Robin's Blog

Converting latitude/longitude co-ordinates to Landsat WRS-2 paths/rows

As part of some work I was doing for my PhD, I needed to automatically find what Landsat scene path and row would contain a pixel with a certain latitude/longitude co-ordinate (this was basically so I could automatically download the relevant Landsat image and do some processing on it).

There is an online converter (provided by the USGS) which allows you to input latitude/longitude and get back path/row, but it doesn’t have an API of any kind, and I couldn’t see an easy to way to automatically submit requests to the form, as they’ve (very sensibly really) included methods to stop people doing that.

Summary: So, I wrote my own code to do the conversion. It’s available on Github and depends on GDAL/OGR and Shapely. See the README file on Github for instructions.

Very helpfully, the USGS have made shapefiles of the WRS-2 scene boundaries available to download, so all my code needs to do is load the shapefile, do some ‘Point in Polygon’ operations to find out which polygon(s) the point is in, and extract the ‘path’ and ‘row’ attributes from those polygons. This is fairly easy to do in Python using the wonderful OGR library to access shapefiles, and Shapely to do the ‘Point in Polygon’ operations. When writing this I used the Python Geospatial Development book as a good reference for how to combine GDAL and Shapely in this way.

The code is available at GitHub, with instructions on how to install it (basically, download the shapefiles from the USGS – I’m deliberately not re-distributing them here – and download the Python script), and it is very easy to use:

>>> import get_wrs
>>> conv = ConvertToWRS()
>>> conv.get_wrs(50.14, -1.7)
[{'path': 202, 'row': 25}]
>>> conv.get_wrs(50.14, -1.43)
[{'path': 201, 'row': 25}, {'path': 202, 'row': 25}]

Beware:

  • Instantiating the class may take a while, as it has to load in the shapefile
  • The get_wrs method may return multiple results, as Landsat scenes overlap at all four edges.

Please let me know (via a comment on this post) if you find this code useful.

For reference, the code is shown below, and is well-commented to show how it works:


Can I atmospherically-correct my images with Py6S?

I’m a big fan of Matt Might’s blog, and thought I’d implement one of his tips for blogging as an academic – namely Reply to Public. I’ve had a number of emails from Py6S users asking me questions about how to atmospherically-correct entire satellite images with Py6S – so I thought ‘d respond online, so that in the future people either find this response without needing to email me (ideally), or at the very least, I can point them to this blog post when they do email me.

Unfortunately, the simple answer to the question is: Py6S cannot (yet!) atmospherically correct satellite images – at least, not in a sensible manner – so I’d suggest using other atmospheric correction software such as ATCOR or FLAASH. The longer answer is below…

If you read the Py6S documentation you’ll find that there is an atmospheric correction option which you can use to take an at-sensor radiance (often called a Top of Atmosphere radiance when you’re dealing with satellite sensors) and atmospherically-correct it to get a corrected surface reflectance (or radiance) value. You could write some code to do that – it might look a bit like this:

from Py6S import *
# Create a SixS object called s
# (used as the standard name by convention)
s = SixS()

# Set the atmospheric conditions as usual
s.aero_profile = AeroProfile.PredefinedType(AeroProfile.Maritime)
s.aot550 = 0.05
s.atmos_profile = AtmosProfile.UserWaterAndOzone(2, 0.318)

# Set the wavelength
s.wavelength=Wavelength(PredefinedWavelengths.MODIS_B6)

# Set the altitudes
s.altitudes.set_target_sea_level()
s.altitudes.set_sensor_satellite_level()

# Set the geometry
s.geometry = Geometry.User()
s.geometry.solar_z= 35.8
s.geometry.solar_a= 149.4
s.geometry.view_z= 5.1
s.geometry.view_a= 106.8
s.geometry.month=06
s.geometry.date=28

# Turn on atmospheric correction mode and set it to do the
# correction assuming a Lambertian surface with a TOA
# radiance of 137.5 W/m^2
s.atmos_corr = AtmosCorr.AtmosCorrLambertianFromRadiance(137.5)   

# Run the model
s.run()

# Print the result of the atmospheric correction
# (assuming Lambertian reflectance)
# This is the ground-reflectance for the given radiance,
# under the given atmospheric conditions
print s.outputs.atmos_corrected_reflectance_lambertian

