gns.tools module

gns.tools.logAddArr(x, y)

logaddexp where x is a scalar and y is an array. Calculates log(exp(x) + sum(exp(y))). Returns a scalar in case that axis = None (exponentiates elements of array then adds them together). np implementation on its own returns an array i.e. doesn’t sum exponentiated elements of array. Axis specifies axis to do summation of exponentials over, and if specified returns an array with shape of the remaining dimensions. Doesn’t try to avoid under/overflow when logaddexp’ing the array y but is more efficient than logAddArr2 as it is vectorised. Axis should be specified such that summation over y results in scalar probably better to use [scipy.misc.]logsumexp(y) and then logaddexp(x,y), although mirculously, this isn’t very fast

gns.tools.logAddArr2(x, y, indexes=(None, ))

Alternative version of logAddArr that avoids over/ underflow errors of exponentiating the array y, to the same extent that np.logaddexp() does Note however that it is slower than logAddArr, so in cases where over/ underflow isn’t an issue, use that Loops over each specified element of y (using rowcol values) and adds to log of sums. Note when trying to avoid under/overflow it only subtracts max(result so far, y_i) for each iteration through y, it doesn’t subtract max(y) from all iterations By default loops over entire array, but to specify a certain row for e.g. a 2d array set indexes to (row_index, slice(None)) or for a certain column (slice(None), col_index)

gns.tools.logAddArr3(x, y, indexes=(None, ))

as above but subtracts max(x, y) when doing logAddExp

gns.tools.logAddExp(a, b, fact)

Calculates fact + log(exp(a - fact) + exp(b - fact)) for scalars a and b. Subtracts fact from a and b before exponentiating in attempt to avoid underflow when a and b are small or overflow when a and b are large, and adds back to final result

gns.tools.logSubArr2(x, y, indexes=(None, ))

Same as logAddArr2 but with logSubExp calculates log(exp(x) - exp(sum(y))). Named …2 for consistency

gns.tools.logSubArr3(x, y, indexes=(None, ))

Same as logAddArr3 but with logSubExp calculates log(exp(x) - exp(sum(y))). Named …3 for consistency

gns.tools.logSubExp(a, b, fact)

Calculates fact + log(exp(a - fact) - exp(b - fact)) for scalars a and b. Subtracts fact from a and b before exponentiating in attempt to avoid underflow when a and b are small or overflow when a and b are large, and adds back to final result