UNIVERSITI PUTRA MALAYSIA

DEVELOPMENT OF A NEW LiDAR DATABASE MANAGEMENT

SYSTEM USING OPEN SOURCE SOFTWARE

KHAIRIL IZWAN BIN AHMAD ARSHAD

FK 2017 87

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USING OPEN SOURCE SOFTWARE

By

KHAIRIL IZWAN BIN AHMAD ARSHAD

Thesis Submitted to the School of Graduate Studies, Universiti Putra Malaysia,

in Fulfilment of the Requirements for the Degree of Master of Science

July 2016

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All material contained within the thesis, including without limitation text, logos, icons,

photographs and all other artwork, is copyright material of Universiti Putra Malaysia

unless otherwise stated. Use may be made of any material contained within the thesis

for non-commercial purposes from the copyright holder. Commercial use of material

may only be made with the express, prior, written permission of Universiti Putra

Malaysia.

Copyright © Universiti Putra Malaysia

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Abstract of thesis presented to the Senate of Universiti Putra Malaysia in fulfilment

of the requirement for the degree of Master of Science

DEVELOPMENT OF A NEW LiDAR DATABASE MANAGEMENT

SYSTEM USING OPEN SOURCE SOFTWARES

By

KHAIRIL IZWAN B AHMAD ARSHAD

July 2016

Chairman: Associate Professor Helmi Zulhaidi Mohd Shafri, PhD

Faculty: Engineering

LiDAR Survey is one alternative method that gives an extra advantage especially to

get coordinate and height value data. It is known as the best way to retrieve coordinate

and height data for the broad area in short period of time. Data produced from LiDAR

is enormous but sadly, they are kept, not in proper relational database management

system. They have been kept in Hard disk or Digital Versatile Disk (DVD) after

serving their purpose. This way of storing make searching difficult because these data

may come from different file versions and varieties of a coordinate system. Survey

Department and Mapping (JUPEM) is the only government agency that has been

given an authority to handle all airborne data based on Circular of Prime Minister

Agency (JPM 1/2007). This researched been carried out to enhanced the way of

LiDAR data been stored. Currently, management of these data is not so effective. Lots

of time and money involved just to know the data availability and retrieves the data.

The objective of this researched is to a developed database using open source software

called LiDAR Database Management System (LiDMS). Next, the evaluation of

LiDMS is based also on its performance via online. This system can work on

windows, iPhone Operating System (iOS) and android which is used the MySQL as

a database. User satisfying test has been carried out to see how the user accepts the

LiDMS. The user experience evaluation test result showed that, LiDMS Portal able to

be used by using Windows, smartphone, ios or others gadget platform smoothly but it

is subject to bandwidth and speed of the processor used. Overall this researched

manage to developed a portal that benefit to the government, researcher, decision

maker, and client either to apply for a new fly permit via online, monitoring the permit

given as follow Prime Minster Circular 1/2007, upload or retrieve the data or just to

browse the data location availability in Malaysia.

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Abstrak tesis yang dikemukakan kepada Senat Universiti Putra Malaysia sebagai

memenuhi keperluan untuk ijazah Master Sains

PEMBANGUNAN PENGURUSAN PANGKALAN DATA LiDAR

BARU MENGGUNAKAN PERISIAN SUMBER TERBUKA

Oleh

KHAIRIL IZWAN B AHMAD ARSHAD

Julai 2016

Pengerusi: Profesor Madya Helmi Zulhaidi Mohd Shafri, PhD

Fakuti: Kejuruteraan

LiDAR menawarkan pelbagai kegunaan dan kelebihan antaranya mendapatkan data

ketinggian kepada ramai pengguna. Ia diakui kaedah terbaik bagi mendapatkan nilai

ketinggian bagi kawasan yang luas dalam masa yang sangat cepat. Namun begitu data

