programming is an active process, you speak out what you see in your head. just looking at the code is not enough to get things done in reasonable time, you got to have a systematic approach. the processing has to be on the conscious mind, not the subconscious. after a few hours of verbal investigation, you understand what's going on.
this is specially relevant when you are dealing with a large codebase. comments are better than separate file worklogs. a worklog helps you externalize the mental model so that you can pick up where you left the last time. an important use of worklog is hierarchies, parent-child hierarchies and relationships of types with the others. so you add the type to your hierarchy as you go on reading and at the end you have a pretty clear picture of how things are laid out.
while reading code, pay special attention to the types, and ask yourself why is this type passed into this function, or in that class's constructor. why this parent class instance keeps a reference to the child etc. these help you build a mental model. thinking in terms of functionality instead of parent-child terms helps as parent-child analogy is just a language construct for who has what functionality, code is always in terms of functionality.