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further speedup tie

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This commit is contained in:
Zhenwen Dai 2014-10-21 22:56:13 +01:00
parent 0ad7259b04
commit 0cef82db29
1 changed files with 42 additions and 25 deletions
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67
GPy/core/parameterization/ties_and_remappings.py
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@ -91,7 +91,7 @@ class Tie(Parameterized):
def _sync_val_p(p, tieparam, read): def _sync_val_p(p, tieparam, read):
if p.tie is not None: if p.tie is not None:
# ltoi = self._label_to_idx # ltoi = self._label_to_idx
ltoi = np.zeros((self.tied_param.size+1,),dtype=np.int32) ltoi = np.zeros((self.tied_param.tie.max()+1,),dtype=np.int32)
ltoi[self.tied_param.tie] = range(self.tied_param.size) ltoi[self.tied_param.tie] = range(self.tied_param.size)
totie = 1 if toTiedParam else 0 totie = 1 if toTiedParam else 0
p_idx = p._raveled_index() p_idx = p._raveled_index()
@ -142,7 +142,7 @@ class Tie(Parameterized):
if p is tieparam: if p is tieparam:
return return
# ltoi = self._label_to_idx # ltoi = self._label_to_idx
ltoi = np.zeros((self.tied_param.size+1,),dtype=np.int32) ltoi = np.zeros((self.tied_param.tie.max()+1,),dtype=np.int32)
ltoi[self.tied_param.tie] = range(self.tied_param.size) ltoi[self.tied_param.tie] = range(self.tied_param.size)
p_tie = p.tie.flatten() p_tie = p.tie.flatten()
p_size = p.size p_size = p.size
@ -195,7 +195,7 @@ class Tie(Parameterized):
if p is tieparam: if p is tieparam:
return return
# ltoi = self._label_to_idx # ltoi = self._label_to_idx
ltoi = np.zeros((self.tied_param.size+1,),dtype=np.int32) ltoi = np.zeros((self.tied_param.tie.max()+1,),dtype=np.int32)
ltoi[self.tied_param.tie] = range(self.tied_param.size) ltoi[self.tied_param.tie] = range(self.tied_param.size)
p_tie = p.tie.flatten() p_tie = p.tie.flatten()
p_size = p.size p_size = p.size
@ -477,6 +477,30 @@ class Tie(Parameterized):
self.buf_idx = self._highest_parent_._raveled_index_for(self.tied_param) self.buf_idx = self._highest_parent_._raveled_index_for(self.tied_param)
self._untie_ = self.label_buf==0 self._untie_ = self.label_buf==0
self._untie_[self.buf_idx] = True self._untie_[self.buf_idx] = True
self.tie_pairs = np.empty(((self.label_buf>0).sum()-self.tied_param.size,2),dtype=np.uint32)
try:
from scipy import weave
self._label_to_idx = np.zeros((self.tied_param.tie.max()+1,),dtype=np.int32)
self._label_to_idx[self.tied_param.tie] = range(self.tied_param.size)
ltoi = self._label_to_idx
t_start=int(self.buf_idx[0])
t_end=int(self.buf_idx[-1])
label_buf = self.label_buf
buf_size = self.label_buf.size
t_pairs = self.tie_pairs
code = """
int j=0;
for(int i=0;i<buf_size;i++) {
if(label_buf[i]>0 && !(i>=t_start && i<=t_end)) {
t_pairs[j*2] = i;
t_pairs[j*2+1] = ltoi[label_buf[i]];
j++;
}
}
"""
weave.inline(code, arg_names=['ltoi','t_start','t_end','label_buf','buf_size','t_pairs'])
except:
pass
assert(np.all(self.tied_param.tie>0)) assert(np.all(self.tied_param.tie>0))
def _keepParamList(self,plist): def _keepParamList(self,plist):
@ -592,23 +616,19 @@ class Tie(Parameterized):
try: try:
from scipy import weave from scipy import weave
pa_grad = self._highest_parent_.gradient pa_grad = self._highest_parent_.gradient
label_buf = self.label_buf
buf_idx = self.buf_idx
tied_grad = self.tied_param.gradient tied_grad = self.tied_param.gradient
t_size = self.tied_param.size t_size = self.tied_param.size
p_size = self._highest_parent_.gradient.size t_pairs = self.tie_pairs
t_pairs_size = self.tie_pairs.size
code=""" code="""
for(int i=0;i<t_size;i++) { for(int i=0;i<t_size;i++) { tied_grad[i]=0;}
int l = label_buf[buf_idx[i]]; for(int i=0;i<t_pairs_size;i+=2) {
tied_grad[i] = 0; int pidx = t_pairs[i];
double g=0; int tidx = t_pairs[i+1];
for(int j=0;j<p_size;j++) { tied_grad[tidx] += pa_grad[pidx];
if(label_buf[j]==l) {g += pa_grad[j];}
}
tied_grad[i] = g;
} }
""" """
weave.inline(code, arg_names=['pa_grad','label_buf','buf_idx','tied_grad','t_size','p_size']) weave.inline(code, arg_names=['pa_grad','t_pairs','t_pairs_size','tied_grad','t_size'])
except: except:
self.tied_param.gradient = 0. self.tied_param.gradient = 0.
[np.put(self.tied_param.gradient, i, self._highest_parent_.gradient[self.label_buf==self.label_buf[self.buf_idx[i]]].sum()) [np.put(self.tied_param.gradient, i, self._highest_parent_.gradient[self.label_buf==self.label_buf[self.buf_idx[i]]].sum())
@ -619,20 +639,17 @@ class Tie(Parameterized):
try: try:
from scipy import weave from scipy import weave
param_array = self._highest_parent_.param_array param_array = self._highest_parent_.param_array
label_buf = self.label_buf
buf_idx = self.buf_idx
tied_param = self.tied_param tied_param = self.tied_param
t_size = self.tied_param.size t_pairs = self.tie_pairs
p_size = param_array.size t_pairs_size = self.tie_pairs.size
code=""" code="""
for(int i=0;i<t_size;i++) { for(int i=0;i<t_pairs_size;i+=2) {
int l = label_buf[buf_idx[i]]; int pidx = t_pairs[i];
for(int j=0;j<p_size;j++) { int tidx = t_pairs[i+1];
if(label_buf[j]==l) {param_array[j] = tied_param[i];} param_array[pidx] = tied_param[tidx];
}
} }
""" """
weave.inline(code, arg_names=['param_array','label_buf','buf_idx','tied_param','t_size','p_size']) weave.inline(code, arg_names=['param_array','t_pairs','t_pairs_size','tied_param'])
except: except:
for i in xrange(self.tied_param.size): for i in xrange(self.tied_param.size):
self._highest_parent_.param_array[self.label_buf==self.label_buf[self.buf_idx[i]]] = self.tied_param[i] self._highest_parent_.param_array[self.label_buf==self.label_buf[self.buf_idx[i]]] = self.tied_param[i]