yang dihasilkan dari LiDAR adalah sangat besar dan selalunya data ini selepas

digunakan ia hanya akan disimpan dalam bentuk storan seperti Cakera Keras atau

Digital Versatiles Disk (DVD). Kaedah ini memberikan kesukaran untuk

mendapatkan data-data tersebut malahan data-data yang disimpan itu kadangkala

terdiri dari pelbagai rujukan sistem koordinat dan versi fail. Jabatan Ukur dan

Pemetaan (JUPEM) adalah agensi kerajaan yang dikhususkan untuk mengawal semua

data bawaan udara termasuk data-data LiDAR berdasarkan Pekeliling Jabatan

Perdana Menteri (JPM 1/2007). Oleh kerana JUPEM memiliki hak keatas data ini

maka pengguna perlu di beritahu berkenaan data ini supaya mereka boleh

mendapatkannya dengan cara yang mudah. Penyelidikan ini dilakukan kerana kaedah

simpanan data di JUPEM sebelumnya kurang efektif dan melibatkan tenaga, kos masa

dan wang bagi mendapatkan data tersebut. Objektif penyelidikan ini adalah untuk

membangunkan satu sistem pangkalan data LiDAR dengan melaksanakan

penggunaan pangkalan data berasaskan perisian terbuka yang dikenali sebagai LiDAR

Database Management System (LiDMS) dan seterusnya menilai prestasi sistem

pangkalan data yang telah dibangunakan tersebut secara atas talian juga menggunakan

platform perisian terbuka sepenuhnya. Sistem ini telah dibangunkan untuk berfungsi

pada sistem operasi Windows, IOS dan android yang mana menggunapakai perisian

pangkalan data terbuka MySQL untuk pangkalan data LiDAR. Ujian kepuasan

pengguna telah dijalankan untuk melihat bagaimana penerimaan oleh pengguna dan

ujian prestasi juga telah dijalankan dalam penyelidikan ini. Penyelidikan ini

menunjukkan bahawa Portal LiDMS berjaya digunakan menggunakan platform

Windows, telefon pintar atau perantian lain berdasarkan faktor-faktor seperti

penggunaan bandwidth dan kelajuan pemproses yang digunakan. Kesimpulannya

penyelidikan ini akan menghasilkan sumbangan yang besar kepada pengawal,

pembuat keputusan, para penyelidik dan pengguna samada bagi permohonan permit

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penerbangan secara atas talian, memantau penghantaran data mengikut pekeliling

1/2007, menghantar dan mendapatkan data LiDAR secara atas talian dan melihat

lokaliti kawasan data LiDAR yang ada di Malaysia.

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ACKNOWLEDGEMENTS

Alhamdulillah, I am very thankful and grateful to Allah for making things possible. I

would like to acknowledge the support and assistance that I have received from so

many people especially from my supervisor, Assoc. Prof. Dr. Helmi Zulhaidi Mohd

Shafri and to thank him for his untiring guidance, advice, help and encouragement

throughout my study in UPM. Many thanks also to Dr Raja Azlina Raja Mohammad

from faculty of Science Information of Technology, UPM that assist me a lot on the

idea and consultation on programming and development the portal. Sincere thanks

also to the guidance and encouragement by my co-supervisor, Prof. Dr. Shattri Mansor

that gave some idea and consultation in LiDAR management works

Sincere thanks to my friends Yun Mohamad Amin, Mohammed Mustafa Al-Habshi,

Nik Mohamad Ramli Nik Yusoff and Mohd Nor Azman for assisting me on preparing

the programming code for my research. Thanks to my colleagues Alireza, Amiruddin,

Kelvin, Malik, Zhoobin, Ebi, Sarah Hanim, Naddia and Bahare who have given any

information and help me during the years of study and make my study in UPM a

valuable one. Finally, I would like to thank my family, especially my wife, my mother

and father, brothers for all their support and encouragement.

