cleanup add_coboundary

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 <typename Column>
 	void add_coboundary(compressed_sparse_matrix<diameter_entry_t>& 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<diameter_index_t>& 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);