feature(filter): Implement filtering class and method #65
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Using class inheritance from `topostats.filter.Filters()` we introduce `SlicingFilter` class which takes as input a `TopoStats` object and performs filtering/flattening on the image. The following methods from TopoStats are used... - Median flattening. - Tilt removal. - Quadratic removal. - Nonlinear polynomial removal. - Scar removal (optional). - Zero average background. - Gaussian filtering. Regression tests are in place that use [syrupy](https://syrupy-project.github.io/syrupy/) and these have been setup as parameterised tests so we can easily add in actual examples once we have some small files on which to base the tests. Other things... - Remove masking parameters in `default_config.yaml` that are carried over from `TopoStats`. - `.pylintrc` > `.pylint.toml` and update `.pre-commit-config.yaml`
We want/need to instantiate an `AFMSlicer` object before we apply `Filter` to it, which takes as input `AFMSlicer` child class which inherits from `topostats.classes.TopoStats`. We can't therefore slice the image before we have done this which was the way `AFMSlicer.__post_init__()` performed. With this pull request we split out setting attributes when creating the class and introduce another method that performs the slicing of the class so that we can first filter/flatten the image.
With recent changes to TopoStats that have refactored and been merged we need to install from `main` branch (for now, this will change when a new TopoStats version is released).
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Using class inheritance from
topostats.filter.Filters()we introduceSlicingFilterclass which takes as input aTopoStatsobject and performs filtering/flattening on the image.The following methods from TopoStats are used...
Regression tests are in place that use syrupy and these have been setup as
parameterised tests so we can easily add in actual examples once we have some small files on which to base the tests.
This required a refactoring of some code because we want/need to instantiate an
AFMSlicerobject before we applyFilterto it, which takes as inputAFMSlicerchild class which inherits fromtopostats.classes.TopoStats.We can't therefore slice the image before we have done this which was the way
AFMSlicer.__post_init__()performed.With this pull request we split out setting attributes when creating the class and introduce another method that
performs the slicing of the class so that we can first filter/flatten the image.
Other things...
default_config.yamlthat are carried over fromTopoStats..pylintrc>.pylint.tomland update.pre-commit-config.yaml