Merge pull request #47 from CovertLab/serialize_rng_state

Serialize PRNG state

Author: U8NWXD

README.md

@@ -70,7 +70,7 @@ given duration. `evolve` returns a dictionary with five keys:
 * outcome - the final state of the system
 
 ```python
-result = system.evolve(state, duration, rates)
+result = system.evolve(duration, state, rates)
 ```
 
 If you are interested in the history of states for plotting or otherwise, these can be

arrow/arrow.py

@@ -23,7 +23,7 @@ def flat_indexes(assorted_lists):
     conjunction with the flat array to recover the original list of lists.
 
     Args:
-        assorted_lists (List[List]): A list of variable length lists. 
+        assorted_lists (List[List]): A list of variable length lists.
 
     Returns numpy arrays:
         flat: The flattened data.
@@ -78,7 +78,7 @@ class StochasticSystem(object):
 
     The stoichiometric matrix has a reaction for each row, with the values in that row
     encoding how many of each substrate are either consumed or produced by the reaction
-    (and zero everywhere else). 
+    (and zero everywhere else).
     '''
 
     def __init__(self, stoichiometry, random_seed=0):
@@ -134,6 +134,7 @@ def __getstate__(self):
 
         return (
             self.random_seed,
+            self.obsidian.get_random_state(),
             self.stoichiometry,
             self.reactants_lengths,
             self.reactants_indexes,
@@ -151,7 +152,7 @@ def __setstate__(self, state):
         Import from pickled state.
         '''
 
-        self.random_seed, self.stoichiometry, self.reactants_lengths, self.reactants_indexes, self.reactants_flat, self.reactions_flat, self.dependencies_lengths, self.dependencies_indexes, self.dependencies_flat, self.substrates_lengths, self.substrates_indexes, self.substrates_flat = state
+        self.random_seed, random_state, self.stoichiometry, self.reactants_lengths, self.reactants_indexes, self.reactants_flat, self.reactions_flat, self.dependencies_lengths, self.dependencies_indexes, self.dependencies_flat, self.substrates_lengths, self.substrates_indexes, self.substrates_flat = state
 
         self.obsidian = Arrowhead(
             self.random_seed,
@@ -166,6 +167,7 @@ def __setstate__(self, state):
             self.substrates_lengths,
             self.substrates_indexes,
             self.substrates_flat)
+        self.obsidian.set_random_state(*random_state)
 
     def evolve(self, duration, state, rates):
         status, steps, time, events, outcome = self.obsidian.evolve(duration, state, rates)

arrow/arrowhead.pyx

@@ -4,7 +4,7 @@ from __future__ import absolute_import, division, print_function
 
 cimport cython
 from cpython.mem cimport PyMem_Malloc, PyMem_Free
-from libc.stdint cimport int64_t
+from libc.stdint cimport int64_t, uint32_t
 from libc.string cimport memset, memcpy
 from libc.stdlib cimport free
 
@@ -132,6 +132,32 @@ cdef class Arrowhead:
         """Returns the number of substrates this system operates on."""
         return self.info.substrates_count
 
+    def get_random_state(self):
+        """Returns the state of the pseudorandom number generator."""
+        cdef mersenne.MTState state
+        obsidian.get_random_state(&self.info, &state)
+
+        mt = copy_c_array(
+            &state.MT[0], mersenne.TWISTER_SIZE, sizeof(uint32_t),
+            np.NPY_UINT32)
+        mt_tempered = copy_c_array(
+            &state.MT_TEMPERED[0], mersenne.TWISTER_SIZE, sizeof(uint32_t),
+            np.NPY_UINT32)
+        index = state.index
+
+        return mt, mt_tempered, index
+
+    def set_random_state(
+            self, uint32_t[::1] mt, uint32_t[::1] mt_tempered,
+            size_t index):
+        cdef mersenne.MTState state
+        memcpy(&state.MT[0], &mt[0], sizeof(state.MT))
+        memcpy(
+            &state.MT_TEMPERED[0], &mt_tempered[0],
+            sizeof(state.MT_TEMPERED))
+        state.index = index
+        obsidian.set_random_state(&self.info, &state)
+
 
 cdef np.ndarray copy_c_array(
         void *source, np.npy_intp element_count, size_t element_size, int np_typenum):

arrow/mersenne.pxd

@@ -5,8 +5,14 @@ from libc.stdint cimport uint32_t
 
 cdef extern from "mersenne.h":
 
