Proshade

This is the version 0.7.6.7 (JUL 2022)

There are only a few modifications in this release, including:
1) Support for the Apple Silicon chipset
2) Removal of two rare bugs, which could cause segmentation faults

NOTE: The examples were not tested on this version, so the expected values in them may be slightly off.

This is the version 0.7.6.6 (JUL 2022).

This version improves on the symmetry detection, specifically by:
a) Allowing for simple and fast symmetry detection using multiple average FSC value thresholds.
b) Resolving the polyhedral symmetries primer selection problem that has re-occured after the introduction of over-sampling in the last version.

Furthermore, this version improves upon the installation of ProSHADE on most platforms by better usage of compiler flags and other minor issues.

The main changes from the previous release are:
1) The FSC computation now uses the first rotation against the original position instead of the average of all pairs of rotations against the original position in most cases. The only situation where the average would be used instead of the single rotation would be where the map resolution is too low for clear distinction of the next rotation and where the first rotation gives high FSC value.
2) The map re-sampling is now done in a way that the map is over-sampled (compared to the Shannon sampling) and therefore allows more accurate interpolation onto the concentric spheres. Also, the E matrices are zero-padded to produce over-sampled rotation function to similarly allow better accuracy of mapping onto the angle-axis space spheres.
3) The symmetry detection now uses a combination of peak height (un-weighted correlation) and FSC (bin-weighted correlation) as opposed to previously used mostly FSC.
4) Seg. fault caused by integration order being supplied by the user while the progressive integration order method is being used has now been resolved.
5) Minor bug fixes and improvements.

This commit introduces the new version 0.7.6.4 (APR 2022). The major changes are:

1) Considerable speed-up in the E-matrix computation.
2) Removal of trace sigma descriptor bug occuring when progressive sphere mapping is used.
3) Improvements in thresholding and deciding the recommended symmetry.
4) Now FSC is used to decide which non-prime axes are to be considered. This may be slightly slower in some cases, but in a few cases this makes 100x time difference.
5) Other minor bug removals and improvements.

This is the new version 0.7.6.3 (FEB 2022).

The main new features include:

1) The stripe on sphere mapped rotation function for angle 180deg around the equator is now gone.
a) The cause was an error in rotation matrix to euler angles conversion in the singularity case.
b) The Euler angles are in ZYZ and NOT in ZXZ format. All references changed.
2) Completely re-worked FSC computation - now it is faster and much more accurate. More specifically:
a) Binning is improved.
b) Resolution cut-off for faster computation.
c) Map rotation now done in reciprocal space (i.e. faster).
3) Improved the symmetry detection logic
a) There was a wrong axis in the pre-computed optimal Icosahedron, now resolved.
b) D symmetries are now not simply taken as the highest fold and passing threshold, now smoothened histogram approach is used.
c) C symmetries and D symmetries are both considered, instead of just taking any D over any C.
4) Speed improvements
a) If mask is supplied, the inner settings (bandwidth) use the non-zero mask size instead of full map size.
b) Radius in which the structure is considered and outside of which it is ignored can now be supplied for faster calculations
c) Improved the peak detection threshold detection, which was causing some structures to take be 10 times slower for symmetry detection.
5) Minor bug fixes and code clean-ups.

This is the new version 0.7.6.2.

The main new features are:
1) Symmetry centre detection can be run using -I option. This allows finding the centre of symmetry
2) Removed boundary condition bug that was causing some extra false positives in the axes list in symmetry detection.
3) General bugs removal and speed-up.