/usr/share/pyshared/fabio/adscimage.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 | #!/usr/bin/env python
#coding: utf8
"""
Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:erik.knudsen@risoe.dk
+ mods for fabio by JPW
"""
# Get ready for python3:
from __future__ import with_statement, print_function
import numpy, logging
from .fabioimage import fabioimage
logger = logging.getLogger("adscimage")
class adscimage(fabioimage):
""" Read an image in ADSC format (quite similar to edf?) """
def __init__(self, *args, **kwargs):
fabioimage.__init__(self, *args, **kwargs)
def read(self, fname, frame=None):
""" read in the file """
infile = self._open(fname, "rb")
try:
self._readheader(infile)
except:
raise Exception("Error processing adsc header")
# banned by bzip/gzip???
try:
infile.seek(int(self.header['HEADER_BYTES']), 0)
except TypeError:
# Gzipped does not allow a seek and read header is not
# promising to stop in the right place
infile.close()
infile = self._open(fname, "rb")
infile.read(int(self.header['HEADER_BYTES']))
binary = infile.read()
infile.close()
#now read the data into the array
self.dim1 = int(self.header['SIZE1'])
self.dim2 = int(self.header['SIZE2'])
if 'little' in self.header['BYTE_ORDER']:
try:
self.data = numpy.reshape(
numpy.fromstring(binary, numpy.uint16),
(self.dim2, self.dim1))
except ValueError:
raise IOError, 'Size spec in ADSC-header does not match ' + \
'size of image data field'
self.bytecode = numpy.uint16
logger.info("adscimage read in using low byte first (x386-order)")
else:
try:
self.data = numpy.reshape(
numpy.fromstring(binary, numpy.uint16),
(self.dim2, self.dim1)).byteswap()
except ValueError:
raise IOError, 'Size spec in ADSC-header does not match ' + \
'size of image data field'
self.bytecode = numpy.uint16
logger.info('adscimage using high byte first (network order)')
self.resetvals()
return self
def _readheader(self, infile):
""" read an adsc header """
line = infile.readline()
bytesread = len(line)
while '}' not in line:
if '=' in line:
(key, val) = line.split('=')
self.header_keys.append(key.strip())
self.header[key.strip()] = val.strip(' ;\n')
line = infile.readline()
bytesread = bytesread + len(line)
def write(self, fname):
"""
Write adsc format
"""
out = '{\n'
for key in self.header_keys:
out += "%s = %s;\n" % (key, self.header[key])
# FIXME ??? - made padding match header bytes keyword
# the cbflib example image has exactly 512...
if self.header.has_key("HEADER_BYTES"):
pad = int(self.header["HEADER_BYTES"]) - len(out) - 2
else:
# integer division
# 1234567890123456789012
# HEADER_BYTES = 1234;\n
hsize = ((len(out) + 23) / 512 + 1) * 512
out += "HEADER_BYTES=%d;\n" % (hsize)
pad = hsize - len(out) - 2
out += pad * ' ' + "}\n"
assert len(out) % 512 == 0 , "Header is not multiple of 512"
outf = open(fname, "wb")
outf.write(out)
# it says "unsigned_short" ? ... jpw example has:
# BYTE_ORDER=big_endian;
# TYPE=unsigned_short;
if "little" in self.header["BYTE_ORDER"]:
outf.write(self.data.astype(numpy.uint16).tostring())
else:
outf.write(self.data.byteswap().astype(
numpy.uint16).tostring())
outf.close()
def test():
""" testcase """
import sys, time
img = adscimage()
begin = time.clock()
while (sys.argv[1:]):
img.read(sys.argv[1])
# rim = img.toPIL16()
img.rebin(2, 2)
img.write('jegErEnFil0000.img')
print(sys.argv[1] + ": max=%d, min=%d, mean=%.2e, stddev=%.2e" % (\
img.getmax(), img.getmin(), img.getmean(), img.getstddev()))
print( 'integrated intensity (%d %d %d %d) =%.3f' % (\
10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))))
sys.argv[1:] = sys.argv[2:]
end = time.clock()
print(end - begin)
if __name__ == '__main__':
test()
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