/usr/share/pyshared/fabio/kcdimage.py is in python-fabio 0.1.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #!/usr/bin/env python
"""
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
logger = logging.getLogger("kcdimage")
DATA_TYPES = {"u16" : numpy.uint16 }
MINIMUM_KEYS = [
'ByteOrder',
'Data type',
'X dimension',
'Y dimension',
'Number of readouts']
DEFAULT_VALUES = { "Data type": "u16" }
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
@
"""
oneLine = infile.readline()
alphanum = string.digits + string.letters + ". "
asciiHeader = True
for oneChar in oneLine.strip():
if not oneChar in alphanum:
asciiHeader = False
if asciiHeader is False:
# This does not look like an edf file
logger.warning("First line of %s does not seam to be ascii text!" % infile.name)
endOfHeaders = False
while not endOfHeaders:
oneLine = infile.readline()
if len(oneLine) > 100:
endOfHeaders = True
break
if oneLine.strip() == "Binned mode":
oneLine = "Mode = Binned"
try:
key, val = oneLine.split('=' , 1)
except:
endOfHeaders = True
break
key = key.strip()
self.header_keys.append(key)
self.header[key] = val.strip()
missing = []
for item in MINIMUM_KEYS:
if item not in self.header_keys:
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.resetvals()
infile = self._open(fname, "rb")
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))
try:
for i in range(nbReadOut):
self.data += numpy.reshape(numpy.fromstring(
block[i * expected_size / nbReadOut:(i + 1) * expected_size / nbReadOut], bytecode),
[self.dim2, self.dim1])
except:
print(len(block), bytecode, self.bpp, self.dim2, self.dim1)
raise IOError(
'Size spec in kcd-header does not match size of image data field')
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)
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