Sentinel_bot – now with NIR vision

A quick blog post as I’m very much in the throes of writing! I took a few minutes today to introduce false colour (Near Infrared – Red – Green) images into @sentinel_bot’s programming, so now there’s a 20% chance that an image it produces will be false colour. In the near future I think I’ll introduce other band combinations (such as PCA band combos for mineral contrast enhancement), but for now I’m going to let it sit and appreciate some of what it comes up with, such as the image below.

Source : https://github.com/JamesOConnor/Sentinel_bot

Twitter : www.twitter.com/sentinel_bot

dgs6xtyxyaadcvj

NIR – R – G image over Argentina

Neural nets in Remote Sensing

Neural nets, a summary: (The chain rule * your GPU RAM)

Around 2 years ago I remember having a discussion with Jan Boehm about photogrammetry after my first meeting as the shadow wavelength rep on the Remote Sensing and Photogrammetry committee. He mentioned Agisoft, which I was already using and familiar with at the time, but then mentioned the movement in dense matching algorithms towards use of neural nets, mentioning one which had been submitted to the KITTI stereo benchmark.

right_cnn

Disparity map using Žbontar’s methods

This piqued my curiosity, and I remember reading and being quite excited by Jure’s paper. While some concepts were new to me, the use of Convolutional neural networks (ConvNets) and the two types of architecture used to initialize the initial results, before moving towards post-processing using semi-global matching. I remember sinking a great deal of time into reading about the methods, exploring the github and methods used within the core of the paper, and subsequently hounding a colleague who was using a Titan-X for some deep learning work for some time with it.

I remember I took the ideas with me to EGU 2016, and even went to the point of acquiring a data set I thought would be worthy of testing it with from a German photogrammetrist, Andreas Kaiser. Alas, it wasn’t to be due to the hardware limitations and the fact that I wasn’t very familiar with the lua programming language. However I had learned a lot about the nature of deep learning, which I felt was a decent investment of my time.

The reason for this blog entry, however, isn’t to enlighten the reader of my failure to get up to speed with neural nets at the time, it’s much more hopeful than that! Fast forward two years, and development within the field of deep learning has come on leaps and bounds. With serious development time going into TensorFlow, and a beautiful and accessible front end in the form of keras, the python user really does have the tools to apply neural nets to all sorts of applications within image-based studies.

Having learned the basic ideas around neural nets from my initial excitement a long time ago I decided to try and get involved with the community once more. A few months back, a well timed kaggle competition came up which involved image classification, which raised an eyebrow. I contacted an old friend of mine who had just finished his PhD in medical imaging and we set to take up the challenge.

river

The task for the competition involved labeling satellite imagery

Since starting the task, I feel like I’ve come on leaps and bounds with not only the concepts behind ConvNets, but their architecture and application in the python framework. Whilst we generated lots of code (will be on github in due course), and had lots of ideas floating about, we finished a decidedly average mid-table – this first pass was as much an experience in learning about organisation as well as about imaging science, but it’s made me rethink about using ConvNets in a Remote Sensing/Photogrammetry environment.

Whilst we are seeing more contributions coming out of the community, and the popularity of other less technical concepts like support vector machines have shown I’m hoping to extend my skill set to include all of these in the future. If anyone who happens to be reading this feel the same, don’t hesitate to get in touch!

 

Django greyscales

Access the application here.

I’ve been learning lots about the django web framework recently as I was hoping to take some of the ideas developed in my PhD and make them into public applications that people can apply to their research. One example of something which could be easily distributed as a web application is the code which serves to generate greyscale image blocks from RGB colour images, a theme touched on in my poster at EGU 2016.

Moving from a suggested improvement (as per the poster) using a complicated non-linear transformation to actually applying it to the general SfM workflow is no mean feat. For this contribution I’ve decided to utilise django along with the methods I use (all written in python, the base language of the framework) to make a minimum working example on a public web server (heroku) which takes an RGB image as a user input and returns the same image with a number of greyscaling algorithms (many discussed in Verhoeven, 2015) as an output. These processed files could then be redownloaded and used in a bundle adjustment to test differences of each greyscale image set. While not set up to do bulk processing, the functionality can easily be extended.

web_out

Landing page of the application, not a lot to look at I’ll admit 😉

To make things more intelligible, I’ve uploaded the application to github so people can see it’s inner workings, and potentially clean up any mistakes which might be present within the code. Many of the base methods were collated by Verhoeven in a Matlab script, which I spent some time translating to the equivalent python code. These methods are seen in the support script im_proc.py.

Many of these aim to maximize the objective information within one channel, and are quite similar in design so it can be quite a difficult game of spot the difference. Also, the scale can often get inverted, which shouldn’t really matter to photogrammetric algorithms processes, but does give an interesting effect. Lastly, the second PC gives some really interesting results, and I’ve spent lots of time poring over them. I’ve certainly learned a lot about PCA over the course of the last few years.

web_out.png

Sample result set from the application

You can access the web version here. All photos are resized so they’re <1,000 pixels in the longest dimension, though this can easily be modified, and the results are served up in a grid as per the screengrab. Photos are deleted after upload. There’s pretty much no styling applied, but it’s functional at least! If it crashes I blame the server.

The result is a cheap and cheerful web application which will hopefully introduce people to the visual differences present within greyscaling algorithms if they are investigating image pre-processing. I’ll be looking to make more simple web applications to support current research I’m working on in the near future, as I think public engagement is a key feature which has been lacking from my PhD thus far.

I’ll include a few more examples below for the curious.

 

This slideshow requires JavaScript.

Sentinel bot source

I’ve been sick the last few days, which hasn’t helped in staying focused so I decided to do a few menial tasks, such as cleaning up my references, and some a little bit more involved but not really that demanding, such as adding documentation to the twitter bot I wrote.