This works fine, and so you might think that all you need to do to correct a satellite image is to take the code above, and run it for each pixel of the image using a for loop, as in the pseudo-code below:

# Load in the image (eg. using GDAL)

for pixel in image:
	reflectance = run_py6s(various, parameters, here)

	# Store reflectance in the output image

# Save output image

Unfortunately, that won’t work very well. Or rather, it will work – it’ll just take a long time! Let’s do some maths to work out roughly how long:

  • As a rough approximation, it takes Py6S around two seconds to atmospherically correct a single pixel in a single band (the exact time depends on how complicated the parameterisation is – for example, a full manual AERONET-based aerosol parameterisation will take longer than a standard aerosol model)
  • A full Landsat scene is roughly 5500 x 6000 pixels (170km x 185km), which is around 33 million pixels
  • 33 million pixels x 2 seconds per pixel = 66 million seconds, or 763 days!
  • If I started running this now – on one band of a Landsat scene – it’d be finished around April 2015. Even if I used a simple parameterisation that only took one second per pixel, it’d still take over a year!

Now, I suspect you’re now thinking the Py6S is really awful because it takes such a long time. Well, unfortunately it’s not down to Py6S (if it was, I could try and improve it!). In fact, the Python bit of Py6S adds very little time  – the vast majority of the time is taken by 6S itself.

So, maybe it’s 6S that is rubbish. Well, again, unfortunately not, or we could switch to something that is better. All other Radiative Transfer Models, such as MODTRAN, SCIATRAN etc, suffer from the same problem.

So, how on earth do people manage to correct satellite images? Obviously people have managed to do it – and there is commercial software available to do it. Well, they use something called a Lookup Table (LUT). This involves running the Radiative Transfer Model many times to produce a table of results, and then looking up the result you want in this table. Creating the table takes a long time (but nowhere near as long as 763 days!) and it often takes a lot of space to store the resulting table (for example, the Lookup Table used in ATCOR is a multi-Gigabyte file), but once you’ve got the table you can correct a pixel in a tiny fraction of a second – rather than one or two seconds – which means the correction of an image is a lot quicker.

A lookup table is a good example of two standard trade-offs in computing:

  • Setup time vs Run time: Often algorithms can either be designed to have a very short (or no) setup time, but then take a long time to run; or they can be designed to have a long setup phase, and then run very quickly from then onwards. Often the decision of which one to focus on depends on how often you’re going to run your process – if you want to run it multiple times (like an atmospheric correction algorithm) then it is normally better to have a long setup time (which you only have to do once!) and then a short run time.
  • Memory vs Time: Again, algorithms often trade speed against memory – a fast algorithm normally requires more memory, and vice-versa. In this case, a Lookup Table trades speed for memory – we have to store the Lookup Table in memory, but once we have access to it, we can do corrections very fast.

I haven’t written any code to use Py6S to create a lookup table and then use that to correct an image (although I will almost certainly write some code to do this sometime during my PhD) – but it wouldn’t be too difficult to do. The procedure would be something like the following:

Setup Phase:

  1. Come up with a list of parameter values for all of the important parameters – choosing a number of parameters across their realistic range (there is a trade-off between accuracy and speed here, as always). For example maybe: AOT = [0.1, 0.2, 0.3, 0.4…]; solar_z = [10, 20, 30, 40, 50…]; radiance = [10, 20, 30, 40, 50, 60, 70] etc.
  2. Write some code to loop over all of these lists and run every possible combination of them
  3. Store the result of all of these runs of Py6S (ie. the atmospherically-corrected reflectance) and the parameters used to get the result in a big table of some sort.

Correction Phase:

Loop through every pixel in the image, and for each pixel:

  1. Get the parameters (AOT, angles, radiance etc) for that pixel
  2. Choose the nearest parameters that were used to create results in the table (for ALL of the parameters you used)
  3. Interpolate between these parameters as needed (eg. for an AOT of 0.15, get the results for an AOT of 0.1 and and AOT of 0.2 and interpolate) to get an interpolated ground reflectance.
  4. Store this reflectance in another image.

