v1.12 Compatibility release

Remove np.string_ from all functions. The package now requires numpy > 2 and h5py > 3 and uses normal str's.

What's Changed

• String compatibility by @ercius in #66

Full Changelog: v1.11.2...v1.12

Version that works with older numpy 1

Install this version of ncempy (1.11.3) if you are currently unable to use numpy v2.

You can install this as:
pip install ncempy==1.11.3

If your code supports numpy version 2 then please install ncempy 1.12 or newer instead.

Numpy and H5py string compatibility.

This is a quick release to limit the version numbers of numpy and h5py for string compatibility. The next release will require numpy >= 2 and h5py >= 3.

Also:

What's Changed

• Update dm.py by @ksytwu in #64

New Contributors

• @ksytwu made their first contribution in #64

Full Changelog: v1.11.1...v1.11.2

Bug fixes

Bug fixes for SMV and remove deprecated ndimage modules.

What's Changed

• Skip tags which cant be converted by _bin2str by @ercius in #56
• Fix smv read by @ercius in #59
• Improve emd warning by @ercius in #60
• add workflow file by @ercius in #61
• Improve io.smv by @ercius in #62
• Fix deprecations by @ercius in #63

Full Changelog: v1.11.0...v1.11.1

v1.11.0

Many new updates to packages old and new!

• Add support for SMV images commonly used in crystallography like microED
• Updates to the Python Titan scripting examples
• Improve the example notebooks
• Added a new ncempy.plot function to simply plot the output of the ncempy.read function
• Improve the metadata returned by the DM class

v1.10.0

Some new features and bug fixes:

New features:

• Added a band_pass function to filter images.
• Simplify imports. You can now use import ncempy and get access to most of the submodules and directly to the read function. This will not impact the traditional ways of importing.
• Add new getMetadata() function to ncempy.io.dm.fileDM to make it easier to get relevant experimental data

Bug fixes:

• An update to python broke the DM reader due to dangling file pointers. This is now fixed.
• EMD files without the name or units attributes can now be read. These default to dim# and pixels instead

v1.9.0

This release adds some new modules to ncempy and features to the io package and some bug fixes.

1. Add peak_find module. This is used for finding peaks (i.e. atoms) in 2D (images) and 3D (volumes) numpy ndarrays. There is code to find peaks, fit peaks to a Gaussian, fit a set of peaks to a lattice, calculate displacements, calculate strain, and calculate a unit cell.
2. Add the gaussND module. This is used for peak fitting 2D and 3D Gaussians.
3. Allow input of an open file object to all io readers.
4. Fix an issue with EMD memmaps being closed when used inside another function
5. Fix issue with int64 data type in DM files

Please create an issue if anything is not working so I can fix it.

io bug fix for py3.6

Bug fix for import issue for python3.6 due to new ncempy.io.read() function.

Documentation and io updates

This release makes many changes to the documentation to help with readability. Check read the docs for the full documentation.

The io mdoule has several updates:

• The new ncempy.io.read() function uses the file suffix to call the correct file reader. No need to choose a reader ahead of time.
• A new simple emdWriter() function has been added
• Parsing of EMD Berkeley files is improved for some special cases
• EMD Berkeley is opened as read only by default

Even more updates

Lots more updates in this version:

1. Fixed an issue with DM memmap() which did not make it into the previous release. memmap with on_memory now works correctly.
2. Improved DM writeTags functionality. Thanks to @koschie for the pull request.
3. Improve speed of EMI meta data reading
4. Fix issue in stack_align with mode='dynamic'. This previously did not work and now its working well.
5. fourier_operations includes shear, shift and rotation for non-interpolated operations
6. Fix the energy output axis for dmReader for spectra. The offset and energy pixel size are now correct and match the expectations from the DM program.
7. Add a Jupyter Notebook with examples of reading all types of files and displaying the data
8. Multicorr image alignment is now moved to the eval subpackage. All related functions remain in algo.multicorr_funcs