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2016 Wang - A Region Growing
2016 Wang - A Region Growing
2016 Wang - A Region Growing
PII: S0098-3004(16)30647-1
DOI: http://dx.doi.org/10.1016/j.cageo.2016.11.002
Reference: CAGEO3862
To appear in: Computers and Geosciences
Received date: 6 May 2016
Revised date: 2 September 2016
Accepted date: 8 November 2016
Cite this article as: Xin Wang, Lejun Zou, Xiaohua Shen, Yupeng Ren and Yi
Qin, A region-growing approach for automatic outcrop fracture extraction from a
three-dimensional point cloud, Computers and Geosciences,
http://dx.doi.org/10.1016/j.cageo.2016.11.002
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A region-growing approach for automatic outcrop
fracture extraction from a three-dimensional point cloud
Xin Wanga , Lejun Zoua , Xiaohua Shena,, Yupeng Rena , Yi Qina
a
Department of Earth Sciences, Zhejiang University Yuquan Campus, 38 Zheda Road,
Hangzhou 310027, China
Abstract
Corresponding author
Email address: shenxh@zju.edu.cn (Xiaohua Shen)
1 1. Introduction
2 The manual surveying of fractures and other planar rock mass surfaces
3 is one of the most fundamental but time-consuming activities performed by
4 eld geologists. The surveyed fracture data usually comprise the fracture lo-
5 cation, orientation, and surface roughness, which can support models and/or
6 hypotheses in various applications (e.g., structural and geomechanical analy-
7 sis, ow modeling, reservoir characterization, and engineering rock mass clas-
8 sication). These surveys are conventionally performed in situ with standard
9 eldwork instruments, such as a handheld compass, clinometer, and possibly
10 a digital camera to record the fracture locations. However, the development
11 of remote sensors (e.g., LiDAR-based scanners) and their availability as re-
12 search equipment have prompted geoscientists to develop new methods that
13 improve the analysis, avoid access problems, reduce time and labor, and re-
14 sult in a more representative dataset. The terrestrial laser scanner (TLS) is
15 one of the most widely used instruments in Earth science applications, and
16 it is very useful for acquiring high-quality, high-resolution, three-dimensional
17 (3D) point clouds from outcrops (Xu et al., 2000; Bellian et al., 2005; Mc-
18 Carey et al., 2005; Olariu et al., 2008; Jones et al., 2009; Mah et al., 2011;
19 Wilson et al., 2011; Pearce et al., 2011; Mah et al., 2013). In addition, the
2
20 GPS receiver module in a typical TLS allows the point cloud, a set of points
21 in a 3D coordinate system, to be transformed into dierent geographic coor-
22 dinate systems, so the data can be processed and used for dierent purposes,
23 such as topographic feature extraction and orientation estimation for planar
24 surfaces.
25 During the last few years, because of the widespread use of TLS in Earth
26 science applications, there has been a growing need for point cloud processing
27 methods to perform analyses and interpretation. The extraction of fractures
28 and other planar surfaces from 3D outcrop point clouds has been the focus
29 of much research by the geological community because fracture data have
30 a wide range of applications. Many semi-automatic and automatic meth-
31 ods have been developed in the last 10 years, and certain algorithms can be
32 used to extract (or segment) the points of fracture surfaces from the point
33 cloud. Slob et al. (2005) and Lato et al. (2009) derived triangulated irreg-
34 ular networks from the point cloud and then grouped neighboring polygons
35 with a similar orientation to obtain planar features. Roncella et al. (2005),
36 Voyat et al. (2006), and Ferrero et al. (2009) used random sample consensus
37 (RANSAC) algorithm-based methods to segment point clouds into subsets,
38 each of which comprise points that belong to the same discontinuity surface.
39 Recently, other methods have also been proposed based on k-means cluster-
40 ing (Olariu et al., 2008), moving sampling cube (Gigli and Casagli, 2011),
41 point attributes (Garca-Selles et al., 2011), neighboring points coplanarity
42 testing (Riquelme et al., 2014), and principal component analysis (PCA)
43 (Gomes et al., 2016). However, using these methods, either the full extent
44 of the individual fracture surface is not extracted (Slob et al., 2005; Olariu
3
45 et al., 2008; Lato et al., 2009) or human supervision is required (Ferrero
46 et al., 2009; Gigli and Casagli, 2011; Garca-Selles et al., 2011; Riquelme
47 et al., 2014). The automatic method proposed by Gomes et al. (2016) splits
48 the point cloud into four subsets (quadrants) iteratively to detect planar
49 structures, but the full extent of the individual fracture surface was not fully
50 extracted and was detected as several planar structures in most cases.
