Mask small regions and calculate regionprops for these #57
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Adds functions to mask small regions. This is done on a per layer basis and the three dimensional arrays are iterated over producing a `numpy.ma.MaskedArray` which holds the original values in the `.data` attribute and the points to be masked in the `.mask` attribute.
- Switches populating `masked_array()` to be pre-assigned dimensions rather than using `np.ma.stack()` as this failed after two layers were added as the dimensions have to match and single layers therefore don't match the two stacked layers. Probably more efficient anyway. - Configuration value for `minimum_size` which should be in nanometres-squared to the `default_config.yaml` - Adds the attribute `AFMSlicer.sliced_segments_clean` which holds a masked array with objects `<= minimum_size` masked. - Region properties are calculated for all and clean - Tests the new attribute, loading masked arrays from `tests/resources/slicer` - Tests for region properties, these are poor though as there are some `NotImplemented` errors raised and some other issues TODO... - Plotting of masked regions.
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Introduces a new additional configuration option
minimum_size(default8000) of the minimum size in nanometressquared. Objects below this are removed/excluded by using Numpy masking.
The region properties are calculated on the whole image and also the masked subset.
Tests are included, although some of the region comparisons fail due to
NotImplementederrors for some of theregionpropsattributes.In future may consider calculating just the metric(s) that are required (at the moment I think this is actually only the
area but things like feret distances may also be useful).
Closes #54