Conversion of Digital Anatomist Movies

The Digital Anatomist Interactive atlases have gone through many iterations since the Hypercard version written in the early 1990's up to the current web cgi version, and including standalone CD-ROM versions that were sold until around 2015. The CD-ROM versions as well as the earlier cgi versions contained Apple Quicktime movies that could be played over the web. However, these movies were encoded in an early version of Quicktime that has not been directly playable for at least 15 years, maybe more.

In this project I decided to see if I could convert the files to a more modern format that could again be played over the web. Basically, even with the help of ChatGPT, I found no way to directly convert the original Quicktime .mov files to a more modern format, so I developed a work-around that, although cumbersome, resulted in a conversion of all 187 original movies from three of the atlases to the more modern mp4 format. At this time I have not been able to convert the Knee atlas movies, but I'm not sure I even have the actual movies. The result is that the movies are now available in the Neuroanatomy, NeuroSyllabus and Thorax atlases, and should play when the "Play Movie" buttons are clicked in these three atlases.

In the following paragraphs I detail the methods I used, both for my own records, and in case anyone else is trying to convert old Quicktime movies and doesn't have access to an old Mac to play and/or convert them. There is probably a better way, (which likely would involve directly editing the binary files), but this method worked for me, and since I'm unlikely to do this again, I probably will just leave it at that. Similarly, I wrote a bunch of python scripts to make this process easier, but I haven't bothered to clean them up or make them widely available on GitHub or elsewhere since I don't plan to do this again.

The methods I describe below make use of several open source programs that can be downloaded on both Mac and Linux. These include VLC, OBS, Reaper, ffmpeg, mediainfo and Handbrake. Although all these programs can be run on either Mac or Linux I ended up running VLC, OBS and Reaper on the Mac, and ffmpeg and mediainfo on Linux, mostly because I already had them installed for other purposes.

The only application I found that can play the old movies is VLC, but VLC is a standalone program that each atlas web user would need to install (I think). In addition, VLC is not able to convert the movies to any other format. In consultation with ChatGPT I tried other ways of converting them, including Handbrake and ffmpeg. I used mediainfo to look at the metadata in these files. It looks like the files are containers for two video streams, each with its own codec: rpza for the titles, and cvid for the remainder of the movie. But ffmpeg can only read the rpza stream, so when it does a conversion, via ffmpeg -i input.mov output.mp4 it only generates the 1 or 2 second title. ChatGTP "thinks" that in the early days of Quicktime Apple had alot of different non-standardized formats that are now unreadable except with legacy Macs.

So after alot of experimentation I decided to break the original 187 mov files into manageable subsets, create a playlist in VLC of each of these subsets, use OBS to screen-capture each playlist as VLC displays the component movies, record the displayed playist as a single long mp4 file, import each long mp4 file into Reaper, create regions in Reaper corresponding to the individual files in the playlist, and then use Reaper to render the regions into mp4 files corresponding to the original mov files. I wrote several python programs to speed up parts of this process. ChatGPT suggested that I could stream the output of each file in the VLC playlist directly to OBS, and save each screen capture directly from OBS to the corresponding mp4 file using the OBS web interface. However, I realized I would have to learn alot to do that since ChatGPT's suggestion didn't work out of the box, so I opted to use the more tedious Reaper approach since I know it works.

All these results and procedures are in a folder on my Mac called ConvertMovies. Within that folder are subfolders da_atlases, convertvideo and convertframes. DA_atlases are a copy of the atlases before conversion, convertvideo does the actual conversion of the movies to mp4, and convertframes modifies the text-based frame files in each atlas so they point to the converted movies. The converted files were then used to replace the original movie and frame files, and then deployed to the web server. Detailed notes are in these subfolders. If anyone wants to see the contents of these folders let me know.