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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been

accepted as fulfilment of the requirement for the degree of Master of Science. The

members of the Supervisory Committee were as follows:

Helmi Zulhaidi Mohd Shafri, PhD

Associate Professor

Faculty of Engineering

Universiti Putra Malaysia

(Chairman)

Shattri Mansor, PhD Professor

Faculty of Engineering

Universiti Putra Malaysia

(Member)

__________________________

ROBIAH BINTI YUNUS, PhD

Professor and Dean

School of Graduate Studies

Universiti Putra Malaysia

Date:

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Declaration by graduate student

I hereby confirm that:

this thesis is my original work;

quotations, illustrations and citations have been duly referenced;

this thesis has not been submitted previously or concurrently for any other degree

at any other institutions;

intellectual property from the thesis and copyright of thesis are fully-owned by

Universiti Putra Malaysia, as according to the Universiti Putra Malaysia

(Research) Rules 2012;

written permission must be obtained from supervisor and the office of Deputy

Vice-Chancellor (Research and Innovation) before thesis is published (in the

form of written, printed or in electronic form) including books, journals, modules,

proceedings, popular writings, seminar papers, manuscripts, posters, reports,

lecture notes, learning modules or any other materials as stated in the Universiti

Putra Malaysia (Research) Rules 2012;

there is no plagiarism or data falsification/fabrication in the thesis, and scholarly

integrity is upheld as according to the Universiti Putra Malaysia (Graduate

Studies) Rules 2003 (Revision 2012-2013) and the Universiti Putra Malaysia

(Research) Rules 2012. The thesis has undergone plagiarism detection software.

Signature: _______________________ Date: ______________________________

Name and Matric No.: _________________________________________________

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Declaration by Members of Supervisory Committee

This is to confirm that:

the research conducted and the writing of this thesis was under our supervision;

supervision responsibilities as stated in the Universiti Putra Malaysia (Graduate

Studies) Rules 2003 (Revision 2012-2013) are adhered to.

Signature:

Name of Chairman

of Supervisory

Committee:

Signature:

Name of Member

of Supervisory

Committee:

