diff --git a/src/feature_creation/feature_space/FeatureSpace.hpp b/src/feature_creation/feature_space/FeatureSpace.hpp
index 05b7d7e6eb1df9ab75f762251aca164c4ef97b7d..0a953d66490f3bcf8b366a8d99800563e6eae90b 100644
--- a/src/feature_creation/feature_space/FeatureSpace.hpp
+++ b/src/feature_creation/feature_space/FeatureSpace.hpp
@@ -34,6 +34,7 @@
#include "mpi_interface/serialize_tuple.h"
#include "utils/project.hpp"
+#include "mpi_interface/MPI_Interface.hpp"
#ifdef PY_BINDINGS
namespace np = boost::python::numpy;
diff --git a/src/inputs/InputParser.hpp b/src/inputs/InputParser.hpp
index 9775b149fce06048c081e633d486533560e61772..ba520cdea62903d3a931cee536d4fd761b935777 100644
--- a/src/inputs/InputParser.hpp
+++ b/src/inputs/InputParser.hpp
@@ -38,9 +38,11 @@
#include "feature_creation/node/FeatureNode.hpp"
#include "mpi_interface/MPI_Interface.hpp"
-#if PARAMETERIZE
+
+#ifdef PARAMETERIZE
#include "nl_opt/NLOptWrapper.hpp"
#endif
+
#ifdef PY_BINDINGS
#include "python/py_binding_cpp_def/conversion_utils.hpp"
diff --git a/src/utils/string_utils.cpp b/src/utils/string_utils.cpp
index dbc7e42d53cf950f27a168a03d40b9916bd9fbb1..8989dc2d76c2bc70df83ca6606c328f671255a39 100644
--- a/src/utils/string_utils.cpp
+++ b/src/utils/string_utils.cpp
@@ -88,3 +88,13 @@ std::string str_utils::matlabify(const std::string str)
}
return to_ret;
}
+
+std::string str_utils::join(std::string join_section, std::string* start, int sz)
+{
+ std::string to_ret = start[0];
+ for(int ii = 1; ii < sz; ++ii)
+ {
+ to_ret += join_section + start[ii];
+ }
+ return to_ret;
+}
diff --git a/src/utils/string_utils.hpp b/src/utils/string_utils.hpp
index 3e0d51a56ccf0cbf4aa9dcdc46b79eb52ae861c3..d022a951fc320e34c5819ba67b4174d80e36563f 100644
--- a/src/utils/string_utils.hpp
+++ b/src/utils/string_utils.hpp
@@ -68,6 +68,28 @@ namespace str_utils
* @return The string with the operators replaced
*/
std::string op2str(const std::string str, const std::string op, const std::string op_str);
+
+ /**
+ * @brief Join a vector of strings together
+ *
+ * @param join_section string to put in between each element
+ * @param start pointer to the first element of the vector to join
+ * @param sz Number of elements of the vector to join
+ * @return The joined string
+ */
+ std::string join(std::string join_section, std::string* start, int sz);
+
+ /**
+ * @brief Join a vector of strings together
+ *
+ * @param join_section string to put in between each element
+ * @param list The vector of strings to join together
+ * @return The joined string
+ */
+ inline std::string join(std::string join_section, std::vector<std::string> list)
+ {
+ return join(join_section, list.data(), list.size());
+ }
}
diff --git a/tests/googletest/inputs/input_parser.cc b/tests/googletest/inputs/input_parser.cc
index 6b9e72663de7ef9d78ca37edf1fd1c0084e67a73..df2485dc02cb8c306a6fe4853a73d764f0095e31 100644
--- a/tests/googletest/inputs/input_parser.cc
+++ b/tests/googletest/inputs/input_parser.cc
@@ -21,11 +21,11 @@ namespace
protected:
void SetUp() override
{
+ std::vector<std::string> filepath = str_utils::split_string_trim(__FILE__, "/");
node_value_arrs::finialize_values_arr();
_sample_ids_train = {"a", "b", "c"};
_sample_ids_test = {"d"};
_task_names = {"task_1", "task_2"};
