def read_CCP4FileWXW(filename):
# Instantize!
tmp = EMap()
with open(filename, mode='rb') as fpointer:
tmp.nc, tmp.nr, tmp.ns = struct.unpack('iii', fpointer.read(12))
tmp.mode = struct.unpack('i', fpointer.read(4))[0]
tmp.ncstart, tmp.nrstart, tmp.nsstart = struct.unpack('iii', fpointer.read(12))
tmp.nx, tmp.ny, tmp.nz = struct.unpack('iii', fpointer.read(12))
tmp.xlen, tmp.ylen, tmp.zlen = struct.unpack('fff', fpointer.read(12))
tmp.alpha, tmp.beta, tmp.gamma = struct.unpack('fff', fpointer.read(12))
tmp.mapc, tmp.mapr, tmp.maps = struct.unpack('iii', fpointer.read(12))
tmp.amin, tmp.amax, tmp.amean = struct.unpack('fff', fpointer.read(12))
tmp.ispg = struct.unpack('i', fpointer.read(4))[0]
tmp.nsymbt = struct.unpack('i', fpointer.read(4))[0]
tmp.lskflg = struct.unpack('i', fpointer.read(4))[0]
tmp.skwmat = struct.unpack('f'*9, fpointer.read(36))
tmp.skwtrn = struct.unpack('fff', fpointer.read(12))
tmp.extra = struct.unpack('i'*15, fpointer.read(60))
tmp.maplabel = ''.join(struct.unpack('cccc', fpointer.read(4)))
tmp.machst = struct.unpack('cccc', fpointer.read(4))
tmp.arms = struct.unpack('f', fpointer.read(4))[0]
tmp.nlabl = struct.unpack('i', fpointer.read(4))[0]
tmp.label = []
for i in range(10):
tmp.label.append(''.join(struct.unpack('c'*80, fpointer.read(80))))
# TODO -- This needs a testcase to debug it!
tmp.symmetry = []
for i in range(tmp.nsymbt/80):
tmp.symmetry.append(''.join(struct.unpack('c'*80, fpointer.read(80))))
# TODO
rawArray = numpy.array(struct.unpack('f'*tmp.nc*tmp.nr*tmp.ns,
fpointer.read(4*tmp.nc*tmp.nr*tmp.ns)))
##
## done with file reading
##
# Map from column/row/section space to x/y/z space
if tmp.mapc == 1 and tmp.mapr == 2 and tmp.maps == 3:
tmp.lx = tmp.nc
tmp.ly = tmp.nr
tmp.lz = tmp.ns
tmp.nxstart = tmp.ncstart
tmp.nystart = tmp.nrstart
tmp.nzstart = tmp.nsstart
def transpose(i, j, k):
return (i, j, k)
def reMap(i, j, k):
return i + j * tmp.nc + k * tmp.nc * tmp.nr
elif tmp.mapc == 1 and tmp.mapr == 3 and tmp.maps == 2:
tmp.lx = tmp.nc
tmp.ly = tmp.ns
tmp.lz = tmp.nr
tmp.nxstart = tmp.ncstart
tmp.nystart = tmp.nsstart
tmp.nzstart = tmp.nrstart
def transpose(i, j, k):
return (i, k, j)
def reMap(i, j, k):
return i + k * tmp.nc + j * tmp.nc * tmp.ns
elif tmp.mapc == 2 and tmp.mapr == 1 and tmp.maps == 3:
tmp.lx = tmp.nr
tmp.ly = tmp.nc
tmp.lz = tmp.ns
tmp.nxstart = tmp.nrstart
tmp.nystart = tmp.ncstart
tmp.nzstart = tmp.nsstart
def transpose(i, j, k):
return (j, i, k)
def reMap(i, j, k):
return j + i * tmp.nr + k * tmp.nr * tmp.nc
elif tmp.mapc == 2 and tmp.mapr == 3 and tmp.maps == 1:
tmp.lx = tmp.ns
tmp.ly = tmp.nc
tmp.lz = tmp.nr
tmp.nxstart = tmp.nsstart
tmp.nystart = tmp.ncstart
tmp.nzstart = tmp.nrstart
def transpose(i, j, k):
return (j, k, i)
def reMap(i, j, k):
return j + k * tmp.nr + i * tmp.nr * tmp.ns
elif tmp.mapc == 3 and tmp.mapr == 1 and tmp.maps == 2:
tmp.lx = tmp.nr
tmp.ly = tmp.ns
tmp.lz = tmp.nc
tmp.nxstart = tmp.nrstart
tmp.nystart = tmp.nsstart
tmp.nzstart = tmp.ncstart
def transpose(i, j, k):
return (k, i, j)
def reMap(i, j, k):
return k + i * tmp.ns + j * tmp.ns * tmp.nc
elif tmp.mapc == 3 and tmp.mapr == 2 and tmp.maps == 1:
tmp.lx = tmp.ns
tmp.ly = tmp.nr
tmp.lz = tmp.nc
tmp.nxstart = tmp.nsstart
tmp.nystart = tmp.nrstart
tmp.nzstart = tmp.ncstart
def transpose(i, j, k):
return (k, j, i)
def reMap(i, j, k):
return k + j * tmp.ns + i * tmp.ns * tmp.nr
else:
raise IOError("NULL: Error with Axis Remapping Data.")
