add database script in c for creation and init

.gitignore

@@ -12,6 +12,7 @@ Code-C/DartConfiguration.tcl
 Code-C/tsl
 
 Makefile
+.vscode
 
 # Created by https://www.toptal.com/developers/gitignore/api/cmake,c
 # Edit at https://www.toptal.com/developers/gitignore?templates=cmake,c

.vscode/launch.json

@@ -1,7 +0,0 @@
-{
-    // Use IntelliSense to learn about possible attributes.
-    // Hover to view descriptions of existing attributes.
-    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
-    "version": "0.2.0",
-    "configurations": []
-}

.vscode/settings.json

@@ -1,26 +0,0 @@
-{
-  "C_Cpp.errorSquiggles": "Disabled",
-  "files.associations": {
-    "time.h": "c",
-    "b2hd.h": "c",
-    "main.h": "c",
-    "stdio.h": "c",
-    "string.h": "c",
-    "initialparameters.h": "c",
-    "filegestion.h": "c",
-    "power.h": "c",
-    "getarray.h": "c",
-    "math.h": "c",
-    "limits": "c",
-    "*.tcc": "c",
-    "type_traits": "c",
-    "simulateflux.h": "c",
-    "pthread.h": "c",
-    "types.h": "c",
-    "average.h": "c",
-    "queue.h": "c",
-    "growthrate.h": "c",
-    "stdbool.h": "c"
-  },
-  "cmake.configureOnOpen": false
-}

.vscode/tasks.json

@@ -1,20 +0,0 @@
-{
-    "tasks": [
-      {
-        "type": "cppbuild",
-        "label": "C/C++: gcc.exe build active file",
-        "command": "C:/msys64/mingw64/bin/gcc.exe",
-        "args": ["-g", "${file}", "-o", "${fileDirname}\\${fileBasenameNoExtension}"],
-        "options": {
-          "cwd": "${fileDirname}"
-        },
-        "problemMatcher": ["$gcc"],
-        "group": {
-          "kind": "build",
-          "isDefault": true
-        },
-        "detail": "compiler: C:/msys64/mingw64/bin/gcc.exe"
-      }
-    ],
-    "version": "2.0.0"
-}

Code-C/.vscode/settings.json

@@ -1,5 +0,0 @@
-{
-    "files.associations": {
-        "power.h": "c"
-    }
-}

Code-C/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
 project(Traitement-signal-plantes C)
 
 include(CTest)
@@ -10,16 +10,21 @@ file(MAKE_DIRECTORY Executable)
 
 set (CMAKE_RUNTIME_OUTPUT_DIRECTORY Executable) #Set Executable directory as default exectutable file location
 
-add_executable(exect fileGestion.c getArray.c average.c growthRate.c power.c queue.c simulateFlux.c main.c)
+add_executable(exect fileGestion.c getArray.c average.c growthRate.c power.c queue.c simulateFlux.c database.c main.c)
 # add_executable(exect main.c simulateFlux.c queue.c power.c growthRate.c average.c getArray.c fileGestion.c)
 
+find_package (SQLite3)
+include_directories(${SQLite3_INCLUDE_DIRS})
+target_link_libraries (exect ${SQLite3_LIBRARIES} m)
+
+
 find_package(Threads)
 target_link_libraries(exect ${CMAKE_THREAD_LIBS_INIT} m)
 
 set(CTEST_MEMORYCHECK_TYPE "AddressSanitizer")
 set(CTEST_MEMORYCHECK_SANITIZER_OPTIONS "verbosity=1:symbolize=1:abort_on_error=1:detect_leaks=1")
 
-add_executable(ctest fileGestion.c getArray.c average.c growthRate.c queue.c simulateFlux.c ctest.c)
+add_executable(ctest fileGestion.c getArray.c average.c growthRate.c queue.c simulateFlux.c database.c ctest.c)
 target_link_libraries(ctest ${CMAKE_THREAD_LIBS_INIT} m)
 
 add_test(test_queueCreateEmpty ./ctest queueCreateEmpty)

Code-C/Include/database.h

@@ -0,0 +1,11 @@
+#include <sqlite3.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <unistd.h>
+#include <math.h>
+
+int createDb();
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot);
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot);

