Mild or wild: robustness through morphological filtering

This guest post (first published here) is by Elwyn Galloway, author of Scibbatical on WordPress. It is the forth in our series of collaborative articles about sketch2model, a project from the 2015 Calgary Geoscience Hackathon organized by Agile Geoscience. Happy reading.

 

We’re highlighting a key issue that came up in our project, and describing what how we tackled it. Matteo’s post on Morphological Filtering does a great job of explaining what we implemented in sketch2model. I’ll build on his post to explain the why and how. In case you need a refresher on sketch2model, look back at sketch2model, Sketch Image Enhancement, Linking Edges with Geomorphological Filtering.

Morphological Filtering

As Matteo demonstrated by example, sketch2model’s ability to segment a sketch properly depends on the fidelity of a sketch.

fill_before_after_closing

An image of a whiteboard sketch (left) divides an area into three sections. Without morphological filtering, sketch2model segments the original image into two sections (identified as orange, purple) (centre). The algorithm correctly segments the area into three sections (orange, purple, green) when morphological filtering is applied (right).

To compensate for sketch imperfections, Matteo suggested morphological filtering on binarized images. Morphological filtering is a set of image modification tools which modify the shape of elements in an image. He suggested using the closing tool for our purposes. Have a look at Matteo’s Post for insight into this and other morphological filters.

One of the best aspects of this approach is that it is simple to apply. There is essentially one parameter to define: a structuring element. Since you’ve already read Matteo’s post, you recall his onion analogy explaining the morphological filtering processes of erosion and dilation – erosion is akin to removing an onion layer, dilation is adding a layer on. You’ll also recall that the size of the structuring element is the thickness of the layer added to, or removed from, the onion. Essentially, the parameterization of this process comes down to choosing the thickness of the onion layers.

Sketch2model uses dilation followed by erosion to fill gaps left between sketch lines (morphological dilation followed by erosion is closing). Matteo created this really great widget to illustrate closing using an interactive animation.

closing_demo1

Matteo’s animation was created using this interactive Jupyter notebook. Closing connects the lines of the sketch.

Some is Good, More is Better?

Matteo showed that closing fails if the structural element used is too small. So just make it really big, right? Well, there can be too much of a good thing. Compare what happens when you use an appropriately sized structuring element (mild) to the results from an excessively large structuring element (wild).

over-morph filtering.png

Comparing the results of mild and wild structuring elements: if the structuring element is too large, the filter compromises the quality of the reproduction.

Using a morphological filter with a structural element that is too small doesn’t fix the sketches, but using a structural element that is too large compromises the sketch too. We’re left to find an element that’s just right. Since one of the priorities for sketch2model was to robustly handle a variety of sketches with as little user input as possible — marker on whiteboard, pencil on paper, ink on napkin — we were motivated to find a way to do this without requiring the user to select the size of the structuring element.

Is there a universal solution? Consider this: a sketch captured in two images, each with their own resolution. In one image, the lines of the sketch appear to be approximately 16 pixels wide. The same lines appear to be 32 pixels wide in the other image. Since the size of the structuring element is defined in terms of pixels, it becomes apparent the ideal structuring element cannot be “one size fits all”.

res_vs_res

High-resolution (left) versus low-resolution (right) image of the same portion of a sketch. Closing the gap between the lines would require a different size structuring element for each image: about 5 pixels for high-resolution or 1 pixel for low-resolution.

Thinking Like a Human

Still motivated to avoid user parameterization for the structuring element, we explored ways to make the algorithm intelligent enough to select an appropriate structuring element on its own. Ultimately, we had to realize a few things before we came up with something that would work:

  1. When capturing an image of a sketch, users compose very similar images (compose in the photographic sense of the word): sketch is centered and nearly fills the captured image.
  2. The image of a sketch is not the same as a user’s perception of a sketch: a camera may record imperfections (gaps) in a sketch that a user does not perceive.
  3. The insignificance of camera resolution: a sketched feature in captured at two different resolutions would have two different lengths (in pixels), but identical lengths when defined as a percentage of image size.

With these insights, we deduced that the gaps we were trying to fill with morphological filtering would be those that escaped the notice of the sketch artist.

Recognizing the importance of accurate sketch reproduction, our solution applies the smallest structuring element possible that will still fill any unintentional gaps in a sketch. It does so in a way that is adaptable.

A discussion about the definition of “unintentional gap” allowed us to create a mandate for the closing portion of our algorithm. Sketch2model should fill gaps the user doesn’t notice. The detail below the limit of the user’s perception should not affect the output model. A quick “literature” (i.e. Google) search revealed that a person’s visual perception is affected by many factors beyond the eye’s optic limits. Without a simple formula to define a limit, we did what any hacker would do… define it empirically. Use a bunch of test images to tweak the structuring element of the closing filter to leave the perceptible gaps and fill in the imperceptible ones. In the sketch2model algorithm, the size of structuring element is defined as a fraction of the image size, so it was the fraction that we tuned empirically.

