def updateHeaderUsingArray(header,
a,
calc_stats=True,
reset_origin=True,
mz=None):
'''
Fills in values of MRC header dictionary using the given array.
'''
ndims = len(a.shape)
nx = a.shape[-1]
ny = nz = 1
if ndims > 1:
ny = a.shape[-2]
if ndims > 2:
nz = a.shape[-3]
header['nx'] = nx
header['ny'] = ny
header['nz'] = nz
mode = numpy2mrc[a.dtype.type]
header['mode'] = mode
if mz is None:
mz = nz
header['mx'] = nx
header['my'] = ny
header['mz'] = mz
try:
psize = weakattr.get(a, 'pixelsize')
except AttributeError:
header['xlen'] = nx
header['ylen'] = ny
header['zlen'] = nz
else:
header['xlen'] = nx * psize['x']
header['ylen'] = ny * psize['y']
header['zlen'] = mz * psize['x']
if calc_stats:
stats = arraystats.all(a)
header['amin'] = stats['min']
header['amax'] = stats['max']
header['amean'] = stats['mean']
header['rms'] = stats['std']
if reset_origin is True:
### changed next lines to be equivalent to proc3d origin=0,0,0
header['xorigin'] = 0
header['yorigin'] = 0
header['zorigin'] = 0
if ndims < 3:
header['nxstart'] = 0
header['nystart'] = 0
header['nzstart'] = 0
else:
header['nxstart'] = nx / -2
header['nystart'] = ny / -2
header['nzstart'] = nz / -2
def updateHeaderUsingArray(header, a, calc_stats=True, reset_origin=True, mz=None):
"""
Fills in values of MRC header dictionary using the given array.
"""
ndims = len(a.shape)
nx = a.shape[-1]
ny = nz = 1
if ndims > 1:
ny = a.shape[-2]
if ndims > 2:
nz = a.shape[-3]
header["nx"] = nx
header["ny"] = ny
header["nz"] = nz
mode = numpy2mrc[a.dtype.type]
header["mode"] = mode
if mz is None:
mz = nz
header["mx"] = nx
header["my"] = ny
header["mz"] = mz
try:
psize = weakattr.get(a, "pixelsize")
except AttributeError:
header["xlen"] = nx
header["ylen"] = ny
header["zlen"] = nz
else:
header["xlen"] = nx * psize["x"]
header["ylen"] = ny * psize["y"]
header["zlen"] = mz * psize["x"]
if calc_stats:
stats = arraystats.all(a)
header["amin"] = stats["min"]
header["amax"] = stats["max"]
header["amean"] = stats["mean"]
header["rms"] = stats["std"]
if reset_origin is True:
### changed next lines to be equivalent to proc3d origin=0,0,0
header["xorigin"] = 0
header["yorigin"] = 0
header["zorigin"] = 0
if ndims < 3:
header["nxstart"] = 0
header["nystart"] = 0
header["nzstart"] = 0
else:
header["nxstart"] = nx / -2
header["nystart"] = ny / -2
header["nzstart"] = nz / -2
def updateHeaderUsingArray(header, a, calc_stats=True, reset_origin=True): ''' Fills in values of MRC header dictionary using the given array. ''' ndims = len(a.shape) nx = a.shape[-1] ny = nz = 1 if ndims > 1: ny = a.shape[-2] if ndims > 2: nz = a.shape[-3] header['nx'] = nx header['ny'] = ny header['nz'] = nz mode = numpy2mrc[a.dtype.type] header['mode'] = mode header['mx'] = nx header['my'] = ny header['mz'] = nz try: psize = weakattr.get(a, 'pixelsize') except AttributeError: header['xlen'] = nx header['ylen'] = ny header['zlen'] = nz else: header['xlen'] = nx * psize['x'] header['ylen'] = ny * psize['y'] header['zlen'] = nz * psize['x'] if calc_stats: stats = arraystats.all(a) header['amin'] = stats['min'] header['amax'] = stats['max'] header['amean'] = stats['mean'] header['rms'] = stats['std'] if reset_origin is True: ### changed next lines to be equivalent to proc3d origin=0,0,0 header['xorigin'] = 0 header['yorigin'] = 0 header['zorigin'] = 0 if ndims < 3: header['nxstart'] = 0 header['nystart'] = 0 header['nzstart'] = 0 else: header['nxstart'] = nx / -2 header['nystart'] = ny / -2 header['nzstart'] = nz / -2
def getHeader(a):
"""
Return the MRC header for the array, if it has one.
"""
return weakattr.get(a, "mrcheader")
def getHeader(a): ''' Return the MRC header for the array, if it has one. ''' return weakattr.get(a, 'mrcheader')
def getCachedStats(a): try: return a.stats except AttributeError: return weakattr.get(a, 'stats')
def getCachedStats(a): try: return a.stats except AttributeError: return weakattr.get(a, 'stats')
