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Monday
Jul162012

Wiki maniacs unite

Last year, we decided to go to at least one non-geoscience conference every year. The idea is to meet other communities, learn about other fields, have some new ideas, and find more ways to be useful. So far, Evan and I have been to symposiums on mathematics, geothermal energy, being more awesome, and science online. Continuing in this vein, I just got home from Wikimania 2012 — the international conference about all things wiki.

Strictly speaking, Wikimania is about the Wikimedia movement, the global effort to "give to every single person on the planet free access to the sum of all human knowledge". This quest is supported by the Wikimedia Foundation, a non-profit organization of professional enthusiasts. Their most conspicuous project is Wikipedia, but it's far from being the only one. Have you heard of Wikimedia Commons? Wikisource? Wikibooks? Read all about them.

The conference was unlike anything I've ever been to. Despite attracting over 950 delegates, it felt more like a meeting of colleagues and friends than a conference of professionals and strangers. I've never felt such a strong undertow of common purpose, and quiet, deliberate action. The phrase intentional community was made for this group.

In short, Wikipedia looks even more awesome from the inside than it does from the outside.

If you too are a Wikipedia enthusiast, here are some things I learned:

  • The number of active editors has fallen by 4000 since 2011, to 85k
  • During the conference, the number of articles in English Wikipedia passed 4 million
  • Developers are working hard to make Wikipedia easier to edit, and big changes are coming
  • Wikipedia Zero is an important effort to make the site available to everyone
  • Developers are working on making Wikipedia available via SMS and other channels
  • Wikis—both private and public—are everywhere: schools, museums, libraries, galleries, academia, government, societies, and corporations

Next time, I'll list a few ways you can get more involved.

The photo is from Wikimedia Commons, licensed CC-BY-SA by User:Awersowy

Tuesday
Jul102012

Fabric facies

I set out to detect patterns in images, with the conviction that they are diagnostic of more telling physical properties of the media. Tea towel textures can indicate absorbency, durability, state of wear and tear, etc. Seismic textures can indicate things like depositional environment, degree of deformation, lithologic content, and so on:

Facies: A rock or stratified body distinguished from others by its appearance or composition.

Facies are clusters distinguishable in all visual media. Geophysicists shouldn't be afraid of using the word normally reserved by geologists—seismic facies. In the seismic case, instead of lithology, grain size, bedding patterns, and so on, we are using attributes such as amplitude, energy, coherency, and Haralick textures for classification.

The brain is good at pattern recognition and picking out subtleties. I can assign facies to the input data (A), based on on hues (B), or patterns (C). I can also count objects (D), interpret boundaries (E), and identify poorly resolved regions of an image (F) caused by shadows or noise. I can even painstakingly draw the pockmarks or divets in the right hand teatowel (G). All of these elements can be simultaneously held in the mind of the viewer and comprise what we naturally perceive as the properties of visual media. Isolating, extracting, and illustrating these visual features by hand remains tedious.

I am not interested in robot vision so computers can replace geophysical interpreters, but I am interested in how image classification can be used to facilitate, enrich, and expedite the interpretive process. You can probably already think of attributes we can use to coincide with this human interpretation from the examples I gave in a previous post.

Identifying absorbency

Let's set an arbitrary goal of classifying the ability to soak up water, or absorbency. Surely a property of interest to anyone studying porous media. Because absorbency is a media-property, not an optical property (like colour) or a boundary property (like edges), it makes sense to use texture classification. From the input image, I can count 5 different materials, each with a distinct pattern. The least tractable might be the rightmost fabric which has alternating waffle-dimple segments, troublesome shadows and contours, and patterns at two different scales. The test of success is seeing how this texture classification compares to the standard approach of visual inspection and manual picking. 

I landed on using 7 classes for this problem. Two for the white tea-towels, two for the green tea-towel, one for the blue, and one that seems to be detecting shadows (shown in dark grey). Interestingly, the counter top on the far left falls into the same texture class as the green tea-towel. Evidence that texture alone isn't a foolproof proxy for absorbency. To improve the classification, I would need to allow more classes (likely 8 or 9). 

