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imageseries overview

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Donald Boyce edited this page Aug 12, 2023 · 3 revisions

Originally, hexrd could only process GE images. We developed the imageseries package to allow for other image formats. The imageseries package provides a standard interface for images coming from different sources. The idea is that we could be working with a large number of images that we don't want to keep in memory. Instead we load the images from a file or generate them dynamically, but the interface is independent of the source.

Here is an example of usage.

Open and Write

The imageseries package has two main functions: open and save.

ims = imageseries.open(file, format, **kwargs)
imageseries.write(ims, file, format, **kwargs):

The format refers to the source of the images; file and kwargs depend on the format. Possible formats currently are:

  • "hdf5" - the images are stored in an HDF5 file and loaded on demand. file is the name of the hdf5 file.
  • "frame-cache" - the images are stored sparse matrices in a numpy .npz file; all of the sparse arrays are loaded on open, and a full (not sparse) array is delivered on request for a frame. There are two ways this can be done. In one, file is the name of the npz, and metadata is stored in the npz file. In the other, file is a YAML file that includes the name of the npz file as well as the metadata.
  • "image-files" - the images are stored as one or more regular image files on the file system. file is a YAML file describing listing a sequence of image files and metadata.
  • "array" - images are stored as a 3D numpy array; used for testing.

See also load options.

Processed Imageseries

This is a subclass of imageseries. It has a number of built-in operations, such as flipping, dark subtraction, restriction to a sub-rectangle. It was intended to be further subclassed by adding more operations. It is instantiated with an existing imageseries and a list of operations. When a frame is requested, the processed imageseries gets the frame from the original image series and applies the operations in order. It can then be saved as a regular imageseries and loaded as usual.

For more detail, see processed imageseries.

Interface

The imageseries provides a standard interface, somewhat like a 3D array.

If ims is an imageseries instance:

  • len(ims) is the number of frames
  • ims[j] returns the j'th frame
  • ims.shape is the shape of each frame
  • ims.dtype is the numpy.dtype of each frame
  • ims.metadata is a dictionary of metadata

Stats module

This module delivers pixel by pixel stats on the imageseries. Functions are:

  • max(ims, nframes=0) gives a single image that is the max over all frames
  • average(ims, nframes=0) gives the mean pixel value over all the frames
  • median(ims, nframes=0) gives median
  • percentile(ims, pct, nframes=0) gives the percentile over all frames

The median is typically used to generate background images, but percentile could also be used too.

Omega module

For the hexrd work, we usually have a sequence of rotations about the vertical axis. Omega refers to the angle of rotation. The OmegaImageSeries is a subclass that has metadata for the rotation angles.

See omega.

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