def _read_kernel(train, standardizer, block_size=None, order='A', dtype=np.float64, force_python_only=False, view_ok=False, return_trained=False):
'''
The method creates a kernel for the in-memory SNP data. It handles these cases
* No standardization is needed & everything is in memory OR uses the FROM-DISK method
'''
from pysnptools.pstreader import PstReader
#Just do a 'python' dot, if no standardization is needed and everything is the right type
if isinstance(standardizer,Identity) and train.val.dtype == dtype:
ts = time.time()
#is_worth_logging = train.val.shape[0] * train.val.shape[1] * test.val.shape[0] > 1e9
#if is_worth_logging: logging.info(" _read_kernel about to multiply train{0} x test{1}".format(train.val.shape,test.val.shape))
if order == 'F': #numpy's 'dot' always returns 'C' order
K = (train.val.dot(train.val.T)).T
else:
K = train.val.dot(train.val.T)
assert PstReader._array_properties_are_ok(K,order,dtype), "internal error: K is not of the expected order or dtype"
#if is_worth_logging: logging.info(" _read_kernel took %.2f seconds" % (time.time()-ts))
if return_trained:
return K, standardizer
else:
return K
else: #Do things the more general SnpReader way.
return SnpReader._read_kernel(train, standardizer, block_size=block_size, order=order, dtype=dtype, force_python_only=force_python_only,view_ok=view_ok, return_trained=return_trained)
def _read_kernel(train, standardizer, block_size=None, order='A', dtype=np.float64, force_python_only=False, view_ok=False, return_trained=False):
'''
The method creates a kernel for the in-memory SNP data. It handles these cases
* No standardization is needed & everything is in memory OR uses the FROM-DISK method
'''
from pysnptools.pstreader import PstReader
#Just do a 'python' dot, if no standardization is needed and everything is the right type
if isinstance(standardizer,Identity) and train.val.dtype == dtype:
ts = time.time()
#is_worth_logging = train.val.shape[0] * train.val.shape[1] * test.val.shape[0] > 1e9
#if is_worth_logging: logging.info(" _read_kernel about to multiply train{0} x test{1}".format(train.val.shape,test.val.shape))
if order == 'F': #numpy's 'dot' always returns 'C' order
K = (train.val.dot(train.val.T)).T
else:
K = train.val.dot(train.val.T)
assert PstReader._array_properties_are_ok(K,order,dtype), "internal error: K is not of the expected order or dtype"
#if is_worth_logging: logging.info(" _read_kernel took %.2f seconds" % (time.time()-ts))
if return_trained:
return K, standardizer
else:
return K
else: #Do things the more general SnpReader way.
return SnpReader._read_kernel(train, standardizer, block_size=block_size, order=order, dtype=dtype, force_python_only=force_python_only,view_ok=view_ok, return_trained=return_trained)
