Created Format package that contains the whole Format interface

MDANSE/Framework/Formats/ASCIIFormat.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 27, 2015
+
+@author: pellegrini
+'''
+
+import os
+import StringIO
+import tarfile
+
+import numpy
+
+from MDANSE.Framework.Formats.IFormat import IFormat
+
+class ASCIIFormat(IFormat):
+    
+    type = 'ascii'
+
+    extension = ".dat"
+
+    extensions = ['.dat','.txt']
+    
+    @classmethod
+    def write(cls, filename, data, header=""):
+                
+        filename = os.path.splitext(filename)[0]
+        filename = "%s_%s.tar" % (filename,cls.type)
+
+        tf = tarfile.open(filename,'w')
+        
+        for var in data.values():
+
+            tempStr = StringIO.StringIO()
+            if header:
+                tempStr.write(header)
+                tempStr.write('\n\n')  
+            tempStr.write(var.info())
+            tempStr.write('\n\n')            
+            cls.write_array(tempStr,var)
+            tempStr.seek(0)
+
+            info = tarfile.TarInfo(name='%s%s' % (var.name,cls.extensions[0]))
+            info.size=tempStr.len
+            tf.addfile(tarinfo=info, fileobj=tempStr)
+                                    
+        tf.close()
+
+    @classmethod
+    def write_array(cls, fileobject, array, slices=None):
+        
+        if slices is None:
+            slices = [0]*array.ndim
+            slices[-2:] = array.shape[-2:]
+
+        if array.ndim > 2:
+        
+            for a in array:
+                cls.write_array(fileobject,a, slices)
+                slices[len(slices)-array.ndim] = slices[len(slices)-array.ndim] + 1
+
+        else:
+            fileobject.write('#slice:%s\n' % slices)
+            numpy.savetxt(fileobject, array)
+            fileobject.write('\n')

MDANSE/Framework/Formats/IFormat.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 27, 2015
+
+@author: pellegrini
+'''
+
+import abc
+
+from MDANSE import REGISTRY
+
+class IFormat(object):
+    '''
+    This is the base class for nmoldyn data.
+    '''
+    
+    __metaclass__ = REGISTRY
+    
+    type = "format"
+    
+    @abc.abstractmethod
+    def write(self, filename, data, header=""):
+        pass

MDANSE/Framework/IO/Formats.py → MDANSE/Framework/Formats/NetCDFFormat.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
 ''' 
-MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-------------------------------------------------------------------------------------------
-Copyright (C)
-2015- Eric C. Pellegrini Institut Laue-Langevin
-BP 156
-6, rue Jules Horowitz
-38042 Grenoble Cedex 9
-France
-pellegrini[at]ill.fr
-
-This library is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or (at your option) any later version.
-
-This library 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
-Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library; if not, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- 
-Created on Mar 23, 2015
+Created on Mar 27, 2015
 
 @author: pellegrini
 '''
 
-import abc
 import os
-import re
-import StringIO
-import tarfile
 
 import numpy
 
-from MDANSE import REGISTRY
-from MDANSE.Core.Error import Error
-from MDANSE.Externals.svgfig.svgfig import _hacks, Frame, Poly
-
-_hacks["inkscape-text-vertical-shift"] = True
-
-class FormatError(Error):
-    pass
-
-def format_unit_string(unitString):
-
-    return re.sub('[%()]','',unitString)
-           
-class Format(object):
-    '''
-    This is the base class for nmoldyn data.
-    '''
-    
-    __metaclass__ = REGISTRY
-    
-    type = "format"
-    
-    @abc.abstractmethod
-    def write(self, filename, data, header=""):
-        pass
-
-            
-class ASCIIFormat(Format):
-    
-    type = 'ascii'
+from Scientific.IO.NetCDF import NetCDFFile
 
