def make_weights(datasets, wtype, make_shared=False, sparse=False):
weights = []
for ds in datasets:
if wtype == 'ichol':
w = num.linalg.inv(ds.covariance.chol)
# print ds.covariance.chol_inverse
elif wtype == 'icov_chol':
w = ds.covariance.chol_inverse
# print w
elif wtype == 'icov':
w = ds.covariance.inverse
else:
raise NotImplementedError('wtype not implemented!')
if make_shared:
sw = shared(w)
if sparse:
sw = ts.csc_from_dense(sw)
weights.append(sw)
else:
weights.append(w)
return weights
def test_sparsevariable(self):
## Re-init counter
Variable.__count__ = count(0)
r1 = sparse.csc_matrix(name='x', dtype='float32')
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_0"
assert r2.auto_name == "auto_1"
assert r3.auto_name == "auto_2"
def test_sparsevariable(self):
## Re-init counter
Variable.__count__ = count(0)
r1 = sparse.csc_matrix(name='x', dtype='float32')
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_0"
assert r2.auto_name == "auto_1"
assert r3.auto_name == "auto_2"
def test_sparsevariable(self):
# Get counter value
autoname_id = next(Variable.__count__)
Variable.__count__ = count(autoname_id)
r1 = sparse.csc_matrix(name="x", dtype="float32")
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_" + str(autoname_id)
assert r2.auto_name == "auto_" + str(autoname_id + 1)
assert r3.auto_name == "auto_" + str(autoname_id + 2)
def test_sparsevariable(self):
## Get counter value
autoname_id = next(Variable.__count__)
Variable.__count__ = count(autoname_id)
r1 = sparse.csc_matrix(name='x', dtype='float32')
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_" + str(autoname_id)
assert r2.auto_name == "auto_" + str(autoname_id + 1)
assert r3.auto_name == "auto_" + str(autoname_id + 2)
def test_sparsevariable(self):
# Get counter value
if not sparse.enable_sparse:
raise SkipTest('Optional package SciPy not installed')
autoname_id = next(Variable.__count__)
Variable.__count__ = count(autoname_id)
r1 = sparse.csc_matrix(name='x', dtype='float32')
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_" + str(autoname_id)
assert r2.auto_name == "auto_" + str(autoname_id + 1)
assert r3.auto_name == "auto_" + str(autoname_id + 2)
def test_sparsevariable(self):
# Get counter value
if not sparse.enable_sparse:
raise SkipTest('Optional package SciPy not installed')
autoname_id = next(Variable.__count__)
Variable.__count__ = count(autoname_id)
r1 = sparse.csc_matrix(name='x', dtype='float32')
r2 = sparse.dense_from_sparse(r1)
r3 = sparse.csc_from_dense(r2)
assert r1.auto_name == "auto_" + str(autoname_id)
assert r2.auto_name == "auto_" + str(autoname_id + 1)
assert r3.auto_name == "auto_" + str(autoname_id + 2)
def test0(self):
a = tensor.as_tensor_variable(numpy.random.rand(5))
s = csc_from_dense(a)
val = eval_outputs([s])
self.assertTrue(str(val.dtype) == "float64")
self.assertTrue(val.format == "csc")
def test_sparse_from_dense(self):
x = tensor.matrix()
self._compile_and_check(
[x], [csc_from_dense(x)], [numpy.random.randn(10, 40).astype(config.floatX)], csc_from_dense.__class__
)
x = T.matrix('x',dtype = 'float32') #T.matrix('x') # the data is presented as rasterized images
#y = T.matrix('y')
#x.tag.test_value = np.random.rand(50,50)
#x.flatten()
#weights1 = gkern2(filter_shape[2],sigma).reshape(filter_shape)
input_shape = (51, 5)
inp_filter_shape = (5,5)
inp_filter_sigma = 7
L0_shape = (31,1)
filter_shape = (9,9)
L1_shape = (15,15)
layer0_input = sparse.csc_from_dense(x)
#final_shape = (s2*s3)
sigma = 1
#i_file = 'Wi_' + str(input_shape) + 'x' + str(L0_shape) + '_' + str(filter_shape[0]) + 's' + str(sigma) + '.npy'
#r_file = 'test_Wr.npy'
LR = np.cast['float32'](0.000001)
#aux = np.array(0.01,dtype='float32')
delta = np.cast['float32'](0.000001)
Wmax =np.cast['float32'](0.9)
Wmin = np.cast['float32'](0.0)
awe = np.cast['float32'](-0.7) # LR * int(W(*)e), usually negative
global generate
