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"""
Module to convert Glue objects to and from JSON descriptions
Example Usage:
s = GlueSerializer(object)
s.dumpo() -> a JSON-serializeable dict
s.dumps() -> a JSON string
s.dump(file) -> dump to a file object
varname = s.id(x) -> string identifier that uniquely labels an object in
the Serialized state
u = GlueUnSerializer.load(file)
u = GlueUnSerializer.loads(str)
u.object(varname) -> A reconstituted version of `x`
u.object('__main__') -> The object passed to the GlueSerializer constructor
Developer Notes:
Custom methods to serialize a class of objects can be registered either by:
- wrapping a serialization function in the @saver decorator::
@saver(TypeToSave)
def save(object, context):
...
- Defining a __gluestate__(self, context) method
These methods should return a JSON-serializable dict representing the
object. context is a GlueSerializer instance. The `context.id` and
`context.do` methods are helpful for referencing or serializing or
dependencies
Unserializer methods can be registered either via:
- wrapping the method in the @loader decorator::
@loader(TypeToLoad)
def load(rec, context)
`rec` is the JSON dict created from the saver, and `context` is a
GlueUnserializer object. context.object() is useful for unserializing
dependencies.
Versions:
Both the @saver and @loader take an optional version keyword. Whenever
you modify the serialization format for an object, you should register a
new saver and loader version. This ensures Glue can still load old
serialization protocols. Versions must be sequential integers,
starting from 1.
"""
from __future__ import absolute_import, division, print_function
import os
import json
import uuid
import types
import logging
from io import BytesIO
from itertools import count
from collections import defaultdict
from base64 import b64encode, b64decode
from inspect import isgeneratorfunction
import numpy as np
from matplotlib.colors import Colormap
from matplotlib import cm
from glue.external import six
from glue import core
from glue.core.data import Data
from glue.core.component_id import ComponentID, PixelComponentID
from glue.core.component import (Component, CategoricalComponent,
DerivedComponent, CoordinateComponent)
from glue.core.subset import (OPSYM, SYMOP, CompositeSubsetState,
SubsetState, Subset, RoiSubsetState,
InequalitySubsetState, RangeSubsetState)
from glue.core import (VisualAttributes, ComponentLink, DataCollection)
from glue.core.component_link import CoordinateComponentLink
from glue.core.roi import Roi
from glue.core import glue_pickle as gp
from glue.core.subset_group import coerce_subset_groups
from glue.utils import lookup_class
literals = tuple([type(None), float, int, bytes, bool, list, tuple])
if six.PY2:
literals += (long,)
literals += np.ScalarType
# We need to make sure that we don't break backward-compatibility when we move
# classes/functions around in Glue, so we have a file that maps the old paths to
# the new location, and we read this in to PATH_PATCHES.
PATCH_FILE = os.path.abspath(os.path.join('/usr/share/glue',
'state_path_patches.txt'))
# For Mac app, need to get file from source directory
if not os.path.exists(PATCH_FILE) and 'site-packages.zip' in PATCH_FILE:
PATCH_FILE = PATCH_FILE.replace('site-packages.zip', 'glue')
PATH_PATCHES = {}
for line in open(PATCH_FILE):
before, after = line.strip().split(' -> ')
PATH_PATCHES[before.strip()] = after.strip()
def lookup_class_with_patches(name):
"""
A wrapper to lookup_class that also patches paths to ensure
backward-compatibility when functions/classes are moved around.
"""
while name in PATH_PATCHES:
name = PATH_PATCHES[name]
return lookup_class(name)
class GlueSerializeError(RuntimeError):
pass
class VersionedDict(object):
"""
A dict-like object which associates (key, version_int) pairs
with an object. Bracket syntax (d[key]) returns the highest-version
value stored with a key.
