Convert to load_from_config() handling Rather than juggling independent configurations, consolidate them under ScanConfig in the style of pyafm.storage. This makes it easy to load a full scanning config from ~/.config/unfold-default.yaml, which is a plain-text file that can easily be tweaked by hand. To generate an initial unfold-default.yaml file, try something like: >>> import unfold_protein.storage as storage >>> config = storage.get_default_config() >>> storage.save_scan_config(config=config)' which uses defaults from unfold_protein.config as well as the default AFM configuration from pyafm.storage.load_config().
.be: Upgrade bugs-everywhere repository from v1.0 to v1.5
unfold.py: Remove config overrides for unfolding distance, etc. These snuck in during 87f12e4 (Update unfold_protein to use the new pyafm.storage._load_afm, 2012-05-11). Obviously, I should be using h5config to load a user-written YAML file instead of hard-coding these values in the unfolding script.
scan: Add stepper_tweaks (--no-stepper-tweaks) to UnfoldScanner.run() This is useful if you're not around to monitor a long run. If the laser is disrupted (e.g. via a bubble in the fluid cell), the photodiode voltage can flatlign, even if you aren't off the surface. A confused UnfoldScanner with *think* it's off the surface, and charge blindly in, crushing the cantilever into itsy bits ;). Laser disruption detection is a great reason to measure the total photodiode voltage. Unfortunately, that signal is not carried on the cable between the MultiMode and the NanoScope. I tried jumping it out of the MultiMode by hand, but after a few weeks like that, the board died. I'm not sure it was related, but I think it's safer to just disable stepper tweaks when you're not around to monitor the signal.
Update unfold_protein to use the new pyafm.storage._load_afm. This is a messy commit to get my Git repo in sync with the version I'm currently using in the lab, but most of the changes have to do with the nested-config overhaul starting with pypiezo's: commit de497a3734372f5fa7c92d6ff7bdb6b2e327c345 Author: W. Trevor King <wking@drexel.edu> Date: Thu Mar 15 10:13:20 2012 -0400 Optional config-based-setup for PiezoAxis, OutputChannel, and InputChannel. See the module docstring for details on why this is useful.