51 In this study, we propose an algorithm using a region-growing approach
52 for the automatic extraction of the full extent of individual outcrop fractures
53 from point clouds and for estimating their orientation. The main novel fea-
54 ture of this algorithm is the application of region growing to the extraction
55 of outcrop fractures from point clouds. Instead of growing the region locally
56 without a global view of the fracture surface, we use a seed point selection
57 criterion to consider the overall fracture occurrence, as well as criteria for
58 determining the initial seed point and controlling the growth of the region.
59 The region-growing concept is simple, and by using carefully designed crite-
60 ria, our algorithm can extract the full extent of every individual fracture in
61 an automatic and robust manner.
63 The study site is a road-cut rock slope located along a country road in
64 Nanbaoxiang, Chengdu, Sichuan Province, China (N 30 24 25.35 , E 103
65 11 8.34 ) (Fig. 1). The rock slope mainly comprises thin to thick layered
66 sandstone, and the area of the study outcrop is about 30 m2 . A RIEGL VZ-
67 1000 terrestrial laser scanning system (mainly comprising a 3D laser scan-
68 ner, digital camera, and GPS receiver) was used to perform a high-resolution
4
69 LiDAR scan of the rock slope. This TLS system uses the time-of-ight tech-
70 nique, which utilizes the emission and return time of highly collimated elec-
71 tromagnetic radiation to calculate the distance from the instruments optical
72 center to a reecting target surface (Baltsavias, 1999). An outcrop 3D point
73 cloud was acquired with an average point spacing of < 1 cm; there were about
74 21 million points. To test the proposed region-growing-based algorithm, we
75 selected the central part of the point cloud (delineated by the white rectangle
76 in Fig. 1), where less vegetation and fallen stone were present. Conventional
77 measurements of fracture surface orientations using a handheld compass were
78 also performed on the rock slope to compare with the results obtained by the
79 proposed algorithm, and 65 orientation measurements (dip direction and dip
80 angle) were acquired from fracture faces distributed over the outcrop.
Figure 1: Picture of the study site: a road-cut rock slope with thin to thick layered
sandstone. The white rectangle delineates the part used to test our algorithm. See the
red notebook for scale.
5
81 3. Methodology
6
105 3.1. Local surface normal and curvature estimation
106 One or more properties of each point in the point cloud are required
107 for region-growing segmentation, i.e., segmenting the regions that comprise
108 points with similar dened properties. The local surface normal and the local
109 surface curvature are two basic properties that can be used to dene planar
110 surfaces such as fractures.
111 To estimate the local surface normal and curvature for each point, its
112 neighboring points, which together form the local topography, are needed.
113 We refer to a point cloud as P , a collection of 3D points pi = {xi , yi , zi } P .
114 Let pq be the query point in the problem of estimating the local surface
115 normal and curvature, and let P k be the K-nearest neighbors of pq , in which
116 k is chosen by the user to nd the k nearest neighbors according to their
117 Euclidean distance to pq .
118 The method we use for estimating the local surface normal is based on
119 least-squares plane tting with P k , as proposed by Berkmann and Caelli
120 (1994). The least-squares plane tting method is based on PCA. The local
121 surface normal nq of point pq is obtained by analyzing the eigenvalues and
122 eigenvectors of P k s covariance matrix C = k1 ki=1 (pi p )T , where
) (pi p
123 = k1 ki=1 pi . If we let 0 , 1 , and 2 be the eigenvalues of C
pi P k and p
124 that satisfy 0 0 1 2 and if v 0 is the corresponding eigenvector of
125 0 , then
v 0 if v 0 (v p pq ) > 0
nq = (1)
v 0 if v 0 (v p pq ) < 0,
126 where v p is the viewpoint from which the point cloud is acquired.
127 The method used to estimate the local surface curvature was proposed
7
128 by Pauly et al. (2002). This method can estimate the curvature directly
129 from the eigenvalues of P k s covariance matrix C without needing to rst
130 create a surface from the point cloud. The local surface curvature q of pq
131 is estimated as follows.
