/usr/lib/python3/dist-packages/csb/bio/io/mrc.py is in python3-csb 1.2.3+dfsg-3.
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Cryo-EM density map I/O
@warning: dragons ahead, this module is experimental
"""
import numpy
import struct
class DensityMapFormatError(ValueError):
pass
class ByteOrder(object):
NATIVE = '='
LITTLE = '<'
BIG = '>'
class DensityInfo(object):
def __init__(self, data, spacing, origin, shape=None, header=None, axes=None):
self.data = data
self.spacing = spacing
self.origin = origin
self.header = header
self.shape = shape
self.axes = axes
if shape is None and data is not None:
self.shape = self.data.shape
class HeaderInfo(object):
def __init__(self, fields):
fields = tuple(fields)
if not len(fields) == 25:
raise ValueError(fields)
self._fields = fields
def __getitem__(self, i):
return self._fields[i]
def __iter__(self):
return iter(self._fields)
@property
def nc(self):
return self._fields[0]
@property
def nr(self):
return self._fields[1]
@property
def ns(self):
return self._fields[2]
@property
def mode(self):
return self._fields[3]
@property
def ncstart(self):
return self._fields[4]
@property
def nrstart(self):
return self._fields[5]
@property
def nsstart(self):
return self._fields[6]
@property
def nx(self):
return self._fields[7]
@property
def ny(self):
return self._fields[8]
@property
def nz(self):
return self._fields[9]
@property
def x(self):
return self._fields[10]
@property
def y(self):
return self._fields[11]
@property
def z(self):
return self._fields[12]
@property
def alpha(self):
return self._fields[13]
@property
def beta(self):
return self._fields[14]
@property
def gamma(self):
return self._fields[15]
@property
def mapc(self):
return self._fields[16]
@property
def mapr(self):
return self._fields[17]
@property
def maps(self):
return self._fields[18]
@property
def amin(self):
return self._fields[19]
@property
def amax(self):
return self._fields[20]
@property
def amean(self):
return self._fields[21]
@property
def ispg(self):
return self._fields[22]
@property
def nsymbt(self):
return self._fields[23]
@property
def lskflg(self):
return self._fields[24]
class DensityMapReader(object):
"""
Binary MRC density map reader.
@param filename: input MRC file name
@type filename: str
"""
HEADER_SIZE = 1024
def __init__(self, filename):
self._filename = filename
@property
def filename(self):
"""
Input MRC file name
@rtype: str
"""
return self._filename
def _rawheader(self, stream):
"""
Read and return the raw binary header.
"""
raw = stream.read(DensityMapReader.HEADER_SIZE)
return bytes(raw)
def _inspect(self, rawheader, order):
"""
Parse a raw binary header.
"""
format = '{0}10l6f3l3f3l'.format(order)
fields = struct.unpack(format, rawheader[:4 * 25])
return HeaderInfo(fields)
def _spacing(self, header):
if header.nx != 0 and header.ny != 0 and header.nz != 0:
return (header.x / header.nx, header.y / header.ny, header.z / header.nz)
else:
return (0, 0, 0)
def _origin(self, header, spacing=None):
if spacing is None:
spacing = self._spacing(header)
origin = header.ncstart, header.nrstart, header.nsstart
return [origin[i] * spacing[i] for i in range(3)]
def _shape(self, header):
return (header.ns, header.nr, header.nc)
def inspect_header(self, order=ByteOrder.NATIVE):
"""
Parse the raw binary header of the density map.
@param order: byte order (defaults to L{ByteOrder.NATIVE})
@type order: str
@return: header information
@rtype: L{HeaderInfo}
"""
with open(self.filename, 'rb') as stream:
raw = self._rawheader(stream)
return self._inspect(raw, order)
def read_header(self):
"""
Read the header of the density map only.
