Source code for fabio.fit2dmaskimage

## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py

#!/usr/bin/env python
"""

Author: Andy Hammersley, ESRF
Translation into python/fabio: Jon Wright, ESRF
"""

import numpy

from fabioimage import fabioimage


[docs]class fit2dmaskimage(fabioimage): """ Read and try to write Andy Hammersley's mask format """ def _readheader(self, infile): """ Read in a header from an already open file """ # 1024 bytes gives 256x32 bit integers header = infile.read(1024) for i, j in [ ("M", 0), ("A", 4), ("S", 8), ("K", 12) ]: if header[j] != i: raise Exception("Not a fit2d mask file") fit2dhdr = numpy.fromstring(header, numpy.int32) self.dim1 = fit2dhdr[4] # 1 less than Andy's fortran self.dim2 = fit2dhdr[5]
[docs] def read(self, fname, frame=None): """ Read in header into self.header and the data into self.data """ fin = self._open(fname) self._readheader(fin) # Compute image size self.bytecode = numpy.uint8 self.bpp = len(numpy.array(0, self.bytecode).tostring()) # integer division num_ints = (self.dim1 + 31) // 32 total = self.dim2 * num_ints * 4 data = fin.read(total) assert len(data) == total fin.close() # Now to unpack it data = numpy.fromstring(data, numpy.uint8) data = numpy.reshape(data, (self.dim2, num_ints * 4)) result = numpy.zeros((self.dim2, num_ints * 4 * 8), numpy.uint8) # Unpack using bitwise comparisons to 2**n bits = numpy.ones((1), numpy.uint8) for i in range(8): temp = numpy.bitwise_and(bits, data) result[:, i::8] = temp.astype(numpy.uint8) bits = bits * 2 # Extra rows needed for packing odd dimensions spares = num_ints * 4 * 8 - self.dim1 if spares == 0: self.data = numpy.where(result == 0, 0, 1) else: self.data = numpy.where(result[:, :-spares] == 0, 0, 1) # Transpose appears to be needed to match edf reader (scary??) # self.data = numpy.transpose(self.data) self.data = numpy.reshape(self.data.astype(numpy.uint16), (self.dim2, self.dim1)) self.pilimage = None return self
[docs] def write(self, fname): """ Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats) """ raise Exception("Not implemented yet")
@staticmethod
[docs] def checkData(data=None): if data is None: return None else: return data.astype(int)