Structure from motion photogrammetry in ecology: Does the choice of software matter?

New Supplementary Photography Methods after the Anomalous of Ground Control Points in UAV Structure-from-Motion Photogrammetry

Recently, multirotor UAVs have been widely used in high-precision terrain mapping, cadastral surveys and other fields due to their low cost, flexibility, and high efficiency. Indirect georeferencing of ground control points (GCPs) is often required to obtain highly accurate topographic products such as orthoimages and digital surface models. However, in practical projects, GCPs are susceptible to anomalies caused by external factors (GCPs covered by foreign objects such as crops and cars, vandalism, etc.), resulting in a reduced availability of UAV images. The errors associated with the loss of GCPs are apparent. The widely used solution of using natural feature points as ground control points often fails to meet the high accuracy requirements. For the problem of control point anomalies, this paper innovatively presents two new methods of completing data fusion by supplementing photos via UAV at a later stage. In this study, 72 sets of experiments were set up, including three control experiments for analysis. Two parameters were used for accuracy assessment: Root Mean Square Error (RMSE) and Multiscale Model to Model Cloud Comparison (M3C2). The study shows that the two new methods can meet the reference accuracy requirements in horizontal direction and elevation direction (RMSEX = 70.40 mm, RMSEY = 53.90 mm, RMSEZ = 87.70 mm). In contrast, the natural feature points as ground control points showed poor accuracy, with RMSEX = 94.80 mm, RMSEY = 68.80 mm, and RMSEZ = 104.40 mm for the checkpoints. This research considers and solves the problems of anomalous GCPs in the photogrammetry project from a unique perspective of supplementary photography, and proposes two new methods that greatly expand the means of solving the problem. In UAV high-precision projects, they can be used as an effective means to ensure accuracy when the GCP is anomalous, which has significant potential for application promotion. Compared with previous methods, they can be applied in more scenarios and have higher compatibility and operability. These two methods can be widely applied in cadastral surveys, geomorphological surveys, heritage conservation, and other fields.

Evaluation of the Influence of Processing Parameters in Structure-from-Motion Software on the Quality of Digital Elevation Models and Orthomosaics in the Context of Studies on Earth Surface Dynamics

The fully automated Structure-from-Motion approach for developing digital elevation models and orthomosaics has been known and used in photogrammetry for at least 15 years. Years of practice and experience have allowed researchers to provide a solid description of the applicability and limitations of this method. That being said, the impact of input processing parameters in software on the quality of photogrammetric products has yet to be fully ascertained empirically. This study is aimed at identifying the most advantageous processing workflow to fill this research gap by testing 375 different setup variations in the Agisoft Metashape software for the same set of images acquired using an unmanned aerial vehicle in a proglacial area. The purpose of the experiment was to determine three workflows: (1) the fastest, which has the shortest calculation time; (2) the best quality, which is as accurate as possible, regardless of the time taken for the calculations; and (3) the optimal, which is a compromise between accuracy and calculation time. Each of the 375 processing setup variations was assessed based on final product accuracy, i.e., orthomosaics and digital elevation models. The three workflows were selected based on calculating the height differences between the digital elevation models and the control points that did not participate in their georeferencing. The analyses of the root mean square errors (RMSE) and standard deviations indicate that excluding some of the optimization parameters during the camera optimization stage results in high RMSE and an increase in the values of standard deviation errors. Furthermore, it was shown that increasing the detail of individual processing steps in software does not always positively affect the accuracy of the resulting models. The experiment resulted in the development of three different workflows in the form of Python scripts for Agisoft Metashape software, which will help users to process image sets efficiently in the context of earth surface dynamics studies.

Monitoring the Structure of Regenerating Vegetation Using Drone-Based Digital Aerial Photogrammetry

Measures of vegetation structure are often key within ecological restoration monitoring programs because a change in structure is rapidly identifiable, measurements are straightforward, and structure is often a good surrogate for species composition. This paper investigates the use of drone-based digital aerial photogrammetry (DAP) for the characterization of the structure of regenerating vegetation as well as the ability to inform restoration programs through spatial arrangement assessment. We used cluster analysis on five DAP-derived metrics to classify vegetation structure into seven classes across three sites of ongoing restoration since linear disturbances in 2005, 2009, and 2014 in temperate and boreal coniferous forests in Alberta, Canada. The spatial arrangement of structure classes was assessed using land cover maps, mean patch size, and measures of local spatial association. We observed DAP heights of short-stature vegetation were consistently underestimated, but strong correlations (rs > 0.75) with field height were found for juvenile trees, shrubs, and perennials. Metrics of height and canopy complexity allowed for the extraction of relatively tall and complex vegetation structures, whereas canopy cover and height variability metrics enabled the classification of the shortest vegetation structures. We found that the boreal site disturbed in 2009 had the highest cover of classes associated with complex vegetation structures. This included early regenerative (22%) and taller (13.2%) wood-like structures as well as structures representative of tall graminoid and perennial vegetation (15.3%), which also showed the highest patchiness. The developed tools provide large-scale maps of the structure, enabling the identification and assessment of vegetational patterns, which is challenging based on traditional field sampling that requires pre-defined location-based hypotheses. The approach can serve as a basis for the evaluation of specialized restoration objectives as well as objectives tailored towards processes of ecological succession, and support prioritization of future inspections and mitigation measures.

