Source Code for Module data.relax_xml

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax is free software; you can redistribute it and/or modify               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing generic fns for creation and parsing of XML representations of python objects.""" 
 25   
 26  # Python module imports. 
 27  from numpy import set_printoptions, array, float32, float64, inf, nan 
 28  try: 
 29      from numpy import float16 
 30  except ImportError: 
 31      float16 = float32    # Support for old numpy versions. 
 32  try: 
 33      from numpy import float128 
 34  except ImportError: 
 35      float128 = float64    # Support for 32-bit numpy versions. 
 36  from re import search 
 37  from string import strip 
 38   
 39  # Modify numpy for better output of numbers and structures. 
 40  set_printoptions(precision=15, threshold=nan) 
 41   
 42  # relax module imports. 
 43  from float import floatAsByteArray, packBytesAsPyFloat 
 44   
 45   
 46 -def fill_object_contents(doc, elem, object=None, blacklist=[]): 
 47      """Place all simple python objects into the XML element namespace. 
 48   
 49      @param doc:         The XML document object. 
 50      @type doc:          xml.dom.minidom.Document instance 
 51      @param elem:        The element to add all python objects to. 
 52      @type elem:         XML element object 
 53      @keyword object:    The python class instance containing the objects to add. 
 54      @type object:       instance 
 55      @keyword blacklist: A list of object names to exclude. 
 56      @type blacklist:    list of str 
 57      """ 
 58   
 59      # Loop over the elements of the object. 
 60      for name in dir(object): 
 61          # Skip blacklisted objects. 
 62          if name in blacklist: 
 63              continue 
 64   
 65          # Skip special objects. 
 66          if search("^_", name): 
 67              continue 
 68   
 69          # Only pack objects in the __mod_attr__ list, if that list exists. 
 70          if hasattr(object, '__mod_attr__') and name not in object.__mod_attr__: 
 71              continue 
 72   
 73          # Create a new element for this object, and add it to the main element. 
 74          sub_elem = doc.createElement(name) 
 75          elem.appendChild(sub_elem) 
 76   
 77          # Get the sub-object. 
 78          subobj = getattr(object, name) 
 79   
 80          # Store floats as IEEE-754 byte arrays (for full precision storage). 
 81          if isinstance(subobj, float) or isinstance(subobj, float16) or isinstance(subobj, float32) or isinstance(subobj, float64) or isinstance(subobj, float128): 
 82              sub_elem.setAttribute('ieee_754_byte_array', repr(floatAsByteArray(subobj))) 
 83   
 84          # Add the text value to the sub element. 
 85          text_val = doc.createTextNode(repr(subobj)) 
 86          sub_elem.appendChild(text_val) 
 87   
 88   
 89 -def node_value_to_python(elem): 
 90      """Convert the node value to a python expression. 
 91   
 92      @param elem:    The XML element. 
 93      @type elem:     xml.dom.minidom.Element instance 
 94      """ 
 95   
 96      # Remove whitespace. 
 97      val = strip(elem.nodeValue) 
 98   
 99      # Convert to python and return. 
100      return eval(val) 
101   
102   
103 -def xml_to_object(elem, base_object=None, set_fn=None, blacklist=[]): 
104      """Convert the XML elements into python objects, and place these into the base object. 
105   
106      @param elem:            The element to extract all python objects from. 
107      @type elem:             xml.dom.minidom.Element instance 
108      @keyword base_object:   The python class instance to place the objects into. 
109      @type base_object:      instance 
110      @keyword set_fn:        A function used to replace setattr for placing the object into the base 
111                              object. 
112      @type set_fn:           function 
113      @keyword blacklist:     A list of object names to exclude. 
114      @type blacklist:        list of str 
115      """ 
116   
117      # Loop over the nodes of the element 
118      for node in elem.childNodes: 
119          # Skip empty nodes. 
120          if node.localName == None: 
121              continue 
122   
123          # The name of the python object to recreate. 
124          name = str(node.localName) 
125   
126          # Skip blacklisted objects. 
127          if name in blacklist: 
128              continue 
129   
130          # IEEE-754 floats (for full precision restoration). 
131          ieee_array = node.getAttribute('ieee_754_byte_array') 
132          if ieee_array: 
133              val = packBytesAsPyFloat(eval(ieee_array)) 
134   
135          # Get the node contents. 
136          else: 
137              val = node_value_to_python(node.childNodes[0]) 
138   
139          # Set the value. 
140          setattr(base_object, name, val) 
141