Thanks for the responses. Unfortunately, I did not inadequately describe the problem, in light of the responses.
I just want the note values to be what was indicated in the MIDI file, you don't have to infer anything.
Noteworthy allows two rhythms on one staff. It puts stems up and down without any input possible from the user. It only allows two note values in one chord, and does not allow you to mix them so that it can cleanly draw one stem up and one stem down without crossing.
As long as these rules are abided by, which is true a substantial majority of the time in vocal sheet music, there is no reason Noteworthy cannot notate it. There is no guessing which part it is. If the MIDI file says that it is a half note, why cut it off as a quarter? The duration is unambiguously indicated in the MIDI file, there is nothing to infer.
MusicXML would be nice, if it was supported by Noteworthy. I have tried the contributed import program that sends Windows events to Noteworthy, but found it to be buggy and it often crashed Noteworthy. As it stands now, there is no way to get a scanned piece of sheet music reliably into Noteworthy, without doing hours of fix up.
When you import a track that has been notated in two parts, which have different rhythms, it cuts off longer notes at the beginning of the next note. I have submitted a bug report, but received no response.
This is a huge problem, and the solution provided by Noteworthy is to split the track into two staffs at particular pitch. It will even do an analysis before you import and find the pitch that results in the fewest mistakes. You can even set your own pitch ranges for each staff. This helps for some kinds of music, but vocal music, and a lot of other music does not work that way. You wind-up with each part split between staffs, which is not useful for most purposes.
I don't understand why the import can't bring in the notes as indicated by the MIDI events. You are allowed to enter two different note values into a chord when you are manually entering the music. Noteworthy notates it as stem-up and stem-down. The "chord" is logically given the note value of the smaller (i.e. if you put a half with a quarter takes the horizontal space of the quarter note). However, it will sound the full value when played as long as there are notes or rests to take up the full value of the time signature. This should always be true. Even if one part starts a measure with a quarter rest, and the other part with a half note, and the part starting with the rest then has a quarter note, the half note can be notated as tied quarter notes, the second of which is part of a chord with the other part. So, you can always implicitly get a rest when needed if done in this way, even though Noteworthy does not have the full concept of parts (including rests) in a single staff.
So, Noteworthy Composer can notate two parts with different rhythms on the same staff. The only problem is that the printed sheet music would not explicitly show some of the rests in fairly rare cases. However, the playback would be perfect. Why can't Noteworthy import what it can notate? You can try notating two parts with different rhythms, export to MIDI, import, and see what happens.
So, what excuse can the Noteworthy people have for having such a broken import? It does not require heuristics or artificial intelligence, it is simple. Why not just import the music as indicated in the MIDI events? Or, at least have the option of importing as written? As long as it has only two parts per channel, not much can go wrong. The vast majority of vocal sheet music (as read in by PhotoScoreMIDI or another product) has two parts per staff, and therefore two parts per MIDI channel, and those parts often have different rhythms. The provided splitting of the track by pitch is not workable. As it stands now you have to import into one staff and then manually go through the score finding all the places where the rhythm differs and fix it. What a headache. Really this should be considered a bug report and not an enhancement request.