Producing Usable Results

Implicit in the implementation is sketch2model’s expectation that the user’s sketch, and their image of the sketch are crafted with some care. The expectations are reasonable: connect lines you’d like connected; get a clear image of your sketch. Like so much else in life, better input gives better results.

paper_pen_wow2_beforeafter.jpg

Input (left) and result (right) of sketch2model.

To produce an adaptable algorithm requiring as little user input as possible, the sketch2model team had to mix a little image processing wizardry with some non-technical insight.

Have you tried it? You can find it at sketch2model.com. Also on GitHub.


Previous posts in the sketch2model series: sketch2model, Sketch Image Enhancement, Linking Edges with Geomorphological Filtering.

sketch2model – linking edges with mathematical morphology

Introduction

As written by Elwyn in the first post of this seriessketch2model was conceived at the 2015 Calgary Geoscience Hackathon as a web and mobile app that would turn an image of geological sketch into a geological model, and then use Agile Geoscience’s modelr.io to create a synthetic seismic model.

original project promo image

The skech2model concept: modelling at the speed of imagination. Take a sketch (a), turn it into an earth model (b), create a forward seismic model (c). Our hack takes you from a to b.

One of the main tasks in sketch2model is to identify each and every geological body in a sketch  as a closed polygon. As Elwyn wrote, “if the sketch were reproduced exactly as imagined, a segmentation function would do a good job. The trouble is that the sketch captured is rarely the same as the one intended – an artist may accidentally leave small gaps between sketch lines, or the sketch medium can cause unintentional effects (for example, whiteboard markers can erase a little when sketch lines cross, see example below). We applied some morphological filtering to compensate for the sketch imperfections.

Morphological filtering can compensate for imperfections in a sketch, as demonstrated in this example. The original sketch (left) was done with a marker on white board. Notice how the vertical stroke erased a small part of the horizontal one. The binarized version of the sketch (middle) shows an unintentional gap between the strokes, but morphological filtering successfully closes the small gap (right).

Morphological filtering can compensate for imperfections in a sketch, as demonstrated in this example. The original sketch (left) was done with a marker on white board. Notice how the vertical stroke erased a small part of the horizontal one. The binarized version of the sketch (middle) shows an unintentional gap between the strokes, but morphological filtering successfully closes the small gap (right).

The cartoon below shows what would be the final output of sketch2model in the two cases in the example above (non closed and closed gap).

fill_before_after_closing

My objective with this post is to explain visually how we correct for some of these imperfections within sketch2model. I will focus on the use of morphological closing,  which consist in applying in sequence a dilation and an erosion, the two fundamental morphological operations.

Quick mathematical morphology review

All morphological operations result from the interaction of an image with a structuring element (a kernel) smaller than the image and typically in the shape of a square, disk, or diamond. In most cases the image is binary, that is pixels take either value of 1, for the foreground objects, or 0 for the background. The structuring element operates on the foreground objects.

Morphological erosion is used to remove pixels on the foreground objects’ boundaries. How ‘deeply’ the boundaries are eroded depends on the size of the structuring element (and shape, but in this discussion I will ignore the effect of changing the shape). This operation is in my mind analogous to peeling off a layer from an onion; the thickness of the layer is related to the structuring element size.

Twan Maintz in his book Digital and medical image processing describes the interaction of image and structuring element during erosion this way: place the structuring element anywhere in the image: if it is fully contained in the foreground object (or in one of the objects) then the origin (central) pixel of the structuring element (and only that one) is part of the eroded output. The book has a great example on page 129.

Dilation does the opposite of erosion: it expands the object boundaries (adding pixels) by an amount that is again related to the size of the structuring element. This is analogous to me to adding back a layer to the onion.

Again, thanks to Maintz the interaction of image and structuring element in dilation can be intuitively described: place the structuring element anywhere in the image: does it touch any of the foreground objects? If yes then the origin of the structuring element is part of the dilated result. Great example on pages 127-128.

Closing is then for me akin to adding a layer to an onion (dilation) and then peeling it back off (erosion) but with the major caveat that some of the changes produced by the dilation are irreversible: background holes smaller than the structuring element that are filled by the dilation are not restored by the erosion. Similarly, lines in the input image separated by an amount of pixels smaller than the size of the structuring element are linked by the dilation and not disconnected by the erosion, which is exactly what we wanted for sketch2model.

Closing demo

If you still need further explanation on these morphological operations, I’d recommend reading further on the ImageMagik user guide the sections on erosion, dilation, and closing, and the examples  on the Scikit-image website.

As discussed in the previous section, when applying closing to a binary image, the external points in any object in the input image will be left unchanged in the output, but holes will be filled, partially or completely, and disconnected objects like edges (or lines in sketches) can become connected.

We will now demonstrate it below with Python-made graphics but without code; however,  you can grab the Jupyter notebook with complete Python code on GitHub.

