Tuesday, December 16. 2014NMO with super resolution
Another old paper is added to the collection of reproducible documents:
A prospect for super resolution Wouldn't it be great if I could take signals of 1030 Hz bandwidth from 100 different offsets and construct a zerooffset trace with 5100 Hz bandwidth? This would not violate Shannon's sampling theorem which theoretically allows us to have a transform from 100 signals of 20 Hz bandwidth to one signal at 2000 Hz bandwidth. The trouble is that simple NMO is not such a transformation. Nevertheless, if the different offsets really did give us any extra information, we should be able to put the information into extra bandwidth. Let us consider noise free synthetic data and see if we can come up with a model where this could happen. Wednesday, December 10. 2014Earthquake stacks
Another old paper is added to the collection of reproducible documents:
Earthquake stacks at constant offset I show Shearer's earthquake stacks over all sourcereceiver locations at constant offset and compare them to exploration seismic data. This electronic document simply reads the stacks and plots them. Sunday, December 7. 2014TXY adaptive filtering for random noise attenuation
A new paper is added to the collection of reproducible documents:
Adaptive prediction filtering in txy domain for random noise attenuation using regularized nonstationary autoregression Many natural phenomena, including geologic events and geophysical data, are fundamentally nonstationary. They may exhibit stationarity on a short timescale but eventually alter their behavior in time and space. We propose a 2D tx adaptive prediction filter (APF) and further extend this to a 3D txy version for random noise attenuation based on regularized nonstationary autoregression (RNA). Instead of using patching, a popular method for handling nonstationarity, we obtain smoothly nonstationary APF coefficients by solving a global regularized leastsquares problem. We use shaping regularization to control the smoothness of the coefficients of APF. 3D spacenoncausal txy APF uses neighboring traces around the target traces in the 3D seismic cube to predict noisefree signal, so it provides more accurate prediction results than the 2D version. In comparison with other denoising methods, such as frequencyspace deconvolution, timespace prediction filter, and frequencyspace RNA, we test the feasibility of our method in reducing seismic random noise on three synthetic datasets. Results of applying the proposed method to seismic field data demonstrate that nonstationary txy APF is effective in practice. This reproducible paper is the first direct contribution from Jilin University, China. Friday, December 5. 2014SCons is “Community Choice” Project of the Month
The favorite tool of all Madagascar users, SCons, is featured as the December 2014 “Community Choice” Project of the Month at SourceForge.
SCons is a software construction tool (build tool, or make tool) implemented in Python, which uses Python scripts as “configuration files” for software builds. It is an easier, more reliable, and faster way to build software, solving a number of problems associated with other build tools, especially including the classic and ubiquitous make itself. Back in 2006, when Madagascar became an opensource project, SourceForge was the dominant platform for such projects. Since then, it has remained a highly useful resource but has lost its popularity to GitHub. Madagascar developers have not yet seen a compelling need to migrate the Madagascar repository from SourceForge to GitHub or to switch from Subversion (SVN) to Git, but will keep all options open. Wednesday, December 3. 2014TX AMO
Another old paper is added to the collection of reproducible documents:
The time and space formulation of azimuth moveout Azimuth moveout (AMO) transforms 3D prestack seismic data from one common azimuth and offset to different azimuths and offsets. AMO in the timespace domain is represented by a threedimensional integral operator. The operator components are the summation path, the weighting function, and the aperture. To determine the summation path and the weighting function, we derive the AMO operator by cascading dip moveout (DMO) and inverse DMO for different azimuths in the timespace domain. To evaluate the aperture, we apply a geometric approach, defining AMO as the result of cascading prestack migration (inversion) and modeling. The aperture limitations provide a consistent description of AMO for small azimuth rotations (including zero) and justify the economic efficiency of the method. Wednesday, November 26. 2014Madagascar Virtual Machine Released
As an alternative to installing Madagascar, you can now run a Crunchbang (Debian) virtual machine (VM) with it preinstalled. Just download, unzip, and run the file with Oracle VirtualBox (free software). Detailed instructions for running the VM for the first time or installing VirtualBox can be found in the readme.
