Defdap

Added
- Add equality check for Quat

Fixed
- Fix bug in boundary line warping

Changed
- Update BCC slip system file and add a separate FCC file with same ordering as in DAMASK
- Refactor boundary lines in `ebsd.map` class and add methods for warping lines to a DIC map
- Refactor `linkEbsdMap` method and pass all arguments to transform estimate method
- Remove IPython and jupyter as requirements
- Move slip systems to `Phase` class and load automatically based on crystal stucture
- Make Oxford bonary loader tolerate of unknown data fields

Fixed
- Fix ebsd grain linker so it works again

Added
- Store EDX data as a dictionary called `EDX` accessible from the EBSD `Map` object
- Add option to change IPF map background colour

Fixed
- Fix bug with reading cpr EBSD file without EDX data
- Fix issue with plotting Schmid factor maps
- Fix bug with maps `component` not updating after masking

Added
- Reading of Channel project files that contain EDX data

Fixed
- Plotting unit cells
- Plotting lines with grain inspector

Added
- Started adding type hinting
- Add save/load support to grainInspector
- Add `drawLineProfile` function. Click and drag a line, then plot an intensity profile across the line

Changed
- Speed up EBSD map data rotation
- Speed up 'warp' grain finding
- Store band slope and MAD arrays from EBSD
- Update nCorrToDavis.m script
- Better description of how to use the function
- Sub-window size is subset radius * 2, as defined in nCorr
- Subset spacing is subset spacing, as defined in nCorr
- Generate phase boundary points and lines at same time as grain boundaries
- Improve histogram plotting
- Options for scatter (as before), step and bar
- Options for logx, logy, loglog and linear
- Updates to example notebook

Fixed
- Fixed docstring links
- Fix bug in 'warp' grain finding algorithm

Added
- Add EBSD file writing to CTF format.
- Add cretation of EBSD maps from runtime data.
- Add method to generate all slip systems in a family from a single system.
- Add grouping of slip systems by family.
- Add mechanism to define default parameter values stored in single loaction.
- Add basic filtering for HRDIC maps.
- Filtering based on threshold of effective shear strain and subsequent binary dilation.
- All current DefDAP functions work with NaN, but the RDR might not work as expected.
- New grain finding algorithm for HRDIC map which warps the EBSD grain map.
- Add `addLegend` command to add a marker size legend to a pole plot.
- Add misorientation calculation between neighbouring EBSD grains.
- Add a `BoundarySegment` class to represent a section of grain boundary between 2 grain in an EBSD map. Objects of this class are assigned to edges of the neighbour network and contain all the boundary points between the grains.
- Add Kuwahara filter for EBSD map noise reduction.
- Add shape property to maps.
- Read EBSD phases from file.
- Add classes to represent phases and crystal structures.

Changed
- Update progress reporting to print elapsed time.
- Speed up grain finding algorithm.
- Update plot IPF and Euler map to consider multiple phasess.
- Drop support of python 3.5.
- Update boundary and grain finding to consider phase boundaries.
- Assign a phase to each grain in an EBSD map.
- Change equality and hash of slip systems, slip plane and direction must now be equal (-ve allowed but not different norms).
- Update slip system plane and direction lables to have overbars - very fancy.
- Updates to example notebook.
- Change docs over to readthedocs.
- Move version number to own file.
- Update neighbour network to use grains as nodes.
- Store grainID in grain objects.
- Split plotGrainDataMap into separate array construction and plotting function.
- Update neighbour network construction to use new EBSD boundary definition.
- Update flood fill algorithm for grain finding in a EBSD map.
- Vertical and horizontal boundary pixels are now considered separately.
- Load phases from CTF file.

Fixed
- Fix bug with comment and blank lines when reading CPR files.
- Fixes to quat class:
- Construction from axis/angle now in passive sense not just a conversion.
- Fix big with transform vector where -ve vector was returned in some cases due to intermediate quat being transformed to northern hemisphere.