I will use this model binary image containing two 1-pixel wide lines. Think of them as lines in a sketch that should have been connected, but are not.

We will attempt to connect these lines using morphological closing with a disk-shaped structuring element of size 2. The result is plotted in the binary image below, showing that closing was successful.

But what would have happened with a smaller structuring element, or with a larger one? In the case of a disk of size 1, the closing magic did not happen:

Observing this result, one would increase the size of the structuring element. However, as Elwyn will show in the next post, also too big a structuring element would have detrimental effects, causing subsequent operations to introduce significant artifacts in the final results. This has broader implications for our sketch2model app: how do we select automatically (i.e. without hard coding it into the program) the appropriate structuring element size? Again, Elwyn will answer that question; in the last section I want to concentrate on explaining how the closing machinery works in this case.

In the next figure I have broken down the closing operation into its component dilation and erosion, and plotted them step by step to show what happens:

non_closed_break_red_two

So we see that the edges do get linked by the dilation, but by only one pixel, which the following erosion then removes.

And now let’s break down the closing with disk of size two into its component. This is equivalent to applying two consecutive passes of dilation with disk of size 1, and then two consecutive passes of erosion with disk of size 1, as in the demonstration in the next figure below (by the way, if we observed carefully the second panel above we could predict that the dilation with a disk of size two would result in a link 3-pixel wide instead of 1-pixel wide, which the subsequent erosion will not disconnect).

closed_break_red

Below is a GIF animated version of this demo, cycling to the above steps; you can also run it yourself by downloading and running the Jupyter notebook on GitHub.

closing_demo

Additional resources

Closing Jupyter notebook with complete Python code on GitHub

sketch2model Jupyter notebook with complete Python code on GitHub 

More reading on Closing, with examples

Related Posts

sketch2model (2015 Geoscience Hackathon, Calgary)

sketch2model – sketch image enhancements

Mapping and validating geophysical lineaments with Python

Google Earth and a 5 minutes book review: Geology Illustrated

A few years ago I bought on e-bay Geology Illustrated – by John S. Shelton, for just 10 US dollars. Every time I look at, and inside the book I can’t but think those were the best 10 dollars I ever invested in books.

There are already reviews and plenty of praise for this book out there – no need to repeat any of that if not briefly. My take is that the geology is clear and well explained. A bit simple, but simple is not always bad. And Shelton himself in the preface recommends this book as a “point of departure rather than something to lean on…” but that is perfect if you are a teacher looking for material, a first year college student, or a non-geologist looking for a high quality introduction.

But the photographs are priceless, and Shelton, who was also a pilot, took them all himself. Again, the author reminds us that nothing can replace field experience, and having  been trained as a field geologist (an average one, but that’s another story) I cannot but agree. However, lacking access or time to go to the field, or both, I find looking at a book like this can be an extraordinary substitute. That is especially true if you combine the reading with using Google Earth (particularly if you are a visual-spatial learner) and that is exactly what I did.

I already praised Google Earth for visualisation in this post. This program is a fantastic tool for learning geology, and today, to reinforce the point, I want to show you a couple of examples of Google Earth views replicating almost exactly figures from Chapter 14 of Geology Illustrated: The works of streams and rivers.

The first view is a replica of Figure 130 in the book, showing a fantastic example of a stream (the Colorado River) deepening its valley at the Marble Canyon.

The second view is a replica of Figure 135, showing many excellent examples of stream capture by headward erosion. Notice that in the 60s, when the photo was taken by Shelton, the highway (US Highway 101 north of San Juan Capistrano, California) was the only visible evidence of human activity.

The last view is a replica of Figure 137 in the book, showing the meander belt of the Animas River a few miles from Durango, Colorado. Looking at this was by far my favourite as it gave me the opportunity to create my own time lapse: a repeat snapshots of the same landscape nearly 50 years apart. Tis is priceless: 50 years are nothing in geological time scale, and yet there are already some significant differences in the two images. For example, it looks like the meander cutoff  in the lower left portion of the image had ‘just’ happened in the 60s, whereas at the time the imagery used by Google Earth was acquired (I imagine in the last few years), the remnant oxbow lake is more clearly defined. Another oxbow lake in the center has nearly disappeared.

I found that this process of looking for and replicating the photos in the book, zooming in and out, then in again changing view was a fantastic way to see the geological features as part of the larger geological context, visualize them, see the interconnection with other elements of the landscape, observe how erosion and deposition, and human processes have modeled the landscape in just a few decades (as in the second and third examples).  As a geophysicist, sitting in the office away from the outcrops, this is  invaluable, and a great aid in finding analogs in support of seismic interpretations. And really you don’t need a book in your lap to start the process.

In a future post I will show my results at creating similar views using HD lidar data, which can be downloaded from the National Center for Airborne Laser Mapping, as done in this blog post on Quest.

Resources

John Shelton’s obituary, August 2008

Geomorphology from space