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TABLE OF CONTENTS

Page

ABSTRACT i

ABSTRAK ii

ACKNOWLEDGEMENTS iv

APPROVAL v

DECLARATION vii

LIST OF TABLES xii

LIST OF FIGURES xiii

LIST OF ABBREVIATIONS xiv

CHAPTER

1. INTRODUCTION 1

1.1 General 1

1.2 Problem Statement 2

1.3 Objectives 3

1.4 Specific Objectives 3

1.5 Scope 3

1.6 Motivation 3

2. LITERATURE REVIEW 5

2.1 Light Detection and Ranging 4

2.2 LiDAR Data 6

2.3 Managing LiDAR Data 7

2.4 LiDAR LAS Data 8

2.5 LiDAR ASCII Data 9

2.6 Boise Center Aerospace Laboratory (BCAL) LiDAR Software 9

2.6.1 ENVI BCAL Extension 10

2.7 Open Source Software For Government Sector 11

2.8 Related research 12

2.9 Summary 14

3. METHODOLOGY 16

3.1 Research Workflow 16

3.2 Materials 18

3.3 System and Architecture Design 20

3.3.1 Client-side Tier 21

3.3.2 Before Login Page 24

3.3.3 After Login Pages 26

3.3.4 Administrator Pages. 28

3.4 Server-side Tier 37

3.4.1 Web Server 37

3.4.2 Server-side Programming Language 37

3.4.3 PHP settings in Apache for this LiDMS 38

3.4.4 Model View Controller (MVC) 38

3.5 MVC History 38

3.5.1 MVC Concept 39

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3.6 CI History 39

3.6.1 CI Structure 40

3.7 Application 40

3.8 System 41

3.9 Benefit of CI 42

3.9.1 Easy Learning Curve 42

3.9.2 Good Documentation 42

3.9.3 Large Support Group 42

3.9.4 Faster Execution 42

3.10 Server Side Structure and Architecture 43

3.11 Database Tier 47

3.11.1 RDBMS 47

3.11.2 MySQL 47

3.11.3 Phpmyadmin 47

3.12 Database Tier Structure 48

3.13 Database ERD 50

3.14 User Flow 51

3.14.1 Download XAMPP 51

3.14.2 Configuration PHP 51

3.14.3 Configuration MySQL 51

3.14.4 Setup The LiDMS 52

3.14.5 Test LiDMS 52

3.15 Evaluation User Acceptance Test 53

3.16 Testing Method 54

3.16.1 Installation 54

3.16.2 Performance 54

3.16.3 Speed 54

4. RESULTS AND DISCUSSION 55

4.1 Introduction 55

4.2 Deployment Test and Result 55

4.2.1 Speed of Deployment 55

4.2.2 Upload Speed Comparison 57

4.2.3 Performance of Deployment 58

4.3 Performance Evaluation Test and Resul 60

4.3.1 Evaluation 60

4.3.2 Data Retrieval Method In JUPEM 61

4.3.3 Result On Type of LiDAR Data Been Requested 62

4.4 Result Discussion 63

4.5 Overall Discussion 64

5. CONCLUSION AND FUTURE RECOMMENDATION 66

5.1 Introduction 66

5.2 Conclusions 66

5.3 Future Work 68

REFERENCES 70

APPENDICES 78

BIODATA OF STUDENT 91

PUBLICATION 92

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LIST OF TABLES

Table Page

2.1 Benefits of Open Source Software 11

2.2 Related studies 13

3.1 Before Login Pages 24

3.2 After Login Pages 26

3.3 Administrator Pages 28

3.4 Table MVC Structure 44

3.5 Database Tables Table 48

4.1 LiDMS upload speed comparison 57

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LIST OF FIGURES

Figure Page

2.1 LiDAR Concept 5

3.1 Methodology Workflow 16

3.2 BCAL On ENVI Software 19

3.3 BCAL To LAS Selection Ascii Output 20

3.4 System Architecture 20

3.5 LiDMS Client-side Architecture Diagram 21

3.6 RBAC Diagram 22

3.7 Basic RBAC Diagram for e-Government 23

3.8 Login Page 23

3.9 Pre-Login User Flow 25

3.10 Front Dashboard 28

3.11 Due Flight Data Submit 32

3.12 Public Search and Vendor's Flight List User Flow 32

3.13 Managers Dashboard User Flow 33

3.14 Manager's Flight User Flow 33

3.15 Administrator's Users User Flow 34

3.16 Roles And User Flow 35

3.17 Classification Userflow 36

3.18 Pages Userflow 36

3.19 Server-side Architecture Diagram 37

3.20 MVC Diagram 38

3.21 Codeigniter Application Flow 40

3.22 Codeigniter Basic Structure Diagram 40

3.23 LiDMS Server-side Structure Diagram 43

3.24 LiDMS Database-tier Structure Diagram 48

3.25 Database ERD 50

4.1 Pekan's Convertion Total Point vs Time 56

4.2 Kuala Lumpur's Conversion Total Point vs Time 56

4.3 Conversion Size for Low Accuracy Data Capture- Pekan 58

4.4 Conversion Size for High Accuracy Data Capture- Kuala Lumpur 59

4.5 LiDMS Deployment Performance Result 60

4.6 Academician, Public Sector and Government Repondents Percentage 61

4.7 Pecentage of Data Retrieving Method 62

4.8 Percentage of LiDAR Data File Type Requested 63

4.9 Performance of Work Efficiency 64

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LIST OF ABBREVIATIONS

3D Three Dimensional

ACID Atomicity, Consistency, Isolation, Durability

ACL Access Control List

AFSM Augmented Finite State Machine

API Application Program Interface

ASCII American Standard Code for Information Interchange

ASPRS American Society for Photogrammetry and Remote Sensing

