/*public void  Start ()
     * {
     *      setupInitialValues ();
     *      writeNavigationMeshToFile ();
     * }*/


    /*
     * setupInitialValue will set up the initial values for the instance variables
     * Parameter:	none
     * Return:	none
     */
    void setupInitialValues()
    {
        positionToStart = -1;

        //goalPosition = GameObject.FindGameObjectWithTag ("Goal").transform.TransformPoint (new Vector3 (0f, 0f, 0f));
        //listOfObjects = GameObject.FindGameObjectsWithTag ("Surface");
        //staticObjects = GameObject.FindGameObjectsWithTag ("Obstacle");
//		GameObject agent = GameObject.FindGameObjectWithTag ("Player");
        //agentStart = agent.transform.position;
        //agentDiameter = agent.GetComponent<CapsuleCollider> ().radius * 2;
        //	agentDiameter = agent.GetComponent<CapsuleCollider> ().radius;
        //objectMesh = new Mesh[listOfObjects.Length];
        //staticObjectMesh = new Mesh[staticObjects.Length];
        //objectsArray = new AIObjects[staticObjects.Length];
        surfacePolygonHolders = new AIPolygonHolder();
        //allSearchs = new string[9];
        //allSearchs [0] = "A*";
        //allSearchs [1] = "A* Optimal";
        //allSearchs [2] = "Bi-Directional";
        //allSearchs [3] = "Bi-Directional Optimal";
        //allSearchs [4] = "FringeSearch";
        //allSearchs [5] = "Beam Search";
        //allSearchs [6] = "Dynamic Weighted A*";
        //allSearchs [7] = "Dynamic Weighted BDBOP";
        //allSearchs [8] = "Dynamic Weighted BDOP";
        //getObjectsArray ();
        getSurfacePolygonHolders();
        //mergeSurfacePolygonHolders ();
    }
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    /*
     *	mergePolygonHolder will merge two AIPolygonHolder objects. This will create a new AIPolygonHolder
     *			place the polygons from each AIPolygonHolder to the new AIPolygonHolder then merge the Polygons
     *			in the new AIPolygonHolder
     *	Parameter:	(AIPolygonHolder)holderToMerge is the AIPolygonHolder that will be merged with this object
     *	Return:			(AIPolygonHolder)
     *									the new AIPolygonHolder that is the two merged AIPolygonHolders
     */
    public AIPolygonHolder mergePolygonHolder(AIPolygonHolder holderToMerge)
    {
        copyAndSrink(polygonArray);
        holderToMerge.copyAndSrink(holderToMerge.getPolygons());
        AIPolygon[]     tempArray = mergeTwoArrays(polygonArray, holderToMerge.getPolygons()); //makes a new AIPolygonHolder with the capacity of both AIPolygonHolders being Merged
        AIPolygonHolder newHolder = new AIPolygonHolder(tempArray.Length);                     //makes a new AIPolygonHolder with the capacity of both AIPolygonHolders being Merged

        for (int count = 0; count < tempArray.Length; count++)
        {
            newHolder.addPolygon(tempArray [count].getVertices());
        }
        newHolder.merge();          // merged the polygons in the new AIPolygonHolders
        return(newHolder);
    }
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    /* mergeSurfacePolygonsHolders calls the merge function to merge all the polygons in
     * the surfacePolygonHolders array.
     * Parameters: none
     * Return: none
     */
    void mergeSurfacePolygonHolders()
    {
        for (int count = 0; count < surfacePolygonHolders.Length; count++)
        {
            surfacePolygonHolders [count].merge();
        }

        for (int count = surfacePolygonHolders.Length - 1; count >= 0; count--)
        {
            if (surfacePolygonHolders [count] != null)
            {
                for (int count2 = surfacePolygonHolders.Length - 1; count2 >= 0; count2--)
                {
                    if (surfacePolygonHolders [count2] != null && count != count2)
                    {
                        surfacePolygonHolders [count]  = surfacePolygonHolders [count].mergePolygonHolder(surfacePolygonHolders [count2]);
                        surfacePolygonHolders [count2] = null;
                    }
                }
            }
        }
        int counter = 0;

        for (int count = 0; count < surfacePolygonHolders.Length; count++)
        {
            if (surfacePolygonHolders [count] != null)
            {
                counter++;
            }
        }

