Unmanned Aerial Vehicle (UAV) photogrammetry as a tool in aquatic ecosystem mapping ...

150 Pages·2016·5.94 MB·English

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Surname, Initial(s). (2012) Title of the thesis or dissertation. PhD. (Chemistry)/ M.Sc. (Physics)/
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Unmanned Aerial Vehicle (UAV) Photogrammetry as a Tool in Aquatic
ecosystem mapping, assessment and planning
BY
MARINUS BOON
THESIS
MINOR DISERTATION SUBMITTED IN PARTIAL FULFILMENT OF REQUIREMENTS FOR THE DEGREE
MAGISTER SCIENTAE
IN
AQUATIC HEALTH
AT THE
UNIVERSITY OF JOHANNESBURG
Supervisor: Dr Richard Greenfield
Co-Supervisor: Dr Solomon Tesfamichael
i
Acknowledgements
I would like to express my sincerest gratitude to the following people who have contributed
immensely towards this degree:
 To Dr. Richard Greenfield for his guidance and assistance throughout the project as my
supervisor.
 Dr. Solomon Tesfamichael of University of Johannesburg Geography department for co-
supervising this project and always being of great assistance during the project and for the
use of the computer to process this large dataset.
 To Aerial Kopter Solutions (AKS) and the RPAS Training Academy who provided the
equipment, resources and expertise to complete the surveying for this project.
 To my wife Hanneke Boon that believes in me, kept motivating me and helped building this
dream.
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Abstract
The understanding of aquatic ecosystems such as wetlands requires that they be examined and understood
from a wide range of perspectives. Unmanned Aerial Vehicle (UAV) photogrammetry using inexpensive digital
cameras has recently become a powerful tool that offers a viable alternative to traditional remote sensing
systems, particularly for applications covering relatively small spatial extents. UAV photography has a high
spatial accuracy needed by scientists and proof to be a valuable tool to enhance our understanding of aquatic
ecosystems. Accurate planning derived from this technological advancement allows for more effective
management and conservation of wetland areas. This thesis presents results of a study that aimed at
investigating the use of UAV photogrammetry as a tool to enhance the assessment of wetland ecosystems.
A baseline wetland delineation, classification and WET-Health assessment (baseline wetland assessment)
was conducted first. Twenty ground control points (GCPs) were then positioned across the site to achieve
geometrical precision and georeferencing accuracy. The XYZ location of each GCP was recorded using a
Trimble SPS985 GNSS GPS. The UAV images were collected during a single flight within 2½ hours over a 100
ha area at the Kameelzynkraal farm, Gauteng Province, South Africa. An AKS Y-6 MKII multi-rotor UAV and a
NIKON D3200 (28 mm) digital camera on a motion compensated gimbal mount were utilised for the survey.
Structure from Motion (SfM) computer vision techniques were used to reconstruct the camera positions,
terrain features and to derive ultra-high resolution point clouds, orthophotos and 3D models from the multi-
view photos using Agisoft Photoscan Professional Version 1.1 software. A spatial resolution of up to 0.018 m
was achieved. The results of the geometric accuracy of the data based on the 20 GCP’s were 0.018 m for the
overall, 0.0025 m for the vertical root mean squared error (RMSE) and an overall root mean square
reprojection error of 0.18 pixel.
The UAV products were then edited using Photoscan and Quick Terrain Modeller (QTM) 805. The edited
products were subsequently analysed, interpreted and key attributes extracted using a selection of tools/
software applications including QGIS 2.2.0 and 2.12.0 application, Google Earth, QTM 805 and Global Mapper
v17. The UAV products were then applied to conduct a wetland delineation and WET-Health assessment
(UAV wetland assessment). The baseline wetland assessment results were then compared with the UAV
assessment results to assess if the latter enhanced wetland delineation and WET-Health.
The UAV products provided a valuable enhancement to the wetland delineation and classification which
would have been difficult to achieve using field studies alone. UAV photogrammetry was successfully applied
to determine the landscape setting (terrain and geomorphic), obtain precise slope profiles, assisted with the
identification of areas of saturation and water accumulation, mapping of hydrophilic vegetation including
surface water sources and surface hydrodynamic analysis. UAV photogrammetry further enhanced the WET-
Health assessment allowing wetland practitioners to better understand the degradation of the study area
where all the wetland indictors were not that apparent by providing accurate data that can assist with
decision making.
