Fix alpha shape

[bertsky]

Some early fixes for the recent #77 – sorry to get back to you so soon @finkf (and thanks for merging so fast).

BTW, if you contemplate making a new release, here is a list of things that have changed since 0.1.5:

Fixed:

* align: fix logging and `--dump-json` #82
* align: avoid superfluous TextEquiv #76
* binarize: traverse regions in reading-order (so derived images are, too)
* ocrolib.morph.spread_labels: fix when no labels exist
* ocrolib.morph.label: :fire: fix ncomps (+1)
* ocrolib.morph.select_regions: fix `dtype` for just 1 label
* binarize/denoise/deskew/dewarp/segment: skip zero-size segments to avoid numpy problems
* common.compute_hlines/separators: fix h/v kernel size
* common.compute_hlines/separators: early length filter must be softer than final criterion
* segment: fix reference before assignment when partitioning
* segment: set correct pageId for image files
* segment (region level): fix and speed up horizontal merging
* segment (page/table level): continue more gracefully when recursive XY-cut fails
* segment (page/table level): fix significance criterion for partitions' line labels
* segment (page level): prevent empty `ReadingOrder` group
* segment (page level): avoid adding existing regions to RO group unless they are immediate children
* resegment: skip empty line polygons
* resegment: prevent overflow in numpy slices due to rounding errors when cropping #79
* resegment: set correct pageId for image files #80
* resegment: use `set_points` to ensure invalidating existing line images
* polygon_for_parent: ensure path validity before checking consistency
* polygon_for_parent: ensure valid polygons for new coords
* segment/polygon_for_parent: skip segment if polygon cannot be made valid

Changed:

* clip: avoid suppressing overlapping components on both sides
* clip: require independence instead of `min_fraction` threshold
* deskew: delegate to OCR-D/core for reflection and rotation
* dewarp: expose `smoothness` parameter
* segment (region level): ignore separators and other existing regions
* segment: do not suppress neighbours if they cover the segment completely
* segment: do not suppress neighbours if already clipped
* segment (region level): annotate clipped images on region level, too
* segment (region level): improve horizontal merging (transitivity, don't cross separators, enlarge region mask, too)
* segment (page/table level): avoid grouping new text lines with existing regions in a XY-cut
* segment (page/table level): re-order grouped new and existing regions in a XY-cut
* segment (page/table level): avoid creating convex hulls for new regions if these would create additional overlaps with existing regions
* segment (page level): hmerge line labels (within each region) here, too
* segment: upgrade segmentation failures from warning to error
* ocrolib.morph: add `dist_labels` (distance transform of semantic segmentation
* ocrolib.morph: for CC analysis, use 4-way instead of 8-way connectivity
* ocrolib.morph: new function `rb_reconstruction` based on repeated dilation and masking
* common.compute_images/hlines/separators: use that instead of `spread_labels`
* re/segment: before spreading lines, assign diacritics to seeds below
* resegment: :tada: complete rewrite (now polygonal and global):
  - polygonal calculus instead of pixel/morphology operations (for efficiency)
  - optimise assignments globally instead of locally (to avoid conflicting assignments)
  - add param `level-of-operation` with new level `page`, also as new default
  - suppress all non-text regions and non-text non-regions before text line segmentation
  - on page level, merge horizontally adjacent labels, but avoid creating new region conflicts in doing so
  - general algorithm: 
    * after line segmentation, find contours and polygonalize, then compare overlaps once
    * allow assigning multiple new labels to existing lines and combine them via a (slightly concave) hull polygon
    * assign existing lines to new lines such that among those candidates covering high fg (90%) and bg (60%) shares of  the new line, the one with the largest fg and bg share of the existing line wins
    * bail out of resegmentation if the new polygon would loose a share of `threshold` fg or `threshold / 3` bg, or if some new, but unassigned line would be lost entirely 
    * subtract matching lines from non-matching lines
* resegment: allow detection of colseps if some regions exist already
* resegment: :tada: compute true alpha shape instead of eroded convex hull
* resegment: :tada: implement alternative `method=ccomps`:
  - calculate connected component analysis
  - calculate distance transform of existing labels
  - find new line seeds by flattening existing labels (via maximum distance)
  - propagate line seeds across connected components (by majority in case of conflict)
  - spread ccomps labels against each other into background
  - for each line,
    * if enough background and foreground wille be retained
    * find the hull polygon of the new line via alpha shape
    * annotate as new coordinates
* resegment: :tada: implement alternative `method=baseline`:
  - calculate connected component analysis
  - find new line seeds based on the existing baselines (by applying dilation above)
  - propagate line seeds across connected components (by majority in case of conflict)
  - spread ccomps labels against each other into the background
  - for each line,
    * if enough background and foreground will be retained
    * find the hull polygon of the new line via alpha shape
    * annotate as new coordinates
* segment (page/table level): :tada: improve splitting by separators:
  - when trying to partition slices by separators,
     * also treat pre-existing regions like separators, and
     * fix the condition on smallest allowed partitions (insignificant but complete lines)
  - fall back to (new) topological partitioning
    * when no cut or separator-split partition can be found for the current slice, then attempt to find another separator-split by grouping lines along their mutual horizontal neighbourship with fg separators
  - repeatedly allow both kinds of partitioning, if interspersed

[lgtm-com]

This pull request introduces 1 alert when merging 200313f into a30ce3b - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com]

This pull request introduces 1 alert when merging b64e66a into a30ce3b - view on LGTM.com

new alerts:

• 1 for Unused import

[bertsky]

dammit, 8841abc contains accidentally commited parts that crash

[bertsky]

Here's some illustration of the recent improvements.

Resegmentation using method=baseline

before	after
steps
1. use existing baselines (dilated mask) as seed	2. propagate to connected components by majority rule
3. spread into background with full scale distance	4. propagate to connected components again (now catching more fg, esp. diacritics)
5. spread into background with only half scale	6. polygonize

Resegmentation using method=lineest (also annotating baselines)

before	after
steps
1. existing line labels with overlaps	2. new line labels
3. new baselines	4. match+assign parts and polygonize

before	after
steps
1. existing line labels with overlaps	2. new line labels
3. new baselines	4. match+assign parts and polygonize

Resegmentation using method=ccomps

before	after
steps
1. use existing segmentation (flattened via maximum of distance transform) as seed	2. propagate to connected components by majority rule
3. spread into background with full scale distance	4. propagate to connected components again (now catching more fg, esp. diacritics)
5. spread into background with only half scale	6. polygonize

Page segmentation with improved separator detection and partitioning

1. input image	2. binarized (SBB)
non-text detection
3. detect images	4. detect separators: medial axis transform
5. connected component labels of skeleton	6. filter by compactness and distance statistics
7. morphological closing of skeleton	8. link newly connected labels if direction is consistent
9. sort and filter candidates by size	10. propagate from skeleton to full components
11. spread separators into background	12. polygonize and suppress images+separators
whitespace separator detection
13. vertical gradients	14. background
15. combined bg seps	16. combined separator mask
textline detection
17. horizontal gradient	18. filtered lineseeds
19. final ordered line labels	20. line labels spread against separators
textregion detection
21. final rlabels	22. final result

1. input image	22. final (not optimal) result