Downloads: README.txt MadagascarVM.zip (~3.0 GB) MadagascarVM.7z (~2.1 GB, but requires 7zip to unpack) Wednesday, November 19. 2014Talitrus saltator
In the excellent reproducible science tutorial at SciPy2014, a reproducible data processing example involved segmenting the eye in an image of Talitrus saltator.
The example is reproduced, with modifications, in rsf/tutorials/talitrus. Madagascar users are encouraged to try improving the results. Thursday, November 13. 2014Madagascar school in Harbin
A Madagascar school will take place on January 78, 2015, in Harbin, China, and will be hosted by the Harbin Institute of Technology (HIT) in conjunction with the International Workshop on Mathematical Geophysics.
More information will be available soon on the school webpage. Wednesday, November 12. 2014Program of the month: sfthreshold
sfthreshold filters the input by soft thresholding (shrinkage).
Soft thresholding is a pointbypoint operation, which can be described mathematically as $\begin{array}{cc}\phantom{\rule{6.0em}{0ex}}& {T}_{\mu}\left[u\right]=\{\begin{array}{ccc}\hfill u\mu \phantom{\rule{0.167em}{0ex}}\text{sign}\left(u\right)& \hfill \phantom{\rule{1.00em}{0ex}}\hfill & \text{if}\phantom{\rule{0.278em}{0ex}}\leftu\right>\mu \hfill \\ \hfill 0& \hfill \phantom{\rule{1.00em}{0ex}}\hfill & \text{if}\phantom{\rule{0.278em}{0ex}}\leftu\right\le \mu \hfill \end{array}\phantom{\}}\hfill \end{array}$ Soft thresholding was analyzed by Donoho (1995) and became particularly popular thanks to the iterative shrinkagethresholding algorithm by Daubechies et al. (2004). Donoho, D. L. (1995). Denoising by softthresholding. Information Theory, IEEE Transactions on, 41(3), 613627. Daubechies, I., Defrise, M., & De Mol, C. (2004). An iterative thresholding algorithm for linear inverse problems with a sparsity constraint. Communications on pure and applied mathematics, 57(11), 14131457. The following example from tccs/seislet/lena shows an image (Seismic Lena) and its reconstruction after soft thresholding in the seislet domain using 5% thresholding (pclip=5). sfthreshold uses percentage parameter pclip= to set thresholding at the corresponding quantile of the data values. To do soft or hard thresholding with a fixed threshold, use sfthr. An alternative thresholdinglike operation is provided by sfsharpen. 10 previous programs of the month:Seismic data analysis using SSWT
A new paper is added to the collection of reproducible documents:
Timefrequency analysis of seismic data using synchrosqueezing wavelet transform Timefrequency (TF) decomposition is used for characterizing the nonstationary relation between time and instantaneous frequency, which is very important in the processing and interpretation of seismic data. The conventional timefrequency analysis approaches suffer from the contradiction between time resolution and frequency resolution. A new timefrequency analysis approach is proposed based on the synchrosqueezing wavelet transform (SSWT). The SSWT is an empiricalmodedecompositionlike tool but uses a different approach in constructing the components. With the help of the synchrosqueezing techniques, the SSWT can obtain obvious higher time and frequency resolution. Synthetic examples show that the SSWT based TF analysis can exactly capture the variable frequency components. Field data tests show the potential of the proposed approach in detecting anomalies of highfrequency attenuation and detecting the deeplayer weak signal. Monday, November 10. 2014Deblending using NMO median filtering
A new paper is added to the collection of reproducible documents:
Deblending using normal moveout and median filtering in commonmidpoint gathers The benefits of simultaneous source acquisition are compromised by the challenges of dealing with intense blending noise. In this paper, we propose a processing workflow for blended data. The incoherent property of blending noise in the commonmidpoint (CMP) gathers is utilized for applying median filtering along the spatial direction after normal moveout (NMO) correction. The key step in the proposed workflow is that we need to obtain a precise velocity estimation which is required by the subsequent NMO correction. Because of the intense blending noise, the velocity scan can not be obtained in one step. We can recursively polish both deblended result and velocity estimation by deblending using the updated velocity estimation and velocity scanning using the updated deblended result. We use synthetic and field data examples to demonstrate the performance of the proposed approach. The migrated image of deblended data is cleaner than that of blended data, and is similar to that of unblended data. Journals unite for reproducibility
Simultaneous editorials in Science and Nature state
