From 0d6fdeb15484392bafc3eb236b13f658c4f53ea1 Mon Sep 17 00:00:00 2001
From: Scott Linderman <slinderman@seas.harvard.edu>
Date: Mon, 18 Jan 2016 17:06:42 -0500
Subject: [PATCH] Adding a flag to specify whether a data objects state
sequence should be resampled'
---
pyhsmm/internals/hmm_states.py | 9 +++++++--
pyhsmm/models.py | 5 +++--
2 files changed, 10 insertions(+), 4 deletions(-)
diff --git a/pyhsmm/internals/hmm_states.py b/pyhsmm/internals/hmm_states.py
index 2ab5362..b138531 100644
--- a/pyhsmm/internals/hmm_states.py
+++ b/pyhsmm/internals/hmm_states.py
@@ -20,7 +20,7 @@ class _StatesBase(object):
__metaclass__ = abc.ABCMeta
def __init__(self,model,T=None,data=None,stateseq=None,
- generate=True,initialize_from_prior=True):
+ generate=True,initialize_from_prior=True, fixed_stateseq=False):
self.model = model
self.T = T if T is not None else data.shape[0]
@@ -28,6 +28,10 @@ class _StatesBase(object):
self.clear_caches()
+ self.fixed_stateseq = fixed_stateseq
+ if fixed_stateseq:
+ assert stateseq is not None, "fixed_stateseq requires a stateseq to be supplied"
+
if stateseq is not None:
self.stateseq = np.array(stateseq,dtype=np.int32)
elif generate:
@@ -353,7 +357,8 @@ class HMMStatesPython(_StatesBase):
self.sample_backwards_normalized(alphan)
def resample(self):
- return self.resample_normalized()
+ if not self.fixed_stateseq:
+ return self.resample_normalized()
@staticmethod
def _sample_forwards_log(betal,trans_matrix,init_state_distn,log_likelihoods):
diff --git a/pyhsmm/models.py b/pyhsmm/models.py
index 5c044ff..9e10134 100644
--- a/pyhsmm/models.py
+++ b/pyhsmm/models.py
@@ -61,11 +61,12 @@ class _HMMBase(Model):
self._clear_caches()
- def add_data(self,data,stateseq=None,**kwargs):
+ def add_data(self,data,stateseq=None,fixed_stateseq=False,**kwargs):
self.states_list.append(
self._states_class(
model=self,data=data,
- stateseq=stateseq,**kwargs))
+ stateseq=stateseq, fixed_stateseq=fixed_stateseq,
+ **kwargs))
return self.states_list[-1]
def generate(self,T,keep=True):
--
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