/usr/share/pyshared/fabio/xsdimage.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
# coding: utf8
"""
Authors: Jérôme Kieffer, ESRF
email:jerome.kieffer@esrf.fr
XSDimge are XML files containing numpy arrays
"""
# Get ready for python3:
from __future__ import with_statement, print_function, division
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import logging, numpy
logger = logging.getLogger("xsdimage")
from .fabioimage import fabioimage
import base64, hashlib
try:
from lxml import etree
except ImportError:
logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format")
etree = None
class xsdimage(fabioimage):
"""
Read the XSDataImage XML File data format
"""
def __init__(self, data=None, header=None, fname=None):
"""
Constructor of the class XSDataImage.
@param _strFilename: the name of the file to open
@type _strFilename: string
"""
fabioimage.__init__(self, data=data, header=header)
self.dims = []
self.size = None
self.coding = None
self.dtype = None
self.rawData = None
self.md5 = None
if fname is not None:
self.filename = fname
self.read(fname)
def read(self, fname, frame=None):
"""
"""
self.header = {}
self.resetvals()
self.filename = fname
infile = self._open(fname, "rb")
self._readheader(infile)
try:
self.dim1, self.dim2 = self.dims[:2]
except:
raise IOError("XSD file %s is corrupt, no dimensions in it" % fname)
try:
self.bytecode = numpy.dtype(self.dtype).type
self.bpp = len(numpy.array(0, self.bytecode).tostring())
except TypeError:
self.bytecode = numpy.int32
self.bpp = 32
logger.warning("Defaulting type to int32")
exp_size = 1
for i in self.dims:
exp_size *= i
assert exp_size == self.size
decData = None
if self.coding == "base64":
decData = base64.b64decode(self.rawData)
elif self.coding == "base32":
decData = base64.b32decode(self.rawData)
elif self.coding == "base16":
decData = base64.b16decode(self.rawData)
else:
logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding)
decData = base64.b64decode(self.rawData)
if self.md5:
assert hashlib.md5(decData).hexdigest() == self.md5
self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims))
if not numpy.little_endian: #by default little endian
self.data.byteswap(inplace=True)
self.resetvals()
# # ensure the PIL image is reset
self.pilimage = None
return self
def _readheader(self, infile):
"""
Read all headers in a file and populate self.header
data is not yet populated
@type infile: file object open in read mode
"""
xml = etree.parse(infile)
self.dims = []
for i in xml.xpath("//shape"):
try:
self.dims.append(int(i.text))
except ValueError, error:
logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i))
for i in xml.xpath("//size"):
try:
self.size = int(i.text)
except Exception, error:#IGNORE:W0703
logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i))
self.dtype = None
for i in xml.xpath("//dtype"):
self.dtype = i.text
self.coding = None
for i in xml.xpath("//coding"):
j = i.find("value")
if j is not None:
self.coding = j.text
self.rawData = None
for i in xml.xpath("//data"):
self.rawData = i.text
self.md5 = None
for i in xml.xpath("//md5sum"):
j = i.find("value")
if j is not None:
self.md5 = j.text
if etree is None:
xsdimage = None
|