BCAL Boise Center Aerospace Laboratory

CI Codeigniter

DAC Discretionary Access Control

DEM Digital Elevation Model

DSM Digital Surface Model

ENVI Exelis Visual Information Solutions

ERD Entity Relationship Diagram

Gb Gigabyte

GHz Gigahertz

GLONASS Global Navigation Satellite System

GNU General Public License

GPS Global Positioning System

GUI Graphical User Interphase

HTML HyperText Markup Language

IDL Interactive Data Language

IMU Inertial Measurement Unit

JUPEM Malaysia Land Surveying and Mapping

LAS Laser

LiDAR Light Detection and Ranging

LiDMS V 1.0 LiDAR Database Management System V 1.0

MAC Mandatory Access Control

MVC Model View Controller

NetCDF Network Common Data Format

NOAA National Oceanic and Atmospheric Administration

PHP Hypertext Preprocessor

RBAC Role Base Access-Control

RDBMS Relational Database Management System

SAN Storage Area Network

SDSC San Diego Supercomputer Center

SQL Structured Query Language

UAT User Acceptance Test

UI User Interface

UX User Experience

XYZ Cartesian Coordinate System( latitude, longitude, and elevation)

http://en.wikipedia.org/wiki/Relational_database_management_system

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CHAPTER 1

INTRODUCTION

1.1 General

Light Detection and Range, LiDAR has been widely used in various applications

(Cao et al., 2015). LiDAR is a rapidly developing measurement technology that has

been extensively applied to feature detection (Tong et al., 2014), terrain monitoring

(Zhou et al., 2012), 3D model reconstruction (Cheng, 2012) and ground object

extraction (Kumar et al., 2013). Aerial laser scanning (ALS) has also been used to

collect topographic data for wide areas and had produced millions of point cloud

data. (Cao et al., 2015). The support for good management of these data is still in the

beginning stages (Mosa et al., 2012).

Airborne LiDAR is widely applied as one kind of survey data source, especially in a

highly automated generation of digital elevation models (DEM) and digital surface

models (DSM) because of its highly accurate three-dimensional (3D) information

acquisition capability (Zhu, 2011). The Global Positioning System (GPS) and Inertial

Measurement Unit (IMU) data recorded on the plane is combined with laser pulse

range measurements to produce point data with x, y-locations and elevations

(ASPRS, 2005).

“The wide use of LiDAR brings about problems in storage, processing, and

application services of massive point cloud data” (Hongchao et al., 2011). LiDAR

data contain a huge amount of points with associated scalar values (Lipus, 2012).

This LAS file format is a public file format for the interchange of 3-dimensional

point cloud data between data users. Although developed primarily for exchange

of LiDAR point cloud data, this format supports the exchange of any 3-dimensional

x,y,z. This binary file format is an alternative to proprietary systems or a generic

ASCII file interchange system used by many companies. The problem with

proprietary systems is that data produced cannot be easily used from one system to

another (Shan et al., 2009).

“The storage and computing patterns in the local file system can no longer meet the

demands, while the networking storage and parallel processing of unstructured

LiDAR data are becoming new requirements for storage, processing and application

of point cloud data” (Wende, 2014).

Restricted by the size and distribution of the point-cloud makes the operation of the

point-cloud time consuming and difficult to deal with (Meijers, 2011). Therefore, the

management and storage research of large-scale 3-D laser scanning data is still rare

around the world (Ehinger, 2011).

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1.2 Problem statement

The large size of LiDAR topography data causes many organizations to struggle with

the managing of relatively large size datasets (Viswananth et al., 2010). No existing

integrated framework solution can exploit the access and storage of these vast data

sets such as LiDAR (Lewis et al., 2010). Users only want a simple and easy method

to store data. The quick and simple solution to just simply save the data is

understandable (Bjorset, 2013)

However, there might be benefits from having the LiDAR data stored in a more

organized manner. Point clouds are versatile and can be reused many times for

different purposes. This becomes more interesting when the acquisition cost is taken

into account. Usually, raw LIDAR data are collected by a variety of vendors.