# Unroll electron density data into flat array
tmp.chargeArray = numpy.zeros(tmp.lx * tmp.ly * tmp.lz)
for n in range(len(rawArray)):
k = n // ( taco.nc * taco.nr)
j = (n % ( taco.nc * taco.nr )) // taco.nc
i = ((n % ( taco.nc * taco.nr )) % taco.nc)
tmp.chargeArray[n] = rawArray[reMap(i, j, k)]
# fin!
return tmp
def read_CCP4File(filename):
"""
ccp4 file specification as per --
http://www.ccp4.ac.uk/html/maplib.html#description
# HEADER VARS
My Var WXW Var Comment
---------------- ---------------- ------------------------
nc, nr, ns lx, ly, lz # of Col/Row/Sect in array
mode mode should be `2` -> Real
ncstart, nrstart, ... nsx, nsy, nsz number of first col in map
nx, ny, nz mx, my, mz number of interval in unit cell
xlen, ylen, zlen xlen, ylen, zlen unit cell dim, in Ang
alpha, beta, gamma alpha, beta, gamma unit cell angles, in Deg
mapc, mapr, maps mapc, mapr, maps col/row/sec -> x/y/z mapping
amin, amax, amean amin, amax, amean eDensity statistics
ispg ispg space group number
nsymbt nsymbt number of bytes for storing sym op
lskflg lskflg flag for skew transformation (=0 none,
=1 if it follows in `symmetry`
skwmat skwmat skew matrix S (in order S11, S12, S13,
S21, etc) if `lskflg` != 0
skwtrn skwtrn skew translation t if `lskflg` != 0
extra extra UNUSED
maplabel maplabel the string 'MAP '
machst machst machine stamp - indicates what wrote file
arms arms rms dev of map from mean density
nlabl # of labels being used
label a list of 10 labels, 80 characters each
symmetry TODO
# NON HEADER VARS
chargeArray A `numpy.array` of dimension lx, ly, lz, whose values are
electron density in coulomb
transposeTuple a tuple of mapc, mapr, maps -- only zero indexed
lx, ly, lz # of x, y, z in array -- it has been mapped from nc, nr, ns
and correctly permutated using mapc, mapr, maps
nxstart, nystart, ... Starting pixel index in the x, y, z directions -- it has been
mapped from ncstart, nrstart, nsstart and correctly permuted
"""
import numpy
# Instantize!
tmp = EMap()
with open(filename, mode='rb') as fpointer:
tmp.nc, tmp.nr, tmp.ns = struct.unpack('iii', fpointer.read(12))
tmp.mode = struct.unpack('i', fpointer.read(4))[0]
tmp.ncstart, tmp.nrstart, tmp.nsstart = struct.unpack('iii', fpointer.read(12))
tmp.nx, tmp.ny, tmp.nz = struct.unpack('iii', fpointer.read(12))
tmp.xlen, tmp.ylen, tmp.zlen = struct.unpack('fff', fpointer.read(12))
tmp.alpha, tmp.beta, tmp.gamma = struct.unpack('fff', fpointer.read(12))
tmp.mapc, tmp.mapr, tmp.maps = struct.unpack('iii', fpointer.read(12))
tmp.amin, tmp.amax, tmp.amean = struct.unpack('fff', fpointer.read(12))
tmp.ispg = struct.unpack('i', fpointer.read(4))[0]
tmp.nsymbt = struct.unpack('i', fpointer.read(4))[0]
tmp.lskflg = struct.unpack('i', fpointer.read(4))[0]
tmp.skwmat = struct.unpack('f'*9, fpointer.read(36))
tmp.skwtrn = struct.unpack('fff', fpointer.read(12))
tmp.extra = struct.unpack('i'*15, fpointer.read(60))
tmp.maplabel = ''.join(struct.unpack('cccc', fpointer.read(4)))
tmp.machst = struct.unpack('cccc', fpointer.read(4))
tmp.arms = struct.unpack('f', fpointer.read(4))[0]
tmp.nlabl = struct.unpack('i', fpointer.read(4))[0]
tmp.label = []
for i in range(10):
tmp.label.append(''.join(struct.unpack('c'*80, fpointer.read(80))))