- _allowed_param_ops = {"log"};
_allowed_ops = {"sq", "cb"};
_prop_train = {1.0, 4.0, 9.0};
_prop_test = {16.0};
@@ -34,8 +34,10 @@ namespace
_task_sizes_test = {1, 0};
_phi_0 = {FeatureNode(0, "feat_1", {1.0, 2.0, 3.0}, {4.0}, Unit("m"))};
_prop_unit = Unit("m");
- _filename = "googletest/inputs/sisso.json";
- _data_file = "googletest/inputs/data.csv";
+ _data_file = (
+ str_utils::join("/", filepath.data(), filepath.size() - 1) +
+ "/data.csv"
+ );
_prop_key = "property";
_prop_label = "property";
_task_key = "task";
@@ -50,18 +52,35 @@ namespace
_n_sis_select = 1;
_n_residual = 1;
_n_models_store = 1;
+
+ _fix_intercept = false;
+
+#ifdef PARAMETERIZE
+ _filename = (
+ str_utils::join("/", filepath.data(), filepath.size() - 1) +
+ "/sisso_param.json"
+ );
+
+ _allowed_param_ops = {"log"};
+
_max_param_depth = 1;
_nlopt_seed = 10;
- _fix_intercept = false;
+
_global_param_opt = true;
_reparam_residual = true;
+
+#else
+ _filename = (
+ str_utils::join("/", filepath.data(), filepath.size() - 1) +
+ "/sisso.json"
+ );
+#endif
}
std::vector<std::string> _sample_ids_train; //!< Vector storing all sample ids for the training samples
std::vector<std::string> _sample_ids_test; //!< Vector storing all sample ids for the test samples
std::vector<std::string> _task_names; //!< Vector storing the ID of the task names
- std::vector<std::string> _allowed_param_ops; //!< Vector containing all allowed operators strings for operators with free parameters
std::vector<std::string> _allowed_ops; //!< Vector containing all allowed operators strings
std::vector<double> _prop_train; //!< The value of the property to evaluate the loss function against for the training set
std::vector<double> _prop_test; //!< The value of the property to evaluate the loss function against for the test set
@@ -97,12 +116,18 @@ namespace
int _n_samp_test; //!< Number of samples in the test set
int _n_residual; //!< Number of residuals to pass to the next sis model
int _n_models_store; //!< The number of models to output to files
+
+ bool _fix_intercept; //!< If true the bias term is fixed at 0
+
+ #ifdef PARAMETERIZE
+ std::vector<std::string> _allowed_param_ops; //!< Vector containing all allowed operators strings for operators with free parameters
+
int _max_param_depth; //!< The maximum depth in the binary expression tree to set non-linear optimization
int _nlopt_seed; //!< The seed used for the nlOpt library
- bool _fix_intercept; //!< If true the bias term is fixed at 0
bool _global_param_opt; //!< True if global optimization is requested for non-linear optimization of parameters (Can break reproducibility)
bool _reparam_residual; //!< If True then reparameterize features using the residuals of each model
+ #endif
};
@@ -124,9 +149,6 @@ namespace
inputs.set_task_names(_task_names);
EXPECT_EQ(inputs.task_names()[0], _task_names[0]);
- inputs.set_allowed_param_ops(_allowed_param_ops);
- EXPECT_EQ(inputs.allowed_param_ops()[0], _allowed_param_ops[0]);
-
inputs.set_allowed_ops(_allowed_ops);
EXPECT_EQ(inputs.allowed_ops()[0], _allowed_ops[0]);
@@ -198,31 +220,36 @@ namespace
inputs.set_n_models_store(_n_models_store);
EXPECT_EQ(inputs.n_models_store(), _n_models_store);
+ inputs.set_fix_intercept(_fix_intercept);