This basic procedure has been used in almost all atmospheric correction tools for the last thirty years, and is described in various papers including Fraser et al. (1992) and Liang et al. (1997). Another way to speed-up the computation even more is by introducing parallel computation. If we can assume that each pixel’s atmospheric correction is entirely independent from every other pixel’s (which may not be the case in the real-world, but is generally assumed by most atmospheric correction algorithms) then we can split the pixels between a number of processors and thus correct many pixels in parallel – which gets an even greater speedup as we can do this both when generating the LUT, and when correcting the image.

Unfortunately, actually implementing this is a bit more complicated than I’ve explained here and various decisions have to be taken (including what ranges of parameters to use, how to interpolate, how best to store the multi-dimensional lookup table and more…) – but it is definitely on my ‘to do’ list as part of my PhD, and as part of Py6S.

So, in conclusion: Py6S can’t do atmospheric correction of satellite imagery in a sensible time at the moment, but should be able to within the next few years. In the meantime, I suggest using other atmospheric correction software (most of which, unfortunately, is commercial software). You may think that not being able to do this makes Py6S useless…but, as my next post will show, Py6S is still very useful for remote-sensing research.

References

Fallah-Adl, Hassan, et al. “Fast algorithms for removing atmospheric effects from satellite images.” Computational Science & Engineering, IEEE 3.2 (1996): 66-77.

Fraser, R. S., Ferrare, R. A., Kaufman, Y. J., Markham, B. L., & Mattoo, S. (1992). Algorithm for atmospheric corrections of aircraft and satellite imagery.International Journal of Remote Sensing13(3), 541-557.

Liang, Shunlin, et al. “An operational atmospheric correction algorithm for Landsat Thematic Mapper imagery over the land.” Journal of Geophysical Research 102.D14 (1997): 17173-17.


Py6S: Run a radiative transfer model with a user-defined input spectrum

Version 1.2 of Py6S has recently been released (including a couple of bug fix releases, taking the most recent version to v1.2.2), and the major new feature in this version is the ability to use any spectrum as the ground reflectance for a model run. Previously, users were restricted to using the built-in 6S ground spectra (vegetation, clear water, lake water and sand) or doing some complicated parameterisation to set the user-defined reflectances up in the correct manner – so complicated that it was almost never worth doing!

Luckily, that has all changed in this version – read on to find out more…

Setting the Ground Reflectance

Setting the ground reflectance parameterisation in Py6S is very simple – you just use one of the methods of the GroundReflectance class. For example, to create a 6S model and set a constant reflectance of 0.5 for all wavelengths, simply run:

from Py6S import *
s = SixS()
s.ground_reflectance = GroundReflectance.HomogeneousLambertian(0.5)
s.run()

In previous versions the parameter given to HomogeneousLambertian (or HeterogeneousLambertian) could be any of:

  • A single reflectance value as a float, which is used as a uniform reflectance for all wavelengths: 
    s.ground_reflectance = GroundReflectance.HomogeneousLambertian(0.7)
  • A constant stating a built-in 6S reflectance value:
    s.ground_reflectance = GroundReflectance.HomogeneousLambertian(GroundReflectance.GreenVegetation)
  • An array giving a user-defined spectrum given in steps of 2.5nm for the wavelength range used for that simulation (the last bit is important!)
    s.ground_reflectance = GroundReflectance.HomogeneousLambertian([0.6, 0.8, 0.34, 0.453])

But now there is one more option:

  • A two-dimensional array containing wavelengths (column 0, in micrometres) and reflectance values (column 1, as a fraction). This array will then be taken by Py6S, resampled to 2.5nm, subset to only the range of wavelengths being used for the current simulation, and used with the underlying 6S model.
    s.ground_reflectance = GroundReflectance.HomogeneousLambertian(spectrum_array)

This saves a lot of time and extra code, compared to doing all of the resampling yourself and using the user-defined spectrum option which was always available in Py6S. However, there are more benefits than this… Py6S will store the whole spectrum that you give, and just re-sample it to the correct wavelength range every time you run the model, which means you can use the lovely helper methods like run_vnir and run_landsat_tm to run simulations for a spectrum for a number of wavelengths with very little code. For example:

from Py6S import *
s = SixS()
# Somehow generate a 2D array called spectrum_array here
s.ground_reflectance = GroundReflectance.HomogeneousLambertian(spectrum_array)
wavelengths, results = SixSHelpers.Wavelengths.run_vnir(s, output_name="apparent_radiance")

