Source Code for Module fabio.xsdimage

  1  #!/usr/bin/env python 
  2  # coding: utf8 
  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 os, logging, struct 
 15  import numpy as np 
 16  from fabioimage import fabioimage 
 17  import base64, hashlib 
 18  try: 
 19      from lxml import etree 
 20  except ImportError: 
 21      logging.warning("lxml library is probably not part of your python installation: disabling xsdimage format") 
 22      etree = None 
 23   
 24 -class xsdimage(fabioimage): 
 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 data: input data 
 33          @type data: numpy.ndarray 
 34          @param header: input metadata 
 35          @type header: dict  
 36          @param fname: the name of the file to open 
 37          @type  fname: string 
 38          """ 
 39          fabioimage.__init__(self, data=data, header=header) 
 40          self.dims = [] 
 41          self.coding = None 
 42          if fname is not None: 
 43              self.filename = fname 
 44              self.read(fname) 
 45   
 46 -    def read(self, fname): 
 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 = np.dtype(self.dtype).type 
 61              self.bpp = len(np.array(0, self.bytecode).tostring()) 
 62          except TypeError: 
 63              self.bytecode = np.int32 
 64              self.bpp = 32 
 65              logging.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              logging.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 = np.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims)) 
 87          if not np.little_endian: #by default little endian 
 88              self.data.byteswap(inplace=True) 
 89          self.resetvals() 
 90  #        # ensure the PIL image is reset 
 91          self.pilimage = None 
 92          return self 
 93   
 94 -    def _readheader(self, infile): 
 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: 
106                  logging.warning("Shape: Unable to convert %s to integer in %s" % (i.text, i)) 
107          for i in xml.xpath("//size"): 
108              try: 
109                  self.size = int(i.text) 
110              except: 
111                  logging.warning("Size: Unable to convert %s to integer in %s" % (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              for j in i.xpath("//value"): 
118                  self.coding = j.text 
119          self.rawData = None 
120          for i in xml.xpath("//data"): 
121              self.rawData = i.text 
122          self.md5 = None 
123          for i in xml.xpath("//md5sum"): 
124              for j in i.xpath("//value"): 
125                  self.md5 = j.text 
126   
127  if etree is None: 
128      xsdimage = None 
129