It seems to me that the manual picks match the classification quite well. The picks lack detail, as with any interpretation, but they also lack noise. On the contrary, there are some locations where the classification has failed. It stuggles in low-light and over-exposed regions. 

If you are asking, "is one approach better than the other?", you are asking the wrong question. These are not mutually exclusive approaches. The ideal scenario is one which uses these methods in concert for detecting geologic features in the fabric of seismic data. 

Thursday
Jul052012

Fabric clusters

There are many reasons we might want to use cluster analysis in our work. Geologists might want to sort hundreds of rock samples into a handful of rock types, a petrophysicist might want to group data points from well logs (as shown here), or a curious kitchen dweller may want to digitally classify patterns found in his (or her) linen collection.

Two algorithms worth knowing about when faced with any clustering problem are called k-means and fuzzy c-means clustering. They aren't the right solution for all clustering problems, but they are a good place to start.

k-means clustering — each data point gets assigned to one of k centroids (or centres) according to the centroid it is closest to. In the image shown here, the number of clusters is 2. The pink dots are closest to the left centroid, and the black dots are closest to the right centroid. To see how the classification is done, watch this short step-by-step video. The main disadvantage with this method is that if the clusters are poorly defined, the result seems rather arbitrary.

Fuzzy c-means clustering — each data point belongs to all clusters, but only to a certain degree. Each data point is assigned a probability of belonging to each cluster, and is thus easily assigned the class for which it has a highest probability. If a data point is midway between two clusters, it is still assigned to its closest cluster, but with lower probability. As the bottom image shows, data points on the periphery of cluster groups, such as those shown in grey may be equally likely to belong to both clusters. Fuzzy c-means clustering provides a way of capturing quantitative uncertainty, and even visualizing it.

Some observations fall naturally into clusters. It is just a matter of the observer choosing an adequate combination of attributes to characterize them. In the fabric and seismic examples shown in the previous post, only two of the four Haralick textures are needed to show a diagnostic arrangement of the data for clustering. Does the distribution of these thumbnail sections in the attribute space align with your powers of visual inspection? 

Friday
Jun292012

Fabric textures

Beyond the traditional, well-studied attributes that I referred to last time, are a large family of metrics from image processing and robot vision. The idea is to imitate the simple pattern recognition rules our brains intuitively and continuously apply when we look at seismic data: how do the data look? How smooth or irregular are the reflections? If you thought the adjectives I used for my tea towels were ambiguous, I assure you seismic will be much more cryptic.

In three-dimensional data, texture is harder to see, difficult to draw, and impossible to put on a map. So when language fails us, discard words altogether and use numbers instead. While some attributes describe the data at a particular place (as we might describe a photographic pixel as 'red', 'bright', 'saturated'), other attributes describe the character of the data in a small region or kernel ('speckled', 'stripy', 'blurry').

Texture by numbers

I converted the colour image from the previous post to a greyscale image with 256 levels (a bit-depth of 8) to match this notion of scalar seismic data samples in space. The geek speak is that I am computing local grey-level co-occurence matrices (or GLCMs) in a moving window around the image, and then evaluating some statistics of the local GLCM for each point in the image. These statistics are commonly called Haralick textures. Choosing the best kernel size will depend on the scale of the patterns. The Haralick textures are not particularly illustrative when viewed on their own but they can be used for data clustering and classification, which will be the topic of my next post.

