Author: bugman
Date: Mon Dec 8 16:04:49 2014
New Revision: 27016
URL: http://svn.gna.org/viewcvs/relax?rev=27016&view=rev
Log:
Created an initial data store object for handling the conversion of nmrglue
data to and from XML.
This is the data_store.nmrglue.Nmrglue data container which inherits from
data_store.data_classes.Element. Custom to_xml() and from_xml() methods have
been added to
specifically convert the numpy data element to and from Base64 format for fast
and efficient
storage.
Added:
branches/nmrglue/data_store/nmrglue.py
Added: branches/nmrglue/data_store/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/data_store/nmrglue.py?rev=27016&view=auto
==============================================================================
--- branches/nmrglue/data_store/nmrglue.py (added)
+++ branches/nmrglue/data_store/nmrglue.py Mon Dec 8 16:04:49 2014
@@ -0,0 +1,102 @@
+###############################################################################
+# #
+# Copyright (C) 2014 Edward d'Auvergne #
+# #
+# This file is part of the program relax (http://www.nmr-relax.com). #
+# #
+# This program is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# This program is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details. #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with this program. If not, see <http://www.gnu.org/licenses/>. #
+# #
+###############################################################################
+
+# Module docstring.
+"""Special relax data storage for nmrglue data."""
+
+# Python module imports.
+from base64 import b64encode, decodestring
+from numpy import float32, frombuffer
+
+# relax module imports.
+from data_store.data_classes import Element
+from lib.xml import object_to_xml, xml_to_object
+
+
+class Nmrglue(Element):
+ """Container for the global GUI data structures."""
+
+ def __init__(self):
+ """Initialise the container info."""
+
+ # Execute the base class __init__() method.
+ super(Gui, self).__init__()
+
+ # Initialise the data.
+ self.dic = None
+ self.udic = None
+ self.data = None
+
+
+ def from_xml(self, nmrglue_node, file_version=1):
+ """Recreate the nmrglue data structure from the XML gui node.
+
+ @param gui_node: The gui XML node.
+ @type gui_node: xml.dom.minicompat.Element instance
+ @keyword file_version: The relax XML version of the XML file.
+ @type file_version: int
+ """
+
+ # Get the data node.
+ data_nodes = nmrglue_node.getElementsByTagName('data')
+
+ # Loop over the info nodes of the Python object.
+ for sub_node in node.childNodes:
+ # Get the value.
+ if sub_node.localName == 'value':
+ # Convert from Base64 to numpy.float32.
+ buffer = decodestring(sub_node.childNodes[0])
+ self.data = frombuffer(buffer, dtype=np.float32)
+
+ # The shape attribute.
+ shape = eval(node.getAttribute('shape'))
+
+ # Reshape the data.
+ self.data.reshape(shape)
+
+ # Recreate all the other data structures.
+ xml_to_object(gui_node, self, file_version=file_version,
blacklist=['data'])
+
+
+ def to_xml(self, doc, element):
+ """Create an XML element for the container.
+
+ @param doc: The XML document object.
+ @type doc: xml.dom.minidom.Document instance
+ @param element: The element to add the data container XML element to.
+ @type element: XML element object
+ """
+
+ # Call the parent class method for all but the data variable.
+ self.blacklist.append('data')
+ super(Nmrglue, self).to_xml(doc, element)
+
+ # Convert the data into a Base64 string.
+ string = b64encode(self.data)
+
+ # Store the value as the string.
+ val_elem = doc.createElement('value')
+ element.appendChild(val_elem)
+ val_elem.appendChild(doc.createTextNode(string))
+
+ # Set the type and shape as attributes.
+ element.setAttribute('type', 'base64, numpy.float32')
+ element.setAttribute('shape', repr(self.data.shape))
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