Versions must be sequential integers starting with 1, and must be
added in order
Examples
--------
v = VersionedDict()
v['key', 1] = 'v1'
v['key', 2] = 'v2'
v['key'] -> 'v2', 2
v.get_version('key', 2) -> 'v2'
v.get_version('key', 1) -> 'v1'
'key' in v -> True
Not allowed:
v['key', 4] = 'cannot skip versions'
v['key', 2] = 'cannot overwrite versions'
v['key', 'bad'] = 'versions must be integers'
"""
def __init__(self):
self._data = defaultdict(dict)
def __contains__(self, key):
return key in self._data
def get_version(self, key, version=None):
"""
Get a specific version of a value stored with a key
:param key: The key to fetch
:param value: the version of the value to fetch. Defaults to latest
"""
if version is None:
if key not in self._data:
raise KeyError("No value associated with any version of %s"
% key)
vs = self._data[key]
return vs[max(vs)]
try:
return self._data[key][version]
except KeyError:
raise KeyError("No value associated with version %s of %s" %
(version, key))
def __getitem__(self, key):
"""Retrieve the highest-version value stored with a key
Returns a tuple of the value, and the version it is associated with
"""
if key not in self._data:
raise KeyError(key)
versions = self._data[key]
return versions[max(versions)], max(versions)
def __delitem__(self, key):
raise ValueError("Cannot remove items from VersionedDict")
def __len__(self):
return len(self._data)
def __setitem__(self, key, value):
""" Assign a new value with a particular key and version
:param key: a tuple of (key, version)
version must be an integer, equal to the previous version + 1 (or 1)
Overwriting versions is not permitted, and will raise a KeyError
:param value: The value to associate with the (key, version) pair
"""
if len(key) != 2:
raise ValueError("Key must be a (item, version) pair")
item, version = key
try:
version = int(version)
except ValueError:
raise ValueError("Version must be an integer: %s" % version)
if version > 1 and (version - 1) not in self._data[item]:
raise KeyError("Cannot assign version %i of item before adding "
"version %i" % (version, version - 1))
if version in self._data[item]:
raise KeyError("Cannot overwrite version %i of %s" %
(version, item))
self._data[item][version] = value
class GlueSerializer(object):
"""
Serialize an object graph
"""
dispatch = VersionedDict()
def __init__(self, obj, include_data=False):
self._names = {} # map id(object) -> name
self._objs = {} # map name -> object
self._working = set()
self._main = obj
self.id(obj)
self.include_data = include_data
@classmethod
def serializes(cls, obj, version=1):
def decorator(func):
cls.dispatch[(obj, version)] = func
return func
return decorator
def _label(self, obj):
if obj is self._main:
return '__main__'
elif hasattr(obj, 'label'):
return self._disambiguate(obj.label)
else:
return self._disambiguate(type(obj).__name__)
def id(self, obj):
"""
Return a unique name for an object, and add it to the ID registry
if necessary.
"""
if isinstance(obj, six.string_types):
return 'st__%s' % obj
if type(obj) in literals:
return obj
oid = id(obj)
if oid in self._names:
return self._names[oid]
name = self._label(obj)
assert name not in self._objs
logging.debug("Registering %r as %s", obj, name)
self._objs[name] = obj
self._names[oid] = name
return name
def object(self, name):
return self._objs[name]
def do_all(self):
sz = -1
while sz != len(self._objs):
sz = len(self._objs)