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Table of Contents
Abstract .......................................................................................................................................................... iii
List of Figures ..................................................................................................................................................vii
List of Tables .................................................................................................................................................... x
List of Abbreviations ....................................................................................................................................... xi
List of Appendices ........................................................................................................................................... xii
Chapter 1: Introduction ................................................................................................................................... 1
1.1 UAV Photogrammetry ...........................................................................................................2
1.1.1 Definition and introduction to Three Dimensional (3D) Models and Orthophotos .................. 2
1.2 Aquatic Ecosystem Assessment .............................................................................................2
1.2.1 Wetland Delineation .................................................................................................................. 3
1.2.2 Wetland Classification ................................................................................................................ 4
1.2.3 WET-Health Present Ecological Status (PES) Assessment .......................................................... 4
1.3 Hypothesis, Aims and Objectives ..........................................................................................4
Chapter 2: Literature Review........................................................................................................................... 6
2.1 Wetland Assessment .............................................................................................................6
2.1.1 Wetland Ecosystems in South Africa.......................................................................................... 6
2.1.2 Wetland Delineation and Classification ..................................................................................... 6
2.1.3 Purpose and key features of wetland health assessment (WET-Health) ................................... 7
2.2 Unmanned aerial vehicle (UAV) photogrammetry and remote sensing ...............................8
2.3 Three dimensional data acquisition based on Structure from Motion (SfM)
photogrammetry ................................................................................................................11
2.4 Further Applications of UAV and Structure from Motion photogrammetry ......................14
2.4.1 Ecological applications ............................................................................................................. 15
2.4.2 Topographical applications ...................................................................................................... 15
2.4.3 Geomorphology and Hydrology ............................................................................................... 16
2.4.4 Vegetation and Wetland related applications ......................................................................... 17
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2.5 Gaps in literature, disadvantages and limitations of UAV photogrammetry ......................19
Chapter 3: Materials and methods ................................................................................................................ 20
3.1 Baseline wetland study ........................................................................................................21
3.1.1 Wetland and riparian delineation ............................................................................................ 22
3.1.2 Wetland Classification .............................................................................................................. 24
3.1.3 Wetland Functionality: Present Ecological Status (PES) – WET-Health ................................... 25
3.2 Unmanned Aerial Vehicle (UAV) flight planning .................................................................27
3.3 Position GCPs and setup of Trimble positioning system .....................................................28
3.4 UAV image collection ...........................................................................................................30
3.5 Structure from Motion (SfM) computer vision techniques .................................................30
3.6 Analysis, interpretation and extraction of necessary attributes from the UAV products ..34
3.6.1 Orthophotos ............................................................................................................................. 37
3.6.2 Point clouds and surface models ............................................................................................. 37
3.7 Study Area ............................................................................................................................40
3.7.1 Background Hydrology ............................................................................................................. 42
3.7.2 Regional Vegetation ................................................................................................................. 43
3.7.3 Geology and Soils ..................................................................................................................... 44
3.7.4 Gauteng Conservation Plan ...................................................................................................... 45
Chapter: 4 Results.......................................................................................................................................... 46
4.1 Wetland Classification and Delineation...............................................................................48
4.1.1 Baseline Study .......................................................................................................................... 48
4.1.2 UAV photogrammetry Enhancement....................................................................................... 51
4.1.3 Discussion ................................................................................................................................. 63
4.2 WET-Health Assessment (ecological status)........................................................................66
4.2.1 Hydrology ................................................................................................................................. 66
4.2.2 Geomorphology ....................................................................................................................... 78
4.2.3 Vegetation ................................................................................................................................ 83
4.2.4 Discussion ................................................................................................................................. 89
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4.2.5 Combined Ecological Status Conclusion................................................................................... 90
Chapter 5: Conclusion ................................................................................................................................... 92
5.1 General Conclusions ............................................................................................................92
5.2 Benefits, Limitations and Potential Future Research ..........................................................93
Chapter 6: References ................................................................................................................................... 96
Appendix A: UAV DATA ............................................................................................................................... 103
Appendix B: Wetland Delineation and WET-Health Data ........................................................................... 109
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List of Figures
Figure 1 The applications of unmanned aerial imagery in the reviewed studies by Shahbazi et al.
(2014). .......................................................................................................................................... 10
Figure 2 Structure-from-Motion (SfM). Instead of a single stereo pair, the SfM technique requires a
series of overlapping photographs as input to feature extraction and 3D reconstruction algorithms
(Westoby et al. 2012). ................................................................................................................... 12
Figure 3 Flow diagram of methodology (Macfarlane et al. 2009, Verhoeven 2011, Lucieer et al. 2013,
AKS 2014, Agisoft LLC 2014 and Applied Imagery 2015) ............................................................. 21
Figure 4: Terrain units (DWAF 2005) ................................................................................................. 22
Figure 5 Typical cross section of a wetland (Ollis et al. 2013) ....................................................... 23
Figure 6: UAV study area and flight lines within the DJI Ground Station software. ........................ 28
Figure 7: 7a Trimble base station setup. 7b Referencing with trigonometrical beacons. 7c Ground
control markers (GCPs) were then laid. ......................................................................................... 29
Figure 8: Ground control markers (arrows) were positioned across the site at the boundaries of the
UAV survey area/study area (red line) including next to the watercourse at different elevations (20
markers equally spaced over the 100ha) ....................................................................................... 29
Figure 9: The UAV survey system used for the study. 9a Ground Control Base 9b AKS Y-6 MKII
multi-rotor UAV ............................................................................................................................. 30
Figure 10: Sparse point cloud generated. 10a Indicate the camera positions and image overlaps.
