ecrc · mahmoudElkarargyBS · Jul 3, 2024 · Jul 3, 2024
diff --git a/inst/include/Rcpp-adapters/FunctionsAdapter.hpp b/inst/include/Rcpp-adapters/FunctionsAdapter.hpp
@@ -22,25 +22,6 @@
 
 namespace exageostat::adapters {
 
-    /**
-     * @brief Retrieves locations from ExaGeoStat data.
-     * @details Extracts and returns the locations stored in an ExaGeoStatData object,
-     * @param[in] apData Pointer to ExaGeoStatData object containing the spatial data.
-     * @return vector of locations coordinates.
-     *
-     */
-    std::vector<std::vector<double>> R_GetLocations(ExaGeoStatData<double> *apData);
-
-    /**
-     * @brief Retrieves descriptive Z values from ExaGeoStat data based on type.
-     * @details Extracts and returns Z values from an ExaGeoStatData object, aiding in targeted spatial data analysis and visualization within ExaGeoStat.
-     * @param[in] apData Pointer to ExaGeoStatData object containing the spatial data.
-     * @param[in] aType String specifying the type of descriptor value to retrieve (e.g., "Chameleon", "HiCMA").
-     * @return Numeric vector of descriptive Z values.
-     *
-     */
-    Rcpp::NumericVector R_GetDescZValues(ExaGeoStatData<double> *apData, const std::string &aType);
-
     /**
      * @brief Function to load ExaGeoStat data.
      * @details This function loads data into an ExaGeoStatData object using the provided configuration and computational settings.
@@ -60,7 +41,7 @@ namespace exageostat::adapters {
      * @return A pointer to an ExaGeoStatData object containing the loaded data.
      *
      */
-    ExaGeoStatData<double> *
+    Rcpp::List
     R_ExaGeoStatLoadData(const std::string &aKernelName, const std::vector<double> &aInitialTheta,
                          const std::string &aDistanceMatrix, const int &aProblemSize, const int &aSeed,
                          const int &aDenseTileSize, const int &aLowTileSize, const std::string &aDimension,

diff --git a/inst/include/utilities/Logger.hpp b/inst/include/utilities/Logger.hpp
@@ -31,17 +31,49 @@
 #define DEFAULT_PRECISION 6
 
 /**
- * @def VERBOSE(msg)
- * @brief Verbose macro for logging and debugging mode.
+ * @def VERBOSE_PRECISION
+ * @brief A fixed precision for the verbose mode.
  */
-#define VERBOSE(msg) \
+#define VERBOSE_PRECISION 12
+
+/**
+ * @def VERBOSE_1(msg)
+ * @brief VERBOSE_1 macro for logging outputs in verbose mode, with double taps at the beginning, a fixed precision and a new line at the end.
+ */
+#define VERBOSE_1(msg) \
+    if(exageostat::configurations::Configurations::GetVerbosity() == exageostat::common::Verbose::DETAILED_MODE && \
+      !exageostat::helpers::CommunicatorMPI::GetInstance()->GetRank()) { \
+        std::ostringstream oss; \
+        oss << "\t\t " << std::fixed << std::setprecision(VERBOSE_PRECISION) << msg << std::endl; \
+        std::cout << oss.str(); \
+    }
+
+/**
+ * @def VERBOSE_2(msg, A)
+ * @brief VERBOSE_2 macro for logging outputs in verbose mode, with double taps at the beginning, a fixed precision and without a new line at the end.
+ */
+#define VERBOSE_2(msg, A) \
     if(exageostat::configurations::Configurations::GetVerbosity() == exageostat::common::Verbose::DETAILED_MODE && \
        !exageostat::helpers::CommunicatorMPI::GetInstance()->GetRank()) { \
         std::ostringstream oss; \
-        oss << "\t\t\t " << msg << std::endl; \
+        oss << "\t\t " << std::fixed << std::setprecision(VERBOSE_PRECISION) << msg ; \
         std::cout << oss.str(); \
     }
 