# TODO -- This needs a testcase to debug it!
tmp.symmetry = []
for i in range(tmp.nsymbt/80):
tmp.symmetry.append(''.join(struct.unpack('c'*80, fpointer.read(80))))
# TODO
rawArray = numpy.array(struct.unpack('f'*tmp.nc*tmp.nr*tmp.ns,
fpointer.read(4*tmp.nc*tmp.nr*tmp.ns)))
##
## done with file reading
##
# Roll raw electron density array data into a 3D matrix
rawMatrix = numpy.zeros((tmp.nc, tmp.nr, tmp.ns))
n = 0
for k in xrange(tmp.ns):
for j in xrange(tmp.nr):
for i in xrange(tmp.nc):
rawMatrix[i, j, k] = rawArray[n]
n += 1
# Map from column/row/section space to x/y/z space
if tmp.mapc == 1 and tmp.mapr == 2 and tmp.maps == 3:
tmp.lx = tmp.nc
tmp.ly = tmp.nr
tmp.lz = tmp.ns
tmp.nxstart = tmp.ncstart
tmp.nystart = tmp.nrstart
tmp.nzstart = tmp.nsstart
transposeTuple = (0, 1, 2)
elif tmp.mapc == 1 and tmp.mapr == 3 and tmp.maps == 2:
tmp.lx = tmp.nc
tmp.ly = tmp.ns
tmp.lz = tmp.nr
tmp.nxstart = tmp.ncstart
tmp.nystart = tmp.nsstart
tmp.nzstart = tmp.nrstart
transposeTuple = (0, 2, 1)
elif tmp.mapc == 2 and tmp.mapr == 1 and tmp.maps == 3:
tmp.lx = tmp.nr
tmp.ly = tmp.nc
tmp.lz = tmp.ns
tmp.nxstart = tmp.nrstart
tmp.nystart = tmp.ncstart
tmp.nzstart = tmp.nsstart
transposeTuple = (1, 0, 2)
elif tmp.mapc == 2 and tmp.mapr == 3 and tmp.maps == 1:
tmp.lx = tmp.ns
tmp.ly = tmp.nc
tmp.lz = tmp.nr
tmp.nxstart = tmp.nsstart
tmp.nystart = tmp.ncstart
tmp.nzstart = tmp.nrstart
transposeTuple = (1, 2, 0)
elif tmp.mapc == 3 and tmp.mapr == 1 and tmp.maps == 2:
tmp.lx = tmp.nr
tmp.ly = tmp.ns
tmp.lz = tmp.nc
tmp.nxstart = tmp.nrstart
tmp.nystart = tmp.nsstart
tmp.nzstart = tmp.ncstart
transposeTuple = (2, 0, 1)
elif tmp.mapc == 3 and tmp.mapr == 2 and tmp.maps == 1:
tmp.lx = tmp.ns
tmp.ly = tmp.nr
tmp.lz = tmp.nc
tmp.nxstart = tmp.nsstart
tmp.nystart = tmp.nrstart
tmp.nzstart = tmp.ncstart
transposeTuple = (2, 1, 0)
else:
raise IOError("NULL: Error with Axis Remapping Data.")
# Remap electron density data
chargeMatrix = numpy.transpose(rawMatrix, transposeTuple)
# Unroll electron density data into flat array
tmp.chargeArray = numpy.zeros(tmp.lx * tmp.ly * tmp.lz)
n = 0
for k in xrange(tmp.lz):
for j in xrange(tmp.ly):
for i in xrange(tmp.lx):
tmp.chargeArray[n] = chargeMatrix[i, j, k]
n += 1
# Generate cartesian data into 'flat' array
tmp._cartArray = numpy.zeros((tmp.lx * tmp.ly * tmp.lz, 3))
n = 0
mz = tmp.zlen / tmp.nz
my = tmp.ylen / tmp.ny
mx = tmp.xlen / tmp.nx
for k in xrange(tmp.nzstart, tmp.nzstart + tmp.lz):
zcart = mz * k
for j in xrange(tmp.nystart, tmp.nystart + tmp.ly):
ycart = my * j
for i in xrange(tmp.nxstart, tmp.nxstart + tmp.lx):
xcart = mx * i
tmp._cartArray[n, 0] = xcart
tmp._cartArray[n, 1] = ycart
tmp._cartArray[n, 2] = zcart
n += 1
# Fin!
tmp._cartArray = tmp._cartArray
tmp.chargeArray = tmp.chargeArray
#tmp.init_cart()
return tmp