Effects of Differences in Structure from Motion Software on Image Processing of Unmanned Aerial Vehicle Photography and Estimation of Crown Area and Tree Height in Forests

This study examines the effects of differences in structure from motion (SfM) software on image processing of aerial images by unmanned aerial vehicles (UAV) and the resulting estimations of tree height and tree crown area. There were 20 flight conditions for the UAV aerial images, which were a combination of five conditions for flight altitude, two conditions for overlap, and two conditions for side overlap. Images were then processed using three SfM programs (Terra Mapper, PhotoScan, and Pix4Dmapper). The tree height and tree crown area were determined, and the SfM programs were compared based on the estimations. The number of densified point clouds for PhotoScan (160 × 105 to 50 × 105) was large compared to the two other two SfM programs. The estimated values of crown area and tree height by each SfM were compared via Bonferroni multiple comparisons (statistical significance level set at p < 0.05). The estimated values of canopy area showed statistically significant differences (p < 0.05) in 14 flight conditions for Terra Mapper and PhotoScan, 16 flight conditions for Terra Mapper and Pix4Dmapper, and 11 flight conditions for PhotoScan and Pix4Dmappers. In addition, the estimated values of tree height showed statistically significant differences (p < 0.05) in 15 flight conditions for Terra Mapper and PhotoScan, 19 flight conditions for Terra Mapper and Pix4Dmapper, and 20 flight conditions for PhotoScan and Pix4Dmapper. The statistically significant difference (p < 0.05) between the estimated value and measured value of each SfM was confirmed under 18 conditions for Terra Mapper, 20 conditions for PhotoScan, and 13 conditions for Pix4D. Moreover, the RMSE and rRMSE values of the estimated tree height were 5–6 m and 20–28%, respectively. Although the estimation accuracy of any SfM was low, the estimated tree height by Pix4D in many flight conditions had smaller RMSE values than the other software. As statistically significant differences were found between the SfMs in many flight conditions, we conclude that there were differences in the estimates of crown area and tree height depending on the SfM used. In addition, Pix4Dmapper is suitable for estimating forest information, such as tree height, and PhotoScan is suitable for detailed monitoring of disaster areas.

Evaluating Feature Extraction Methods with Synthetic Noise Patterns for Image-Based Modelling of Texture-Less Objects

Image-based three-dimensional (3D) reconstruction is a process of extracting 3D information from an object or entire scene while using low-cost vision sensors. A structure-from-motion coupled with multi-view stereo (SFM-MVS) pipeline is a widely used technique that allows 3D reconstruction from a collection of unordered images. The SFM-MVS pipeline typically comprises different processing steps, including feature extraction and feature matching, which provide the basis for automatic 3D reconstruction. However, surfaces with poor visual texture (repetitive, monotone, etc.) challenge the feature extraction and matching stage and affect the quality of reconstruction. The projection of image patterns while using a video projector during the image acquisition process is a well-known technique that has been shown to be successful for such surfaces. In this study, we evaluate the performance of different feature extraction methods on texture-less surfaces with the application of synthetically generated noise patterns (images). Seven state-of-the-art feature extraction methods (HARRIS, Shi-Tomasi, MSER, SIFT, SURF, KAZE, and BRISK) are evaluated on problematic surfaces in two experimental phases. In the first phase, the 3D reconstruction of real and virtual planar surfaces evaluates image patterns while using all feature extraction methods, where the patterns with uniform histograms have the most suitable morphological features. The best performing pattern from Phase One is used in Phase Two experiments in order to recreate a polygonal model of a 3D printed object using all of the feature extraction methods. The KAZE algorithm achieved the lowest standard deviation and mean distance values of 0.0635 mm and −0.00921 mm, respectively.