+    size_t TWISTER_SIZE
+
     ctypedef struct MTState:
-        pass
+        # mersenne.h defines TWISTER_SIZE to be 624.
+        uint32_t MT[624]
+        uint32_t MT_TEMPERED[624]
+        size_t index
+
 
     void seed(MTState *state, uint32_t seed_value)
 

arrow/obsidian.c

@@ -200,7 +200,7 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
       choice = -1;
       break;
 
-    // Otherwise we need to find the next reaction to perform. 
+    // Otherwise we need to find the next reaction to perform.
     } else {
 
       // First, sample two random values, `point` from a linear distribution and
@@ -310,6 +310,14 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
   return result;
 }
 
+void get_random_state(const Info *info, MTState *exported_random_state) {
+  memcpy(exported_random_state, info->random_state, sizeof(MTState));
+}
+
+void set_random_state(Info *info, const MTState *state) {
+  memcpy(info->random_state, state, sizeof(MTState));
+}
+
 // Print an array of doubles
 int
 print_array(double *array, int length) {

arrow/obsidian.h

@@ -38,6 +38,10 @@ typedef struct Info {
 // arrays that the caller must free().
 evolve_result evolve(Info *info, double duration, int64_t *state, double *rates);
 
+void get_random_state(const Info *info, MTState *exported_random_state);
+
+void set_random_state(Info *info, const MTState *state);
+
 // Supporting print utilities
 int print_array(double *array, int length);
 

arrow/obsidian.pxd

@@ -1,6 +1,6 @@
 # cython: language_level=3str
 
-from libc.stdint cimport int64_t
+from libc.stdint cimport int64_t, uint32_t
 
 from mersenne cimport MTState
 
@@ -37,4 +37,8 @@ cdef extern from "obsidian.h":
 
     evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
 
+    void get_random_state(Info *info, MTState *exported_random_state)
+
+    void set_random_state(Info *info, MTState *state)
+
     int print_array(double *array, int length)

arrow/test/test_arrow.py

@@ -273,6 +273,32 @@ def test_flagella():
 
     print('flagella result: {}'.format(result))
 
+def test_get_set_random_state():
+    stoich = np.array([[1, 1, -1, 0], [-2, 0, 0, 1], [-1, -1, 1, 0]])
+    system = StochasticSystem(stoich)
+
+    state = np.array([1000, 1000, 0, 0])
+    rates = np.array([3.0, 1.0, 1.0])
+
+    system.evolve(1, state, rates)
+
+    rand_state = system.obsidian.get_random_state()
+
+    result_1 = system.evolve(1, state, rates)
+    result_2 = system.evolve(1, state, rates)
+
+    with np.testing.assert_raises(AssertionError):
+        for key in ('time', 'events', 'occurrences', 'outcome'):
+            np.testing.assert_array_equal(
+                result_1[key], result_2[key])
+
+    system.obsidian.set_random_state(*rand_state)
+    result_1_again = system.evolve(1, state, rates)
+
+    for key in ('time', 'events', 'occurrences', 'outcome'):
+        np.testing.assert_array_equal(
+            result_1[key], result_1_again[key])
+
 
 def main(args):
     systems = (

setup.py

@@ -39,7 +39,7 @@
 
 setup(
 	name='stochastic-arrow',
-	version='0.4.3',
+	version='0.4.4',
 	packages=['arrow'],
 	author='Ryan Spangler, John Mason, Jerry Morrison',
 	author_email='spanglry@stanford.edu',