Update serialization for all classes

- Use attrs for storing metadata
- Remove pickle usage from Field and PowerSpace

nifty/field.py

 from __future__ import division
-import pickle
 import numpy as np
 
 from keepers import Versionable
@@ -893,14 +892,13 @@ class Field(Loggable, Versionable, object):
     # ---Serialization---
 
     def _to_hdf5(self, hdf5_group):
-        # pickling for nested tuples
-        hdf5_group['field_type_axes'] = pickle.dumps(self.field_type_axes)
-        hdf5_group['domain_axes'] = pickle.dumps(self.domain_axes)
-
-        hdf5_group['dtype'] = self.dtype.name
-        hdf5_group['distribution_strategy'] = self.distribution_strategy
-        hdf5_group['num_domain'] = len(self.domain)
-        hdf5_group['num_ft'] = len(self.field_type)
+        # metadata
+        hdf5_group.attrs['dtype'] = self.dtype.name
+        hdf5_group.attrs['distribution_strategy'] = self.distribution_strategy
+        hdf5_group.attrs['field_type_axes'] = str(self.field_type_axes)
+        hdf5_group.attrs['domain_axes'] = str(self.domain_axes)
+        hdf5_group.attrs['num_domain'] = len(self.domain)
+        hdf5_group.attrs['num_ft'] = len(self.field_type)
 
         ret_dict = {
             'val' : self.val
@@ -923,20 +921,20 @@ class Field(Loggable, Versionable, object):
         new_field.__class__ = cls
         # set values
         temp_domain = []
-        for i in range(hdf5_group['num_domain'][()]):
+        for i in range(hdf5_group.attrs['num_domain']):
             temp_domain.append(loopback_get('s_' + str(i)))
         new_field.domain = tuple(temp_domain)
 
         temp_ft = []
-        for i in range(hdf5_group['num_ft'][()]):
+        for i in range(hdf5_group.attrs['num_ft']):
             temp_domain.append(loopback_get('ft_' + str(i)))
         new_field.field_type = tuple(temp_ft)
 
-        new_field.domain_axes = pickle.loads(hdf5_group['domain_axes'][()])
-        new_field.field_type_axes = pickle.loads(hdf5_group['field_type_axes'][()])
+        exec('new_field.domain_axes = ' + hdf5_group.attrs['domain_axes'])
+        exec('new_field.field_type_axes = ' + hdf5_group.attrs['field_type_axes'])
         new_field._val = loopback_get('val')
-        new_field.dtype = np.dtype(hdf5_group['dtype'][()])
-        new_field.distribution_strategy = hdf5_group['distribution_strategy'][()]
+        new_field.dtype = np.dtype(hdf5_group.attrs['dtype'])
+        new_field.distribution_strategy = hdf5_group.attrs['distribution_strategy']
 
         return new_field
 

nifty/spaces/gl_space/gl_space.py

 from __future__ import division
 
-import pickle
-
 import itertools
 import numpy as np
 
@@ -217,7 +215,8 @@ class GLSpace(Versionable, Space):
     def _to_hdf5(self, hdf5_group):
         hdf5_group['nlat'] = self.nlat
         hdf5_group['nlon'] = self.nlon
-        hdf5_group['dtype'] = self.dtype.name
+        # metadata
+        hdf5_group.attrs['dtype'] = self.dtype.name
 
         return None
 
@@ -226,7 +225,7 @@ class GLSpace(Versionable, Space):
         result = cls(
             nlat=hdf5_group['nlat'][()],
             nlon=hdf5_group['nlon'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
 
         return result

nifty/spaces/hp_space/hp_space.py

@@ -209,13 +209,16 @@ class HPSpace(Versionable, Space):
 
     def _to_hdf5(self, hdf5_group):
         hdf5_group['nside'] = self.nside
-        hdf5_group['dtype'] = self.dtype.name
+        # metadata
+        hdf5_group.attrs['dtype'] = self.dtype.name
+
         return None
 
     @classmethod
     def _from_hdf5(cls, hdf5_group, loopback_get):
         result = cls(
             nside=hdf5_group['nside'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
+
         return result

nifty/spaces/lm_space/lm_space.py

@@ -187,13 +187,15 @@ class LMSpace(Versionable, Space):
 
     def _to_hdf5(self, hdf5_group):
         hdf5_group['lmax'] = self.lmax
-        hdf5_group['dtype'] = self.dtype.name
+        # metadata
+        hdf5_group.attrs['dtype'] = self.dtype.name
+
         return None
 
     @classmethod
     def _from_hdf5(cls, hdf5_group, loopback_get):
         result = cls(
             lmax=hdf5_group['lmax'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
         return result

nifty/spaces/power_space/power_space.py

 # -*- coding: utf-8 -*-
 
-import pickle
 import numpy as np
 
 from keepers import Versionable
@@ -161,13 +160,14 @@ class PowerSpace(Versionable, Space):
     # ---Serialization---
 
     def _to_hdf5(self, hdf5_group):
-        hdf5_group['log'] = self.log
-        hdf5_group['nbin'] = pickle.dumps(self.nbin)
-        hdf5_group['binbounds'] = pickle.dumps(self.binbounds)
         hdf5_group['kindex'] = self.kindex
         hdf5_group['rho'] = self.rho
         hdf5_group['pundex'] = self.pundex
-        hdf5_group['dtype'] = self.dtype.name
+        # metadata
+        hdf5_group.attrs['dtype'] = self.dtype.name
+        hdf5_group.attrs['log'] = self.log
+        hdf5_group.attrs['nbin'] = str(self.nbin)
+        hdf5_group.attrs['binbounds'] = str(self.binbounds)
 
         return {
             'harmonic_domain': self.harmonic_domain,
@@ -182,11 +182,11 @@ class PowerSpace(Versionable, Space):
         # reset class
         new_ps.__class__ = cls
         # set all values
-        new_ps.dtype = np.dtype(hdf5_group['dtype'][()])
+        new_ps.dtype = np.dtype(hdf5_group.attrs['dtype'])
         new_ps._harmonic_domain = loopback_get('harmonic_domain')
-        new_ps._log = hdf5_group['log'][()]
-        new_ps._nbin = pickle.loads(hdf5_group['nbin'][()])
-        new_ps._binbounds = pickle.loads(hdf5_group['binbounds'][()])
+        new_ps._log = hdf5_group.attrs['log']
+        exec('new_ps._nbin = ' + hdf5_group.attrs['nbin'])
+        exec('new_ps._binbounds = ' + hdf5_group.attrs['binbounds'])
 
         new_ps._pindex = loopback_get('pindex')
         new_ps._kindex = hdf5_group['kindex'][:]

nifty/spaces/rg_space/rg_space.py

@@ -328,8 +328,9 @@ class RGSpace(Versionable, Space):
         hdf5_group['shape'] = self.shape
         hdf5_group['zerocenter'] = self.zerocenter
         hdf5_group['distances'] = self.distances
-        hdf5_group['harmonic'] = self.harmonic
-        hdf5_group['dtype'] = self.dtype.name
+        # metadata
+        hdf5_group.attrs['harmonic'] = self.harmonic
+        hdf5_group.attrs['dtype'] = self.dtype.name
 
         return None
 
@@ -339,7 +340,7 @@ class RGSpace(Versionable, Space):
             shape=hdf5_group['shape'][:],
             zerocenter=hdf5_group['zerocenter'][:],
             distances=hdf5_group['distances'][:],
-            harmonic=hdf5_group['harmonic'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            harmonic=hdf5_group.attrs['harmonic'],
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
         return result