The legend on the right represents the number of images in which a point appears. 10b Sparse point
cloud with ground control points/marker visible. ............................................................................ 31
Figure 11: Dense point cloud reconstructed with Photoscan; (a) with camera positions, (b) without
camera positions. .......................................................................................................................... 32
Figure 12: Identification of the GCP’s to achieve geometrical precision and georeferencing accuracy
within Photoscan. .......................................................................................................................... 32
Figure 13: The automatic division of all the points into two classes - ground points (brown) and the
rest (grey) was performed within Photoscan .................................................................................. 33
Figure 14: A section of the wireframe mesh buildt on the ground points only. ............................... 34
Figure 15: Editing of the study area surface model within QTM version 805 (Applied Imagery 2015).
...................................................................................................................................................... 38
Figure 16: Locality of the Cors-Air study area to the east of Pretoria, Gauteng Province. The location
of the study area is indicated by the black dot. .............................................................................. 41
Figure 17 17a: Infilling and infestation with black wattle 17b: and the construction of earthen dams
within the wetland .......................................................................................................................... 41
Figure 18: Sections of the system still represent typical characteristics of a wetland such as wetland
soils and vegetation. ..................................................................................................................... 42
Figure 19: River Catchments of South Africa Quaternary Catchment B20C (green area) located
within the Olifants Water Management Area (pink area). The study area location is indicated by the
black dot (DWAF 1994). ................................................................................................................ 43
Figure 20: Study area soil forms from the Gauteng Soil survey (AGIS 2015) ................................ 44
Figure 21: The study area in relation to the Gauteng Conservation Plan (Important Area and
Ecological Support Area) ............................................................................................................... 45
Figure 22: The 0.038 m ground spatial resolution Digital Terrain Model (DTM) derived from the UAV
the point cloud and aerial photographs respectively. ..................................................................... 47
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Figure 23: The valley-bottom landscape setting of the wetland visible looking towards the study area
from the nearest trigonometric beacon .......................................................................................... 49
Figure 24: The average slope of the study area (white line) is 2.4% and the maximum slope is 4.9%.
...................................................................................................................................................... 49
Figure 25 25a The presence of hydrophytic species such as Bullrushes (Typha capensis) and (25b)
Pragmites australis dominated the permanent and semi-permanent zone of the wetland. ............. 50
Figure 26: Wetland soil indicators 33a Willowbrook soil form a typical form associated with the
permanent zone of a wetland found on the lower section of the wetland. 33b The freely upper solum
with mottling clearly visible in the upper section of the HGM. ........................................................ 50
Figure 27: Wetland areas delineated (baseline study). .................................................................. 51
Figure 28: A 0.29 m ground pixel resolution DTM of the study area with QTM height colouration and
2.5 m contours .............................................................................................................................. 52
Figure 29: The average slope (profile analysis) of the study area (red line) as indicated in the graph
in Figure 30. .................................................................................................................................. 53
Figure 30: The average slope (profile analysis) calculated for the study area with QTM is 1.013° or
1.77 % slope. ................................................................................................................................ 53
Figure 31: Small scale 3D representation of the 0.29 m DTM using Global Mapper v17 with baseline
delineation (blue line). ................................................................................................................... 54
Figure 32: Cross section placement within the 0.29 m DTM and derived as indicated in Figure 41.
...................................................................................................................................................... 54
Figure 33: Cross section placement within the 0.038 m DTM and derived as indicated in Figure 42.
