Merge pull request #711 from VincentRouvreau/bug/persistence_utilities_default_output

persistence diagram default output is std::cout, not std::clog. Modify utilities help to be in agreement with this

16 files changed, 17 insertions, 17 deletions

diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 91899040..e65d8c6f 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -263,7 +263,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
       "cuboid-file,c", po::value<std::string>(&cuboid_file),
       "Name of file describing the periodic domain. Format is:\n  min_hx min_hy min_hz\n  max_hx max_hy max_hz")(
       "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-alpha-square-value,r",
       po::value<Filtration_value>(&alpha_square_max_value)
           ->default_value(std::numeric_limits<Filtration_value>::infinity()),
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index e86b34e2..29edbd8e 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -163,7 +163,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
       "weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()),
       "Name of file containing a point weights. Format is one weight per line:\n  W1\n  ...\n  Wn ")(
       "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
                                       ->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal alpha square value for the Alpha complex construction.")(
diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp
index a07ba212..e6419f3d 100644
--- a/src/Cech_complex/utilities/cech_persistence.cpp
+++ b/src/Cech_complex/utilities/cech_persistence.cpp
@@ -118,7 +118,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, bool&
       "fast,f", po::bool_switch(&fast),
       "To activate fast version of Cech complex (default is false, not available if exact is set)")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-radius,r",
       po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Cech complex construction.")(
diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp
index 38efb9e6..70b489b5 100644
--- a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp
+++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp
@@ -111,7 +111,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-edge-length,r",
       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Rips complex construction.")(
diff --git a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp
index d8f42ab6..a8fd6f14 100644
--- a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp
+++ b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp
@@ -140,7 +140,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::cout")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-edge-length,r",
       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Rips complex construction.")(
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index 38c44514..7f89c001 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -93,7 +93,7 @@ void program_options(int argc, char * argv[]
   visible.add_options()
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::clog")
+       "Name of file in which the persistence diagram is written. Default print in standard output")
       ("field-charac,p", po::value<int>(&p)->default_value(11),
        "Characteristic p of the coefficient field Z/pZ for computing homology.")
       ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index ca26a5b9..84453898 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -96,7 +96,7 @@ void program_options(int argc, char * argv[]
   visible.add_options()
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::clog")
+       "Name of file in which the persistence diagram is written. Default print in standard output")
       ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index a503d983..6f37cf5c 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -112,7 +112,7 @@ void program_options(int argc, char * argv[]
   visible.add_options()
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::clog")
+       "Name of file in which the persistence diagram is written. Default print in standard output")
       ("max-edge-length,r",
        po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
        "Maximal length of an edge for the Rips complex construction.")
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 8c5742aa..6b60f603 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -109,7 +109,7 @@ void program_options(int argc, char * argv[]
   visible.add_options()
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::clog")
+       "Name of file in which the persistence diagram is written. Default print in standard output")
       ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
index b473738e..72ddc797 100644
--- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
@@ -118,7 +118,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "min-edge-corelation,c", po::value<Filtration_value>(&correlation_min)->default_value(0),
       "Minimal corelation of an edge for the Rips complex construction.")(
       "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
index 6306755d..77ad841a 100644
--- a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
@@ -79,7 +79,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-edge-length,r",
       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Rips complex construction.")(
diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp
index 9d7490b3..43194821 100644
--- a/src/Rips_complex/utilities/rips_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_persistence.cpp
@@ -81,7 +81,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-edge-length,r",
       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Rips complex construction.")(
diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
index ac935b41..829c85e6 100644
--- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp
+++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
@@ -84,7 +84,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   po::options_description visible("Allowed options", 100);
   visible.add_options()("help,h", "produce help message")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-edge-length,r",
       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Rips complex construction.")(
diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index 614de0d4..b2ecad82 100644
--- a/src/Witness_complex/utilities/strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
@@ -108,7 +108,7 @@ void program_options(int argc, char* argv[], int& nbL, std::string& file_name, s
   visible.add_options()("help,h", "produce help message")("landmarks,l", po::value<int>(&nbL),
                                                           "Number of landmarks to choose from the point cloud.")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
       "Maximal squared relaxation parameter.")(
       "field-charac,p", po::value<int>(&p)->default_value(11),
diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index 5ea31d6b..c7ead7de 100644
--- a/src/Witness_complex/utilities/weak_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -108,7 +108,7 @@ void program_options(int argc, char* argv[], int& nbL, std::string& file_name, s
   visible.add_options()("help,h", "produce help message")("landmarks,l", po::value<int>(&nbL),
                                                           "Number of landmarks to choose from the point cloud.")(
       "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-      "Name of file in which the persistence diagram is written. Default print in std::clog")(
+      "Name of file in which the persistence diagram is written. Default print in standard output")(
       "max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
       "Maximal squared relaxation parameter.")(
       "field-charac,p", po::value<int>(&p)->default_value(11),
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
index 3a3a7d83..e994e0b8 100644
--- a/src/Witness_complex/utilities/witnesscomplex.md
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -29,7 +29,7 @@ and `p` is the characteristic of the field *Z/pZ* used for homology coefficients
 

 * `-h [ --help ]` Produce help message

 * `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

-* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::clog.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in standard output.

 * `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

 * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

 * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

@@ -60,7 +60,7 @@ and `p` is the characteristic of the field *Z/pZ* used for homology coefficients
 

 * `-h [ --help ]` Produce help message

 * `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

-* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::clog.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in standard output.

 * `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

 * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

 * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.