@return: density info without any actual data (density.data is None)
@rtype: L{DensityInfo}
"""
with open(self.filename, 'rb') as stream:
raw = self._rawheader(stream)
header = self._inspect(raw, ByteOrder.NATIVE)
spacing = self._spacing(header)
origin = self._origin(header, spacing)
shape = self._shape(header)
return DensityInfo(None, spacing, origin, shape=shape, header=raw)
def read(self):
"""
Read the entire density map.
@return: complete density info
@rtype: L{DensityInfo}
"""
with open(self.filename, 'rb') as stream:
raw = self._rawheader(stream)
header = self._inspect(raw, ByteOrder.NATIVE)
if header.mode == 2 or header.mode == 1:
byte_order = ByteOrder.NATIVE
elif header.mode == 33554432:
header = self._inspect(raw, ByteOrder.BIG)
byte_order = ByteOrder.BIG
if header.mode == 33554432:
header = self._inspect(raw, ByteOrder.LITTLE)
byte_order = ByteOrder.LITTLE
else:
raise DensityMapFormatError("Not a mode 2 CCP4 map file")
stream.read(header.nsymbt) # symmetry_data
count = header.ns * header.nr * header.nc
map_data = stream.read(4 * count)
if byte_order == ByteOrder.NATIVE:
array = numpy.fromstring(map_data, numpy.float32, count)
else:
array = numpy.zeros((count,), numpy.float32)
index = 0
while len(map_data) >= 4 * 10000:
values = struct.unpack(byte_order + '10000f', map_data[:4 * 10000])
array[index:index + 10000] = numpy.array(values, numpy.float32)
index += 10000
map_data = map_data[4 * 10000:]
values = struct.unpack(byte_order + '%df' % (len(map_data) / 4), map_data)
array[index:] = numpy.array(values, numpy.float32)
del map_data
array.shape = self._shape(header)
data = array.T
spacing = self._spacing(header)
origin = self._origin(header, spacing)
return DensityInfo(data, spacing, origin, header=raw)
class DensityMapWriter(object):
"""
Binary MRC density map writer.
"""
def reconstruct_header(self, density):
"""
Attempt to reconstruct the header, given L{DensityInfo}'s
data shape, spacing and origin.
@param density: density info
@type density: L{DensityInfo}
@return: reconstructed binary header
@rtype: bytes
"""
N = list(density.data.shape)
MODE = 2
if isinstance(density.spacing, float):
spacing = 3 * [density.spacing]
else:
spacing = density.spacing
if density.origin is None:
origin = 3 * [0.]
else:
origin = density.origin
if density.axes is None:
MAP = list(range(1, 4))
else:
MAP = list(density.axes)
start = [int(round(origin[i] / spacing[i], 0)) for i in range(3)]
M = [density.data.shape[i] for i in range(3)]
cella = [density.data.shape[i] * spacing[i] for i in range(3)]
cellb = 3 * [90.]
stats = [density.data.min(), density.data.max(), density.data.mean()]
ISPG = 0
NSYMBT = 0
LSKFLG = 0
JUNK = [0] * 25
ORIGIN = [0., 0., 0.]
MACHST = 0
args = N + [MODE] + start + M + cella + cellb + \
MAP + stats + [ISPG, NSYMBT, LSKFLG] + JUNK + \
ORIGIN + [0, MACHST, 0., 0] + [b' ' * 796]
return struct.pack('=10l6f3l3f3l25l3f2l1f1l796s', *args)
def write(self, stream, density):
"""
Write C{density} to a binary C{stream}.
@param stream: destination binary stream
@type stream: stream
@param density: input density info
@type density: L{DensityInfo}
"""
if density.header is not None:
stream.write(density.header)
else:
stream.write(self.reconstruct_header(density))
data = density.data.T.flatten()
x = struct.pack('=%df' % len(data), *data.tolist())
stream.write(x)
def write_file(self, filename, density):
"""
Write C{density} to a binary file.
@param filename: destination file name
@type filename: str
@param density: input density info
@type density: L{DensityInfo}
"""
with open(filename, 'wb') as stream:
self.write(stream, density)
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