+/**
+ * @def VERBOSE_CONTROL(x, A, B, FUNC, ...)
+ * @brief VERBOSE_CONTROL is The internal macro that simply strips the excess and ends up with the required macro
+ */
+#define VERBOSE_CONTROL(x, A, B, FUNC, ...) FUNC
+
+/**
+ * @def VERBOSE(...)
+ * @brief VERBOSE macro that's called, Used to logging outputs in a verbose mode.
+ */
+#define VERBOSE(...) VERBOSE_CONTROL(,##__VA_ARGS__, \
+                       VERBOSE_2(__VA_ARGS__),         \
+                       VERBOSE_1(__VA_ARGS__),       \
+                                         )
 /**
  * @def LOGGER_1(msg)
  * @brief LOGGER_1 macro for logging outputs with double taps and new line at the end.

diff --git a/man/get_Z_measurement_vector.Rd b/man/get_Z_measurement_vector.Rd
@@ -1,4 +1,3 @@
-// TODO: dots
 % Copyright (c) 2017-2024 King Abdullah University of Science and Technology,
 % All rights reserved.
 % ExaGeoStat is a software package, provided by King Abdullah University of Science and Technology (KAUST).

diff --git a/scripts/Benchmarking.sh b/scripts/Benchmarking.sh
@@ -47,13 +47,13 @@ for N in "${desired_N[@]}"; do
       time_prediction=$(echo "$time_prediction" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
       time_modeling_iteration=$(echo "$command_output" | awk -F "#Average Time Modeling per Iteration: " '{print $2}' | awk -F "," '{print $1}')
       time_modeling_iteration=$(echo "$time_modeling_iteration" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
-      flops_generation=$(echo "$command_output" | awk -F "#Total Data Generation Gflop/s: " '{print $2}' | awk -F "," '{print $1}')
+      flops_generation=$(echo "$command_output" | awk -F "#Total Data Generation GFlop/s: " '{print $2}' | awk -F "," '{print $1}')
       flops_generation=$(echo "$flops_generation" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
-      flops_modeling=$(echo "$command_output" | awk -F "#Total MLE Gflop/s: " '{print $2}' | awk -F "," '{print $1}')
+      flops_modeling=$(echo "$command_output" | awk -F "#Total MLE GFlop/s: " '{print $2}' | awk -F "," '{print $1}')
       flops_modeling=$(echo "$flops_modeling" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
       flops_modeling_iteration=$(echo "$command_output" | awk -F "#Average Flops per Iteration: " '{print $2}' | awk -F "," '{print $1}')
       flops_modeling_iteration=$(echo "$flops_modeling_iteration" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
-      flops_mspe=$(echo "$command_output" | awk -F "#MSPE Gflop/s: " '{print $2}' | awk -F "," '{print $1}')
+      flops_mspe=$(echo "$command_output" | awk -F "#MSPE GFlop/s: " '{print $2}' | awk -F "," '{print $1}')
       flops_mspe=$(echo "$flops_mspe" | tr -d '\n' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
 
     echo "$command_output"

diff --git a/src/Rcpp-adapters/FunctionsAdapter.cpp b/src/Rcpp-adapters/FunctionsAdapter.cpp
@@ -25,60 +25,7 @@ using namespace exageostat::configurations;
 