+ EXPECT_EQ(inputs.fix_intercept(), _fix_intercept);
+
+ #ifdef PARAMETERIZE
+ inputs.set_allowed_param_ops(_allowed_param_ops);
+ EXPECT_EQ(inputs.allowed_param_ops()[0], _allowed_param_ops[0]);
+
inputs.set_max_param_depth(_max_param_depth);
EXPECT_EQ(inputs.max_param_depth(), _max_param_depth);
inputs.set_nlopt_seed(_nlopt_seed);
EXPECT_EQ(inputs.nlopt_seed(), _nlopt_seed);
- inputs.set_fix_intercept(_fix_intercept);
- EXPECT_EQ(inputs.fix_intercept(), _fix_intercept);
-
inputs.set_global_param_opt(_global_param_opt);
EXPECT_EQ(inputs.global_param_opt(), _global_param_opt);
inputs.set_reparam_residual(_reparam_residual);
EXPECT_EQ(inputs.reparam_residual(), _reparam_residual);
+ #endif
}
TEST_F(InputParserTests, FileConsructor)
{
boost::property_tree::ptree propTree;
boost::property_tree::json_parser::read_json(_filename, propTree);
+ propTree.put("data_file", _data_file);
InputParser inputs(propTree, _filename, mpi_setup::comm);
EXPECT_EQ(inputs.sample_ids_train()[0], _sample_ids_train[0]);
EXPECT_EQ(inputs.sample_ids_test()[0], _sample_ids_test[0]);
EXPECT_EQ(inputs.task_names()[0], _task_names[0]);
- EXPECT_EQ(inputs.allowed_param_ops()[0], _allowed_param_ops[0]);
EXPECT_EQ(inputs.allowed_ops()[0], _allowed_ops[0]);
EXPECT_EQ(inputs.prop_train()[0], _prop_train[0]);
EXPECT_EQ(inputs.prop_test()[0], _prop_test[0]);
@@ -251,10 +278,14 @@ namespace
EXPECT_EQ(inputs.n_sis_select(), _n_sis_select);
EXPECT_EQ(inputs.n_residual(), _n_residual);
EXPECT_EQ(inputs.n_models_store(), _n_models_store);
+ EXPECT_EQ(inputs.fix_intercept(), _fix_intercept);
+
+#ifdef PARAMETERIZE
+ EXPECT_EQ(inputs.allowed_param_ops()[0], _allowed_param_ops[0]);
EXPECT_EQ(inputs.max_param_depth(), _max_param_depth);
EXPECT_EQ(inputs.nlopt_seed(), _nlopt_seed);
- EXPECT_EQ(inputs.fix_intercept(), _fix_intercept);
EXPECT_EQ(inputs.global_param_opt(), _global_param_opt);
EXPECT_EQ(inputs.reparam_residual(), _reparam_residual);
+#endif
}
}
diff --git a/tests/googletest/inputs/sisso.json b/tests/googletest/inputs/sisso.json
index f41261dc992d0c1d090c254ae5530fee190504b2..2e655b860bda6796662d0cc9186eed6563eaf6e2 100644
--- a/tests/googletest/inputs/sisso.json
+++ b/tests/googletest/inputs/sisso.json
@@ -10,12 +10,7 @@
"task_key": "task",
"leave_out_inds": [3],
"opset": ["sq", "cb"],
- "param_opset": ["log"],
"fix_intercept": false,
"min_abs_feat_val": 1e-5,
- "max_abs_feat_val": 1e8,
- "max_param_depth": 1,
- "nlopt_seed": 10,
- "global_param_opt": true,
- "reparam_residual": true
+ "max_abs_feat_val": 1e8
}
diff --git a/tests/googletest/inputs/sisso_param.json b/tests/googletest/inputs/sisso_param.json
new file mode 100644
index 0000000000000000000000000000000000000000..f41261dc992d0c1d090c254ae5530fee190504b2
--- /dev/null
+++ b/tests/googletest/inputs/sisso_param.json
@@ -0,0 +1,21 @@
+{
+ "desc_dim": 2,
+ "n_sis_select": 1,
+ "max_rung": 1,
+ "n_residual": 1,
+ "n_models_store": 1,
+ "n_rung_store": 1,
+ "data_file": "googletest/inputs/data.csv",
+ "property_key": "property",
+ "task_key": "task",
+ "leave_out_inds": [3],
+ "opset": ["sq", "cb"],
+ "param_opset": ["log"],
+ "fix_intercept": false,
+ "min_abs_feat_val": 1e-5,
+ "max_abs_feat_val": 1e8,
+ "max_param_depth": 1,
+ "nlopt_seed": 10,
+ "global_param_opt": true,
+ "reparam_residual": true
+}