Reproducibility, rigour, transparency and independent verification are cornerstones of the scientific method. Of course, just because a result is reproducible does not make it right, and just because it is not reproducible does not make it wrong. A transparent and rigorous approach, however, will almost always shine a light on issues of reproducibility. This light ensures that science moves forward, through independent verifications as well as the course corrections that come from refutations and the objective examination of the resulting data. The editorials describe Proposed Principles and Guidelines for Reporting Preclinical Research developed this summer and endorsed by dozens of leading scientific journals publishing in the field of biomedical research. The guidelines focus on the issue of reproducibility of scientific experiments and include provisions for sharing data and software. Nature explains its software sharing policy further in the following statement: Nature and the Nature journals have decided that, given the diversity of practices in the disciplines we cover, we cannot insist on sharing computer code in all cases. But we can go further than we have in the past, by at least indicating when code is available. Accordingly, our policy now mandates that when code is central to reaching a paper’s conclusions, we require a statement describing whether that code is available and setting out any restrictions on accessibility. Editors will insist on availability where they consider it appropriate: any practical issues preventing code sharing will be evaluated by the editors, who reserve the right to decline a paper if important code is unavailable. These changes in publication policies by the leading scientific journals may lead to a fundamental change in scientific standards for reproducibility of computational experiments in different fields. See also:
Sunday, November 9. 2014Robust timetodepth conversion
A new paper is added to the collection of reproducible documents:
A robust approach to timetodepth conversion and interval velocity estimation from time migration in the presence of lateral velocity variations The problem of conversion from timemigration velocity to an interval velocity in depth in the presence of lateral velocity variations can be reduced to solving a system of partial differential equations. In this paper, we formulate the problem as a nonlinear leastsquares optimization for seismic interval velocity and seek its solution iteratively. The input for inversion is the Dix velocity which also serves as an initial guess. The inversion gradually updates the interval velocity in order to account for lateral velocity variations that are neglected in the Dix inversion. The algorithm has a moderate cost thanks to regularization that speeds up convergence while ensuring a smooth output. The proposed method should be numerically robust compared to the previous approaches, which amount to extrapolation in depth monotonically. For a successful timetodepth conversion, imageray caustics should be either nonexistent or excluded from the computational domain. The resulting velocity can be used in subsequent depthimaging model building. Both synthetic and field data examples demonstrate the applicability of the proposed approach. Wednesday, October 22. 2014Tutorial on parameter testing
The example in rsf/tutorials/parameters reproduces the tutorial from Matt Hall on parameter testing.
Madagascar users are encouraged to try improving the results. In his blog post and in the discussion that follows, Matt brings up an interesting question about finding the best way for parameter selection. For the lack of a better approach, parameter selection in seismic attributes is just an interactive game. In the Madagascar version, the key parameter for the Canny edge detector is the amount of prior anisotropicdiffusion smoothing, controlled by the smoothing radius (rect= parameter.) We can do different things with it: for example, make a movie of different images looping through different values of the radius, or, by exposing the parameter to the commandline SCons interface, build a simple GUI script for controlling it. The question posted by Matt waits for a better answer. See also: Saturday, October 18. 2014Tutorial on colormaps
The example in rsf/tutorials/colormaps reproduces the tutorial from Matteo Niccoli on how to evaluate and compare color maps. The tutorial was published in the August 2014 issue of The Leading Edge.
Madagascar users are encouraged to try improving the results. See also:
Several new color palettes have been recently added to Madagascar (thanks to Aaron Stanton): color=seismic (redyellowwhiteblack, popular among seismic interpreters), color=owb (orangewhiteblack), and color=rwb (redwhiteblack).
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