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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""
Author: Andy Hammersley, ESRF
Translation into python/fabio: Jon Wright, ESRF.
Writer: Jérôme Kieffer
"""
__authors__ = ["Jon Wright", "Jérôme Kieffer"]
__contact__ = "Jerome.Kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__version__ = "06/01/2015"
import io
import numpy
import struct
from .fabioimage import FabioImage
class Fit2dMaskImage(FabioImage):
""" Read and try to write Andy Hammersley's mask format """
DESCRIPTION = "Fit2d mask file format"
DEFAULT_EXTENSIONS = ["msk"]
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 [(b"M", 0),
(b"A", 4),
(b"S", 8),
(b"K", 12)]:
if header[j] != i[0]:
raise Exception("Not a fit2d mask file")
fit2dhdr = numpy.frombuffer(header, numpy.int32)
# Enforce little endian
if not numpy.little_endian:
fit2dhdr.byteswap(True)
dim1 = fit2dhdr[4] # 1 less than Andy's fortran
dim2 = fit2dhdr[5]
self._shape = dim2, dim1
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._dtype = numpy.dtype(numpy.uint8)
# integer division
dim2, dim1 = self._shape
num_ints = (dim1 + 31) // 32
total = dim2 * num_ints * 4
data = fin.read(total)
assert len(data) == total
fin.close()
# Now to unpack it
data = numpy.frombuffer(data, numpy.uint8)
if not numpy.little_endian:
data.byteswap(True)
data = numpy.reshape(data, (dim2, num_ints * 4))
result = numpy.zeros((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 - dim1
if spares == 0:
data = numpy.where(result == 0, 0, 1)
else:
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.ascontiguousarray(data, dtype=numpy.uint8)
self.data.shape = self._shape
self._shape = None
return self
def write(self, fname):
"""
Try to write a file
"""
dim2, dim1 = self.shape
header = bytearray(b"\x00" * 1024)
header[0] = 77 # M
header[4] = 65 # A
header[8] = 83 # S
header[12] = 75 # K
header[24] = 1 # 1
header[16:20] = struct.pack("<I", dim1)
header[20:24] = struct.pack("<I", dim2)
compact_array = numpy.zeros((dim2, ((dim1 + 31) // 32) * 4), dtype=numpy.uint8)
large_array = numpy.zeros((dim2, ((dim1 + 31) // 32) * 32), dtype=numpy.uint8)
large_array[:dim2,:dim1] = (self.data != 0)
for i in range(8):
order = (1 << i)
compact_array += large_array[:, i::8] * order
with self._open(fname, mode="wb") as outfile:
outfile.write(bytes(header))
if isinstance(outfile, io.BufferedWriter):
compact_array.tofile(outfile)
else:
outfile.write(compact_array.tobytes())
@staticmethod
def check_data(data=None):
if data is None:
return None
else:
return (data != 0).astype(numpy.uint8)
fit2dmaskimage = Fit2dMaskImage
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