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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
"""
Authors: Jerome Kieffer, ESRF
email:jerome.kieffer@esrf.fr
kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's
Based on the edfimage.py parser.
"""
import numpy
import logging
import os
import string
from .fabioimage import FabioImage
logger = logging.getLogger(__name__)
import io
if not hasattr(io, "SEEK_END"):
SEEK_END = 2
else:
SEEK_END = io.SEEK_END
DATA_TYPES = {"u16": numpy.uint16}
MINIMUM_KEYS = [
# 'ByteOrder', Assume little by default
'Data type',
'X dimension',
'Y dimension',
'Number of readouts']
DEFAULT_VALUES = {"Data type": "u16"}
ALPHANUM = bytes(string.digits + string.ascii_letters + ". ", encoding="ASCII")
class KcdImage(FabioImage):
"""
Read the Nonius kcd data format """
DESCRIPTION = "KCD file format from Nonius's KappaCCD diffractometer"
DEFAULT_EXTENSIONS = ["kcd"]
def _readheader(self, infile):
"""
Read in a header in some KCD format from an already open file
"""
one_line = infile.readline()
asciiHeader = True
for oneChar in one_line.strip():
if oneChar not in ALPHANUM:
asciiHeader = False
if asciiHeader is False:
# This does not look like an KappaCCD file
logger.warning("First line of %s does not seam to be ascii text!" % infile.name)
end_of_headers = False
while not end_of_headers:
one_line = infile.readline()
try:
one_line = one_line.decode("ASCII")
except UnicodeDecodeError:
end_of_headers = True
else:
if len(one_line) > 100:
end_of_headers = True
if not end_of_headers:
if one_line.strip() == "Binned mode":
one_line = "Mode = Binned"
if "=" in one_line:
key, val = one_line.split('=', 1)
key = key.strip()
self.header[key] = val.strip()
else:
end_of_headers = True
missing = []
for item in MINIMUM_KEYS:
if item not in self.header:
missing.append(item)
if len(missing) > 0:
logger.debug("KCD file misses the keys " + " ".join(missing))
def read(self, fname, frame=None):
"""
Read in header into self.header and
the data into self.data
"""
self.header = self.check_header()
self.resetvals()
with self._open(fname, "rb") as infile:
self._readheader(infile)
# Compute image size
try:
dim1 = int(self.header['X dimension'])
dim2 = int(self.header['Y dimension'])
self._shape = dim2, dim1
except (KeyError, ValueError):
raise IOError("KCD file %s is corrupt, cannot read it" % fname)
try:
bytecode = DATA_TYPES[self.header['Data type']]
except KeyError:
bytecode = numpy.uint16
logger.warning("Defaulting type to uint16")
self._dtype = numpy.dtype(bytecode)
try:
nbReadOut = int(self.header['Number of readouts'])
except KeyError:
logger.warning("Defaulting number of ReadOut to 1")
nbReadOut = 1
expected_size = dim1 * dim2 * self._dtype.itemsize * nbReadOut
try:
infile.seek(-expected_size, SEEK_END)
except Exception:
logger.debug("Backtrace", exc_info=True)
logger.warning("seeking from end is not implemeneted for file %s", fname)
if hasattr(infile, "measure_size"):
fileSize = infile.measure_size()
elif hasattr(infile, "size"):
fileSize = infile.size
elif hasattr(infile, "getSize"):
fileSize = infile.getSize()
else:
logger.warning("Unable to guess the file-size of %s", fname)
fileSize = os.stat(fname)[6]
infile.seek(fileSize - expected_size - infile.tell(), 1)
block = infile.read(expected_size)
# infile.close()
# now read the data into the array
self.data = numpy.zeros((dim2, dim1), numpy.int32)
stop = 0
for i in range(nbReadOut):
start = stop
stop = (i + 1) * expected_size // nbReadOut
data = numpy.frombuffer(block[start: stop], self._dtype).copy()
data.shape = dim2, dim1
if not numpy.little_endian:
data.byteswap(True)
self.data += data
self._dtype = None
self._shape = None
self.resetvals()
return self
@staticmethod
def checkData(data=None):
if data is None:
return None
else:
return data.astype(int)
kcdimage = KcdImage
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