  • Step 1: Reduce the image to 256 grey-levels
  • Step 2: For every pixel, compute a co-occurrence matrix from a p by q kernel (p, q = 15 for my tea towel photo)
  • Step 3: For every pixel, compute the Haralick textures (Contrast, Correlation, Energy, Homogeneity) from the GLCM

Textures in seismic data

Here are a few tiles of seismic textures that I have loosely labeled as "high-amplitude continous", "high-amplitude discontinuous", "low-amplitude continuous", etc. You certainly might choose different words to describe them, but each has a unique and objective set of Haralick textures. I have explicitly represented the value of each's texture as a color; using cyan for contrast, magenta for correlation, yellow for energy, and black for homogeneity. Thus, the four Haralick textures span the CMYK color space. Merging these components back together into a single color gives you a sense of the degree of difference across the tiles. For instance, the high-amplitude continuous tile, is characterized by high contrast and high energy, but low correlation, relative to the low-amplitude continuous tile. Their textures are similar, so obviously, they map to similar color values in CMYK color space. Whether or not they are truly discernable is the challenge we offer to data clustering; be it employed by visual inspection or computational force.

Further reading:
Gao, D., 2003, Volume texture extraction for 3D seismic visualization and interpretation, Geophysics, 64, No. 4, 1294-1302
Haralick, R., Shanmugam, K., and Dinstein, I., 1973, Textural features for image classification: IEEE Tran. Systems, Man, and Cybernetics, SMC-3, 610-621.
Mryka Hall-Beyer has a great tutorial at http://www.fp.ucalgary.ca/mhallbey/tutorial.htm for learning more about GLCMs.
Images in this post were made using MATLAB, FIJI and Inkscape.

Thursday
Jun212012

Fabric attributes

The catch-all term seismic interpretation, often used to refer to the labour of digitizing horizons and faults, is almost always spatially constrained. Picking seismic line-by-line means collapsing complex 3D patterns and volumes onto 2D maps and surfaces. It hurts me to think about what we are discarding. Take a second and imagine looking at a photograph one row of pixels at a time. So much is lost in the simplification.

Attributes, on the other hand, can either quantify the nature of a horizon, probe between horizons, or characterize an entire 3D space. Single-trace attributes can tell us about waveform shape and magnitude which allegedly responds to true physical impedance contrasts. Multi-trace attributes (coherency, curvature, etc.) pull information from neighbouring traces.

The fabric test model

In a spirited act of geeky indulgence, I went to my linen closest, grabbed some tea towels, pulled out my phone (obviously), and captured this scene. A set of four folded tea towels overlapping and spread across my counter top—reverse engineering what I thought to be a suitable analogy for training my seismic inutition. The left (blue) tea towel is a honeycomb texture, the second (green) is speckled like a wash cloth, the third is a high thread-count linen, and the fourth has a grid of alternating cross-hatches and plain print. Don't laugh! It turns out to be quite difficult to verbally describe the patterns in these fabrics. Certainly, you will describe them differently to me, and that is the problem. 

Perhaps image processing can transcend our linguistic limitations. In seismic, as in image processing in general, there are attributes that work on each sample (or trace) independently, and there are attributes that use an ensemble of neighbouring samples in their computation. See if you can think a seismic analogy in the for each of these image attributes.

  • Spectral decomposition shows the component of the RGB color spectrum at each sample location. I subsequently clipped and enhanced the red panel to show curves, wrinkles and boundaries caused by the interplay of light, shadows, and morphology.
  • Spectral filtering extracts or removes hues. In this instance, I have selected all the color triplets that make up the blue tea towel. You could also select a range to say, show where the shadows are.
  • Edge detection, after smoothing, shows sharp edges in white and yellow, soft edges in purple and blue. The wrinkles and subtle folds on the right most fabric have also been detected. 

My question: can you manually draw the morphology, or the blues, or the edges and discontinuities? Manual interpretation is time consuming, prone to error, seldom reproducible, and that makes it flawed. Furthermore, none of these attributes actually tell us about the nature of the textures in the fabric. Indeed, we don't know if any of them are relevant at all. Colour happens to be one proxy for texture in this case, but it fails in delineating the two whitish fabrics.

Artistically and computationally speaking, I submit to you that seismic data are nothing but images. In the next post I will extend this fabric-photograph model to explore the utility of textural attributes. 

Theses images were made using the open source FIJI and the illustrations were done in Inkscape. The attributes were computed in MATLAB and FIJI.