        AIPolygonHolder[] tempArray = new AIPolygonHolder[counter];

        for (int count = 0, tempCount = 0; count < surfacePolygonHolders.Length; count++)
        {
            if (surfacePolygonHolders [count] != null)
            {
                tempArray [tempCount] = surfacePolygonHolders [count];
                tempCount++;
            }
        }
    }
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    /* getSurgavePolygonHolders gets all the triangle polygons that compose all objects in a Unity map,
     * and loads them into the triangleArray. Then creates new AIObjects from those triangles out of the walkable
     * polygons and loads them into surfacePolygonHolders to be used for nav mesh construction.
     * Parameters: none
     * Return: none
     */
    void getSurfacePolygonHolders()
    {
        Vector3[] WorldPositionArray = new Vector3[3];
        for (int count = 0; count < listOfObjects.Length; count++)
        {
            objectMesh [count]           = listOfObjects [count].GetComponent <MeshFilter> ().mesh;
            vectorArray                  = objectMesh[count].vertices;
            triangleArray                = objectMesh[count].GetTriangles(0);
            surfacePolygonHolders[count] = new AIPolygonHolder(triangleArray.Length / 3);

            for (int count1 = 0, count2 = 1, count3 = 2; count1 < triangleArray.Length; count1 += 3, count2 += 3, count3 += 3)
            {
                WorldPositionArray [0] = listOfObjects [count].transform.TransformPoint(vectorArray [triangleArray [count1]]);
                WorldPositionArray [1] = listOfObjects [count].transform.TransformPoint(vectorArray [triangleArray [count2]]);
                WorldPositionArray [2] = listOfObjects [count].transform.TransformPoint(vectorArray [triangleArray [count3]]);
                if (checkVertex(WorldPositionArray) == false)
                {
                    surfacePolygonHolders[count].addPolygon(WorldPositionArray);
                }
            }
        }
    }
    /*
     * writeAfterDataToFile method will write all the data from the navigation mesh and the search agent to the
     *      end of the file
     * parameters:	none
     * return:	none
     */
    /*void writeAfterDataToFile ()
     * {
     *      string filePath = "data.txt";
     *      StreamReader inputStream = new StreamReader(filePath);
     *      string tempString = "";
     *      tempString += inputStream.ReadToEnd();
     *      tempString += "\n";
     *      inputStream.Close ();
     *      tempString += Application.loadedLevelName + "\t";
     *      if (AINavigationMeshAgent.loadNavigationMesh == true)
     *              tempString += "load Navigation Mesh\t";
     *      else
     *              tempString += "build Navigation Mesh\t";
     *      tempString += AINavigationMeshData.timeTaken + "\t";
     *      tempString += AINavigationMeshData.initialPolygonCount + "\t";
     *      tempString += AINavigationMeshData.obstacleCount + "\t";
     *      tempString += AINavigationMeshData.finalPolygonCount + "\t";
     *      tempString += AISearchAgentData.searchType + "\t";
     *      tempString += AISearchAgentData.timeTaken + "\t";
     *      tempString += AISearchAgentData.nodesVisited + "\t";
     *      tempString += AISearchAgentData.maxQueueSize + "\t";
     *      tempString += AISearchAgentData.finalPathLength + "\t";
     *      tempString += AISearchAgentData.finalPathCost + "\t";
     *      StreamWriter writer = new StreamWriter (filePath);
     *      writer.Write (tempString);
     *      writer.Close ();
     *
     *
     *
     * }*/

    /*
     * doAISearchMethods will make a search agent to start searching though the navigation mesh
     * Parameter:	none
     * Return:	none
     */
    /*void doAISearchMethods()
     * {
     *
     *              AINavigationMeshAgent.polygonLengthMin = surfacePolygonHolders [positionToStart].getMinPolygonLength ();
     *              AINavigationMeshAgent.polygonLengthAvg = surfacePolygonHolders [positionToStart].getAveragePolygonLength ();
     *              if (positionToStart != -1)
     *                      tempSearch = new AISearch (searchType, goalPosition, surfacePolygonHolders [positionToStart].getPolygons ());
     *              if (tempSearch != null) {
     *                      Vector3[] vertices = tempSearch.getWayPoints ();
     *                      if (vertices != null)
     *                              for (int count = 0; count < vertices.Length; count++)
     *                                      Instantiate (sphere, vertices [count], new Quaternion (0f, 0f, 0f, 0f));
     *              }
     * }*/



