]
if mode == 1 and N.sometrue(dm):
inds = N.empty_like(irs)
# print 'translate', dm
for d, ind in enumerate(irs):
U.trans2d(ind, inds[d], (-dm[1], -dm[0], 0, 1, 0, 1))
else:
inds = irs
INDS_DIC[shapeTuple] = inds
r_inds = N.empty_like(inds)
for d, ld in enumerate(LD):
r_inds[d] = inds[d] + ld
return r_inds, LD