 namespace exageostat::adapters {
 
-    vector<vector<double>> R_GetLocations(ExaGeoStatData<double> *apData) {
-
-        // Number of points per each dimension
-        int length = apData->GetLocations()->GetSize();
-        bool is3D = apData->GetLocations()->GetDimension() == Dimension3D;
-
-        double *locationXArray = apData->GetLocations()->GetLocationX();
-        double *locationYArray = apData->GetLocations()->GetLocationY();
-        double *locationZArray = nullptr;
-        if (is3D) {
-            locationZArray = apData->GetLocations()->GetLocationZ();
-        }
-
-        vector<vector<double>> locations_matrix;
-        for (int i = 0; i < length; ++i) {
-            vector<double> point;
-            point.push_back(locationXArray[i]);
-            point.push_back(locationYArray[i]);
-            if (is3D) {
-                point.push_back(locationZArray[i]);
-            }
-            locations_matrix.push_back(point);
-        }
-        return locations_matrix;
-    }
-
-    NumericVector R_GetDescZValues(ExaGeoStatData<double> *apData, const string &aType) {
-
-        DescriptorType descriptorType;
-        void *pDescriptor;
-
-        if (aType == "chameleon" || aType == "Chameleon") {
-            descriptorType = CHAMELEON_DESCRIPTOR;
-        } else if (aType == "hicma" || aType == "Hicma" || aType == "HICMA") {
-#ifdef USE_HICMA
-            descriptorType = HICMA_DESCRIPTOR;
-#else
-            throw runtime_error("Please enable HiCMA to use HiCMA descriptors.");
-#endif
-        } else {
-            throw domain_error("Invalid type of descriptor, please use chameleon or hicma.");
-        }
-
-        // Obtain the pointer to the array of doubles
-        double *data = apData->GetDescriptorData()->GetDescriptorMatrix(descriptorType, DESCRIPTOR_Z);
-        int length = apData->GetLocations()->GetSize();
-        // Create an empty NumericVector of the appropriate length
-        NumericVector vec(length);
-        // Copy data from the double array to the NumericVector
-        copy(data, data + length, vec.begin());
-        return vec;
-    }
-
-    ExaGeoStatData<double> *
+    List
     R_ExaGeoStatLoadData(const string &aKernelName, const vector<double> &aInitialTheta, const string &aDistanceMatrix,
                          const int &aProblemSize, const int &aSeed, const int &aDenseTileSize, const int &aLowTileSize,
                          const string &aDimension, const string &aLogPath, const string &aDataPath,
@@ -110,8 +57,59 @@ namespace exageostat::adapters {
         unique_ptr<ExaGeoStatData<double>> data;
         ExaGeoStat<double>::ExaGeoStatLoadData(configurations, data);
 
+        // Obtain the pointer to the array of doubles
+        double *descriptor_data = data->GetDescriptorData()->GetDescriptorMatrix(CHAMELEON_DESCRIPTOR, DESCRIPTOR_Z);
+        int length = data->GetLocations()->GetSize();
+        // Create an empty NumericVector of the appropriate length
+        NumericVector vec(length);
+        // Copy data from the double array to the NumericVector
+        copy(descriptor_data, descriptor_data + length, vec.begin());
+
+        // Number of points per each dimension
+        bool is3D = data->GetLocations()->GetDimension() == Dimension3D;
+
+        double *locationXArray = data->GetLocations()->GetLocationX();
+        double *locationYArray = data->GetLocations()->GetLocationY();
+        double *locationZArray = nullptr;
+        if (is3D) {
+            locationZArray = data->GetLocations()->GetLocationZ();
+        }
+
+        vector<vector<double>> locations_matrix;
+        for (int i = 0; i < length; ++i) {
+            vector<double> point;
+            point.push_back(locationXArray[i]);
+            point.push_back(locationYArray[i]);
+            if (is3D) {
+                point.push_back(locationZArray[i]);
+            }
+            locations_matrix.push_back(point);
+        }
+
+        // Create NumericVectors for location coordinates
+        NumericVector locationX(length);
+        NumericVector locationY(length);
+        NumericVector locationZ(length);
+
+        for (int i = 0; i < length; ++i) {
+            locationX[i] = locationXArray[i];
+            locationY[i] = locationYArray[i];
+            if (is3D) {
+                locationZ[i] = locationZArray[i];
+            }
+        }
+
+        // Create a list of vectors including z_values and locations
+        Rcpp::List result = Rcpp::List::create(
+                _["m"] = vec,
+                _["x"] = locationX,
+                _["y"] = locationY,
+                _["z"] = locationZ
+        );
         // We can safely return the raw pointer, but we need to release it from data to avoid deletion.
-        return data.release();
+        data.release();
+
+        return result;
     }
 
     vector<double>

diff --git a/src/Rcpp-adapters/RcppModules.cpp b/src/Rcpp-adapters/RcppModules.cpp
@@ -66,8 +66,4 @@ RCPP_MODULE(ExaGeoStatCPP) {
              List::create(_["kernel"], _["distance_matrix"] = "euclidean", _["estimated_theta"], _["dts"], _["lts"] = 0,
                           _["dimension"] = "2D", _["train_data"], _["test_data"], _["test_measurements"]));
 
