stempy 3.2.2

What's Changed

• Add analysis functions by @ercius in #272
• com_sparse and nans by @ercius in #271

Full Changelog: 3.2.1...3.2.2

stempy 3.2.0

What's Changed

• Skip python 3.11 wheels by @psavery in #263
• Fix binning scans with multiple frames per scan by @psavery in #262
• Fix com sparse parameters by @ercius in #264
• Add row dark algorithm to electron counting by @psavery in #260
• Add SparseArray.to_dense() by @psavery in #266

Full Changelog: 3.1.0...3.2.0

stempy 3.1.0

What's Changed

• Remove references to <= 3.6 ( no longer supported by cibw ) by @cjh1 in #257
• Add two new options to com_sparse. by @ercius in #256
• Update examples by @ercius in #255

Full Changelog: 3.0.0...3.1.0

stempy 3.0.0

What's Changed

• The data format used by SparseArray and electron counting methods changes. This simplifies a lot of the logic involving multiple frames per scan position, and completely removes the need for manipulating the scan positions array that the SparseArray previously held. The data shape from a flat array of sparse frames to a 2D array, where the first dimension is the scan position, and the second dimension is the index of a frame at that scan position.

  Backwards compatibility has been maintained so that the SparseArray class can load in HDF5 files saved in versions 1, 2, or 3 and correctly convert them to version 3 upon loading.

• A num_frames_per_scan property has been added to SparseArray.num_frames_per_scan

• All scan processing functions have been updated to use the new data format.

Example notebooks updated

• Check out the examples directory for useful Jupyter notebooks for common 4D-STEM processing tasks. All calculations are done in the sparse domain providing significant speed-up and reduced memory use.
  • center_of_mass_sparse.ipynb: Calculates the center of mass (intensity) of each diffraction pattern and then calculates the phase for a Differential Phase Contrast (DPC) image
  • radial_sum_display.ipynb: Calculate the radial sum of every pattern and interactively choose the inner and outer angle of a virtual detector to explore different types of image contrast in a 4D-STEM scan.
  • vacuum_scan_subtract.ipynb: Compensate for beam motion at each scan position using a separate scan acquired without a sample known as a "vacuum scan." The vacuum scan can be smaller in the number of scan positions but must be acquired at the same STEM magnification and camera length.
  • A set of examples in the py4dstem directory show how to use the SparseArray class to analyze sparse data sets in this popular 4D-STEM analysis package.

Full Changelog: 2.0.2...3.0.0

stempy 2.0.0

This release contains breaking changes that may require code updates.

What's Changed

• For consistency and ease of use, the ElectronCountedData namedtuple has been replaced by the SparseArray class. The SparseArray has similar attributes as the ElectronCountedData, but scan_dimensions is now scan_shape[::-1], and frame_dimensions is now frame_shape.

  Here are the functions that are effected:

  • stempy.image.electron_count() now returns a SparseArray instead of the namedtuple
  • stempy.io.load_electron_counts() now also returns a SparseArray
  • stempy.io.save_electron_counts() now requires a SparseArray argument instead of the namedtuple

• SparseArray now also supports attaching metadata. This metadata will be included in any of the HDF5 files written from a SparseArray instance. The various electron counting parameters used in stempy.image.electron_count() are now also automatically added to the metadata of the SparseArray instance.

• When performing electron counting on a dataset that contains multiple frames at each scan position, the electron events are now stored in separate arrays for each frame, rather than being append to a single array.

Full Changelog: 1.1.1...2.0.0

stempy 1.0.4

This release improves electron counting with a new multi-pass approach the reduce memory usage and make it more amenable to parallelization.

Infrastructure and changes have been implemented to allow binary wheels to be built and pushed to the Python Package Index (PyPI). This allow stempy to be install using pip on Windows, Mac and Linux.

stable version

This is the initial stable release of stempy.