# csc_matrix and csr_matrix. These can be called with the usual name # and dtype parameters, but no broadcastable flags are allowed. This is # forbidden since the sparse package, as the SciPy sparse module, does not # provide any way to handle a number of dimensions different from two. The # set of all accepted dtype for the sparse matrices can be found in # sparse.all_dtypes. print sparse.all_dtypes # 2.1 To and Fro # To move back and forth from a dense matrix to a sparse matrix # representation, Theano provides the dense_from_sparse and csc_from_dense # functions. No additional detail must be provided. Here is an example # that performs a full cycle from sparse to sparse: x = sparse.csc_matrix(name='x', dtype='float32') y = sparse.dense_from_sparse(x) z = sparse.csc_from_dense(y) # 2.2 Properties and Construction # Although sparse variables do not allow direct to their properties, this # can be accomplished using the csm_properties function. This will return # a tuple of one-dimensional tensor variables that represents the internal # characteristics of the sparse matrix. # In order to reconstruct a sparse matrix from some properties, the # function CSC and CSR can be used. This will create the sparse matrix in # desired format. As an example, the following code reconstructs a csc # matrix into a csr one. x = sparse.csc_matrix(name='x', dtype='int64') data, indices, indptr, shape = sparse.csm_properties(x) y = sparse.CSR(data, indices, indptr, shape) f = theano.function([x], y)
import numpy as np import scipy.sparse as sp import theano from theano import sparse # pylint: disable = bad-whitespace, invalid-name, no-member, bad-continuation, assignment-from-no-return # if shape[0] > shape[1], use csr. Otherwise, use csc # but, not all ops are available for both yet # so use the one that has what you need # to and fro x = sparse.csc_matrix(name='x', dtype='float32') y = sparse.dense_from_sparse(x) z = sparse.csc_from_dense(y) # resconstruct a csc from a csr x = sparse.csc_matrix(name='x', dtype='int64') data, indices, indptr, shape = sparse.csm_properties(x) y = sparse.CSR(data, indices, indptr, shape) f = theano.function([x], y) a = sp.csc_matrix(np.asarray([[0, 1, 1], [0, 0, 0], [1, 0, 0]])) print a.toarray() print f(a).toarray() # "structured" operations # act only on (originally) nonzero elements x = sparse.csc_matrix(name='x', dtype='float32')
def test0(self):
a = tensor.as_tensor_variable(numpy.random.rand(5))
s = csc_from_dense(a)
val = eval_outputs([s])
self.assertTrue(str(val.dtype) == 'float64')
self.assertTrue(val.format == 'csc')
def __init__(self,fname,constants={},sparse=False):
# parse model specification
with open(fname,'r') as fid:
mod = json.load(fid,object_pairs_hook=OrderedDict)
self.mod = mod
# constants
self.con_dict = OrderedDict()
for name in mod['constants']:
value = constants[name]
self.con_dict[name] = np.array(value) if type(value) is list else value
# arguments
self.arg_info = OrderedDict()
self.arg_dict = OrderedDict()
for (name,spec) in mod['arguments'].items():
asize = spec['size']
(amin,amax) = spec['range']
agrid = np.linspace(amin,amax,asize)
info = OrderedDict()
info['size'] = asize
info['grid'] = agrid
self.arg_info[name] = info
self.arg_dict[name] = agrid
# parameters
self.par_info = OrderedDict()
self.par_sizes = []
for (name,spec) in mod['parameters'].items():
ptype = spec.get('type','scalar')
psize = 1 if ptype == 'scalar' else spec['size']
info = OrderedDict()
info['type'] = ptype
info['size'] = psize
self.par_info[name] = info
self.par_sizes.append(psize)
# variables
self.var_info = OrderedDict()
self.var_sizes = []
for (name,spec) in mod['variables'].items():
vtype = spec['type']
info = OrderedDict()
info['type'] = vtype
if vtype == 'scalar':
vsize = 1
self.var_sizes.append(vsize)
elif vtype == 'vector':
vsize = spec['size']
self.var_sizes.append(vsize)
elif vtype == 'function':
vder = spec.get('derivs',[])
nder = len(vder)
args = spec['args']
ainfo = [self.arg_info[arg] for arg in args]
vsize = np.prod([ai['size'] for ai in ainfo])
info['vder'] = vder
info['nder'] = nder
info['args'] = args
info['shape'] = [self.arg_info[a]['size'] for a in args]
info['grid'] = map(lambda v: v.transpose().flatten(),np.meshgrid(*[self.arg_info[a]['grid'] for a in args])) if len(args) > 1 else [self.arg_info[args[0]]['grid']]
self.var_sizes.append(vsize)
self.var_sizes += sum(map(len,vder))*[vsize]
info['size'] = vsize
