Amoeba: Automated Molecular Excitation Bayesian Line-fitting Algorithm

The hyperfine transitions of the ground-rotational state of the hydroxyl radical (OH) have emerged as a versatile tracer of the diffuse molecular interstellar medium. We present a novel automated Gaussian decomposition algorithm designed specifically for the analysis of the paired on-source and off-source optical depth and emission spectra of these OH transitions. In contrast to existing automated Gaussian decomposition algorithms, Amoeba (Automated Molecular Excitation Bayesian line-fitting Algorithm) employs a Bayesian approach to model selection, fitting all four optical-depth and four emission spectra simultaneously. Amoeba assumes that a given spectral feature can be described by a single centroid velocity and full width at half maximum, with peak values in the individual optical-depth and emission spectra then described uniquely by the column density in each of the four levels of the ground-rotational state, thus naturally including the real physical constraints on these parameters. Additionally, the Bayesian approach includes informed priors on individual parameters that the user can modify to suit different data sets. Here we describe Amoeba and establish its validity and reliability in identifying and fitting synthetic spectra with known (but hidden) parameters, finding that the code performs very well in a series of practical tests. Amoeba’s core algorithm could be adapted to the analysis of other species with multiple transitions interconnecting shared levels (e.g., the 700 MHz lines of the first excited rotational state of CH). Users are encouraged to adapt and modify Amoeba to suit their own use cases.

Updates to LUCI: A New Fitting Paradigm Using Mixture Density Networks

LUCI is an general-purpose spectral line-fitting pipeline which natively integrates machine learning algorithms to initialize fit functions. LUCI currently uses point-estimates obtained from a convolutional neural network (CNN) to inform optimization algorithms; this methodology has shown great promise by reducing computation time and reducing the chance of falling into a local minimum using convex optimization methods. In this update to LUCI, we expand upon the CNN developed in Rhea et al. so that it outputs Gaussian posterior distributions of the fit parameters of interest (the velocity and broadening) rather than simple point-estimates. Moreover, these posteriors are then used to inform the priors in a Bayesian inference scheme, either emcee or dynesty. The code is publicly available at crhea93:LUCI (https://github.com/crhea93/LUCI).

Accurate Morphology Characterization Using Atomic Force Microscopy via Vertical Drift Correction and Illusory Slope Elimination

Thanks to the ability to perform imaging and manipulation at the nanoscale, atomic force microscopy (AFM) has been widely used in biology, materials, chemistry, and other fields. However, as common error sources, vertical drift and illusory slope severely impair AFM imaging quality. To address this issue, this paper proposes a robust algorithm to synchronously correct the image distortion caused by vertical drift and slope, thus achieving accurate morphology characterization. Specifically, to eliminate the damage of abnormal points and feature areas on the correction accuracy, the laser spot voltage error acquired in the AFM scanning process is first utilized to preprocess the morphology height data of the sample, so as to obtain the refined alternative data suitable for line fitting. Subsequently, this paper proposes a novel line fitting algorithm based on sparse sample consensus, which accurately simulates vertical drift and slope in the cross-sectional profile of the topographic image, thereby achieving effective correction of the image distortion. In the experiments and applications, a nanoscale optical grating sample and a biological cell sample are adopted to perform topography imaging and distortion correction, so as to verify the ability of the proposed algorithm to promote AFM imaging quality.

Least Squares Adjustment with a Rank-Deficient Weight Matrix and Its Applicability to Image/Lidar Data Processing

This article proposes a solution to special least squares adjustment (LSA) models with a rank-deficient weight matrix, which are commonly encountered in geomatics. The two sources of rank deficiency in weight matrices are discussed: naturally occurring due to the inherent characteristics of LSA mathematical models and artificially induced to eliminate nuisance parameters from LSA estimation. The physical interpretation of the sources of rank deficiency is demonstrated using a case study to solve the problem of 3D line fitting, which is often encountered in geomatics but has not been addressed fully to date. Finally, some geomatics-related applications—mobile lidar system calibration, point cloud registration, and single-photo resection—are discussed along with respective experimental results, to emphasize the need to assess LSA models and their weight matrices to draw inferences regarding the effective contribution of observations. The discussion and results demonstrate the vast applications of this research in geomatics as well as other engineering domains.

A Novel coarse-to-fine Localization Algorithm for Automated Vickers Hardness Measurement

Vickers hardness testing is one of the most useful methods to determine the hardness of materials. To calculate the hardness of materials, the key is to measure the diagonal length of the Vickers indentation on the surface accurately. However, since this length is extremely minuscule, there are many challenges to achieve accurate measurement. Especially, when the indentation corner is cracked, the precise position of the corner cannot be obtained by conventional methods. In this paper, we proposed a method of coarse-to-fine localization to accurately locate the indentation corner. The coarse localization process can be used to determine the position and size of the indentation. During fine localization, the linear equations of the indentation edges are calculated by the line fitting method. The capabilities of the proposed method are compared to manual measurement and results are presented.

ChainLineNet: Deep-Learning-Based Segmentation and Parameterization of Chain Lines in Historical Prints

The paper structure of historical prints is sort of a unique fingerprint. Paper with the same origin shows similar chain line distances. As the manual measurement of chain line distances is time consuming, the automatic detection of chain lines is beneficial. We propose an end-to-end trainable deep learning method for segmentation and parameterization of chain lines in transmitted light images of German prints from the 16th Century. We trained a conditional generative adversarial network with a multitask loss for line segmentation and line parameterization. We formulated a fully differentiable pipeline for line coordinates’ estimation that consists of line segmentation, horizontal line alignment, and 2D Fourier filtering of line segments, line region proposals, and differentiable line fitting. We created a dataset of high-resolution transmitted light images of historical prints with manual line coordinate annotations. Our method shows superior qualitative and quantitative chain line detection results with high accuracy and reliability on our historical dataset in comparison to competing methods. Further, we demonstrated that our method achieves a low error of less than 0.7 mm in comparison to manually measured chain line distances.

Intelligent Measurement of Morphological Characteristics of Fish Using Improved U-Net

In the smart mariculture, batch testing of breeding traits is a key issue in the breeding of improved fish varieties. The body length (BL), body width (BW) and body area (BA) features of fish are important indicators. They are of great significance in breeding, feeding and classification. To accurately and intelligently obtain the morphological characteristic sizes of fish in actual scenes, data augmentation is first used to greatly expand the published fish dataset, thereby ensuring the robustness of the training model. Then, an improved U-net segmentation and measurement algorithm is proposed, which uses a dilated convolution with a dilation rate 2 and a convolution to partially replace the convolution in the original U-net. This operation can enlarge the partial convolution receptive field and achieve more accurate segmentation for large targets in the scene. Finally, a line fitting method based on the least squares method is proposed, which is combined with the body shape features of fish and can accurately measure the BL and BW of inclined fish. Experimental results show that the Mean Intersection over Union (mIoU) is 97.6% and the average relative error of the area is 0.69%. Compared with the unimproved U-net, the average relative error of the area is reduced to about half. Moreover, with the improved U-net and the line fitting method, the average relative error of BL and the average relative error of BW of inclined fish decrease to 0.37% and 0.61%, respectively.