Jan Caron authored 5 years ago and Jan Caron committed 5 years ago

Moved .mplstyle files inside vis.
setup.cfg: added options.packages.find
    removed 3Dplot requirements (for now).
setup.py: moved stylesheet installation to vis.tools, now optional.
vis.tools: also added a use_style contextmanager that dynamically uses
    local styles (in package) or styles installed in user config folder.
colors/decorators/plot2d: now use the new use_style contextmanager.

Jan Caron authored 5 years ago and Jan Caron committed 5 years ago

setup.py: use matplotlib AFTER setup()
(otherwise matplotlib is not available, despite being in setup_requires)

Moved .mplstyle files inside vis.
setup.cfg: added options.packages.find
    removed 3Dplot requirements (for now).
setup.py: moved stylesheet installation to vis.tools, now optional.
vis.tools: also added a use_style contextmanager that dynamically uses
    local styles (in package) or styles installed in user config folder.
colors/decorators/plot2d: now use the new use_style contextmanager.

setup.py: use matplotlib AFTER setup()
(otherwise matplotlib is not available, despite being in setup_requires)

Deleted print statements, superfluous log, TODOs, added a few comments.

Added the fields submodule with field, shapes and vectors!
Added the vis module (not viz) with colors, decorators, plot2d, tools.
Added version.
Minor changes in pyramid.

removed last artefact of hg usage ages ago...
removed syntax error in setup.py...

conf.py: uncommented path  finding for sphinx to find docs folder.
index.rst: Added modules.rst as an overview.
make.bat, Makefile, pyramid.rst: Deleted!
utils: put many functions in convenience.py
environment.py: Added stuff for documentation
README.md: deleted badges (directly on GitLab now!)
setup.py: Further streamline!

put most options into setup.cfg

Installing EVERYTHING with pip was not a smart idea...

Added environment.yml and requirement.txt.
GitLab should now produce html coverage artifacts.
io_vectordata: now warns if grid spacing is not equal in all directions.

And deleted/ignored pyramid.egg-info

phasemap: Now supports flips, rotations and shifts with ndimage.
          Added plot_phase_with_hist to plot histograms (for difference plots).
fielddata: FieldData now properly plots contours and masks (new).
dataset: set_3d_mask now uses the new mask capability of FieldData.
         Default is no longer "logical backprojection".
io_phasemap: Now includes .tif (although that does not always work).
setup.py: Deleted deprecated depencencies.
Renamed a few plot commands to plot_...
Rollback to RdBu as colormap (back from Spectral).

Renaming of variables in PhaseMapperRDFC.jac_T_dot to make more sense...

GUIs now import .ui-files directly.

Added .idea folder with PyCharms settings.
Changed icon.ico (now round).
PhaseMap and MagData: Now use h5py to load/save data (via HyperSpy).
Deprecated loading routines (x3d) are gone now!
tests: All tests now reflect this change.
scripts: Streamlined some scripts. Many are now in separate project:
Script-Vault

colormap: Added TransparentColormap.
magdata: Added get_magslice method, to_emd and from_emd.
phasemap: Added to_emd and from_emd.
gui: New GUI "PhaseMap Creator".
tests: Moved from ./tests to ./pyramid/tests. Not a package anymore!

Phase maps now also have a mask and a confidence matrix.
Began new script structure (temporary folders created).
Cleanup, logging and documentation done.
config: NTHREADS is now set here.
dataset: Method for creating 3D masks added.
phasemap: Mask and confidence matrix added. Padding and cropping supported.
forwardmodel: Stubs for multiprocessing added (next TODO!).
kernel: Added support for perturbed reference wave.
magdata: Padding and cropping supported.
projector: New property 'sparsity' introduced.
regularisator: Stub for ComboRegularisator added (next TODO!).
tests: Changed accordingly.

kernel, phasemapper: now use the new pyramid.fft module.
MagData, PhaseMap: now use np.float32 instead of np.float64
MagData: new quiver_plot3d with just matplotlib (buggy and still WOP).
logging: deleted several logging.debug prompts for speed up.
util: deleted module!

setup: Changes to setup.py, pyramid.version to fit to numpy and jutil
       now uses __all__ magic and supports from pyramid import *
tests: changes to test_compliance/magcreator/analytic (should now work)
collaborations: added several scripts for Patrick
reconstruction: added batch file for the reconstruction of several configs
test methods: (unfinished) scripts for fftw tests and kernel comparisons
paper 1: ch5-4 changed padding values to 0, 1, 3 and 7
plotting: deleted plt.show() lines (have to be done manually now or via Spyder)
logging: now named _log instead of LOG (private variable instead of constant)
         also some logs were disabled, because Pylint says they are slow...
reconstruction: now has info argument (pass a list in which cost info is copied)
phasemapper: changed sign of constant PHI_0, is now correctly positive (instead
             the negative z-integration is taken into account which was not done
             before!)
kernel: now uses FFTW, numpy code was changed accordingly and is still available
phasemapper: also uses FFTW now, work in progress: FFTW for jac_T_dot

package: some minor corrections (mainly import statements), some old functions
         were revived (e.g. in MagData)

scripts: adaption to the new structure and sorting (more work is to do here...)

_version: __version__ string is now imported from this file

phasemapper_core.pyx: added to separate the corresponding numcore_functions
                      from kernel_core.pyx

regrid: Added many scripts for regridding by Jörn
logging: Introduced logging
scripts: Added Scripts for regridding and simulating stuff for cooperations
removed: Unused test scripts
structure: Many new restructuring aspects already implemented

holoimage: changed colorwheel (now without axes)
magcreator: create_vortex now also allows a 3D-center (2D is extracted)
magdata: new methods: get_mask() and scale_down()
phasemap: changed plotting defaults (new kwargs)
phasemapper: started on electrical contribution

setup.py: Final cleanup
deleted initpyximport, compare_method_errors and get_revision (now in setup.py)