From b909e6c124b8d83e759793991f9db391103ebb0b Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Tue, 2 Jul 2019 12:52:59 +0200 Subject: cleanup add_coboundary --- benchmarks/Dockerfile | 16 +++++++++++----- ripser.cpp | 21 +++++++++++---------- 2 files changed, 22 insertions(+), 15 deletions(-) diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile index 40c654f..3d6e952 100644 --- a/benchmarks/Dockerfile +++ b/benchmarks/Dockerfile @@ -52,7 +52,7 @@ RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphe && curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/random_point_cloud_50_16_.txt \ && curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/random_50_16.bin - +COPY o3_1024.txt . FROM benchmark-setup as benchmark-ripser @@ -65,10 +65,11 @@ ENV PATH="${PATH}:/ripser/ripser" WORKDIR /benchmark RUN time -v -o sphere_3_192.ripser.txt ripser sphere_3_192.distance_matrix --dim 2 -RUN time -v -o random.ripser.txt ripser random_point_cloud_50_16_.txt --dim 7 +RUN time -v -o random.ripser.txt ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7 RUN time -v -o fractal-r.ripser.txt ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2 -RUN time -v -o dragon-2.ripser.txt ripser dragon_vrip.ply.txt_2000_.txt --dim 1 +RUN time -v -o dragon-2.ripser.txt ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1 # RUN time -v -o genome.ripser.txt ripser human_gene_distmat.txt --dim 1 +RUN time -v -o o3_1024.ripser.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 @@ -175,8 +176,13 @@ RUN time -v -o fractal-r.eirene.txt \ julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt")), record="none", maxdim=2))' >fractal-r.eirene.out.txt #RUN time -v -o random.eirene.txt \ # julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("random_point_cloud_50_16_.txt")), model="pc", record="none", maxdim=7))' >random.eirene.out.txt - - +RUN time -v -o o3_1024.eirene.txt \ + julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("o3_1024.txt")), model="pc", record="none", maxdim=3, maxrad=1.8))' > o3_1024.eirene.out.txt +# +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_1024.txt")), model="pc", record="none", maxdim=3, maxrad=1.8)) +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_2048.txt")), model="pc", record="none", maxdim=3, maxrad=1.6)) +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_4096.txt")), model="pc", record="none", maxdim=3, maxrad=1.4)) +# FROM benchmark-setup as benchmark-dionysus2 diff --git a/ripser.cpp b/ripser.cpp index 3f19858..b10ec07 100644 --- a/ripser.cpp +++ b/ripser.cpp @@ -539,12 +539,18 @@ public: if (get_diameter(coface) <= threshold) working_coboundary.push(coface); } } - + template void add_coboundary(compressed_sparse_matrix& reduction_matrix, - const index_t index_column_to_add, const coefficient_t factor, - Column& working_reduction_column, Column& working_coboundary, - const index_t& dim) { + std::vector& columns_to_reduce, + const index_t index_column_to_add, const coefficient_t factor, + Column& working_reduction_column, Column& working_coboundary, + const index_t& dim) { + diameter_entry_t column_to_add(columns_to_reduce[index_column_to_add], + factor); + add_coboundary(column_to_add, working_reduction_column, working_coboundary, + dim); + for (auto it = reduction_matrix.cbegin(index_column_to_add); it != reduction_matrix.cend(index_column_to_add); ++it) { diameter_entry_t simplex = *it; @@ -598,12 +604,7 @@ public: modulus - get_coefficient(pivot) * multiplicative_inverse[get_coefficient(other_pivot)] % modulus; - diameter_entry_t column_to_add(columns_to_reduce[index_column_to_add], - factor); - - add_coboundary(column_to_add, working_reduction_column, working_coboundary, - dim); - add_coboundary(reduction_matrix, index_column_to_add, factor, + add_coboundary(reduction_matrix, columns_to_reduce, index_column_to_add, factor, working_reduction_column, working_coboundary, dim); pivot = get_pivot(working_coboundary, modulus); -- cgit v1.2.3