...................................................................................................................................................... 55
Figure 34: Cross sections derived from the 0.29 m DTM indicating the profile of the wetland and
associated landscape. ................................................................................................................... 55
Figure 35: Cross sections derived from the 0.038 m DTM indicating the profile of the the wetland and
associated landscape. ................................................................................................................... 56
Figure 36: The visualisation of the 0.29 m DTM with floating cross sections. The red line within the
wetland is the slope path more accurately placed within the watercourse through visualisation within
QTM. ............................................................................................................................................. 56
Figure 37: The accumulation of water in small puddles is visible in the 10 cm orthophoto. ........... 57
Figure 38: The watercourse visible in the 10 cm orthophoto by taking into consideration that this
imagery was acquired in the winter when the flow and water levels were low. .............................. 58
Figure 39: Point cloud (small extent 0.038 m) with QTM height coloration and intensity enabled. The
red line indicates the baseline delineation. .................................................................................... 58
Figure 40: Orthophoto (1.8 cm) with hydrophilic vegetation (KMZ format displayed with Google Earth)
...................................................................................................................................................... 59
Figure 41: The remaining intact hydrophilic vegetation sections delineated (red delineations in the
centre) in the DEM (0.038 m) is clearly visible. The QTM visualisation and height coloration was also
used here. ..................................................................................................................................... 60
Figure 42: The classified (ground and low points only) point cloud provides useful hydrodynamic
information of the wetland section below the dam with the spillway. .............................................. 61
Figure 43: The section of the wetland just below the Kikuyu cultivation displayed using the classified
point cloud (ground and low points only). The seepage of the water from the Kikuyu that is under
irrigation can be determined. The red line indicates the baseline delineation. .............................. 61
Figure 44: Local watershed and surface water drainage determination from the DTM (0.29 m) with
the baseline delineation displayed. ................................................................................................ 62
Figure 45: Flood simulation using the QTM flood analysis tool with the 0.038 m DTM with the baseline
delineation displayed (red line). ..................................................................................................... 63
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Figure 46: Wetland areas delineated. Baseline and UAV wetland delineation displayed on the 10 cm
orthophoto. .................................................................................................................................... 65
Figure 47: UAV delineation presented in the 0.038 m DTM with texture (10 cm orthophoto) overlay
in QTM. ......................................................................................................................................... 66
Figure 48: Historical aerial imagery of 1958 (Surveyor General) presenting the study area (red line).
...................................................................................................................................................... 67
Figure 49: 3D mensuration of the drains in the wetland using QTM mensuration tool (0.038 m DTM
with orthophoto texture). ................................................................................................................ 74
Figure 50: The 0.038 m DTM with orthophoto overlay used to determine the density of drains in the
wetland. Note the measurement line and also the contours. ......................................................... 75
Figure 51: The DEM (0.038 m) with a visual overview of the UAV delineation and the location of
some of the dams and the interruption the dams may cause. ........................................................ 75
Figure 52: Visualisation of a section of the surface roughness delineated within the wetland and
channel (10 cm orthophoto as a texture over the DEM 0.038 m). .................................................. 76
Figure 53: Above ground level (AGL) analysis of the surface roughness using the QTM AGL analyst
tool. ............................................................................................................................................... 76
Figure 54: A section of the surface roughness that was cut from the point cloud for more detailed
inspection using the height coloration function. ............................................................................. 77
Figure 55: The areas with a minimum point intensity score of just below 45 (green coloration)
correlated with areas observed in the field and on the HROs as areas with a relative surface
roughness. .................................................................................................................................... 77
Figure 56: The Black wattle (Acacia mearnsii) trees could be determined from the HROs (2.5 cm
orthophoto displayed using Global Mapper v17 note the red UAV delineation line). ...................... 78
Figure 57: QTM point cloud intensity deviation map with orthophoto texture and the UAV delineation.
Areas with a low deviation score 1,119 (blue and light blue) included areas which was and still
currently is subjected to anthropogenic activities such as infilling and compaction. ....................... 82
Figure 58: Sediment deposition within the earthen dam visible in the HRO (2.5 cm orthophoto
displayed using Global Mapper v17 note the red UAV delineation line). ........................................ 82
Figure 59: Identification and estimation of disturbance classes with the HRO (2.5 cm orthophoto
displayed using Global Mapper v17 note the red UAV delineation line). Infrastructure such as the
internal roads, deep flooding by dams areas of pasture and cultivation can be identified. ............. 87
Figure 60: Identification and estimation of disturbance classes with the HRO (2.5 cm orthophoto
displayed using Global Mapper v17 note the red UAV delineation line). The deep flooding by dams
(dam overgrown with Kikuyu grass) and the drains within the wetland can be identified................ 88
Figure 61: QTM intensity deviation point cloud. Areas with a low deviation score 0-10 (orange to
yellow/green) included areas which were and currently are subjected to anthropogenic
disturbance. One needs to note that the other end of the deviation intensity scores include the blue
which indicates intact wetland areas and alien tree stands such as black wattle, which is also a
disturbance class (although this sections include more purple and pink), therefore the need to
visualise this calculations in conjunction with the HROs for confirmation. The two earthen dams
with orange should also be ignored due to reconstruction errors of these two
features. ........................................................................................................................................ 89
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