Data Acquisition

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:

git clone --recursive git://github.com/openchemistry/tomviz.git
cd tomviz/acquisition
python -m venv tomviz-acq
source tomviz-acq/bin/activate
pip install -e .
pip install -e .[tiff]
pip install -e .[test]

Starting the Acquisition Server

Once everything is installed you can start the acquisition server:

source tomviz-acq/bin/activate
tomviz-acquisition -a tomviz.acquisition.vendors.passive.PassiveWatchSource

This will start 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. 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 /tmp/test and the file name regex of .*.

Once ready click on Connect, and 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 re-executed when new images are available.

Starting a Test Sequence

Image stacks already acquired can be used for testing. The following command writes an image from a stack every five seconds:

tomviz-tiltseries-writer -p /tmp/test -d 5 -t tiff

It supports dm3 type as well. The path, delay, and type can all be modified.

Active Development

This feature is under active development and the interfaces may change.