Code-C/cmake/FindSQLite3.cmake

@@ -0,0 +1,37 @@
+# Copyright (C) 2007-2009 LuaDist.
+# Created by Peter Kapec <kapecp@gmail.com>
+# Redistribution and use of this file is allowed according to the terms of the MIT license.
+# For details see the COPYRIGHT file distributed with LuaDist.
+#	Note:
+#		Searching headers and libraries is very simple and is NOT as powerful as scripts
+#		distributed with CMake, because LuaDist defines directories to search for.
+#		Everyone is encouraged to contact the author with improvements. Maybe this file
+#		becomes part of CMake distribution sometimes.
+
+# - Find sqlite3
+# Find the native SQLITE3 headers and libraries.
+#
+# SQLITE3_INCLUDE_DIRS	- where to find sqlite3.h, etc.
+# SQLITE3_LIBRARIES	- List of libraries when using sqlite.
+# SQLITE3_FOUND	- True if sqlite found.
+
+# Look for the header file.
+FIND_PATH(SQLITE3_INCLUDE_DIR NAMES sqlite3.h)
+
+# Look for the library.
+FIND_LIBRARY(SQLITE3_LIBRARY NAMES sqlite)
+
+# Handle the QUIETLY and REQUIRED arguments and set SQLITE3_FOUND to TRUE if all listed variables are TRUE.
+INCLUDE(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+
+# Copy the results to the output variables.
+IF(SQLITE3_FOUND)
+	SET(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})
+	SET(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
+ELSE(SQLITE3_FOUND)
+	SET(SQLITE3_LIBRARIES)
+	SET(SQLITE3_INCLUDE_DIRS)
+ENDIF(SQLITE3_FOUND)
+
+MARK_AS_ADVANCED(SQLITE3_INCLUDE_DIRS SQLITE3_LIBRARIES)

