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Pattern Matching: Compare experimental with simulated data (#233)

* feat(SimilarityMetric): ZNCC, NDP and user defined metrics

Framework for calculating similarities between 2D gray-tone images of equal size.

* fix(SimilarityMetric): squeeze dimensions of similarity matrix

* fix(SimiliarityMetric): rechunk dask arrays after type conversion

* refactor(SimilarityMetric)

length of shape -> ndim, and removed unnecessary squeeze call.

* test(SimilarityMetric): Many to many ZNCC

Produce value of 1 with equal pattern and template

* refactor: removed metricscopes including ANY

* wip: tests cover most cases

* test: remove print statement

* refactor: indexation -> indexing

* Reformat docstrings, add Ole to credits, add indexing module to doc

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* refactor: renamed variables and made functions private

* refactor: underscore prefix

* refactor: underscore prefix

* Update docstring table, and more

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Add indexing module to kikuchipy/__init__.py

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Add static dictionary indexing note in changelog

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* fix: change standard shape of similarity matrix

Change data shape from (N,nm) to (nm,N) to correspond better with cdist in scipy and general logic.

* test: update tests to new output standard

* fix: _is_compatible to be working for all scopes

* Clarify parameters in docstrings, some minor syntax changes, repr

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Docstring explanation of _is_compatible()

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Return numpy where only numpy arrays are passed, test repr

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Improve return numpy/dask test

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* feat(template_match): Keep... (continued)

187 of 187 new or added lines in 5 files covered. (100.0%)

6087 of 6087 relevant lines covered (100.0%)

5.0 hits per line

Jobs
ID Job ID Ran Files Coverage
1 465.1 (DEPS="dask[array] hyperspy[learning] h5py matplotlib numpy numba scikit-image scipy" TEST_DEPS="pytest pytest-cov coveralls coverage" DEPLOY=false ENV=conda PYTHON_VERSION=3.8) 0
100.0
 Travis Job 465.1
2 465.2 (DEPS="dask[array] hyperspy[learning] h5py matplotlib numpy numba scikit-image scipy" TEST_DEPS="pytest pytest-cov coveralls coverage" DEPLOY=false ENV=pip DEPLOY=true) 0
100.0
 Travis Job 465.2
3 465.3 (DEPS="dask[array] hyperspy[learning] h5py matplotlib numpy numba scikit-image scipy" TEST_DEPS="pytest pytest-cov coveralls coverage" DEPLOY=false ENV=conda PYTHON_VERSION=3.8) 0
100.0
 Travis Job 465.3
5 465.5 (DEPS="dask[array] hyperspy[learning] h5py matplotlib numpy numba scikit-image scipy" TEST_DEPS="pytest pytest-cov coveralls coverage" DEPLOY=false ENV=conda PYTHON_VERSION=3.8 PATH="/c/tools/miniconda3/:/c/tools/miniconda3/Scripts:$PATH") 0
100.0
 Travis Job 465.5
6 465.6 (DEPS="dask[array] hyperspy[learning] h5py matplotlib numpy numba scikit-image scipy" TEST_DEPS="pytest pytest-cov coveralls coverage" DEPLOY=false ENV=pip PYTHON_VERSION=3.7.5 PATH="/c/Python37:/c/Python37/Scripts:$PATH") 0
100.0
 Travis Job 465.6
Source Files on build 465
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