Well, there isn't any faster way than to compute them, it takes the time it takes
However, depending on exactly how you set up the script, you may be introducing various amounts of overhead. To determine that, however, you would have to post the script.
Generally speaking, your approach should be
1. Converge the self-consistent two-probe calculation. Never mind any "analysis", just make sure to store the NetCDF (checkpoint) file.
2. Perform all analysis from the checkpoint file, using the function
restoreSelfConsistentCalculation() to restore the SCF object, then calculate what you want from that, just as if it were at the end of the main script
3. You don't have to give the k-points one by one to
calculateTransmissionEigenvalues(). As you can see from its
manual entry, you can in fact give it your entire list of k-points in one single call. Then just loop over the results instead, to print them for instance.
You will still have to loop over energies in my point 3, but you can skip the loop in your point 2.1.