Linking the Remote Sensing of Geodiversity and Traits Relevant to Biodiversity—Part II: Geomorphology, Terrain and Surfaces

The status, changes, and disturbances in geomorphological regimes can be regarded as controlling and regulating factors for biodiversity. Therefore, monitoring geomorphology at local, regional, and global scales is not only necessary to conserve geodiversity, but also to preserve biodiversity, as well as to improve biodiversity conservation and ecosystem management. Numerous remote sensing (RS) approaches and platforms have been used in the past to enable a cost-effective, increasingly freely available, comprehensive, repetitive, standardized, and objective monitoring of geomorphological characteristics and their traits. This contribution provides a state-of-the-art review for the RS-based monitoring of these characteristics and traits, by presenting examples of aeolian, fluvial, and coastal landforms. Different examples for monitoring geomorphology as a crucial discipline of geodiversity using RS are provided, discussing the implementation of RS technologies such as LiDAR, RADAR, as well as multi-spectral and hyperspectral sensor technologies. Furthermore, data products and RS technologies that could be used in the future for monitoring geomorphology are introduced. The use of spectral traits (ST) and spectral trait variation (STV) approaches with RS enable the status, changes, and disturbances of geomorphic diversity to be monitored. We focus on the requirements for future geomorphology monitoring specifically aimed at overcoming some key limitations of ecological modeling, namely: the implementation and linking of in-situ, close-range, air- and spaceborne RS technologies, geomorphic traits, and data science approaches as crucial components for a better understanding of the geomorphic impacts on complex ecosystems. This paper aims to impart multidimensional geomorphic information obtained by RS for improved utilization in biodiversity monitoring.

Comparison of Spectral Reflectance-Based Smart Farming Tools and a Conventional Approach to Determine Herbage Mass and Grass Quality on Farm

The analysis of multispectral imagery (MSI) acquired by unmanned aerial vehicles (UAVs) and mobile near-infrared reflectance spectroscopy (NIRS) used on-site has become increasingly promising for timely assessments of grassland to support farm management. However, a major challenge of these methods is their calibration, given the large spatiotemporal variability of grassland. This study evaluated the performance of two smart farming tools in determining fresh herbage mass and grass quality (dry matter, crude protein, and structural carbohydrates): an analysis model for MSI (GrassQ) and a portable on-site NIRS (HarvestLabTM 3000). We compared them to conventional look-up tables used by farmers. Surveys were undertaken on 18 multi-species grasslands located on six farms in Switzerland throughout the vegetation period in 2018. The sampled plots represented two phenological growth stages, corresponding to an age of two weeks and four to six weeks, respectively. We found that neither the performance of the smart farming tools nor the performance of the conventional approach were satisfactory for use on multi-species grasslands. The MSI-model performed poorly, with relative errors of 99.7% and 33.2% of the laboratory analyses for herbage mass and crude protein, respectively. The errors of the MSI-model were indicated to be mainly caused by grassland and environmental characteristics that differ from the relatively narrow Irish calibration dataset. The On-site NIRS showed comparable performance to the conventional Look-up Tables in determining crude protein and structural carbohydrates (error ≤ 22.2%). However, we identified that the On-site NIRS determined undried herbage quality with a systematic and correctable error. After corrections, its performance was better than the conventional approach, indicating a great potential of the On-site NIRS for decision support on grazing and harvest scheduling.

Accuracy of 3D Landscape Reconstruction without Ground Control Points Using Different UAS Platforms

The rapid increase of low-cost consumer-grade to enterprise-level unmanned aerial systems (UASs) has resulted in the exponential use of these systems in many applications. Structure from motion with multiview stereo (SfM-MVS) photogrammetry is now the baseline for the development of orthoimages and 3D surfaces (e.g., digital elevation models). The horizontal and vertical positional accuracies (x, y and z) of these products in general, rely heavily on the use of ground control points (GCPs). However, for many applications, the use of GCPs is not possible. Here we tested 14 UASs to assess the positional and within-model accuracy of SfM-MVS reconstructions of low-relief landscapes without GCPs ranging from consumer to enterprise-grade vertical takeoff and landing (VTOL) platforms. We found that high positional accuracy is not necessarily related to the platform cost or grade, rather the most important aspect is the use of post-processing kinetic (PPK) or real-time kinetic (RTK) solutions for geotagging the photographs. SfM-MVS products generated from UAS with onboard geotagging, regardless of grade, results in greater positional accuracies and lower within-model errors. We conclude that where repeatability and adherence to a high level of accuracy are needed, only RTK and PPK systems should be used without GCPs.