-    function("get_locations", &exageostat::adapters::R_GetLocations, List::create(_["data"]));
-
-    function("get_Z_measurement_vector", &exageostat::adapters::R_GetDescZValues, List::create(_["data"], _["type"]));
-
 }
diff --git a/src/api/ExaGeoStat.cpp b/src/api/ExaGeoStat.cpp
@@ -71,6 +71,18 @@ T ExaGeoStat<T>::ExaGeoStatDataModeling(Configurations &aConfigurations, std::un
     optimizing_function.optimize(aConfigurations.GetStartingTheta(), opt_f);
     aConfigurations.SetEstimatedTheta(aConfigurations.GetStartingTheta());
 
+    auto theta = aConfigurations.GetStartingTheta();
+
+    LOGGER("--> Final Theta Values (", true)
+    for (int i = 0; i < parameters_number; i++) {
+        LOGGER_PRECISION(theta[i])
+        if (i != parameters_number - 1) {
+            LOGGER_PRECISION(", ")
+        }
+    }
+    LOGGER_PRECISION(")")
+    LOGGER("")
+
     delete pKernel;
     delete modeling_data;
     return optimizing_function.last_optimum_value();

diff --git a/src/configurations/Configurations.cpp b/src/configurations/Configurations.cpp
@@ -623,6 +623,7 @@ void Configurations::InitTheta(vector<double> &aTheta, const int &size) {
 
 void Configurations::PrintSummary() {
 
+#ifndef USING_R
     Verbose temp = this->GetVerbosity();
     mVerbosity = STANDARD_MODE;
 
@@ -674,9 +675,10 @@ void Configurations::PrintSummary() {
             LOGGER("#Out Of Core (OOC) technology is enabled")
         }
         LOGGER("*************************************************")
-        mVerbosity = temp;
         mFirstInit = true;
     }
+    mVerbosity = temp;
+#endif
 }
 
 int Configurations::CalculateZObsNumber() {

diff --git a/src/linear-algebra-solvers/LinearAlgebraMethods.cpp b/src/linear-algebra-solvers/LinearAlgebraMethods.cpp
@@ -813,16 +813,16 @@ void LinearAlgebraMethods<T>::ExaGeoStatMLETileMLOEMMOM(Configurations &aConfigu
 
     int n_z_miss = aConfigurations.GetUnknownObservationsNb();
     int num_par = aKernel.GetParametersNumbers();
-    LOGGER("\t\t- Truth Theta: ", true)
+    VERBOSE("\t\t- Truth Theta: ", true)
     for (int num = 0; num < num_par; num++) {
-        LOGGER_PRECISION(apTruthTheta[num] << " ")
+        VERBOSE(apTruthTheta[num] << " ",true)
     }
-    LOGGER("")
-    LOGGER("\t\t- Estimated Theta: ", true)
+    VERBOSE("")
+    VERBOSE("\t\t- Estimated Theta: ", true)
     for (int num = 0; num < num_par; num++) {
-        LOGGER_PRECISION(apEstimatedTheta[num] << " ")
+        VERBOSE(apEstimatedTheta[num] << " ",true)
     }
-    LOGGER("")
+    VERBOSE("")
     int p;
     double all_time, cholesky1, cholesky2, matrix_gen, vecs_gen, copy_vecs, trsm1, trsm2, trsm3, trsm4, gevv1, gevv2, gevv3, gevv4, gevv5;
 
@@ -1109,7 +1109,7 @@ void LinearAlgebraMethods<T>::ExaGeoStatMLETileMLOEMMOM(Configurations &aConfigu
     *mloe /= n_z_miss;
     *mmom /= n_z_miss;
     STOP_TIMING(all_time);
-    LOGGER("\t\t- MLOE = " << *mloe << "\t\t- MMOM = " << *mmom)
+    VERBOSE("\t\t- MLOE = " << *mloe << "\t\t- MMOM = " << *mmom)
     VERBOSE("\t---- MLOE MMOM Time: " << all_time << " seconds.")
 