Getting spectral data

Of course, that example won’t work until we add in some code to generate this 2D array for us. There are a two ways we could get this array:

  • Generate it within our code somehow – for example, using a simple model, or interpolation between some hard-coded values.
  • Load it from some sort of external datafile, for example from a CSV file using np.loadtxt

Both of those are ways that you might want to use, but I’ve added functions to Py6S to simplify a couple of ways of doing this that may be useful to people.

Firstly, the functions in the Spectra module make it easy to import spectra from the USGS Spectral Library and the ASTER Spectral Library. These two libraries seem to be the most commonly used – as far as I am aware, at least – and have a very wide range of spectra in them. The two functions are very simple to use – you simply pass the URL or file path to the spectrum data file, and it returns the right sort of array. Thus you can do:

spectrum_array = Spectra.import_from_usgs("http://speclab.cr.usgs.gov/spectral.lib06/ds231/ASCII/V/russianolive.dw92-4.30728.asc")
s.ground_reflectance = GroundReflectance.HomogeneousLambertian(spectrum_array)

Or

s.ground_reflectance = GroundReflectance.HomogeneousLambertian(Spectra.import_from_usgs("http://speclab.cr.usgs.gov/spectral.lib06/ds231/ASCII/V/russianolive.dw92-4.30728.asc"))

(Either of the URLs could be replaced with a simple local file path instead, which is particularly useful if you have downloaded the USGS Spectral Library archive file, or obtained the CD of the ASTER Spectral Library).

The other way to get data is to use a model. Many models can produce spectral data, and most will output in a format like CSV that can be imported into a NumPy array really easily – but to make things even easier I have also released a Python interface to the ProSAIL called – you guessed it – PyProSAIL. Again, the methods have been carefully designed to return the right sort of arrays, so you can simply do:

# Make sure you have both PyProSAIL and Py6S installed
import pyprosail
from Py6S import *

spectrum = pyprosail.run(1.5, 40, 8, 0, 0.01, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile)
s = SixS()
s.ground_reflectance = GroundReflectance.HomogeneousLambertian(spectrum)
s.run()

So, hopefully that has been a useful introduction to how to use user-defined spectra with Py6S. I’ll leave you with an example of how to put all of this together to do something useful – that is, to run a Py6S simulation with the ground reflectance set to the spectra from every USGS spectral library file in a directory, and store the results:

from Py6S import *
import glob
import numpy as np

# Create the SixS model and set some parameters
s = SixS()
s.aero_profile = AeroProfile.PredefinedType(AeroProfile.NoAerosols)
s.altitudes.set_sensor_satellite_level()
s.altitudes.set_target_sea_level()

# Get a list of files that have the extension .asc
# (the extension used by the USGS spectral library files)
files = glob.glob("./USGSSpecLib/Selected/*.asc")

results = []

# Run the model using each filename as the ground reflectance spectrum
# using the Landsat ETM+ bands
for filename in files:
	s.ground_reflectance = GroundReflectance.HomogeneousLambertian(Spectra.import_from_usgs(filename))
	wvs, res = SixSHelpers.Wavelengths.run_landsat_etm(s, output_name='apparent_radiance')
	results.append(res)

# Stack all of the results into an array
results_arr = np.vstack(results)

# Write the results out to a CSV file for further analysis
np.savetxt("results.csv", results_arr, delimeter=",")

My first academic paper – on Py6S

Another exciting update for this new year: my first academic journal paper has been published!

It’s called Py6S: A Python interface to the 6S Radiative Transfer Model, and is published in Computers and Geosciences. If you’re reading this from a university with a subscription to Computers and Geosciences then you can read it at ScienceDirect – if you don’t, then you can read the post-peer-review (but pre-publisher-typsetting) version at my website.

The paper describes the Py6S python module that I wrote to assist me in running simulations using the Second Simulation of the Satellite Signal in the Solar Spectrum (6S) model, and is fairly short, but – I hope – fairly useful. It also gives a good way for people to cite Py6S when (if…) they use it in their work – they simply cite this paper.