0
q = (2)
0 + 1 + 2
133 Let Pr P be the set of points that have not yet been assigned to any
134 fracture regions. For each fracture region, the initial seed point that starts
135 this regions growth is selected from Pr , and the point pmin Pr with the
136 minimum curvature is selected as a reasonable initial seed point for planar
137 surfaces such as fractures.
138 Next, the criterion that controls the growth from the seed points to their
139 neighboring points is dened as the local surface normal deviation threshold
140 th given by the user. For the neighboring point pi , the local surface normal
141 is ni , and the seed points local surface normal is ns , so pi is added to the
142 current region if cos1 ( nnssn
ni
i
) < th , i.e., if the angle between ns and ni is
143 less than th .
144 The new seed points are then selected from the newly added points. The
145 criterion dened as the transmission error threshold tth , which is also given
146 by the user, determines whether the newly added pi is selected as a new
147 seed point. For the newly added pi , the local surface normal is ni and the
148 initial seed point pmin s local surface normal is nmin , so the newly added pi
149 is selected as a new seed point if cos1 ( nnmin
min ni
ni
) < tth , i.e., if the angle
150 between nmin and ni is less than tth . Therefore, the overall occurrence of the
8
151 fracture, which is represented by nmin , serves to control the growth of the
152 region instead of its being allowed to grow blindly.
153 The regions growth from the newly selected seed points and the selection
154 of new seed points are then performed iteratively until no new seed point
155 can be selected and the regions growth is complete. The growth of the other
156 regions is completed for those remaining in the point cloud until all of the
157 points in the point cloud have been processed.
158 The local surface normal deviation threshold th and the transmission
159 error threshold tth that yield the best segmentation result are related to the
160 fracture surfaces geometrical nature and the weathering condition of the
161 outcrop. According to their denitions and the functions described above,
162 th is related to the local roughness, whereas tth is related to the overall
163 atness of the fracture. For example, if a at fracture has a rough local
164 surface, then th should be suciently large to allow small protrusions and
165 dents in the fracture region. If the uneven fracture has a smooth local surface,
166 such as weathered fracture surfaces, then tth should be suciently large to
167 allow the uneven fracture to grow into one region. The ow chart for the
168 region-growing step of the proposed method is shown in Fig. 2.
9
Input: P ; nq and q for all pq P ; th and tth
yes
Is A empty?
no
The Current Fracture Region Rc
The Seed Points List Sc
From A nd the minimum curvature point pmin ; add it to Sc and Rc
Get pmin s local surface normal nmin
Remove pmin from A
yes
Is Sc empty?
no
Get a seed point ps from Sc
From A nd ps s neighboring points Psk
Get ps s local surface normal ns
yes
Is Psk empty?
no
Get pi from Psk and its local surface normal ni
no
cos1 ( nnssn
ni
i
) < th ?
yes
Add pi to Rc
Remove pi from A
cos1 ( nnmin
min ni no
ni ) < tth ?
yes
Add pi to Sc
Remove ps from Sc
Add Rc to R
Output: R
170 For a patch of a point cloud that has completed its growth, many features
171 of the extracted fracture can be estimated, such as the fracture orientation.
172 The fracture orientation can be estimated as the normal nx , ny , nz of the
173 least-squares tting plane in the point cloud patch that represents the frac-
174 ture. The normal can also be transformed into the Dip direction, Dip ,
175 and the transformation may vary with the geographic coordinate systems
176 employed for the point cloud. For example, if the y-axis of the coordinate
177 system points north, the x-axis points east, and the z-axis points vertically
178 up, then the Dip direction and Dip will be as follows.
0 if nx = 0 & ny 0
180 if nx = 0 & ny < 0
Dip direction = (3)
90 tan1 (ny /nx ) if nx > 0
270 tan1 (n /n ) if n < 0
y x x
0 if n2x + n2y = 0
Dip = (4)
90 tan1 ( |nz | ) if n2x + n2y = 0
n2x +ny2
180 The point cloud used to test our algorithm and the conventional measure-
181 ments of the fracture surface orientations for the same outcrop were described
182 in Section 2. The application of the proposed algorithm to the entire point
183 cloud will provide a great number of planar regions with various dimensions,
11
184 and this makes it dicult to show the detailed results obtained by the pro-
185 posed algorithm. Therefore, before applying the proposed algorithm to the
186 entire point cloud, we tested the algorithm with a portion of the point cloud,
187 as described in Section 4.1. The results obtained for the entire point cloud
188 and comparisons with manual eld survey results are discussed in Section 4.2.