     Results::GetInstance()->SetMLOE(*mloe);

diff --git a/src/prediction/Prediction.cpp b/src/prediction/Prediction.cpp
@@ -93,16 +93,16 @@ void Prediction<T>::PredictMissingData(unique_ptr<ExaGeoStatData<T>> &aData, Con
         VERBOSE("\t\t- CI for nu: " << aConfigurations.GetEstimatedTheta()[2] - Q_NORM * sqrt(fisher_results[8]) << " "
                                     << aConfigurations.GetEstimatedTheta()[2] + Q_NORM * sqrt(fisher_results[8]))
 
-        LOGGER("\t\t- Fisher Matrix:")
+        VERBOSE("\t\t- Fisher Matrix:")
         for (i = 0; i < num_params; i++) {
-            LOGGER("\t\t  ", true)
+            VERBOSE("\t\t ", true)
             for (j = 0; j < num_params; j++) {
-                LOGGER_PRECISION(fisher_results[i * num_params + j], 18)
+                VERBOSE(fisher_results[i * num_params + j],true)
                 if (j != num_params - 1) {
-                    LOGGER_PRECISION(", ")
+                    VERBOSE(", ",true)
                 }
             }
-            LOGGER("")
+            VERBOSE("")
         }
         delete[] fisher_results;
     }
@@ -159,7 +159,7 @@ void Prediction<T>::PredictMissingData(unique_ptr<ExaGeoStatData<T>> &aData, Con
 
     // MSPE Prediction Function Call
     if (aConfigurations.GetIsMSPE()) {
-        LOGGER("\t---- Using MSPE ----")
+        LOGGER("\t---- Using Prediction Function MSPE ----")
         T *prediction_error_mspe;
         if (aConfigurations.GetIsNonGaussian()) {
             prediction_error_mspe = linear_algebra_solver->ExaGeoStatMLENonGaussianPredictTile(aData,
@@ -187,7 +187,7 @@ void Prediction<T>::PredictMissingData(unique_ptr<ExaGeoStatData<T>> &aData, Con
         }
         Results::GetInstance()->SetPredictedMissedValues(z_miss_vector);
         if (z_actual) {
-            LOGGER("\t\t- MSPE: " << avg_pred_value[0])
+            LOGGER("\t\t- Prediction value: " << avg_pred_value[0])
         }
         delete[] prediction_error_mspe;
     }

diff --git a/src/prediction/PredictionAuxiliaryFunctions.cpp b/src/prediction/PredictionAuxiliaryFunctions.cpp
@@ -61,5 +61,5 @@ void PredictionAuxiliaryFunctions<T>::PredictIDW(T *apZMiss, T *apZActual, T *ap
     for (int index = 0; index < aZMissNumber; index++) {
         VERBOSE(" (" << apZActual[index] << ", " << apZMiss[index] << ")")
     }
-    LOGGER("\t\t- Prediction Error (IDW): " << apMSPE[0] << " - " << apMSPE[1] << " - " << apMSPE[2])
+    VERBOSE("\t\t- Prediction Error (IDW): " << apMSPE[0] << " - " << apMSPE[1] << " - " << apMSPE[2])
 }
diff --git a/tests/R-tests/TestDataGeneration.R b/tests/R-tests/TestDataGeneration.R
@@ -40,9 +40,14 @@ hardware <- new(Hardware, computation, ncores, ngpus, p, q)
 exageostat_data <- simulate_data(kernel=kernel, initial_theta=initial_theta, problem_size=problem_size, dts=dts, dimension=dimension, log_path=log_path)
 
 # Print the data..
-paste("** Locations X - Y - Z")
-locations <- get_locations(data=exageostat_data)
-paste(locations)
+paste("Z Values")
+paste(exageostat_data$m)
+paste("Locations X")
+paste(exageostat_data$x)
+paste("Locations Y")
+paste(exageostat_data$y)
+paste("Locations Z")
+paste(exageostat_data$z)
 
 paste("---------------------------------------------------------------------------------------------")
 paste("ExaGeoStat with Data Generation - Reading Data")
@@ -52,6 +57,13 @@ data_path <- "./synthetic_ds/SYN_16_1"
 
 exageostat_data <- simulate_data(kernel=kernel, initial_theta=initial_theta, problem_size=problem_size, dts=dts, dimension=dimension, data_path=data_path)
 
-paste("** Locations X - Y - Z - after reading")
-locations <- get_locations(data=exageostat_data)
-paste(locations)
+paste("** after reading")
+# Print the data..
+paste("Z Values")
+paste(exageostat_data$m)
+paste("Locations X")
+paste(exageostat_data$x)
+paste("Locations Y")
+paste(exageostat_data$y)
+paste("Locations Z")
+paste(exageostat_data$z)