Of course, the issue with journal papers is that they are static – indeed, a number of things changed in Py6S during the time between submitting the paper and it coming out in print (which was around nine months!). None of those affected the example code given in the paper – and to be honest, they were mostly bugfixes – but there are some new features gradually working their way into the code.

I’m planning to start a series of posts about Py6S on this blog, showing how various things work ‘under the hood’, announcing new features, and showing examples of how to use Py6S well. Hopefully this will be useful for me and also useful for other people who may be interested in using Py6s, but may require a bit of help.

So… stay tuned for the next post which will be on a new feature involving user-defined spectra.


Major update to Free GIS Data site

The New Year is a time of new beginnings – and so it is rather appropriate to launch the complete redesign of my Free GIS Data list today.

 

Free GIS Data site - updated design

 

As you can see from the screenshot above, it looks far nicer than before – but it is also far easier to navigate. The dropdown menus at the top allow easy access to all of the categories (and also, incidentally, make it easier for me to add new categories as needed). I’ve also added quite a few new datasets, and tidied up some of the descriptions and categorisations of links that were already there.

Doing the re-design was around an evening’s work – mainly because I used the wonderful Bootstrap framework for the page. There were a few niggles I had to sort out (particularly regarding the header bar sticking at the top when you scroll down, and what that does for within-page anchors) but generally it was a fairly painless experience.

So, I hope the list is useful to you during 2013 and beyond!


Review: Code – The Hidden Language of Computer Hardware and Software by Charles Petzold

Summary: This book takes you all the way from Morse Code to a fully working computer, explaining everything along the way. What’s more, it’s a great read too! If you ever wondered how a computer worked then buy this and read it – even if you think you already know (unless you’re, you know, a chip designer at Intel or something!) Front Cover

Reference: Petzold, C., 2000, Code: The Hidden Language of Computer Hardware and Software, Microsoft Press, 395pp Amazon Link

As you’ll probably know if you’ve read many articles on this site: I’m a computer programmer and general ‘geek’. So, it won’t surprise you to know that I am quite interested in how computers work – and picked up this book thinking that I’d already know quite a lot of it. I knew a fair bit – but I learnt a huge amount from reading it, and it helped me gain a full understanding of what is going on when I write computer programs – right down to the level of the electricity inside the processor. By the end of the book I was itching to buy lots of relays or transformers and make a computer on my living room table!

The book starts by looking at the ways you, as a child, might try and communicate with your best friend who lives across the street – after your parents think you’ve gone to bed. The natural solution to this is Morse code using a torch, and Petzold takes this simple code as a good starting point to explain the concepts of a code. He then moves on to Braille, which is significantly more complex than I thought, and which gives the opportunity to look at some of the more complex things you find in codes (eg. shift characters and escape characters – both of which Braille has). You’ll note that nothing about computers has been introduced yet – and that is a key feature of the first part of the book, it doesn’t go straight in to “this is how a computer works”, it starts at a very basic (but still interesting) level that becomes useful when thinking about computers later in the book, but isn’t too scary.

Electricity and electrical circuits are introduced when describing how you might communicate with another friend whose window you can’t see from yours. This is introduced almost entirely from scratch – explaining how circuits work, what voltage is, how batteries work etc – but it actually went beyond my previous knowledge in electricity fairly quickly, and taught me much of interest. Whenever circuits are drawn in the book – from here onwards – they are shown with the wires that have current in them in red, making it very easy to see what is going on.

The discussion of electricity for sending messages leads into the history of telegraph networks, and then the concept of relays. I’d never really understood relays before, but Petzold introduces them with a very good analogy as a ‘labour saving device’ at a telegraph station. Around this point a number of other key – but rather unrelated – topics are covered like Boolean logic (True/False, AND, OR etc) and number systems (particularly number bases and binary). There is a very practical emphasis on everything – and the point about the importance of binary as on/off, true/false, open/closed and so on, is very much emphasised. After these introductions, the relays discussed earlier are combined to produce logic gates (AND, OR, NOT, NAND, XOR and so on) with the aim of producing a circuit to help you choose a cat (yes, it sounds strange, but works well as an example!). Here you can start to see how this is moving towards a computer…

I’m not going to go much further into detail about the rest of the book, except to say that you move towards being able to ‘build’ (conceptually if not actually physically) a fully-working computer gradually, one step at a time. From logic gates, to adding circuits and subtracting circuits and from clocks to flip-flops and RAM you gradually work up to a full, programmable computer which you have basically built by page 260! Given how much detail everything is explained in – and how little knowledge is assumed – fitting it into 260 pages is very impressive!

