8545078607

Committed 03 Apr 2024 08:26PM UTC coverage: 96.51% (+0.09%) from 96.417%

Build # 8545078607

Build Type

Pull #166

github

Committed by

web-flow

Commit Message

Merge ed46e50d4 into 3f2d63fae

Pull Request Pull Request #166: Better homology

Run Details

245 of 250 new or added lines in 5 files covered. (98.0%)

3 existing lines in 3 files now uncovered.

1770 of 1834 relevant lines covered (96.51%)

3302629.22 hits per line

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93.33

/src/computation/involuted.jl

"""
    compute_death_simplices!(matrix::CoboundaryMatrix{true}, verbose, cutoff)

Fully reduce `matrix`, but only compute (homological) death simplices. Return all death
simplices up to the last that produces an interval with persistence greater than `cutoff`.

Used for involuted homology.
"""
function compute_death_simplices!(matrix::CoboundaryMatrix{true}, verbose, cutoff)
    columns, apparent = find_apparent_pairs(
        matrix.filtration, matrix.columns_to_reduce, verbose
    )
    bulk_insert!(matrix.reduced, apparent)
    deaths = simplex_type(matrix.filtration, dim(matrix) + 1)[]
    inf_births = simplex_type(matrix.filtration, dim(matrix))[]
    if isempty(columns)
        return deaths, inf_births
    else
        dim(matrix) > 1 && sort!(columns; rev=true)
        thresh = typemin(birth(first(columns)))
        for pair in apparent
            if birth(pair[2]) - birth(pair[1]) > cutoff
                thresh = max(thresh, birth(pair[2]))
            end
            push!(deaths, pair[2])
        end
        if verbose
            progbar = Progress(length(columns); desc="Precomputing columns...   ")
        end
        for column in columns
            pivot = reduce_column!(matrix, column)
            if !isnothing(pivot)
                if birth(pivot) - birth(column) > cutoff
                    thresh = max(thresh, birth(pivot))
                end
                push!(deaths, simplex(pivot))
            else
                push!(inf_births, column)
            end
            verbose && next!(progbar; showvalues=((:simplices, length(deaths)),))
        end
        return filter!(x -> birth(x) ≤ thresh, deaths), inf_births
    end
end

function _ripserer(
    ::Val{:involuted}, filtration, cutoff, verbose, field, dim_max, reps, implicit
)
    result = PersistenceDiagram[]
    zeroth, to_reduce, to_skip = zeroth_intervals(
        filtration, cutoff, verbose, field, _reps(reps, 0)
    )
    push!(result, zeroth)
    if dim_max > 0
        comatrix = CoboundaryMatrix{true}(field, filtration, to_reduce, to_skip)
        for dim in 1:dim_max
            columns, inf_births = compute_death_simplices!(comatrix, verbose, cutoff)
            birth_candidates = comatrix.columns_to_reduce
            matrix = BoundaryMatrix{implicit}(
                field, filtration, birth_candidates, columns; infinite_intervals=false
            )
            diagram = compute_intervals!(matrix, cutoff, verbose, _reps(reps, dim))
            for birth_simplex in inf_births
                push!(
                    diagram.intervals,
                    interval(comatrix, birth_simplex, nothing, 0, _reps(reps, dim)),
                )
            end
            push!(result, diagram)
            if dim < dim_max
                comatrix = next_matrix(comatrix, verbose)
            end
        end
    end
    return result
end

1	"""
2	compute_death_simplices!(matrix::CoboundaryMatrix{true}, verbose, cutoff)
3
4	Fully reduce `matrix`, but only compute (homological) death simplices. Return all death
5	simplices up to the last that produces an interval with persistence greater than `cutoff`.
6
7	Used for involuted homology.
8	"""
9	function compute_death_simplices!(matrix::CoboundaryMatrix{true}, verbose, cutoff)	12✔
10	columns, apparent = find_apparent_pairs(	12✔
11	matrix.filtration, matrix.columns_to_reduce, verbose
12	)
13	bulk_insert!(matrix.reduced, apparent)	12✔
14	deaths = simplex_type(matrix.filtration, dim(matrix) + 1)[]	12✔
15	inf_births = simplex_type(matrix.filtration, dim(matrix))[]	12✔
16	if isempty(columns)	12✔
NEW 17	return deaths, inf_births	×
18	else
19	dim(matrix) > 1 && sort!(columns; rev=true)	14✔
20	thresh = typemin(birth(first(columns)))	12✔
21	for pair in apparent	12✔
22	if birth(pair[2]) - birth(pair[1]) > cutoff	118✔
NEW 23	thresh = max(thresh, birth(pair[2]))	×
24	end
25	push!(deaths, pair[2])	118✔
26	end	118✔
27	if verbose	12✔
NEW 28	progbar = Progress(length(columns); desc="Precomputing columns... ")	×
29	end
30	for column in columns	12✔
31	pivot = reduce_column!(matrix, column)	3,899✔
32	if !isnothing(pivot)	7,758✔
33	if birth(pivot) - birth(column) > cutoff	3,859✔
34	thresh = max(thresh, birth(pivot))	336✔
35	end
36	push!(deaths, simplex(pivot))	3,859✔
37	else
38	push!(inf_births, column)	40✔
39	end
40	verbose && next!(progbar; showvalues=((:simplices, length(deaths)),))	3,899✔
41	end	3,899✔
42	return filter!(x -> birth(x) ≤ thresh, deaths), inf_births	3,989✔
43	end
44	end
45
46	function _ripserer(	9✔
47	::Val{:involuted}, filtration, cutoff, verbose, field, dim_max, reps, implicit
48	)
49	result = PersistenceDiagram[]	9✔
50	zeroth, to_reduce, to_skip = zeroth_intervals(	9✔
51	filtration, cutoff, verbose, field, _reps(reps, 0)
52	)
53	push!(result, zeroth)	9✔
54	if dim_max > 0	9✔
55	comatrix = CoboundaryMatrix{true}(field, filtration, to_reduce, to_skip)	9✔
56	for dim in 1:dim_max	9✔
57	columns, inf_births = compute_death_simplices!(comatrix, verbose, cutoff)	12✔
58	birth_candidates = comatrix.columns_to_reduce	12✔
59	matrix = BoundaryMatrix{implicit}(	12✔
60	field, filtration, birth_candidates, columns; infinite_intervals=false
61	)
62	diagram = compute_intervals!(matrix, cutoff, verbose, _reps(reps, dim))	12✔
63	for birth_simplex in inf_births	12✔
64	push!(	80✔
65	diagram.intervals,
66	interval(comatrix, birth_simplex, nothing, 0, _reps(reps, dim)),
67	)
68	end	40✔
69	push!(result, diagram)	12✔
70	if dim < dim_max	12✔
71	comatrix = next_matrix(comatrix, verbose)	3✔
72	end
73	end	15✔
74	end
75	return result	9✔
76	end

mtsch / Ripserer.jl / 8545078607

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