pias 0.1.0.dev0

Interactive agglomeration scheme for paintera

Paintera Interactive Agglomeration Server

pias provides a server for interactive updates of a nifty-based agglomeration model for fragments in EM segmentation (but could probably be used in other scenarios, as well). Clients provide positive (two fragments are in the same segment) and negative (two fragments should not be in the same segment) examples for edges (fragment-pairs). Random forest classifiers are trained on these examples to infer weights for all edges of neighboring fragments in a multi-cut problem (constraints for the enforcement of positive/negative examples provided by the client is modeled via appropriate weights).

Installation

The minimum python version is 3.6.

Besides the packages specified in setup.py, you will need to install the following packages that are not installable via pip:

• nifty available on conda through the cpape channel
• z5py available on conda through the conda-forge channel

You can install these dependencies through conda via the aforementioned channels. Otherwise, follow the build instructions on the linked github repositories.

If you do not install pyzmq through conda make sure that libzmq is installed on your system.

pip install git+https://github.com/saalfeldlab/pias

Server Details

pyzmq is used for communication between server and client. Data should be sent as big endian. The server can be started with the pias command that is installed with the python package. See pias --help for usage details. Once started, the server will start multiple sockets, addressed by extensions of the address_base parameter:

• ${address_base}-ping - ping the server at this address to see if it is alive (REQ/REP)
• ${address_base}-current-solution - request current solution (REQ/REP)
• ${address_base}-set-edge-labels - set labels for edges: (multiples of) (e1, e2, label) (REQ/REP) where label is one of {0, 1}
• ${address_base}-update-solution - request update of current solution (REQ/REP)
• ${address_base}-new-solution - be notified about updates of the current solution (PUB/SUB)

NOTE: This scheme probably works (reliably) with ipc:// zmq-addresses.

Socket Details

TBD: What kind of input/output does each socket expect/provide?