Inspired by David Mastronarde's framewatcher. moviewatcher monitors the current working directory for any files with the mrcs or tif/tiff extensions. While moviewatcher is running, any new files that appear in the running directory will automatically be processed by a command specified in a command file.
- Python
- The Python package, Watchdog
pip install watchdog
- Download the repository and cd into it.
git clone https://github.com/alberttxu/moviewatcher
cd moviewatcher
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Download an example unaligned micrograph stack from the Relion 2.1 tutorial test data; https://drive.google.com/uc?export=download&id=0BwXH3eSej0nHam5jZWNuOHlxeWc
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Start moviewatcher. Done. The original movie and all the output files will end up in done_folder.
./moviewatcher --command command_file.txt --dest done_folder
Add moviewatcher anywhere in your PATH to install.
sudo mv moviewatcher /usr/local/bin
Warning! Do not make DEST the same as the current working directory. This will cause an infinite loop.
COMMAND is the command file
DEST is the directory to move each initial mrcs/tif file after MotionCor2 finishes processing it. A new folder will be created if DEST does not already exist.
The syntax is sh shell with a few differences. Multiple lines are joined together with spaces. To add comments, use # as the first non-whitespace character of a line.
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(filename) is replaced with a discovered mrcs/tif file. e.g. Falcon_2012_06_12-15_56_10_0_movie.mrcs
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(basename) is the same as (filename) without the extension. e.g. Falcon_2012_06_12-15_56_10_0_movie
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(dest) is replaced with the --dest argument in the moviewatcher command. e.g. done_folder
- If you just want to automatically move the originial data without processing, don't use --command.
- The MotionCor2 output files don't have to go in the same folder as the DEST folder for the original data.
- You can use other programs to align such as Unblur and alignframes.