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# coding: utf-8
#
# Project: FabIO X-ray image reader
#
# Copyright (C) 2010-2016 European Synchrotron Radiation Facility
# Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""
Authors: Jérôme Kieffer, ESRF
email:jerome.kieffer@esrf.fr
XSDimge are XML files containing numpy arrays
"""
__author__ = "Jérôme Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import logging
import numpy
import base64
import hashlib
from .fabioimage import FabioImage
logger = logging.getLogger(__name__)
try:
import lxml.etree as etree
except ImportError:
try:
# Try using the standard library
import xml.etree.ElementTree as etree
except ImportError:
logger.warning("xml/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
"""
DESCRIPTION = "XSDataImage XML file format"
DEFAULT_EXTENSIONS = ["xml", "xsd"]
def __init__(self, data=None, header=None, fname=None):
"""
Constructor of the class XSDataImage.
:param str fname: the name of the file to open
"""
FabioImage.__init__(self, data=data, header=header)
self._shape = []
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
with self._open(fname, "rb") as infile:
self._readheader(infile)
exp_size = 1
for i in self.shape:
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
data = numpy.frombuffer(decData, dtype=self._dtype)
data.shape = self.shape
self.data = data
if not numpy.little_endian: # by default little endian
self.data.byteswap(inplace=True)
self.resetvals()
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._shape = []
for i in xml.findall(".//shape"):
try:
self._shape.insert(0, int(i.text))
except ValueError as error:
logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i))
self._shape = tuple(self._shape)
for i in xml.findall(".//size"):
try:
self.size = int(i.text)
except Exception as error:
logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i))
self._dtype = None
for i in xml.findall(".//dtype"):
self._dtype = numpy.dtype(i.text)
self.coding = None
for i in xml.findall(".//coding"):
j = i.find("value")
if j is not None:
self.coding = j.text
self.rawData = None
for i in xml.findall(".//data"):
self.rawData = i.text.encode("latin-1")
self.md5 = None
for i in xml.findall(".//md5sum"):
j = i.find("value")
if j is not None:
self.md5 = j.text
if etree is None:
# Hide the class if it can't work
XsdImage = None
xsdimage = XsdImage
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