def pad_mapByPixel(self, lessI, moreI, lessJ, moreJ, lessK, moreK):
lessI = int(lessI)
moreI = int(moreI)
lessJ = int(lessJ)
moreJ = int(moreJ)
lessK = int(lessK)
moreK = int(moreK)
assert lessI >= 0
assert moreI >= 0
assert lessJ >= 0
assert moreJ >= 0
assert lessK >= 0
assert moreK >= 0
#
tmp = self._new()
tmp.nxstart = self.nxstart - (lessI + moreI - 1)
tmp.nystart = self.nystart - (lessJ + moreJ - 1)
tmp.nzstart = self.nzstart - (lessK + moreK - 1)
tmp.ncstart = tmp.nxstart
tmp.nrstart = tmp.nystart
tmp.nsstart = tmp.nzstart
#
chargeArray3d = ext.padZero(self.chargeArray3d, lessI, moreI, lessJ, moreJ, lessK, moreK)
tmp.lx, tmp.ly, tmp.lz = chargeArray3d.shape
tmp.nc, tmp.nr, tmp.ns = chargeArray3d.shape
tmp.chargeArray = chargeArray3d.flatten('F')
#
tmp.cartArray = ext.build_cart(tmp.lx, tmp.ly, tmp.lz,
tmp.nxstart, tmp.nystart, tmp.nzstart,
tmp.xres, tmp.yres, tmp.zres)
#
return tmp
def combine_maps(emap1, emap2):
"""
Loop over all the grid points of emap1, and interpolate them into grid points of emap2.
"""
# (1) Find Min/Max cartesian values of emap1 and emap2
xm1, ym1, zm1 = emap1.cartArray.min(axis=0)
xm2, ym2, zm2 = emap2.cartArray.min(axis=0)
#
xmin = xm1 if xm1 < xm2 else xm2
ymin = ym1 if ym1 < ym2 else ym2
zmin = zm1 if zm1 < zm2 else zm2
#
xm1, ym1, zm1 = emap1.cartArray.max(axis=0)
xm2, ym2, zm2 = emap2.cartArray.max(axis=0)
#
xmax = xm1 if xm1 > xm2 else xm2
ymax = ym1 if ym1 > ym2 else ym2
zmax = zm1 if zm1 > zm2 else zm2
# (2) create valid metadata
newmap = emap2._new()
newmap.nxstart = np.int(np.floor(xmin/emap2.xres)) - 1
newmap.nystart = np.int(np.floor(ymin/emap2.yres)) - 1
newmap.nzstart = np.int(np.floor(zmin/emap2.zres)) - 1
newmap.lx = np.int(np.ceil(xmax/emap2.xres)) - newmap.nxstart + 1
newmap.ly = np.int(np.ceil(ymax/emap2.yres)) - newmap.nystart + 1
newmap.lz = np.int(np.ceil(zmax/emap2.zres)) - newmap.nzstart + 1
newmap.nc = newmap.lx
newmap.nr = newmap.ly
newmap.ns = newmap.lz
newmap.ncstart = newmap.nxstart
newmap.nrstart = newmap.nystart
newmap.nsstart = newmap.nzstart
# (3) Create a new blank 3d array using the min/max cartesian values
# (4) copy data from emap2
lessX = emap2.nxstart - newmap.nxstart
moreX = newmap.lx + newmap.nxstart - (emap2.lx + emap2.nxstart)
lessY = emap2.nystart - newmap.nystart
moreY = newmap.ly + newmap.nystart - (emap2.ly + emap2.nystart)
lessZ = emap2.nzstart - newmap.nzstart
moreZ = newmap.lz + newmap.nzstart - (emap2.lz + emap2.nzstart)
chargeArray = ext.padZero(emap2.chargeArray3d,
lessX, moreX, lessY, moreY, lessZ, moreZ)
newmap.cartArray = ext.build_cart(newmap.lx, newmap.ly, newmap.lz,
newmap.nxstart, newmap.nystart, newmap.nzstart,
newmap.xres, newmap.yres, newmap.zres)
# (5) interpolate data from emap1
newmap.chargeArray = ext.interpolate(emap1.cartArray, emap1.chargeArray, chargeArray,
newmap.xres, newmap.yres, newmap.zres).flatten('F')
return newmap
def get_lap(emap):
rho_1 = ext.padZero(emap.chargeArray3d, 1, 1, 1, 1, 1, 1)
tmpArray = np.zeros(emap.lx * emap.ly * emap.lz, dtype=np.float64)
iterator = ( (i, j, k) for k in xrange(1, 1+emap.lz)
for j in xrange(1, 1+emap.ly) for i in xrange(1, 1+emap.lx) )
for n, (i, j, k) in enumerate(iterator):
tmp = np.float64(0)
tmp += rho_1[i+1, j, k]
tmp += rho_1[i-1, j, k]
tmp += rho_1[i, j+1, k]
tmp += rho_1[i, j-1, k]
tmp += rho_1[i, j, k+1]
tmp += rho_1[i, j, k-1]
tmp -= 6*rho_1[i, j, k]
tmpArray[n] = tmp
return tmpArray
def get_core(emap):
# initialize
chargeMatrix = emap.chargeArray3d
lapMatrix = emap.laplacianArray3d
rhocut = emap.rhocut
tmpArray = np.ones((emap.lx-2, emap.ly-2, emap.lz-2), dtype=np.int)
tmpArray = ext.padZero(tmpArray, 1)
#
def minF(i, j, k):
tmp = []
tmp.append(tmpArray[i+1, j, k])
tmp.append(tmpArray[i-1, j, k])
tmp.append(tmpArray[i, j+1, k])
tmp.append(tmpArray[i, j-1, k])
tmp.append(tmpArray[i, j, k+1])
tmp.append(tmpArray[i, j, k-1])
return min(tmp)
#
iteration = 1
while True:
print "Iteration: %d" % iteration
nextArray = tmpArray.copy()
iterator = ( (i, j, k) for k in xrange(1, emap.lz-1) for j in xrange(1, emap.ly-1) for i in xrange(1, emap.lx-1) )
for i, j, k in iterator:
if chargeMatrix[i, j, k] <= rhocut and minF(i, j, k) == 0:
nextArray[i, j, k] = 0
elif lapMatrix[i, j, k] > 0 and minF(i, j, k) == 0:
nextArray[i, j, k] = 0
else:
nextArray[i, j, k] = minF(i, j, k) + 1
#
if (tmpArray == nextArray).all():
return tmpArray.flatten('F')
else:
iteration += 1
tmpArray = nextArray