# we need to construct this in two steps otherwise we get a
# 'dictionary changed size during iteration' error.
result = [(oid, self.do(obj)) for oid, obj in list(self._objs.items())]
result = dict(result)
return result
def do(self, obj):
"""
Serialize an object, but do not add it to
the ID registry
"""
if isinstance(obj, six.string_types):
return 'st__' + obj
if type(obj) in literals:
return obj
oid = id(obj)
if oid in self._working:
raise GlueSerializeError("Circular reference detected")
self._working.add(oid)
fun, version = self._dispatch(obj)
logging.debug("Serializing %s with %s", obj, fun)
result = fun(obj, self)
if isinstance(obj, types.FunctionType):
result['_type'] = 'types.FunctionType'
elif isinstance(obj, types.MethodType):
result['_type'] = 'types.MethodType'
else:
result['_type'] = "%s.%s" % (type(obj).__module__,
type(obj).__name__)
if version > 1:
result['_protocol'] = version
self._working.remove(oid)
return result
def _dispatch(self, obj):
if hasattr(obj, '__gluestate__'):
return type(obj).__gluestate__, 1
try:
for typ in type(obj).mro():
if typ in self.dispatch:
return self.dispatch[typ]
except TypeError: # no mro
pass
raise GlueSerializeError("Don't know how to serialize"
" %r of type %s" % (obj, type(obj)))
def _disambiguate(self, name):
if name not in self._objs:
return name
for i in count(0):
newname = "%s_%i" % (name, i)
if newname not in self._objs:
return newname
def dumpo(self):
"""
Dump an object (with needed dependencies) into a
JSON Serializable data structure.
Note: If eventually dumping to a string or file, dumps or dump
are more robust
"""
return self.do_all()
@staticmethod
def json_default(o):
"""Default JSON enconding, to handle some special cases
In particular, coerces numpy scalars to the equivalent
python types
Can be used as default kwarg in json.dumps/json.dump
"""
if np.isscalar(o) and isinstance(o, np.generic):
return np.asscalar(o) # coerce numpy number to pure-python type
if isinstance(o, (tuple, set)):
return list(o)
return o
def dumps(self, indent=None):
result = self.dumpo()
return json.dumps(result, indent=indent, default=self.json_default)
def dump(self, outfile, indent=None):
result = self.dumpo()
return json.dump(result, outfile, default=self.json_default,
indent=indent)
class GlueUnSerializer(object):
dispatch = VersionedDict()
def __init__(self, string=None, fobj=None):
if string is None and fobj is None:
raise ValueError("Most provide either a string or a file")
self._names = {} # map id(object) -> name
self._objs = {} # map name -> object
self._working = set()
self._rec = json.loads(string) if string else json.load(fobj)
@classmethod
def loads(cls, string):
return cls(string=string)
@classmethod
def load(cls, fobj):
return cls(fobj=fobj)
@classmethod
def unserializes(cls, obj, version=1):
def decorator(func):
cls.dispatch[(obj, version)] = func
return func
return decorator
def _dispatch(self, rec):
typ = lookup_class_with_patches(rec['_type'])
if typ is None:
raise GlueSerializeError("Unkonwn type %s" % rec['_type'])
version = rec.get('_protocol', 1)
if hasattr(typ, '__setgluestate__'):
return typ.__setgluestate__
for t in typ.mro():
try:
return self.dispatch.get_version(t, version)
except KeyError:
continue
raise GlueSerializeError("Don't know how to load"
" objects of type %s" % typ)
def register_object(self, obj_id, obj):
self._objs[obj_id] = obj
@core.registry.disable
def object(self, obj_id):
if isinstance(obj_id, six.string_types):
if obj_id.startswith('st__'): # a string literal
return obj_id[4:]
if obj_id in self._objs:
return self._objs[obj_id]
if obj_id not in self._rec:
raise GlueSerializeError("Unrecognized object %s" % obj_id)
if obj_id in self._working:
raise GlueSerializeError(
"Circular Reference detected: %s" % obj_id)
self._working.add(obj_id)
rec = self._rec[obj_id]
elif isinstance(obj_id, literals):
return obj_id
else:
rec = obj_id
func = self._dispatch(rec)
obj = func(rec, self)
# loader functions might yield the constructed value,
# and then futher populate it. This deals with circular
# dependencies.
if isgeneratorfunction(func):
gen, obj = obj, next(obj) # get the partially-constructed value...
if isinstance(obj_id, six.string_types): # ... add it to the registry ...
