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SimStore: Support for OpenMM snapshots #949

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Merged
dwhswenson merged 15 commits into from
Dec 23, 2020
Merged

SimStore: Support for OpenMM snapshots #949

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a67f164
Refactor for attribute handler factories
dwhswenson Dec 1, 2020
51cbccd
redo attribute handlers; integrate for ndarray
dwhswenson Dec 3, 2020
31892e9
complete transition to attribute handlers (numpy)
dwhswenson Dec 3, 2020
1a2ae80
support for simtk units (needs tests)
dwhswenson Dec 3, 2020
c4d0ade
most of the way to storing OpenMM snapshots
dwhswenson Dec 4, 2020
d4546e2
Add engine to StaticContainer/KineticContainer
dwhswenson Dec 4, 2020
b8fa05d
Seems like I can store/load OpenMM snapshots now!
dwhswenson Dec 5, 2020
1523850
move proxy and UUID stuff to their own files
dwhswenson Dec 12, 2020
7224f2e
Fix test for new file locs
dwhswenson Dec 12, 2020
4e29269
docstrings
dwhswenson Dec 12, 2020
c5b6f78
Misc fixes to get the new tutorial to work
dwhswenson Dec 12, 2020
1bf7a16
tests for attribute_handler.py
dwhswenson Dec 19, 2020
9e901bf
Additional test for scalarize_singletons
dwhswenson Dec 19, 2020
8f97732
tests for simstore/simtk-quantity serialization
dwhswenson Dec 20, 2020
62d09d6
integration tests for openmm snapshots
dwhswenson Dec 20, 2020
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Refactor for attribute handler factories
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@dwhswenson
dwhswenson committed Dec 1, 2020
commit a67f1644bd1fcceb4cc8185dc50e23c64b41244c
34 changes: 34 additions & 0 deletions openpathsampling/experimental/simstore/attribute_handlers.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
from .my_types import parse_ndarray_type


class HandlerFactory(object):
def is_my_type(self, type_str):
pass

def serializer(self, type_str):
pass

def deserializer(self, type_str):
pass

class NDArrayHandlerFactory(HandlerFactory):
def is_my_type(self, type_str):
as_ndarray = parse_ndarray_type(type_str)

def serializer(self, type_str):
as_ndarray = self.is_my_type(type_str)
if as_ndarray:
dtype, shape = as_ndarray
handler = lambda data, _: \
np.fromstring(data, dtype=dtype).reshape(shape)
return handler

def deserializer(self, type_str):
as_ndarray = self.is_my_type(type_str)
if as_ndarray:
dtype, shape = as_ndarray
return lambda arr: \
arr.astype(dtype=dtype, copy=False).tostring()



37 changes: 27 additions & 10 deletions openpathsampling/experimental/simstore/serialization.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import numpy as np
from .my_types import parse_ndarray_type
from . import serialization_helpers as serialization
from .attribute_handlers import NDArrayHandlerFactory
import json

import logging
Expand Down Expand Up @@ -96,6 +97,9 @@ def make_all_lazies(self, lazies):


class SchemaDeserializer(object):
handler_factories = [
NDArrayHandlerFactory(),
]
default_handlers = {
'lazy': serialization.search_caches,
'uuid': serialization.search_caches,
Expand All @@ -113,9 +117,15 @@ def __init__(self, schema, table, cls):
self.attribute_handlers = self.init_attribute_handlers()

# TODO: move this external
@staticmethod
def make_numpy_handler(dtype, shape):
return lambda data, _: np.fromstring(data, dtype=dtype).reshape(shape)
# @staticmethod
# def make_numpy_handler(dtype, shape):
# return lambda data, _: np.fromstring(data, dtype=dtype).reshape(shape)

def get_handler_from_factories(self, type_name):
for factory in self.handler_factories:
handler = factory.serializer(type_name)
if handler is not None:
return handler

def init_attribute_handlers(self):
attribute_handlers = {}
Expand All @@ -124,10 +134,11 @@ def init_attribute_handlers(self):
if type_name in self.default_handlers:
handler = self.default_handlers[type_name]
else:
as_ndarray = parse_ndarray_type(type_name)
if as_ndarray:
(dtype, shape) = as_ndarray
handler = self.make_numpy_handler(dtype, shape)
handler = self.get_handler_from_factories(type_name)
# as_ndarray = parse_ndarray_type(type_name)
# if as_ndarray:
# (dtype, shape) = as_ndarray
# handler = self.make_numpy_handler(dtype, shape)
if handler:
attribute_handlers[attr] = handler
return attribute_handlers
Expand Down Expand Up @@ -158,9 +169,15 @@ class ToDictSerializer(SchemaDeserializer):

# TODO: move this external; that will allow us to remove this class
# (use it as input to SchemaSerializer or a class factory for that)
@staticmethod
def make_numpy_handler(dtype, shape):
return lambda arr: arr.astype(dtype=dtype, copy=False).tostring()
# @staticmethod
# def make_numpy_handler(dtype, shape):
# return lambda arr: arr.astype(dtype=dtype, copy=False).tostring()

def get_handler_from_factories(self, type_name):
for factory in self.handler_factories:
handler = factory.serializer(type_name)
if handler is not None:
return handler

def __call__(self, obj):
dct = obj.to_dict()
Expand Down