While it’s still a bit messy, I think it’s due time I started putting up some code online, particularly because I love doing it so much. When you code for yourself, however, you don’t have to face the wrath of the computer scientists telling you what you’re doing wrong! It’s actually similar in feeling to editing writing, the more you do it the better you get.

As such, I’ve been using Pycharm lately which has forced me to start using PEP8 styling and I have to say it’s been a blessing. There are so many more reasons than I ever thought for using a very high level IDE and I’ll never go back to hacky notepad++ scripts, love it as I may.

In any case, I hope to have some time someday to add functionality – for example have people tweet coordinates + a date @sentinel_bot and have it respond with a decent image close to the request. This kind of very basic engagement for people who mightn’t be bothered going to Earth Explorer or are dissatisfied with Google Earth’s mosaicing or lack of coverage over a certain time period.

The Sentinel missions offer a great deal of opportunity for scientists in the future, and I’ll be trying my best to think of more ways to engage the community as a result.

Find the source code here, please be gentle, it was for fun 🙂

dainlptxkaajaaw

WhatsApp Images

One thing I’ve noticed since sharing images across a range of formats/websites, is that image compression algorithms on various platforms vary noticeably. This is most evident, from my experience, with WhatsApp, where images tend to be resized without even an anti-aliasing filter. The results are images with huge amounts of speckle in them when they are not resized before uploading.

Obviously the target market for WhatsApp and its user base isn’t people using high end cameras to share their images on the application, but it still seems like a couple of functions could fix a lot of the visual problems that I see, which would save me having to do it locally.

It seems astounding to me that such a big company wouldn’t put more time into sensible image compression/resizing, or perhaps they have and I am catching exceptions. The blocky artifacts I’ve written about being associated with the algorithm on this blog before are evident. Even with the third example included, where the image was resized to 20% of it’s sized before compression applied produces a much better result qualitatively, even with the smaller pixel count upon redownload of the latter.

Whilst whatever algorithm they are using is likely directed towards smartphone camera users it still seems like an oversight by the developers. Hopefully WordPress doesn’t apply a similar type of compression when I post this now!

MP map

Just a quick entry detailing an interactive map showing MPs’ constituencies and party membership created at the request of a friend. It uses leaflet.js and geojson to draw the map, meaning it’s standalone html code which can be easily moved and modified.

mp_map.png

It’s based largely on the chloropleth example included in the leaflet documentation and was pretty interesting to make!

You can see it at my website here.

Leafiness

I thought it might be fun to try something different, and delve back into the world of satellite remote sensing (outside of Sentinel_bot, which isn’t a scientific tool). It’s been a while since I’ve tried anything like this, and my skills have definitely degraded somewhat, but I decided to fire up GrassGIS and give it a go with some publicly available data.

I set myself a simple task of trying to guess how ‘leafy’ streets are within an urban for urban environment from Landsat images. Part of the rationale was that whilst we could count trees using object detectors, this requires high resolution images. While I might do a blog on this at a later date, it was outside the scope of what I wanted to achieve here which is at a very coarse scale. I will be using a high resolution aerial image for ground truthing!

For the data, I found an urban area on USGS Earth Explorer with both high resolution orthoimagery and a reasonably cloud free image which were within 10 days of one another in acquisition. This turned out to be reasonably difficult to find, with the aerial imagery being the main limiting factor, but I found a suitable area in Cleveland, Ohio.

The aerial imagery is a 30 cm resolution having been acquired using a Williams ZI Digital Mapping Camera, and was orthorectified prior to download. For the satellite data, a Landsat 5 Thematic Mapper raster was acquired covering the area of interest, with a resolution of 30 m in the bands we are interested in.

This experiment sought to use the much researched NDVI, a simple index used for recovering an estimate of vegetation presence and health.

Initially, I loaded both datasets into QGIS to get an idea of the resolution differences

jezzer.png

Aerial image overlain on Landsat 5 TM data (green channel)

So a decent start, looks like our data is valid in some capacity and should be an interesting mini-experiment to run! The ground truth data is resolute enough to let us know how the NDVI is doing, and will be used farther downstream.

 

Onto GrassGIS, which I’ve always known has great features for processing satellite imagery, though I’ve never used. It’s also largely built on python, which is my coding language of choice, so I feel very comfortable troubleshooting the many errors fired at me!

The bands were loaded, DN -> reflectance conversion done (automatically, using GrassGIS routines) and a subsequent NDVI raster derived.

ndvi2.png

Aerial image overlain on NDVI values. Lighter pixels denote a higher presence of vegetation

Cool! We’ve got our NDVI band, and can ground truth it against the aerial photo as planned.

ndvi1

Lighter values were seen around areas containing vegetation

Last on the list is grabbing a vector file with street data for the area of interest so we can limit the analysis to just pixels beside or on streets. I downloaded the data from here and did a quick clip to the area of interest.

roads1.png

Vector road network (in yellow) for our aerial image. Some new roads appear to have been built.

I then generated a buffer from the road network vector file, and generated a raster mask from this so only data within 20 m of a road would be included in analyses. The result is a first stab at our leafy streets index!

map1.jpg

Visual inspection suggests it’s working reasonably well when compared with the reference aerial image, a few cropped examples are shown below.

This slideshow requires JavaScript.

Lastly, we can use this this data to scale things up, and make a map of the wider area in Cleveland. This would be simple to do for anywhere with decent road data.

map3.jpgThis might be useful for sending people on the scenic route, particularly in unfamiliar locations. Another idea might be to use it in a property search, or see if there’s a correlation with real estate prices. Right now I’ve run out of time for this post, but might return to the theme at a later date!