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better algorithm for keeping zero entires #5

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50 changes: 37 additions & 13 deletions src/helper.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -150,23 +150,47 @@ macro timing(cond,code)
end

function SparseMatrix.sparse(I,J,V, M, N;keepzeros=false)
@assert length(I) == length(J) == length(V)
if(!keepzeros)
return sparse(I,J,V,M,N)
else
full = sparse(I,J,ones(Float64,length(I)),M,N)
actual = sparse(I,J,V,M,N)
fill!(full.nzval,0.0)
mergednnz = [0]
mergedmap = zeros(Int,length(I))
idxmap = zeros(Int,length(I))
mergedindices = zeros(Int,length(I))
function combine(idx1,idx2)
# @show idx1, idx2
idx1 = round(Int,idx1)
idx2 = round(Int,idx2)
@inbounds @assert mergedmap[idx2] == 0 && (mergedmap[idx1] == idx1 || mergedmap[idx1] == 0)
@inbounds mergednnz[1] += 1
@inbounds mergedmap[idx1] = idx1
@inbounds mergedmap[idx2] = idx1
@inbounds mergedindices[mergednnz[1]] = idx2
return idx1
end

full = sparse(I,J,[float(i) for i in 1:length(I)],M,N,combine)
for col in 1:N
@inbounds for pos in full.colptr[col]:(full.colptr[col+1]-1)
@inbounds row = full.rowval[pos]
@inbounds origidx = round(Int,full.nzval[pos]) # this is the original index (on JJ) of this element
@inbounds idxmap[origidx] = pos
end
end

for c = 1:N
for i=nzrange(actual,c)
r = actual.rowval[i]
v = actual.nzval[i]
if(v!=0)
full[r,c] = v
end
end
# full.nzval[crange] = actual.nzval[crange]
end
@inbounds for k in 1:mergednnz[1]
@inbounds origidx = mergedindices[k]
@inbounds mergedwith = mergedmap[origidx]
@inbounds @assert idxmap[origidx] == 0
@inbounds @assert idxmap[mergedwith] != 0
@inbounds idxmap[origidx] = idxmap[mergedwith]
end

fill!(full.nzval,0.0)
for i in 1:length(I)
@inbounds full.nzval[idxmap[i]] += V[i]
end
return full
end
end
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