Datasets may also available in different formats, with different schemes, different

attributes, and different compression schemes.

There are cases of data recorded in different geographic projections even within the

same dataset (Viswanath et al., 2010). Gathered data is processed after the flight and

every measured point is referenced with its geospatial position (Zlatanova, 2006).

Processed point clouds are then written into output files of different formats, with the

preferred format being the open LAS file format (Qing et al., 2001). The LAS format

is currently the common way of storing and managing LiDAR point clouds (ASPRS,

2010).

Various ASCII formats exist, depending on the information available. It could be a

basic XYZ file, XYZI or an extended version with intensity. Other features could be

added as ASCII columns in any possible order. The most frequent features are the

GPS acquisition time, pulse number or classification field (ISPRS, 2012).

Additionally, a file can represent different things, such as a tile of lidar data or a strip

(raw acquisition geometry). Lastly, some formats also propose spatial indexing

(McGaughey, 2007). Convincingly, it becomes clear that a modern lidar library

should be able to manage this two standards and also provide extended ASCII import

and export functionalities for ensuring compatibility with toolkits and current

software packages (David et al., 2008).

Even though the intention to organize LiDAR data is there, directions for selecting a

system that can manage the data is problematic. Software solutions for storing and

working with LiDAR data are still in their very early stages. As a result of many

current spatial databases and Geographical Information Systems having poor support

for LiDAR data, it is not thoroughly clear-cut for researchers to easily use these as

data management solutions (Bjorset, 2013).

An effective organization and management of a vast point-cloud data would be the

key obstacle in point-cloud storage research. It is an urgent problem to define the

point-cloud data type and the organization in 3-D spatial databases (Ming, 2007,

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Wang, 2008). The choice of the right and appropriate database is always crucial for

any information system (Kulshrestha, 2014

This research explores the possibility of using an open source in the development of

the web application based on a database structure using Graphical User Interface

(GUI) to make information accessible to users. However, the main target group of

this research will be the vendor and managers in JUPEM.

1.3 Objectives

The objective of this research is to improve and develop a new method for managing

LiDAR database system using open source platforms to accommodate future needs

by JUPEM and Industries develop a LiDAR database management system using

open source platforms. The purpose of developing LiDAR Database Management

System (LiDMS V 1.0) is to be used by operators and managers at JUPEM as well as

public and researchers to get information on LiDAR data via a web application.

1.4 Specific Objectives

The specific objectives of this study are as follows:

1. To develop a LiDAR Database management system. 2. To implement the database system using an open software system. 3. To evaluate the performance of the system

1.5 Scope

This thesis aims to investigate how LiDAR data can be stored in an efficient,

organized and user-friendly manner especially for users who do not possess full

knowledge of LiDAR. This was done by, firstly, developing a thorough

understanding of the challenges related to the structure, acquisition, data conversion

and storage of the LiDAR data. A LiDAR database prototype will be developed,

followed by an assessment of what can be done from the system’s implementation.

The study will focus only on data available from the Malaysian Department of

Surveying and Mapping (JUPEM). JUPEM as a proprietary data holder or library

data for aerial photography receives a lot of aerial photography data from other

government agencies or the private sector who captures data year every year, and this

includes LiDAR data (Circular Document of Classified Security Geospatial

Instructions, 2007).

1.6 Motivation

The motivation of this research is to provide access to LiDAR data in Malaysia to

users such as university students, researchers, the army, the police, managers and

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decision makers through the online portal. The current methods practiced acquiring

LiDAR data from JUPEM are either by making phone calls asking for data or

sending formal letters to management requesting so. While this is manageable at the

moment, it is important to explore the usage of open source platforms because it is

available freely and has the required capabilities to function the same as commercial

software like Oracle. A LiDMS v1.0 is customized to address the needs of JUPEM

operators to manage LiDAR data and to provide access to researchers for their

studies. LiDMS v1.0 gathers LiDAR data that been received from JUPEM in

Malaysia for public access.

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