Of course, the book continues past page 260, going on to cover topics including input and output (from keyboards and to the screen), high and low level programming languages, graphics, multimedia and more. Interestingly, transistors aren’t mentioned until after you’ve got almost all of the way to building a computer – but this is almost certainly because relays are far easier to understand, and accomplish the same job. Once they have been introduced, a couple of important processors (the Intel 8080 and the Motorola 6800) are examined in detail – a really interesting opportunity to see how the concepts you’ve learnt about have been applied in real life by chip designers.

I can think of very few issues with this book – although the last chapter does read rather strangely, as if the author was trying to fit far too much into far too little space (trying to cover multimedia, networking, WIMP interfaces and more in one chapter is a bit of a tall order though!), but I very much like the book as a whole. It is one of those rare books that is suitable for a very wide range of audiences – from those with almost no knowledge of the subject at all (it starts from the very beginning, so that isn’t a problem) right up to those who are experienced programmers and know some of it (they will still find a lot they don’t know, and realise a lot of things). Overall: a great read, very interesting and very educational. You won’t be disappointed.


Validating the validation?

So, I’ve been pondering an interesting scientific dilemma recently: how do you validate a validation technique? That is, if you’re using a certain procedure to validate some data (that is, check how correct/accurate it is), how can you validate the validation procedure itself?

This has come up in my work recently in relation to validating Aerosol Optical Thickness (AOT) data from satellites. Validation is normally performed by comparing satellite-derived data to data from the Aerosol Robotic Network (AERONET). However, this is challenging for a number of reasons: the main one being that AERONET measurements are point measurements of the AOT above the measurement site, whereas the satellite will measure AOT averaged over a large pixel area (10 x 10km for MODIS). A number of validation methods have been proposed to deal with this, and they are all based on spatial and temporal averaging of the data, to bring it into a comparable state.

MODIS AOT data

Example MODIS AOT data for Europe

The big question then becomes:

If there are a number of different methods for validating this data, then how do we choose which one is best?

This is a big problem because the results of the validation will be used to infer the accuracy and uncertainty of the dataset – and if we use a validation that gives misleading results then we will have a misleading opinion of the dataset. This gets even more difficult when you need to choose parameter values for use in these validation procedures. For example, if the validation involves temporal or spatial averaging then what period/distance should the averaging be done over? 30 minutes? 1 hour? 5 hours?

So, how should we deal with this?

Unfortunately, I don’t know. I know that I have a problem with some of the current methods (for example, trying a wide range of parameter values and choosing the ones that give you the best validation results – that is, the lowest error) as some of them really do seem to be ‘cheating the system’. This is something that I’m hoping to come back to over time – I already have some preliminary ideas on how to ‘fix’ the AOT validation system – but I think it is a problem which won’t go away.


Updated Snow GIS data

A while back I released a GIS dataset containing Snow’s Cholera analysis data in modern GIS formats, and georeferenced to the British National Grid (see my previous post). Unfortunately, there was an error in some of the attributes of the Cholera Deaths shapefile which caused issues when using the data.

This error has now been fixed, and the updated data are available to download here: SnowGIS_v2.zip. The link on the previous post has also been updated.

Please accept my apologies for this error.


I signed the Science Code Manifesto – and you should too!

I’ve just signed the Science Code Manifesto because I firmly believe in what it says. Ok well, that probably doesn’t tell you much – generally I tend to believe in things that I sign – but I’d like to tell you why I signed it, and why I think it’s really important.

A lot of my PhD life is spent writing code (a lot of my life outside of my PhD is also spent writing code, but that’s another story). When I tell people this quite a few of them are surprised that I’m not doing a computer science PhD – because surely they’re the only ones who spend their time writing code? Well…no! A lot of scientists spend a lot of time writing code for research in almost every subject.

