Merge commit '5adf0472e278034d155395cb8a95c017b30f0acb' into sparse-distance-matrix

* commit '5adf0472e278034d155395cb8a95c017b30f0acb':
  rearranged reduction columns code
  suppress output of 0-persistence pairs in dim 0
  fixed license header

1 files changed, 32 insertions, 27 deletions

diff --git a/ripser.cpp b/ripser.cpp
index 561f7bf..a5d6c7c 100644
--- a/ripser.cpp
+++ b/ripser.cpp
@@ -1,19 +1,23 @@
-/*  Ripser: a lean C++ code for the computation of Vietoris-Rips persistence barcodes
+/*
 
-    Copyright 2015-2016 Ulrich Bauer.
+Ripser: a lean C++ code for computation of Vietoris-Rips persistence barcodes
 
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
+Copyright 2015-2016 Ulrich Bauer.
 
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the
+Free Software Foundation, either version 3 of the License, or (at your option)
+any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along
+with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
 
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>. */
 
 //#define ASSEMBLE_REDUCTION_MATRIX
 //#define USE_COEFFICIENTS
@@ -602,7 +606,7 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in
 #endif
 
 #ifdef ASSEMBLE_REDUCTION_MATRIX
-	compressed_sparse_matrix<diameter_entry_t> reduction_matrix;
+	compressed_sparse_matrix<diameter_entry_t> reduction_coefficients;
 #else
 #ifdef USE_COEFFICIENTS
 	std::vector<diameter_entry_t> reduction_coefficients;
@@ -640,9 +644,9 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in
 		diameter_entry_t pivot(0, -1, -1 + modulus);
 
 #ifdef ASSEMBLE_REDUCTION_MATRIX
-		// initialize reduction_matrix as identity matrix
-		reduction_matrix.append_column();
-		reduction_matrix.push_back(diameter_entry_t(column_to_reduce, 1));
+		// initialize reduction_coefficients as identity matrix
+		reduction_coefficients.append_column();
+		reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, 1));
 #else
 #ifdef USE_COEFFICIENTS
 		reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, 1));
@@ -655,18 +659,18 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in
 			const coefficient_t factor = modulus - get_coefficient(pivot);
 
 #ifdef ASSEMBLE_REDUCTION_MATRIX
-			for (auto it = reduction_matrix.cbegin(j); it != reduction_matrix.cend(j); ++it)
-#endif
-			{
-#ifdef ASSEMBLE_REDUCTION_MATRIX
-				diameter_entry_t simplex = *it;
+			auto coeffs_begin = reduction_coefficients.cbegin(j), coeffs_end = reduction_coefficients.cend(j);
 #else
 #ifdef USE_COEFFICIENTS
-				diameter_entry_t simplex = reduction_coefficients[j];
+			auto coeffs_begin = &reduction_coefficients[j], coeffs_end = &reduction_coefficients[j] + 1;
 #else
-				diameter_entry_t simplex = columns_to_reduce[j];
+			auto coeffs_begin = &columns_to_reduce[j], coeffs_end = &columns_to_reduce[j] + 1;
 #endif
 #endif
+
+			for (auto it = coeffs_begin; it != coeffs_end; ++it)
+			{
+				diameter_entry_t simplex = *it;
 				set_coefficient(simplex, get_coefficient(simplex) * factor % modulus);
 
 #ifdef ASSEMBLE_REDUCTION_MATRIX
@@ -734,9 +738,9 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in
 #endif
 
 #ifdef ASSEMBLE_REDUCTION_MATRIX
-			// replace current column of reduction_matrix (with a single diagonal 1 entry)
+			// replace current column of reduction_coefficients (with a single diagonal 1 entry)
 			// by reduction_column (possibly with a different entry on the diagonal)
-			reduction_matrix.pop_back();
+			reduction_coefficients.pop_back();
 			while (true) {
 				diameter_entry_t e = pop_pivot(reduction_column, modulus);
 				if (get_index(e) == -1) break;
@@ -744,7 +748,7 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in
 				set_coefficient(e, inverse * get_coefficient(e) % modulus);
 				assert(get_coefficient(e) > 0);
 #endif
-				reduction_matrix.push_back(e);
+				reduction_coefficients.push_back(e);
 			}
 #else
 #ifdef USE_COEFFICIENTS
@@ -1010,7 +1014,8 @@ int main(int argc, char** argv) {
 
 			if (u != v) {
 #ifdef PRINT_PERSISTENCE_PAIRS
-				std::cout << " [0," << get_diameter(e) << ")" << std::endl;
+				if (get_diameter(e) > 0)
+					std::cout << " [0," << get_diameter(e) << ")" << std::endl;
 #endif
 				dset.link(u, v);
 			} else