/usr/lib/python2.7/dist-packages/fabio/kcdimage.py is in python-fabio 0.3.0+dfsg-1build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 | # coding: utf-8
#
# Project: X-ray image reader
# https://github.com/kif/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
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.
"""
# Get ready for python3:
from __future__ import with_statement, print_function
import numpy, logging
import os, string
from .fabioimage import FabioImage
from .fabioutils import six
logger = logging.getLogger("kcdimage")
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" }
if six.PY2:
ALPHANUM = string.digits + string.letters + ". "
else:
ALPHANUM = bytes(string.digits + string.ascii_letters + ". ", encoding="ASCII")
class KcdImage(FabioImage):
"""
Read the Nonius kcd data format """
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 not oneChar 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 as err:
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:
self.dim1 = int(self.header['X dimension'])
self.dim2 = int(self.header['Y dimension'])
except:
raise Exception("KCD file %s is corrupt, cannot read it" % fname)
try:
bytecode = DATA_TYPES[self.header['Data type']]
self.bpp = len(numpy.array(0, bytecode).tostring())
except KeyError:
bytecode = numpy.uint16
self.bpp = 2
logger.warning("Defaulting type to uint16")
try:
nbReadOut = int(self.header['Number of readouts'])
except KeyError:
logger.warning("Defaulting number of ReadOut to 1")
nbReadOut = 1
fileSize = os.stat(fname)[6]
expected_size = self.dim1 * self.dim2 * self.bpp * nbReadOut
infile.seek(fileSize - expected_size)
block = infile.read()
assert len(block) == expected_size
# infile.close()
# now read the data into the array
self.data = numpy.zeros((self.dim2, self.dim1), numpy.int32)
stop = 0
for i in range(nbReadOut):
start = stop
stop = (i + 1) * expected_size // nbReadOut
data = numpy.fromstring(block[start: stop], bytecode)
data.shape = self.dim2, self.dim1
if not numpy.little_endian:
data.byteswap(True)
self.data += data
self.bytecode = self.data.dtype.type
self.resetvals()
# ensure the PIL image is reset
self.pilimage = None
return self
@staticmethod
def checkData(data=None):
if data is None:
return None
else:
return data.astype(int)
kcdimage = KcdImage
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