An experimental feature adds the ability to passively watch a directory for new files in order to facilitate a passive mode of acquisition where another program is acquiring data from the microscope. The Tomviz acquisition interface will watch files in a specified directory using a regular expression to match the file name.
The process watching the directory is a small, self-contained Python server with a simple programming interface that can be called over the network. The process should be started on a machine with access to files as they are acquired, this can then be used from the Tomviz user interface.
Installing the Acquisition Server
Get a copy of the Tomviz source repository, and ensure the machine has Python available. You can install everything in a Python virtual environment, or add the dependencies globally if preferred (in which case you will need elevated prvileges).
git clone --recursive git://github.com/openchemistry/tomviz.git cd tomviz/acquisition mkvirtualenv tomviz pip install 'git+https://firstname.lastname@example.org/cjh1/pydm3reader.git@filelike' pip install https://github.com/bottlepy/bottle/archive/41ed6965.zip pip install -e . pip install -e .[tiff] pip install -e .[test]
At this point you will have a Python environment with the required Python tools.
Starting the Acquisition Server
Once everything is installed you can start the acquisition server with the following commands.
workon tomviz tomviz-acquisition -a tomviz.acquisition.vendors.passive.PassiveWatchSource
This will result in a process running in the terminal on the machine that has a directory to be watched passively.
Connecting from the Application
Start the Tomviz application, click on the
Tools menu, and then select
Acquisition. This will open a dialog, from there click on
Introspect at the
bottom, and fill in the details. Typical testing parameters might be the default
host name of
localhost, port number of
8080, watch path of
the file name regex of '.*'.
Once ready click on
Watch to begin observing the directory. A
preview of the last image to be acquired will be shown, and the pipeline will
get a 'Live' data source. This will be appended to, and the pipeline reexecuted
when new images are available.
Starting a Test Sequence
We don't have any microscopes, and many of these features can be simulated using image stacks already acquired. We have made a couple available in the testing interface to aid in development. The following (from within the 'tomviz' Python virtual environment) will cause an image to be written from a stack every five seconds:
tomviz-tiltseries-writer -p /tmp/test -d 5 -t tiff
It supports type of
dm3 too, the path, delay, and type can all be modified. At
present the angle information is not being fed through, this will be added next.
None of these interfaces are set in stone, they are being developed to aid in the extension of the pipeline to support use cases where data is being actively acquired.