    /* getObjectsArray gets all the triangle polygons that compose all objects in a Unity map,
     * and loads them into the triangleArray. Then creates new AIObjects from those triangles and loads
     * them into objectsArray to be used for nav mesh construction.
     * Parameters: none
     * Return: none
     */
    /*void getObjectsArray ()
     * {
     *      Vector3[] WorldPositionArray = new Vector3[3];
     *      for (int count = 0; count < staticObjects.Length; count++) {
     *              staticObjectMesh [count] = staticObjects [count].GetComponent<MeshFilter> ().mesh;
     *              vectorArray = staticObjectMesh[count].vertices;
     *              triangleArray = staticObjectMesh[count].GetTriangles (0);
     *              objectsArray[count] = new AIObjects(triangleArray.Length/3, staticObjects[count]);
     *              for (int count1 = 0, count2 = 1, count3 = 2; count1 < triangleArray.Length; count1 += 3, count2 += 3, count3 += 3) {
     *                      WorldPositionArray [0] = staticObjects [count].transform.TransformPoint (vectorArray [triangleArray [count1]]);
     *                      WorldPositionArray [1] = staticObjects [count].transform.TransformPoint (vectorArray [triangleArray [count2]]);
     *                      WorldPositionArray [2] = staticObjects [count].transform.TransformPoint (vectorArray [triangleArray [count3]]);
     *                      objectsArray[count].addPolygon(WorldPositionArray);
     *              }
     *      }
     * }*/



    /* getSurgavePolygonHolders gets all the triangle polygons that compose all objects in a Unity map,
     * and loads them into the triangleArray. Then creates new AIObjects from those triangles out of the walkable
     * polygons and loads them into surfacePolygonHolders to be used for nav mesh construction.
     * Parameters: none
     * Return: none
     */
    void getSurfacePolygonHolders()
    {
        Vector3[]            WorldPositionArray  = new Vector3[3];
        NavMeshTriangulation triangulatedNavMesh = NavMesh.CalculateTriangulation();

        //Mesh mesh = new Mesh ();
        //mesh.vertices = triangulatedNavMesh.vertices;
        //mesh.triangles = triangulatedNavMesh.indices;
        vectorArray           = triangulatedNavMesh.vertices;
        triangleArray         = triangulatedNavMesh.indices;
        surfacePolygonHolders = new AIPolygonHolder(triangleArray.Length / 3);

        for (int count1 = 0, count2 = 1, count3 = 2; count1 < triangleArray.Length; count1 += 3, count2 += 3, count3 += 3)
        {
            WorldPositionArray [0] = vectorArray [triangleArray [count1]];
            WorldPositionArray [1] = vectorArray [triangleArray [count2]];
            WorldPositionArray [2] = vectorArray [triangleArray [count3]];
            //if (checkVertex (WorldPositionArray) == false) {
            surfacePolygonHolders.addPolygon(WorldPositionArray);
            //}
        }
    }
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    /*
     * loadNavigationMeshFromFile method will load all the data for the navigation mesh from the file
     * Paramters:	none
     * Return:	none
     */
    public void loadNavigationMeshFromFile()
    {
        startTime = Time.realtimeSinceStartup;
        string          filePath       = Application.loadedLevelName + "NavigationMesh.dat";
        Stream          TestFileStream = File.OpenRead(filePath);
        BinaryFormatter deserializer   = new BinaryFormatter();

        positionToStart = 0;
        AIPolygonHolderData dataholder = (AIPolygonHolderData)deserializer.Deserialize(TestFileStream);

        AIPolygon[] polygons = new AIPolygon[dataholder.polygonData.Length];
        for (int count = 0; count < dataholder.polygonData.Length; count++)
        {
            Vector3[] vertices      = new Vector3[dataholder.polygonData [count].vertices.Length / 3];
            int       id            = dataholder.polygonData [count].id;
            int[]     neighbors     = dataholder.polygonData [count].neighbors;
            int       neighborsHeld = dataholder.polygonData [count].neighborCount;
            bool      gotGoal       = dataholder.polygonData [count].gotGoal;
            bool      gotAgent      = dataholder.polygonData [count].gotAgent;
            int       agentID       = dataholder.polygonData[count].agentID;
            for (int count2 = 0; count2 < vertices.Length; count2++)
            {
                vertices [count2] = new Vector3(dataholder.polygonData [count].vertices [count2, 0], dataholder.polygonData [count].vertices [count2, 1], dataholder.polygonData [count].vertices [count2, 2]);
            }
            polygons [count] = new AIPolygon();
            polygons [count].setData(vertices, id, neighborsHeld, neighbors, gotGoal, gotAgent, agentID);
        }
        AINavigationMeshData.initialPolygonCount = getSurfacePolygonCount();
        AINavigationMeshData.obstacleCount       = staticObjects.Length;
        surfacePolygonHolders     = new AIPolygonHolder[1];
        surfacePolygonHolders [0] = new AIPolygonHolder();
        surfacePolygonHolders [0].setAll(polygons, polygons.Length);
        positionToStart = 0;
        AINavigationMeshData.timeTaken         = Time.realtimeSinceStartup - startTime;
        AINavigationMeshData.finalPolygonCount = getSurfacePolygonCount();
        TestFileStream.Close();
        writeNavigationMeshToFile();
    }