syncAndCrunchis the function that processes data during acquisition, sends images of the most recently completed section to the web, and stitches data automatically once acquisition is complete. This page describes in detail how to set it up and run it. Note that in day to day use, all you will need to run is:
However, the details are:
- 2.Start MATLAB. Run
help syncAndCrunchif you are not familiar with the command.
- 3.The acquisition system should be mounted on the analysis machine and at this mount point you should find your sample directory. Use the
lscommand to find your sample.
- 4.Create a variable containing the name of you experiment directory on the acquisition machine or server. e.g.S = ’/mnt/acqMachine/Data/Sample_0123’;(obviously substituting this with your own data directory).
- 5.Now you can run
syncAndCrunch. In one of these ways:
MICROSCOPE_NAMEis the name of your microscope (e.g.
organator, ... whatever). The
syncAndCrunchcommand looks for files coming from this system.
You can also run:
This will copy the contents of
Sto the so-called "landing directory" on the analysis machine on which
syncAndCrunchis running. The landing directory is defined in your INI file or can be manually set when you run
syncAndCrunchwith an optional input argument. The
2indicates that the second channel will be sent to the web to monitor progress. Read the help for the command if it's not clear why it does that. You should now see stuff scrolling down the screen and it should appear to be doing things. After a bit you’ll see it say that it’s building the web images. You can the navigate to the URL to which the images are sent. This is set vi a the INI file. It will just keep looping. If running on a remote server you can detach from your screen session or VNC connection. When all sections have been acquired, it will stop pulling in data and automatically start stitching. If you finish the acquisition early, you can manually trigger stitching by creating a file called ‘FINISHED ’ in the experiment root directory.
syncAndCrunchwill automatically start stitching when it finds the
FINISHEDfile. Alternatively, you can quit with
ctrl+cand run the stitching commands manually. It is important that you keep an eye on the progress of the experiment by looking on the web from time to time.
syncAndCrunchwill usually send messages to Slack (if you have configured this) if it crashes. You can then re-start it.