Code-C/database.c

@@ -0,0 +1,248 @@
+#include "./Include/simulateFlux.h"
+#include "./Include/database.h"
+
+int initializeTrialsTable()
+{
+    sqlite3 *db;
+    int rc;
+    sqlite3_stmt *stmt;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    // char *sql = "CREATE TABLE Test(Id INT)";
+
+    char *sql =
+        "CREATE TABLE Trials(Id INTEGER PRIMARY KEY AUTOINCREMENT, Position TEXT, Start INT, Frequency NUMBER);";
+
+    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+    return 0;
+}
+
+int initializeCaptorMetadataTable()
+{
+    sqlite3 *db;
+    int rc;
+    sqlite3_stmt *stmt;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    // char *sql = "CREATE TABLE Test(Id INT)";
+
+    char *sql =
+        "CREATE TABLE CaptorMetadata(Id INTEGER PRIMARY KEY AUTOINCREMENT, CaptorNumber INT, TrialId INT, FOREIGN KEY (TrialId) REFERENCES Trials(Id));";
+
+    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+    return 0;
+}
+
+char *generateDataTableName(int trialId, int captorNumber)
+{
+
+    char *tableName;
+    tableName = (char *)malloc(8 * sizeof(char));
+    strcpy(tableName, "T");
+    strcat(tableName, convertIntegerToChar(trialId));
+    strcat(tableName, "C");
+    strcat(tableName, convertIntegerToChar(captorNumber));
+    strcat(tableName, "Data");
+    return tableName;
+}
+
+int createCaptorDataTable(int trialId, int captorNumber)
+{
+    sqlite3 *db;
+    int rc;
+    sqlite3_stmt *stmt;
+
+    // Create Table Name
+    char *tableName = generateDataTableName(trialId, captorNumber);
+
+    rc = sqlite3_open("robotgowest.db", &db);
+    if (rc != SQLITE_OK)
+    {
+        return 1;
+    }
+
+    char sql[101] = "CREATE TABLE ";
+    strcat(sql, tableName);
+    strcat(sql, " (Id INTEGER PRIMARY KEY AUTOINCREMENT, Lux NUMBER, Mean NUMBER , Power NUMBER);");
+
+    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+
+    return 0;
+}
+
+int insertTrailElement(char *position, int start, double frequency)
+{
+
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+
+    int rc;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    rc = sqlite3_prepare_v2(db, "INSERT INTO Trials(Position,Start,Frequency) VALUES ( :position , :start , :frequency )", -1, &stmt, NULL);
+    if (rc != SQLITE_OK)
+        return 1;
+
+    sqlite3_bind_text(stmt, 1, position, -1, SQLITE_STATIC);
+
+    sqlite3_bind_int(stmt, 2, start);
+
+    sqlite3_bind_double(stmt, 3, frequency);
+
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+    return 0;
+}
+
+int updateTrailElement(int id, char *position, int start, double frequency)
+{
+
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+
+    int rc;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    rc = sqlite3_prepare_v2(db, "UPDATE Trials SET Position = :position, Start = :start, Frequency = :frequency WHERE Id = :id", -1, &stmt, NULL);
+    if (rc != SQLITE_OK)
+        return 1;
+
+    sqlite3_bind_text(stmt, 1, position, -1, SQLITE_STATIC);
+
+    sqlite3_bind_int(stmt, 2, start);
+
+    sqlite3_bind_double(stmt, 3, frequency);
+
+    sqlite3_bind_int(stmt, 4, id);
+
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+    return 0;
+}
+
+int insertCaptorMetadataElement(int captorNumber, int trialId)
+{
+
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+
+    int rc;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    rc = sqlite3_prepare_v2(db, "INSERT INTO CaptorMetadata(CaptorNumber,TrialId) VALUES ( :captorNumber , :trialId)", -1, &stmt, NULL);
+    if (rc != SQLITE_OK)
+        return 1;
+
+    sqlite3_bind_int(stmt, 1, captorNumber);
+
+    sqlite3_bind_int(stmt, 2, trialId);
+
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+
+    sqlite3_close(db);
+    return 0;
+}
+
+int insertCaptorDataElement(int trialId, int captorNumber, double lux, double mean, double power)
+{
+
+    char *tableName = generateDataTableName(trialId, captorNumber);
+
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+
+    int rc;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+
+    char sql[70] = "INSERT INTO ";
+    strcat(sql, tableName);
+    strcat(sql, "(Lux,Mean,Power) VALUES ( :lux , :mean , :power)");
+
+    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
+    if (rc != SQLITE_OK)
+        return 1;
+
+    sqlite3_bind_double(stmt, 1, lux);
+    sqlite3_bind_double(stmt, 2, mean);
+    sqlite3_bind_double(stmt, 3, power);
+
+    rc = sqlite3_step(stmt);
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+    return 0;
+}
+
+int createDb()
+{
+    char *dbPosition = "./robotgowest.db";
+    if (access(dbPosition, F_OK))
+    {
+        initializeTrialsTable();
+        initializeCaptorMetadataTable();
+        return 0;
+    }
+    else
+    {
+        printf("Database already initialized");
+        return 1;
+    }
+}
+
+int getMaxTrialIdRow()
+{
+    int rc;
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+    int data = -1;
+
+    rc = sqlite3_open("robotgowest.db", &db);
+    if (rc != SQLITE_OK)
+    {
+        return -1;
+    }
+
+    rc = sqlite3_prepare_v2(db, "SELECT MAX(Id) FROM Trials", -1, &stmt, NULL);
+
+    if (sqlite3_step(stmt) == SQLITE_ROW)
+    {
+        data = sqlite3_column_int(stmt, 0);
+    }
+
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+
+    return data;
+}
+
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot)
+{
+    insertTrailElement(position, -1, frequency);
+    int trialId = getMaxTrialIdRow();
+    for (int i = 0; i < 8; i++)
+    {
+        if (captorOneHot[i])
+        {
+            insertCaptorMetadataElement(i, trialId);
+            createCaptorDataTable(trialId, i + 1);
+        }
+    }
+    return 0;
+}

Code-C/main.c

@@ -8,6 +8,7 @@
 #include "./Include/average.h"
 #include "./Include/growthRate.h"
 #include "./Include/getArray.h"
+#include "./Include/database.h"
 
 bool rawDataWriteFlag;
 int nRowRawData = 5000;
@@ -160,6 +161,11 @@ int main(int argc, char **argv)
     invTimeBandWidth = 1 / (nRowRawData * period);
     firstRawDataQueue = queueCreateEmpty(); // change this for create empty
 
+    // launch DB related function
+    sqlite3_initialize();
+    createDb();                                           // Created the Db if not exist
+    initiaizeNewTrial("test", freqEch, selectionCaptors); // Initialize Trials data and tables
+
     pthread_t rawData;
     if (pthread_create(&rawData, NULL, threadSimulateFlux, "threadSimulflux") != 0)
     {
@@ -182,4 +188,6 @@ int main(int argc, char **argv)
     // }
 
     pthread_exit(NULL);
+
+    sqlite3_shutdown();
 }

Code-C/simulateFlux.c

@@ -152,11 +152,11 @@ bool writeOneRawData(FILE *rawDataFile)
             {
                 if (selectionCaptors[i - 1])
                 {
-                    quartet value;
-                    value.octet1 = buff[3 * i + 1];
-                    value.octet2 = buff[3 * i + 2];
-                    value.octet3 = buff[3 * i + 3];
-                    value.octet4 = 0;
+                    // quartet value;
+                    // value.octet1 = buff[3 * i + 1];
+                    // value.octet2 = buff[3 * i + 2];
+                    // value.octet3 = buff[3 * i + 3];
+                    // value.octet4 = 0;
 
                     valbin[i] = buff[3 * i + 1] * 256 * 256 * 256 + buff[3 * i + 2] * 256 * 256 + buff[3 * i + 3] * 256;
                     memcpy(&values[i], &valbin[i], sizeof(uint32_t));