-    extension = ".dat"
+from MDANSE.Framework.Formats.IFormat import IFormat
 
-    extensions = ['.dat','.txt']
-    
-    @classmethod
-    def write(cls, filename, data, header=""):
-                
-        filename = os.path.splitext(filename)[0]
-        filename = "%s_%s.tar" % (filename,cls.type)
-
-        tf = tarfile.open(filename,'w')
-        
-        for var in data.values():
-
-            tempStr = StringIO.StringIO()
-            if header:
-                tempStr.write(header)
-                tempStr.write('\n\n')  
-            tempStr.write(var.info())
-            tempStr.write('\n\n')            
-            cls.write_array(tempStr,var)
-            tempStr.seek(0)
-
-            info = tarfile.TarInfo(name='%s%s' % (var.name,cls.extensions[0]))
-            info.size=tempStr.len
-            tf.addfile(tarinfo=info, fileobj=tempStr)
-                                    
-        tf.close()
-
-    @classmethod
-    def write_array(cls, fileobject, array, slices=None):
-        
-        if slices is None:
-            slices = [0]*array.ndim
-            slices[-2:] = array.shape[-2:]
-
-        if array.ndim > 2:
-        
-            for a in array:
-                cls.write_array(fileobject,a, slices)
-                slices[len(slices)-array.ndim] = slices[len(slices)-array.ndim] + 1
-
-        else:
-            fileobject.write('#slice:%s\n' % slices)
-            numpy.savetxt(fileobject, array)
-            fileobject.write('\n')
-
-
-class NetCDFFormat(Format):
+class NetCDFFormat(IFormat):
 
     type = 'netcdf'
 
@@ -136,9 +59,6 @@ class NetCDFFormat(Format):
 
         filename = "%s%s" % (filename,cls.extensions[0])
        
-        # Import the NetCDFFile function.
-        from Scientific.IO.NetCDF import NetCDFFile
-
         # The NetCDF output file is opened for writing.
         outputFile = NetCDFFile(filename, 'w')
         
@@ -170,45 +90,3 @@ class NetCDFFormat(Format):
         
         # The NetCDF file is closed.
         outputFile.close()
-
-class SVGFormat(Format):
-
-    type = 'svg'
-    
-    extension = ".svg"
-    
-    extensions = ['.svg']
-        
-    @classmethod
-    def write(cls,filename,data, header=""):
-
-        filename = os.path.splitext(filename)[0]
-        filename = "%s.tar" % filename
-
-        tf = tarfile.open(filename,'w')
-                                
-        for var in data.values():
-                        
-            if var.ndim != 1:
-                continue
-            
-            if var.axis in data:
-                axis = data[var.axis]
-                xtitle = "%s (%s)" % (axis.name,format_unit_string(axis.units))
-            else:
-                axis = numpy.arange(len(var))
-                xtitle = 'index'
-                
-            ytitle = "%s (%s)" % (var.name,format_unit_string(var.units))
-                        
-            pl = Poly(zip(axis,var),stroke='blue')
-
-            svgfilename = os.path.join(os.path.dirname(filename),'%s%s' % (var.name,cls.extensions[0]))
-            
-            Frame(min(axis),max(axis),min(var),max(var),pl,xtitle=xtitle,ytitle=ytitle).SVG().save(svgfilename)
-
-            tf.add(svgfilename, arcname='%s%s' % (var.name,cls.extensions[0]))
-            
-            os.remove(svgfilename)
-    
-        tf.close()

MDANSE/Framework/Formats/SVGFormat.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 27, 2015
+
+@author: pellegrini
+'''
+
+import os
+import re
+import tarfile
+
+import numpy
+
+from MDANSE.Externals.svgfig.svgfig import _hacks, Frame, Poly
+from MDANSE.Framework.Formats.IFormat import IFormat
+
+_hacks["inkscape-text-vertical-shift"] = True
+
+def format_unit_string(unitString):
+
+    return re.sub('[%()]','',unitString)
+
+class SVGFormat(IFormat):
+
+    type = 'svg'
+    
+    extension = ".svg"
+    
+    extensions = ['.svg']
+        
+    @classmethod
+    def write(cls,filename,data, header=""):
+
+        filename = os.path.splitext(filename)[0]
+        filename = "%s.tar" % filename
+
+        tf = tarfile.open(filename,'w')
+                                
+        for var in data.values():
+                        
+            if var.ndim != 1:
+                continue
+            
+            if var.axis in data:
+                axis = data[var.axis]
+                xtitle = "%s (%s)" % (axis.name,format_unit_string(axis.units))
+            else:
+                axis = numpy.arange(len(var))
+                xtitle = 'index'
+                
+            ytitle = "%s (%s)" % (var.name,format_unit_string(var.units))
+                        
+            pl = Poly(zip(axis,var),stroke='blue')
+
+            svgfilename = os.path.join(os.path.dirname(filename),'%s%s' % (var.name,cls.extensions[0]))
+            
+            Frame(min(axis),max(axis),min(var),max(var),pl,xtitle=xtitle,ytitle=ytitle).SVG().save(svgfilename)
+
+            tf.add(svgfilename, arcname='%s%s' % (var.name,cls.extensions[0]))
+            
+            os.remove(svgfilename)
+    
+        tf.close()