1
2
3 """
4 Authors: Jérôme Kieffer, ESRF
5 email:jerome.kieffer@esrf.fr
6
7 XSDimge are XML files containing numpy arrays
8 """
9 __author__ = "Jérôme Kieffer"
10 __contact__ = "jerome.kieffer@esrf.eu"
11 __license__ = "GPLv3+"
12 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
13
14 import logging, numpy
15 logger = logging.getLogger("xsdimage")
16 from fabioimage import fabioimage
17 import base64, hashlib
18 try:
19 from lxml import etree
20 except ImportError:
21 logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format")
22 etree = None
23
25 """
26 Read the XSDataImage XML File data format
27 """
28 - def __init__(self, data=None, header=None, fname=None):
29 """
30 Constructor of the class XSDataImage.
31
32 @param _strFilename: the name of the file to open
33 @type _strFilename: string
34 """
35 fabioimage.__init__(self, data=data, header=header)
36 self.dims = []
37 self.size = None
38 self.coding = None
39 self.dtype = None
40 self.rawData = None
41 self.md5 = None
42 if fname is not None:
43 self.filename = fname
44 self.read(fname)
45
46 - def read(self, fname, frame=None):
47 """
48 """
49 self.header = {}
50 self.resetvals()
51 self.filename = fname
52 infile = self._open(fname, "rb")
53 self._readheader(infile)
54
55 try:
56 self.dim1, self.dim2 = self.dims[:2]
57 except:
58 raise IOError("XSD file %s is corrupt, no dimensions in it" % fname)
59 try:
60 self.bytecode = numpy.dtype(self.dtype).type
61 self.bpp = len(numpy.array(0, self.bytecode).tostring())
62 except TypeError:
63 self.bytecode = numpy.int32
64 self.bpp = 32
65 logger.warning("Defaulting type to int32")
66
67 exp_size = 1
68 for i in self.dims:
69 exp_size *= i
70 assert exp_size == self.size
71
72 decData = None
73 if self.coding == "base64":
74 decData = base64.b64decode(self.rawData)
75 elif self.coding == "base32":
76 decData = base64.b32decode(self.rawData)
77 elif self.coding == "base16":
78 decData = base64.b16decode(self.rawData)
79 else:
80 logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding)
81 decData = base64.b64decode(self.rawData)
82 if self.md5:
83 assert hashlib.md5(decData).hexdigest() == self.md5
84
85
86 self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims))
87 if not numpy.little_endian:
88 self.data.byteswap(inplace=True)
89 self.resetvals()
90
91 self.pilimage = None
92 return self
93
95 """
96 Read all headers in a file and populate self.header
97 data is not yet populated
98 @type infile: file object open in read mode
99 """
100 xml = etree.parse(infile)
101 self.dims = []
102 for i in xml.xpath("//shape"):
103 try:
104 self.dims.append(int(i.text))
105 except ValueError, error:
106 logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i))
107 for i in xml.xpath("//size"):
108 try:
109 self.size = int(i.text)
110 except Exception, error:
111 logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i))
112 self.dtype = None
113 for i in xml.xpath("//dtype"):
114 self.dtype = i.text
115 self.coding = None
116 for i in xml.xpath("//coding"):
117 j = i.find("value")
118 if j is not None:
119 self.coding = j.text
120 self.rawData = None
121 for i in xml.xpath("//data"):
122 self.rawData = i.text
123 self.md5 = None
124 for i in xml.xpath("//md5sum"):
125 j = i.find("value")
126 if j is not None:
127 self.md5 = j.text
128
129 if etree is None:
130 xsdimage = None
131