Db-Script/database.c

@@ -1,118 +0,0 @@
-#include "./database.h"
-
-int initializeTrailsTable()
-{
-    sqlite3 *db;
-    char *err_msg;
-    int rc;
-    sqlite3_stmt *stmt;
-
-    rc = sqlite3_open("robotgowest.db", &db);
-
-    // char *sql = "CREATE TABLE Test(Id INT)";
-
-    char *sql =
-        "CREATE TABLE Trials(Id INTEGER PRIMARY KEY AUTOINCREMENT, Position TEXT, Start INT, Frequency NUMBER, Duration INT);";
-
-    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
-    rc = sqlite3_step(stmt);
-    rc = sqlite3_finalize(stmt);
-    sqlite3_close(db);
-}
-
-int initializeCaptorMetadataTable()
-{
-    sqlite3 *db;
-    char *err_msg;
-    int rc;
-    sqlite3_stmt *stmt;
-
-    rc = sqlite3_open("robotgowest.db", &db);
-
-    // char *sql = "CREATE TABLE Test(Id INT)";
-
-    char *sql =
-        "CREATE TABLE CaptorMetadata(Id INTEGER PRIMARY KEY AUTOINCREMENT, CaptorNumber INT, TrialId INT, FOREIGN KEY (TrialId) REFERENCES Trials(Id));";
-
-    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
-    rc = sqlite3_step(stmt);
-    rc = sqlite3_finalize(stmt);
-    sqlite3_close(db);
-}
-
-int createCaptorDataTable(int trialId, int captorNumber)
-{
-    sqlite3 *db;
-    char *err_msg;
-    int rc;
-    sqlite3_stmt *stmt;
-
-    // Create Table Name
-    char tableName[8];
-    strcpy(tableName, "T");
-    strcat(tableName, convertIntegerToChar(trialId));
-    strcat(tableName, "C");
-    strcat(tableName, convertIntegerToChar(captorNumber));
-    strcat(tableName, "Data");
-
-    rc = sqlite3_open("robotgowest.db", &db);
-    if (rc != SQLITE_OK)
-    {
-        return 1;
-    }
-
-    char sql[101] = "CREATE TABLE ";
-    strcat(sql, tableName);
-    strcat(sql, " (Id INTEGER PRIMARY KEY AUTOINCREMENT, Lux NUMBER, Mean NUMBER , Power NUMBER);");
-
-    rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
-    rc = sqlite3_step(stmt);
-    rc = sqlite3_finalize(stmt);
-    sqlite3_close(db);
-
-    return 0;
-}
-
-/**
- * @brief convert an interger N into a char*
- *
- * @param N
- * @return char*
- */
-char *convertIntegerToChar(int N)
-{
-    // Count digits in number N
-    int m = N;
-    int digit = 0;
-    while (m)
-    {
-        digit++;
-        m /= 10;
-    }
-    char *arr;
-    char arr1[digit];
-    arr = (char *)malloc(digit * sizeof(char));
-    int index = 0;
-    while (N)
-    {
-        arr1[++index] = N % 10 + '0';
-        N /= 10;
-    }
-    int i;
-    for (i = 0; i < index; i++)
-    {
-        arr[i] = arr1[index - i];
-    }
-    arr[i] = '\0';
-    return (char *)arr;
-}
-
-int main(void)
-{
-    sqlite3_initialize();
-
-    initializeTrailsTable();
-    initializeCaptorMetadataTable();
-    createCaptorDataTable(12, 8);
-    sqlite3_shutdown();
-}

Db-Script/database.h

@@ -1,14 +0,0 @@
-#include <sqlite3.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-
-// Duplication from simulFlux.c
-
-/**
- * @brief convert an interger N into a char*
- *
- * @param N
- * @return char*
- */
-char *convertIntegerToChar(int N);

Db-Script/database.py

@@ -1 +1,3 @@
-##This mist include all fetch function and also init and insert function for nn training annd testing result 
+##This mist include all fetch function and also init and insert function for nn training annd testing result 
+
+import numpy