189 The performance of the proposed algorithm in terms of time consumption
190 was tested using a set of outcrop point cloud data, and the number of planes
191 detected from the same point cloud data with dierent congurations of th
192 and tth was also investigated. These are discussed in Section 4.3.
194 A portion of the outcrop (Fig. 3a and its point cloud Fig. 3b) was pro-
195 cessed using our method. The local surface normal deviation threshold th
196 was set to 6 , and the transmission error threshold tth was set to 20 , which
197 were tuned to obtain the best results. These settings for th and tth can
198 be applied to similar outcrop conditions. Fig. 3c is the result of the pro-
199 posed algorithm; it shows the fracture regions having more than 800 points
200 so that they can be conveniently compared with the manually identiable
201 fractures in Fig. 3a. The threshold value of 800 can be modied if smaller or
202 larger fracture regions are required. Dierent fracture regions are indicated
203 by dierent colors; the non-fracture regions are shown in red.
204 The results show that most of the fractures extracted by the proposed
205 algorithm could be identied as real fractures in Fig. 3a and also that most
206 of the major fractures identied in Fig. 3a were extracted by the proposed
207 algorithm. In addition, the results show that unlike other existing methods,
208 the proposed region-growing-based algorithm can extract the full extent of
12
209 every individual fracture automatically.
210 The estimated fracture planes and the least-squares tting planes for the
211 extracted fracture regions are shown in Fig. 3d. The fracture orientations
212 were estimated using these planes according to the methods described in
213 Section 3.3.
13
1m 1m
(a) (b)
1m 1m
(c) (d)
Figure 3: Detailed results obtained from a portion of the point cloud. (a) A portion of
the outcrop and (b) its point cloud. (c) Segmentation results obtained using the proposed
algorithm. Dierent fracture regions are shown in various colors, and the non-fracture
regions are shown in red. (d) Estimated fracture planes obtained from the segmentation
results.
14
214 4.2. Results for entire point cloud and comparison with manual eld survey
215 results
216 We applied the proposed method, with the local surface normal deviation
217 threshold th set to 6 and the transmission error threshold tth set to 20 , to
218 the entire point cloud (Fig. 4a). The resulting fracture regions having more
219 than 100 points are shown by dierent colors in Fig. 4b, and the non-fracture
220 regions are shown in red.
221 The results demonstrate that our proposed algorithm can extract many
222 small fracture faces, cases for which conventional measurements cannot be
223 obtained. Thus, besides accurately extracting fractures in the same manner
224 as a conventional manual survey as demonstrated by the detailed results
225 shown in Section 4.1, our method may also provide additional information
226 about fractures (particularly small fractures) that cannot be acquired from
227 conventional manual surveys.
15
1m
(a)
1m
(b)
Figure 4: (a) The outcrop used to test the proposed algorithm and (b) the segmentation
results. Dierent fracture regions are shown by dierent colors, and the non-fracture
regions are shown in red.
228 We extracted 157 fracture regions having more than 100 points and es-
229 timated their orientations. To compare the performance of the manual eld
230 survey and our proposed algorithm, we stereographically projected 65 orien-
231 tations from the manual eld survey and 157 orientations from the results
232 obtained by the proposed algorithm and plotted the density of their poles
233 (Fig. 5a and Fig. 5b, respectively).
16
0
f7 % of total
f5 per 0.6% area
f3 12.1
9.90
f4 f2 7.70
270 90
5.50
f6 3.30
f1
f8 1.10
Equal Area
bedding Lower Hemisphere
180 65 Poles
(a)
0
a9 % of total
a5 per 0.5% area
a3 a7
6.60
a11 5.40
a2
a4 4.20
270 90
a10 3.00
a6 a1 1.80
a8 0.60
Equal Area
bedding Lower Hemisphere
180 157 Poles
(b)
Figure 5: Pole density plots for the fracture orientations obtained from (a) the manual eld
survey and (b) the results produced using the proposed algorithm. The beddings pole
and arc plot are each shown in red in both (a) and (b). f1 , ..., f8 and a1 , ..., a8 represent
dierent sets of corresponding fractures.