Why do they do that? Well, nearly every research project involves at least one of the following activities:

  • Data processing
  • Plotting graphs
  • Calculating statistics
  • Running models
  • Building new models, simulations and so on

All of these activities can easily be done through code, and in fact it’s often far more efficient to do them through code than by other methods. However, mistakes can be made in code, and people will often want to check the results of other people’s papers (that is, to ensure reproducibility – a key factor in science) – but to do that they need the code. That is what the first tenet of the Science Code Manifesto says: “All source code written specifically to process data for a published paper must be available to the reviewers and readers of the paper”. That means that as a reader (or reviewer) I can read the code (to check it looks like it does what it’s meant to do), and run the code (to check it actually does what its meant to do). It also means that if I have the code to do the processing, plus the input data, I can generate the output data that they got, and check it against the results in the paper. I was reading a paper today which examined aerosol optical depth variations across Europe. They had really high resolution data, and I’d love to have seen a map of the distribution across the UK in detail, but it wasn’t included in the paper (they had a lower-resolution map of the whole of Europe instead). If I’d had access to the code (and the data) then I could have generated the data myself, plotted a map over the whole of Europe (to check that it looked the same as their published map) and then zoomed in on the UK to examine it in more detail.

Scientific papers are designed to be built upon. As Newton said, “If I have seen further it is only by standing on the shoulders of giants”  – as scientists we all need to stand on the shoulders of those who came before us (giants or not). If you have the code that other scientists have used to produce the results in their paper, it is likely that you might want to modify it (for example, to fix some errors you’ve found), extend it (to make it applicable to your particular study area), and share it or its modifications with your colleagues. You won’t be able to do this unless you know what license the code was originally released under – hence the second tenet of “The copyright ownership and license of any released source code must be clearly stated”.

The next two tenets are very important as they place scientific code at the same level as scientific papers, books and other more ‘traditional’ academic outputs. They state that Researchers who use or adapt science source code in their research must credit the code’s creators in resulting publications and Software contributions must be included in systems of scientific assessment, credit, and recognition. This is important because if we believe that scientific code is important (which I, and the 846 people who have signed the manifesto so far believe) then we need to recognise it. This means two things: firstly citing it, so that we give the proper attribution to the authors, and let people see how it is being used; and secondly giving credit for writing code when we assess how good researchers are. This is something that varies significantly by department and research area – but it is something which I think should be standard across all fields. If you write a good piece of scientific software (not a 10 line Python script in a random file somewhere, but something which is properly released, useful, documented and sustainable) then you should be given credit for it, just as if you had written a paper or a journal article! As a number of people have commented before: a scientific paper which describes a new algorithm is not the scientific work itself – it is just an advert for the work. The real scientific work, and scientific product, is the code that implements the algorithm.

Finally, the manifesto touches on the subject of software sustainability – something that I will (hopefully) be doing a lot more work on in the near future. This refers to the practice of sustaining software so that it can continue to be used (and, ideally, continue to be improved) in the future. Software is a funny thing – it is susceptible to rotting away, just like organic material. This is known as software decay and is primarily caused by the rapid progress made in technology: it may be that the ‘latest, greatest’ technology that you used to write your software in 2012 can’t be run in 2020, or 2025, but the job the software does may still be very important. I think (hope) that all of my code will be able to run for the foreseeable future as I’ve written it in fairly standard programming languages (such as Python and R), but this may not be the case – for example, libraries can easily break as standards evolve, and if the author is no longer maintaining their libraries then they may not get fixed. This can be a big issue, and leads on to the other part of sustaining software: that of generating a community around the software, which will help sustain it in the years to come. The manifesto is actually fairly limited in what it says: Source code must remain available, linked to related materials, for the useful lifetime of the publication, but I feel that it a lot of the other things I’ve raised in this paragraph are also relevant.

So, there we go. That’s why I signed the manifesto – now have a think about it, and if you agree go and sign it too!


In praise of ProjectTemplate for reproducible research

As you might know from some of my previous posts, I’m a big fan of making my scientific work reproducible. My main reasons for being so keen on this are:

1. Reproducibility is key to science – if it can’t be reproduced then it can not be verified (that is, the experiment can’t be tried again to determine if the same result was produced then no-one can verify your work, and no-one can falsify it if it was incorrect), and therefore (according to various scientific philosophers such as Popper) it isn’t science.

