Source code for fabio.xsdimage
#!/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
[docs]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)
[docs] 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