Real-Time Defect Identification

This package is a service for real-time defect identification from TEM images.

The key component is a server that will watch a specific folder on a file system and send images to be processed by a Tensorflow-based image process pipeline. The results of the labeling will be saved to disk, and the summaries will be made available via a web service.

The server is intended to use FuncX to perform image processing on remote resources. This package also includes the environment needed to service image processing requests.

Installation

The environment can be installed via Anaconda: conda env create --file environment.yml --force

Change the tensorflow dependency in environment.yml to tensorflow-gpu if GPU support is desired.

See below for setting up a remote compute service for running the machine learning model. It is entirely possible to run everything locally, but external resources may provide faster image throughput.

Running Image Analysis

Run the image segmentation and analysis code by calling the rtdefects command line application.

The full version of the application will run new images as they appear in a certain folder, delegate processing to a remote system, and deploy a web server that displays a status page. Launch it by calling:

rtdefects ./path/to/watch

rtdefects will write the segmentation files and a JSON file containing the defect statstics to a directory named "masks" within the watched directory.

If you want to run segmentation on a directory of files, use the "run" command

rtdefects run --local --no-server ./path/to/files.tiff

• --local turns off remote computing
• --timeout 0 stops watching for new files after 0 seconds have passed.
• --redo-existing runs analysis of all images, even if they have been processed before
• --no-server turns off the status server

Call rtdefects start -h or rtdefects run -h for a complete list of options.

Setting up Remote Computing

Our system requires configuring both an endpoint to run the image analysis and one where the images are generated.

Compute Provider

The Compute Provider should be a system with the ability to process images quickly and need not have access to the filesystem that stores the images. It only needs internet access. To set up the ability to run the functions:

1. Install and activate the computational environment, as described above.
2. Configure a FuncX endpoint to receive image processing commands. Follow the directions on the Funcx documentation to configure the system.
   1. Record the ID produced by your endpoint, which should look something like 8c01d13c-cfc1-42d9-96d2-52c51784ea17.
3. Place the Keras .h5 file with the model in the rtdefects directory and name it segment-model.h5
4. Launch the FuncX service (e.g., funcx-endpoint start default).

Once you are done processing images, you may stop the FuncX endpoint. You will need to stop and re-start each time you change the Keras model.

Image Analyzer

The Image Analyzer must have access to the images and an internet connection.

First, install and activate the computational environment, as described above.

Before any image analysis runs, you must tell the system what computations to run and where to run them:

1. Register the analysis function by calling rtdefects register
2. Configure where to run them using the endpoint ID for the Compute Provider and setting it using rtdefects config --funcx-endpoint <the endpoint id>
   1. You may later change this endpoint using rtdefects config

Begin an analysis run by calling rtdefects start. The single argument for this command is a directory to watch for new files, though more will soon be implemented.

The process will watch for files to be created, send those files to be processed via FuncX, and then collect the completed results. It will run until you exit by pressing Ctrl+C, which will require up to 15s to register on a Windows system.

Support

This material is based upon work supported by Laboratory Directed Research and Development (LDRD) funding from Argonne National Laboratory, provided by the Director, Office of Science, of the U.S. Department of Energy under Contract No. DE-AC02-06CH11357.