self._objs[obj_id] = obj
self._working.remove(obj_id)
if isgeneratorfunction(func):
for _ in gen: # ... and finish constructing it
pass
return obj
saver = GlueSerializer.serializes
loader = GlueUnSerializer.unserializes
@saver(dict)
def _save_dict(state, context):
return dict(contents=json.dumps(state))
@loader(dict)
def _load_dict(rec, context):
return json.loads(rec['contents'])
@saver(CompositeSubsetState)
def _save_composite_subset_state(state, context):
return dict(state1=context.id(state.state1),
state2=context.id(state.state2))
@loader(CompositeSubsetState)
def _load_composite_subset_state(rec, context):
cls = lookup_class_with_patches(rec['_type'])
result = cls(context.object(rec['state1']),
context.object(rec['state2']))
return result
@saver(SubsetState)
def _save_subset_state(state, context):
return {}
@loader(SubsetState)
def _load_subset_state(rec, context):
return SubsetState()
@saver(RangeSubsetState)
def _save_range_subset_state(state, context):
return dict(lo=state.lo, hi=state.hi, att=context.id(state.att))
@loader(RangeSubsetState)
def _load_range_subset_state(rec, context):
return RangeSubsetState(rec['lo'], rec['hi'], context.object(rec['att']))
@saver(RoiSubsetState)
def _save_roi_subset_state(state, context):
return dict(xatt=context.id(state.xatt),
yatt=context.id(state.yatt),
roi=context.id(state.roi))
@loader(RoiSubsetState)
def _load_roi_subset_state(rec, context):
return RoiSubsetState(context.object(rec['xatt']),
context.object(rec['yatt']),
context.object(rec['roi']))
@saver(InequalitySubsetState)
def _save_inequality_subset_state(state, context):
return dict(left=context.id(state.left),
right=context.id(state.right),
op=OPSYM.get(state.operator))
@loader(InequalitySubsetState)
def _load_inequality_subset_state(rec, context):
return InequalitySubsetState(context.object(rec['left']),
context.object(rec['right']),
SYMOP[rec['op']])
@saver(Roi)
def _save_roi(roi, context):
raise NotImplementedError
@loader(Roi)
def _laod_roi(roi, context):
raise NotImplementedError
@saver(VisualAttributes)
def _save_style(style, context):
return dict((a, getattr(style, a)) for a in style._atts)
@loader(VisualAttributes)
def _load_style(rec, context):
result = VisualAttributes()
for attr in result._atts:
setattr(result, attr, rec[attr])
return result
@saver(Subset)
def _save_subset(subset, context):
return dict(style=context.do(subset.style),
state=context.id(subset.subset_state),
label=subset.label)
@loader(Subset)
def _load_subset(rec, context):
result = Subset(None)
result.style = context.object(rec['style'])
result.subset_state = context.object(rec['state'])
result.label = rec['label']
return result
@saver(DataCollection)
def _save_data_collection(dc, context):
cids = [c for data in dc for c in data.component_ids()]
components = [data.get_component(c)
for data in dc for c in data.component_ids()]
return dict(data=list(map(context.id, dc)),
links=list(map(context.id, dc.links)),
cids=list(map(context.id, cids)),
components=list(map(context.id, components)))
@saver(DataCollection, version=2)
def _save_data_collection_2(dc, context):
result = _save_data_collection(dc, context)
result['groups'] = list(map(context.id, dc.subset_groups))
return result
@saver(DataCollection, version=3)
def _save_data_collection_3(dc, context):
result = _save_data_collection_2(dc, context)
result['subset_group_count'] = dc._sg_count
return result
@loader(DataCollection)
def _load_data_collection(rec, context):
dc = DataCollection(list(map(context.object, rec['data'])))
for link in rec['links']:
dc.add_link(context.object(link))
coerce_subset_groups(dc)
return dc
@loader(DataCollection, version=2)
def _load_data_collection_2(rec, context):
result = _load_data_collection(rec, context)
result._subset_groups = list(map(context.object, rec['groups']))
for grp in result.subset_groups:
grp.register_to_hub(result.hub)