17
234 A comparison of the pole density plots shows that the major clusters of
235 poles representing dierent sets of fractures from the eld manual survey,
236 such as f1 , ..., f8 in Fig. 5a, can also be found in the results obtained using
237 our algorithm (a1 , ..., a8 in Fig. 5b). The comparison also shows that the
238 proposed algorithm has the advantage of locating clusters of fracture sets
239 more accurately. For example, if many fractures are perpendicular to the
240 bedding (as was found at the study site considered), then the stereographic
241 plot poles of those fractures should be near the arc of the bedding, and
242 obviously the proposed algorithm has better descriptions than the manual
243 eld survey. Thus, the red arc of bedding in Fig. 5b ts the distribution
244 of poles better than the red arc of bedding in Fig. 5a, which indicates that
245 our algorithm was better at locating the cluster of bedding and the other
246 clusters of fracture sets. Therefore, in general, our algorithm was able to
247 obtain fracture data whose quality was as good as or better than that from
248 the manual eld survey.
249 Furthermore, our algorithm provides additional information about frac-
250 tures, which may be useful for the analysis. For example, clusters a9 , a10 and
251 a11 in Fig. 5b, as well as the symmetries between a6 and a7 , a9 and a10 , a6
252 and a10 , and a7 and a9 , may be interesting information that merits further
253 discussion and study.
254 The only disadvantage of the proposed algorithm may be the presence
255 of some possible outlier clusters in the fracture sets (examples can be seen
256 in Fig. 5b). The nature and removal of these outliers should be studied in
257 future work.
18
258 4.3. Performance and parameter conguration of the proposed algorithm
259 A set of point cloud data (Table 1) was used to test the performance of our
260 algorithm using a desktop computer with a CPU of 3.60 GHz and 4 GB RAM.
261 The average point spacing in all the point cloud datasets used was 0.01 m, the
262 dataset size ranged from 134,067 points to 1,096,948 points, and the outcrop
263 areas ranged from 5.5 m2 to 67.3 m2 . The same processing parameters were
264 used for all the point cloud datasets to highlight the variation in the time
265 consumption.
Table 1: Point cloud datasets used to test the performance of the proposed region-growing-
based algorithm
266 The performance testing result is shown in Fig. 6. The gure shows that
267 there was a steep increase in time consumption as the point cloud size reached
268 1 million points, but the time consumption is still acceptable. Therefore, we
269 conclude that our algorithm is suitable for point cloud datasets whose outcrop
270 area 70 m2 . For datasets larger than that, the computing power should be
271 increased or the algorithm should be modied.
19
600
500
Time consumption (seconds)
400
300
200
100
0
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1
Number of points (million)
272 Using the same point cloud as the one shown in Fig. 4a, we investigated
273 the number of planes detected using dierent congurations of th and tth .
274 The results are shown in Fig. 7, which shows that an increase in th or tth
275 resulted in a decrease in the number of planes detected. It is interesting to
276 note that th = 6 in Fig. 7a and tth = 20 in Fig. 7b, the conguration we
277 judged to yield the best results, are turning points: before these points, the
278 number of planes detected decreases quickly; after these points, the number
279 of planes detected decreases much more slowly. As we know, small changes
280 in the conguration of th and tth should not greatly inuence the number
281 of planes detected, so the point cloud may be over-segmented before these
282 turning points. Thus, an analysis of the number of planes detected under
283 dierent congurations of th and tth may help nd the conguration that
20
284 yields the best results.
21
3200
3000
2800
Number of planes
2600
2400
2200
2000
2 3 4 5 6 7 8 9
(with
th W=
th 20)
(a)
6000
5500
5000
4500
Number of planes
4000
3500
3000
2500
2000
1500
4 6 8 10 12 14 16 18 20 22 24 26 28 30
t th (with =
th 6)
(b)
Figure 7: Number of planes detected from the same point cloud under dierent congu-
rations of (a) th and (b) tth .
22
285 5. Conclusion
23
310 Further research should focus on improving the proposed method by re-
311 moving possible non-fracture regions (outlier clusters in the fracture sets) and
312 analyzing the results obtained by the region-growing-based algorithm, such
313 as the relationship between the roughness of the fracture and the weathering
314 condition, fracture type, and orientation, as well as assessing the performance
315 of the proposed method with dierent rock types and weathering conditions.
316 Acknowledgments
317 This study was funded by the Chinese National Science and Technology
318 Major Project (2011ZX05009001). We are grateful to Prof. Changjiang Li
319 for valuable comments on earlier drafts. We would like to thank the editor
320 and two anonymous reviewers for their valuable comments and suggestions,
321 which have improved the paper.
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