self.var_info[name] = info
# totals
self.n_pars = len(self.par_info)
self.n_vars = len(self.var_info)
self.sz_pars = np.sum(self.par_sizes)
self.sz_vars = np.sum(self.var_sizes)
# input vectors
self.par_vec = T.dvector('parvec')
self.var_vec = T.dvector('varvec')
# unpack and map out variables
self.par_dict = OrderedDict()
piter = iter(split(self.par_vec,self.par_sizes))
for (name,info) in self.par_info.items():
ptype = info['type']
par = next(piter)
if ptype == 'scalar':
par = par[0]
par.name = name
self.par_dict[name] = par
else:
par.name = name
self.par_dict[name] = par
self.var_dict = OrderedDict()
self.der_dict = OrderedDict()
viter = iter(split(self.var_vec,self.var_sizes))
for (name,info) in self.var_info.items():
var = next(viter)
vtype = info['type']
if vtype == 'scalar':
var = var[0]
var.name = name
self.var_dict[name] = var
elif vtype == 'vector':
var.name = name
self.var_dict[name] = var
elif vtype == 'function':
var.name = name
self.var_dict[name] = var
vder = info.get('vder',[])
nder = len(vder)
self.der_dict[var] = {'': var}
for der in vder:
for s in prefixes(der):
dvar = viter.next()
dvar.name = name+'_'+s
self.der_dict[var][s] = dvar
# define operators
def diff(var,*args):
name = ''.join([getkey(self.arg_dict,v) for v in args])
return self.der_dict[var][name]
def vslice(var,arg,point):
var_name = var.name
arg_name = getkey(self.arg_dict,arg)
var_info = self.var_info[var_name]
args = var_info['args']
(idx, _) = filter(lambda ia: ia[1]==arg_name, enumerate(args))[0]
shape = var_info['shape']
idx_list = slice_dim([point],idx,shape)
return var[idx_list]
def grid(var,arg):
var_name = var.name
arg_name = getkey(self.arg_dict,arg)
var_info = self.var_info[var_name]
args = var_info['args']
(idx, _) = filter(lambda ia: ia[1]==arg_name, enumerate(args))[0]
return var_info['grid'][idx]
def interp(var,arg,x):
i = icut(arg,x)
t = np.clip((arg[i+1]-x)/(arg[i+1]-arg[i]),0.0,1.0)
return t*vslice(var,arg,i) + (1.0-t)*vslice(var,arg,i+1)
self.func_dict = {'diff': diff, 'slice': vslice, 'grid': grid, 'interp': interp}
# combine them all
self.sym_dict = merge(op_dict,self.con_dict,self.par_dict,self.var_dict,self.func_dict,self.arg_dict)
# evaluate
self.equations = []
# regular equations
for eq in mod['equations']:
self.equations.append(eval(eq,{},self.sym_dict))
# derivative relations
for (name,info) in self.var_info.items():
if info['type'] == 'function':
var = self.var_dict[name]
size = info['size']
# derivative relations - symmetric except at 0
vder = info.get('vder','')
args = info['args']
shape = info['shape']
for der in vder:
v0 = '' # function value
for v1 in prefixes(der):
# collect argument info
arg = v1[-1]
(adx, _) = filter(lambda ia: ia[1]==arg, enumerate(args))[0]
s = shape[adx]
grid = info['grid'][adx]
# generate accessors
zer_idx = slice_dim([0],adx,shape)
one_idx = slice_dim([1],adx,shape)
beg_idx = slice_dim(range(s-2),adx,shape)
mid_idx = slice_dim(range(1,s-1),adx,shape)
end_idx = slice_dim(range(2,s),adx,shape)
# calculate derivatives
d0 = self.der_dict[var][v0]
d1 = self.der_dict[var][v1]
self.equations.append(d0[one_idx]-d0[zer_idx]-(grid[one_idx]-grid[zer_idx])*d1[zer_idx])
self.equations.append((d0[end_idx]-d0[beg_idx])-(grid[end_idx]-grid[beg_idx])*d1[mid_idx])
# to next level
v0 = v1
# repack
self.eqn_vec = T.join(0,*map(ensure_vector,self.equations))
# jacobians
self.par_jac = T.jacobian(self.eqn_vec,self.par_vec)
self.var_jac = T.jacobian(self.eqn_vec,self.var_vec)
# sparse?
if sparse:
self.par_jac = S.csc_from_dense(self.par_jac)
self.var_jac = S.csc_from_dense(self.var_jac)
self.linsolve = spsolve
else:
self.linsolve = np.linalg.solve
# compile
print('Compiling...')
self.eqn_fun = theano.function([self.par_vec,self.var_vec],self.eqn_vec)
self.parjac_fun = theano.function([self.par_vec,self.var_vec],self.par_jac)
self.varjac_fun = theano.function([self.par_vec,self.var_vec],self.var_jac)
# newtonian path
t = T.dscalar('t')
start = T.dvector('start')
finish = T.dvector('finish')
path = (1.0-t)*start + t*finish
dpath = T.jacobian(path,t)
self.path_fun = theano.function([start,finish,t],path)
self.dpath_fun = theano.function([start,finish,t],dpath)