return result
@loader(DataCollection, version=3)
def _load_data_collection_3(rec, context):
result = _load_data_collection_2(rec, context)
result._sg_count = rec['subset_group_count']
return result
@saver(Data)
def _save_data(data, context):
return dict(components=[(context.id(c),
context.id(data.get_component(c)))
for c in data._components],
subsets=[context.id(s) for s in data.subsets],
label=data.label,
coords=context.id(data.coords))
@saver(Data, version=2)
def _save_data_2(data, context):
result = _save_data(data, context)
result['style'] = context.do(data.style)
return result
@loader(Data)
def _load_data(rec, context):
label = rec['label']
result = Data(label=label)
result.coords = context.object(rec['coords'])
# we manually rebuild pixel/world components, so
# we override this function. This is pretty ugly
result._create_pixel_and_world_components = lambda: None
comps = [list(map(context.object, [cid, comp]))
for cid, comp in rec['components']]
comps = sorted(comps,
key=lambda x: isinstance(x[1], (DerivedComponent,
CoordinateComponent)))
for cid, comp in comps:
if isinstance(comp, CoordinateComponent):
comp._data = result
result.add_component(comp, cid)
assert result._world_component_ids == []
coord = [c for c in comps if isinstance(c[1], CoordinateComponent)]
coord = [x[0] for x in sorted(coord, key=lambda x: x[1])]
assert len(coord) == result.ndim * 2
result._world_component_ids = coord[:len(coord) // 2]
result._pixel_component_ids = coord[len(coord) // 2:]
for s in rec['subsets']:
result.add_subset(context.object(s))
return result
@loader(Data, version=2)
def _load_data_2(rec, context):
# adds style saving
result = _load_data(rec, context)
result.style = context.object(rec['style'])
return result
@saver(Data, version=3)
def _save_data_3(data, context):
result = _save_data_2(data, context)
result['_key_joins'] = [[context.id(k), context.id(v0), context.id(v1)]
for k, (v0, v1) in data._key_joins.items()]
return result
@loader(Data, version=3)
def _load_data_3(rec, context):
result = _load_data_2(rec, context)
yield result
result._key_joins = dict((context.object(k), (context.object(v0), context.object(v1)))
for k, v0, v1 in rec['_key_joins'])
@saver(Data, version=4)
def _save_data_4(data, context):
result = _save_data_2(data, context)
def save_cid_tuple(cids):
return tuple(context.id(cid) for cid in cids)
result['_key_joins'] = [[context.id(k), save_cid_tuple(v0), save_cid_tuple(v1)]
for k, (v0, v1) in data._key_joins.items()]
result['uuid'] = data.uuid
return result
@loader(Data, version=4)
def _load_data_4(rec, context):
result = _load_data_2(rec, context)
yield result
def load_cid_tuple(cids):
return tuple(context.object(cid) for cid in cids)
result._key_joins = dict((context.object(k), (load_cid_tuple(v0), load_cid_tuple(v1)))
for k, v0, v1 in rec['_key_joins'])
if 'uuid' in rec and rec['uuid'] is not None:
result.uuid = rec['uuid']
else:
result.uuid = str(uuid.uuid4())
@saver(ComponentID)
def _save_component_id(cid, context):
return dict(label=cid.label, hidden=cid.hidden)
@loader(ComponentID)
def _load_component_id(rec, context):
return ComponentID(rec['label'], rec['hidden'])
@saver(PixelComponentID)
def _save_component_id(cid, context):
return dict(axis=cid.axis, label=cid.label, hidden=cid.hidden)
@loader(PixelComponentID)
def _load_component_id(rec, context):
if 'axis' in rec:
axis = rec['axis']
else: # backward-compatibility
axis = int(rec['label'].split()[2])
return PixelComponentID(axis, rec['label'], rec['hidden'])
@saver(Component)
def _save_component(component, context):
if not context.include_data and hasattr(component, '_load_log'):
log = component._load_log
return dict(log=context.id(log),
log_item=log.id(component))
return dict(data=context.do(component.data),
units=component.units)
@loader(Component)
def _load_component(rec, context):
if 'log' in rec:
return context.object(rec['log']).component(rec['log_item'])
return Component(data=context.object(rec['data']),
units=rec['units'])
@saver(CategoricalComponent)
def _save_categorical_component(component, context):
if not context.include_data and hasattr(component, '_load_log'):
log = component._load_log
return dict(log=context.id(log),
log_item=log.id(component))
return dict(categorical_data=context.do(component.labels),
categories=context.do(component.categories),
jitter_method=context.do(component._jitter_method),
units=component.units)
@loader(CategoricalComponent)
def _load_categorical_component(rec, context):
if 'log' in rec:
return context.object(rec['log']).component(rec['log_item'])
return CategoricalComponent(categorical_data=context.object(rec['categorical_data']),
categories=context.object(rec['categories']),
jitter=context.object(rec['jitter_method']),
units=rec['units'])
@saver(DerivedComponent)
def _save_derived_component(component, context):
return dict(link=context.id(component.link))
@loader(DerivedComponent)
def _load_derived_component(rec, context):
return DerivedComponent(None, link=context.object(rec['link']))
@saver(ComponentLink)
def _save_component_link(link, context):
frm = list(map(context.id, link.get_from_ids()))
to = list(map(context.id, [link.get_to_id()]))
using = context.do(link.get_using())
inverse = context.do(link.get_inverse())
hidden = link.hidden
return dict(frm=frm, to=to, using=using, inverse=inverse, hidden=hidden)
@loader(ComponentLink)
def _load_component_link(rec, context):
frm = list(map(context.object, rec['frm']))
to = list(map(context.object, rec['to']))[0]
using = context.object(rec['using'])
inverse = context.object(rec['inverse'])
result = ComponentLink(frm, to, using, inverse)
result.hidden = rec['hidden']
return result
@saver(CoordinateComponentLink)
def _save_coordinate_component_link(link, context):
frm = list(map(context.id, link._from_all))
to = list(map(context.id, [link.get_to_id()]))
coords = context.id(link.coords)
index = link.index
pix2world = link.pixel2world
return dict(frm=frm, to=to, coords=coords, index=index,
pix2world=pix2world)
@loader(CoordinateComponentLink)
def _load_coordinate_component_link(rec, context):
to = list(map(context.object, rec['to']))[0] # XXX why is this a list?
coords = context.object(rec['coords'])
index = rec['index']
pix2world = rec['pix2world']
frm = list(map(context.object, rec['frm']))
return CoordinateComponentLink(frm, to, coords, index, pix2world)
@saver(types.FunctionType)
def _save_function(function, context):
ref = "%s.%s" % (function.__module__, function.__name__)
if lookup_class_with_patches(ref) is function:
l = lookup_class_with_patches(ref)
return {'function': ref}
return {'pickle': gp.dumps(function).encode('base64')}
@loader(types.FunctionType)
def _load_function(rec, context):
if 'pickle' in rec:
return gp.loads(rec['pickle'].decode('base64'))
return lookup_class_with_patches(rec['function'])
@saver(types.MethodType)
def _save_method(method, context):
# Note: this only works for methods for which the class can be serialized
return {'instance': context.id(method.__self__), 'method': method.__name__}
@loader(types.MethodType)
def _load_method(rec, context):
instance = context.object(rec['instance'])
return getattr(instance, rec['method'])
@saver(core.Session)
def _save_session(session, context):
# we will rely on GlueApplication to re-populate
return {}
@loader(np.ndarray)
def _load_numpy(rec, context):
s = BytesIO(b64decode(rec['data']))
return np.load(s)
@saver(np.ndarray)
def _save_numpy(obj, context):
f = BytesIO()
np.save(f, obj)
data = b64encode(f.getvalue()).decode('ascii')
return dict(data=data)
@saver(Colormap)
def _save_cmap(cmap, context):
return {'cmap':cmap.name}
@loader(Colormap)
def _load_cmap(rec, context):
return cm.get_cmap(rec['cmap'])
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