Commit f84243a0 authored by eric pellegrini's avatar eric pellegrini
Browse files

Created Format package that contains the whole Format interface

parent a6012205
#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 : 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 : 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 Created on Mar 27, 2015
------------------------------------------------------------------------------------------
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
@author: pellegrini @author: pellegrini
''' '''
import abc
import os import os
import re
import StringIO
import tarfile
import numpy import numpy
from MDANSE import REGISTRY from Scientific.IO.NetCDF import NetCDFFile
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'
extension = ".dat" from MDANSE.Framework.Formats.IFormat import IFormat
extensions = ['.dat','.txt'] class NetCDFFormat(IFormat):
@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):
type = 'netcdf' type = 'netcdf'
...@@ -136,9 +59,6 @@ class NetCDFFormat(Format): ...@@ -136,9 +59,6 @@ class NetCDFFormat(Format):
filename = "%s%s" % (filename,cls.extensions[0]) 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. # The NetCDF output file is opened for writing.
outputFile = NetCDFFile(filename, 'w') outputFile = NetCDFFile(filename, 'w')
...@@ -170,45 +90,3 @@ class NetCDFFormat(Format): ...@@ -170,45 +90,3 @@ class NetCDFFormat(Format):
# The NetCDF file is closed. # The NetCDF file is closed.
outputFile.close() 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 : 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()
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