2. It’s actually really useful for me as a researcher. Have you ever come back to a project six months after stopping work on it (possibly because you’d submitted a paper on it, and had to wait ages for the reviewers comments) and found it almost impossible to work out how to produce a certain graph or table, or which data was used to produce a certain result? Making your work reproducible by other scientists also means it will be reproducible by you when you’ve forgotten all about how it worked!

Basically reproducibility in scientific research these days means code. You could write a long Word document saying exactly how you processed all of your data (good luck keeping it up-to-date) and then run through all of that again, but in most of my work I use code in a variety of languages (Python, R and IDL mostly) to do the processing for me.

The beauty of this (aside from not spending ages clicking around in frustrating dialog boxes) is that doing your research through code gets it a long way to being reproducible without any other work on your part. You created your original outputs through code, so you can reproduce them just by running the code again! Simple isn’t it?

Well, unfortunately, it’s not quite that simple. Do you know which exact bit of data you used to create that code? Did you pre-process the data before using it in your code? Did you some processing on the data that the code produced before putting into a table/graph in your paper? Will you remember these things in six months/six years if you need to reproduce that bit of work yourself (or, more scarily, if someone emails you to tell you that they think your results were wrong…)? Unfortunately, I think that’s unlikely.

Anyway, to get to the point of this post: I have recently been using a R package called ProjectTemplate which has really helped me make my research properly reproducible. This package generates a standard folder structure for your R code, and provides a range of useful functionality for automatically loading data and caching the results of computations. I’ve been using this for a report that I wrote recently for my PhD supervisors (something which may turn into a paper sometime – hopefully), and it’s been great.

I’m not going to give a full overview of all of the functionality of ProjectTemplate here, but I’ll show you a bit about how I use it. Firstly, here is my folder structure for this project:

Folder structure

Folder structure for my ProjectTemplate project

As you can see there are quite a few folders here with code in:

  • data: scripts for loading in data (or data files themselves, which will be loaded automatically if they are of certain file types)
  • lib: functions that will be used throughout the project
  • munge: scripts to manipulate or ‘munge’ before use in the rest of the project (ie. pre-processing)
  • src: scripts used to actually do the processing and analysis of the data

There are also quite a few folders that I use that I haven’t shown expanded above:

  • cache: stores cached R objects (eg. results from time-consuming processing steps)
  • graph: stores graphical outputs from the analysis

So, what we’ve got here is a place to put re-usable functions (basically functions that could eventually go into a separate R package – eg. for reading specific format data files etc), a place to put pre-processing code, and a place to put actually scientific analysis code. You’ll see there are loads of other folders that I haven’t mentioned that I don’t really use, but I suspect I will probably use them in new projects in the future.

The beauty of this folder structure is that the folder that contains the structure above can be simply zipped up, given to someone else and then they can run it themselves. How do they do that? Simple, change the working directory to the folder and run:

library(ProjectTemplate)
load.project()

That will load all of the library needed, load the data (from files or cache), pre-process it (or load the results from the cache) and get it to the stage where you can run any of the files in src. Great!

The brilliant thing is that each of my scripts in the src folder will produce one or two outputs for my report. All of my graphs are saved as PDFs into the graphs folder, ready to be included directly into a LaTeX document, and my tables are produced as R data frames and then converted to LaTeX tables using the xtable package.

So, what’s the practical upshot of this? Well, if I come back to this in six months I can run any analysis that I use for my report by typing a couple of lines of code and then running the relevant file. It also meant that when I realised half-way through my writing up that I had accidentally done all of my results (about 5 graphs, and 4 big tables) based on some incorrect input data (basically I had data for half of Europe rather than just the UK, which makes a big difference to the ranges of atmospheric data!) it took me about 30 minutes to generate all of the new results by simply changing a line of code where the data was imported, running the pre-processing again (which took about 20 minutes of the 30 minutes time!) and then running each file to generate the required graph PDF files or xtable LaTeX code.

Hopefully this will have made sense to you all – stay tuned for some more reproducible research posts in the near future.