LiberTEM currently focuses on pixelated STEM and scanning electron beam diffraction data processing, both interactive and offline. The processing back-end supports any n-dimensional binary data. As concrete supported operations, we started with everything that can be expressed as the application of one or more masks and summation, i.e. virtual detector, center of mass etc. These operations are embarrassingly parallel and can be scaled to a distributed system very well. Furthermore, we support User-defined functions that process well-defined subsets of a dataset following a simplified MapReduce programming model.
For our task, data locality is one of the most important factors for achieving good performance and scalability. With a traditional distributed storage solution (like Lustre or NFS), the network will quickly become the bottleneck.
LiberTEM is distributing the data to the local storage of each compute node. One possible implementation is using the Hadoop filesystem (HDFS), although we are working on a transparent caching layer as an alternative. The general idea is to split the dataset into (usually disjoint) partitions, which are assigned to worker nodes.
The execution is structured into Tasks and Jobs. A Job represents the computation on a whole dataset, and is divided into Tasks for each partition. The scheduler executes Tasks on the available worker nodes. For fast execution on each node, the Task reads the data in small Tiles (~1MB).
For distributing the workload, we are using dask.distributed. The Future API allows us to control our computation in a flexible way, with little overhead. With dask Futures, we can assure that computation on a partition of the dataset is scheduled on the node(s) that hold the partition on their local storage.
For ingesting data into the cluster, a caching layer (WIP) will transparently read a dataset from a primary source (via a shared network file system, HTTP, …) and stores it on fast local storage in a format that is best suited for efficient processing. The cached data can also be pre-processed, for example for offset correction or applying a gain map.
An important part of the architecture is the API server. Through the API server, the client gets access to the resources of the cluster, by running analyses. It uses a protocol based on HTTP and/or websockets. Processing is initiated by HTTP calls, and results are streamed back to the browser via web sockets.
The API server keeps some state in memory, like information about the currently opened datasets. Traditionally this would be done with an external in-memory database, but for ease of deployment, we decided to integrate this into the API server.
Processing is done in an asynchronous fashion; if you start an analysis using the HTTP API, the request immediately returns, but you get notifications about status changes and results on the websocket channel, or you can explicitly query the API server about a specific analysis. API calls in the Python API are synchronous for keeping it easy to use. Please contact us or add a comment to Issue #216 if you are interested in an asynchronous Python API for LiberTEM!
As UI, we use a web-based interface. This allows LiberTEM to work in cloud environment as well as locally on a single node. We can benefit from existing FOSS frameworks and infrastructure for communication, authentication etc. of the web.
LiberTEM is also suited for running on your laptop or workstation. In this case, all parts can run on a single node. We can also skip the caching step, if the data is already available locally.
When taking care to avoid needless copying and buffering, we can achieve native throughput on each node. With NVMe SSDs, this means we can process multiple gigabytes per second per node.
Mathematical expression for applying masks¶
The most basic operation with pixelated STEM data is multiplying each frame element-wise with a mask of the same size and summing up the result for each frame. This way one can implement virtual detectors, center of mass and darkfield imaging, to name a few examples.
Since each frame is processed individually and there’s a 1:1 match between mask element and detector pixel, the processing can be simplified by flattening the 4D dataset to a 2D matrix, i.e. a list of vectors where each vector is one flattened detector frame. Correspondingly, each mask is flattened to a 1D vector as well. The result of element-wise multiplication and summation is a 1D vector for each mask, where each entry corresponds to the result of one frame. To display the result, the data can be re-shaped to the scan dimension again.
With those extra dimensions flattened, let
c be the number of pixels per
n the number of frames and
m the number of masks. Let (
n x c matrix with the scanned data, and
c x m matrix with the
masks. Applying the masks in
B to the detector data in
A can be
expressed as a rectangular matrix product of
That means we can use the BLAS function GEMM. to
process the flattened data and we can choose from wide array of highly
optimized implementations of this operation. LiberTEM supports both dense and
sparse masks (sparse.pydata.org and scipy.sparse) for this purpose.
This functionality is available through
create_mask_analysis() and a number of more
specialized analysis functions in