Today we are gonna work with bulk downloaded data from MODIS. The MODIS satellites Terra and Aqua have been floating around the earth since the year 2000 and provide a reliable and free-to-obtain source of remote sensing data for ecologists and conservationists. Among the many MODIS products, Indices of Vegetation Greenness such as NDVI or EVI have been used in countless ecological studies and are the first choice of most ecologists for relating field data to remote sensing data. Here we gonna demonstrate 3 different ways how to acquire and calculate the mean EVI for a given Region and time-period. For this we are using the MOD13Q1 product. We focus on the area a little bit south of Mount Kilimanjaro and the temporal span around May 2014.
The first handy R-package we gonna use is MODISTools. It is able to download spatial-temporal data via a simple subset command. The nice advantage of using *MODISTools* is that it only downloads the point of interest as the subsetting and processing is done server-wise. This makes it excellent to download only what you need and reduce the amount of download data. A disadvantage is that it queries a perl script on the daac.ornl.gov server, which is often horrible slow and stretched to full capacity almost every second day.
# Using the MODISTools Package library(MODISTools) # MODISTools requires you to make a query data.frame coord <- c(-3.223774, 37.424605) # Coordinates south of Mount Kilimanjaro product <- "MOD13Q1" bands <- c("250m_16_days_EVI","250m_16_days_pixel_reliability") # What to query. You can get the names via GetBands savedir <- "tmp/" # You can save the downloaded File in a specific folder pixel <- c(0,0) # Get the central pixel only (0,0) or a quadratic tile around it period <- data.frame(lat=coord,long=coord,start.date=2013,end.date=2014,id=1) # To download the pixels MODISSubsets(LoadDat = period,Products = product,Bands = bands,Size = pixel,SaveDir = "",StartDate = T) MODISSummaries(LoadDat = period,FileSep = ",", Product = "MOD13Q1", Bands = "250m_16_days_EVI",ValidRange = c(-2000,10000), NoDataFill = -3000, ScaleFactor = 0.0001,StartDate = TRUE,Yield = T,Interpolate = T, QualityScreen = TRUE, QualityThreshold = 0,QualityBand = "250m_16_days_pixel_reliability") # Finally read the output read.table("MODIS_Summary_MOD13Q1_2014-08-10.csv",header = T,sep = ",")
The Mean EVI between the year 2013 up to today on the southern slope of Kilimanjaro was .403 (SD=.036). The Yield (integral of interpolated data between start and end date) is 0.05. MODISTools is a very much suitable for you if you want to get hundreds of individual point locations, but less suitable if you want to extract for instance values for a whole area (eg. a polygon shape) or are just annoyed by the frequent server breakdowns…
If you want to get whole MODIS tiles for your area of interest you have another option in R available. The MODIS package is particularly suited for this job in R and even has options to incorporate ArcGis as path for additional processing. It is also possible to use the MODIS Reprojection Tool or gdal (our choice) as underlying workhorse.
library(MODIS) dates <- as.POSIXct( as.Date(c("01/05/2014","31/05/2014"),format = "%d/%m/%Y") ) dates2 <- transDate(dates,dates) # Transform input dates from before # The MODIS package allows you select tiles interactively. We however select them manually here h = "21" v = "09" runGdal(product=product,begin=dates2$beginDOY,end = dates2$endDOY,tileH = h,tileV = v,) # Per Default the data will be stored in # ~homefolder/MODIS_ARC/PROCESSED # After download you can stack the processed TIFS vi <- preStack(path="~/MODIS_ARC/PROCESSED/MOD13Q1.005_20140810192530/", pattern="*_EVI.tif$") s <- stack(vi) s <- s*0.0001 # Rescale the downloaded Files with the scaling factor # And extract the mean value for our point from before. # First Transform our coordinates from lat-long to to the MODIS sinus Projection sp <- SpatialPoints(coords = cbind(coord,coord),proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84")) sp <- spTransform(sp,CRS(proj4string(s))) extract(s,sp) # Extract the EVI values for the available two layers from the generated stack #> 0.2432 | 0.3113
If all the packages and tools so far did not work as expected, there is also an alternative to use a combination of R and Python to analyse your MODIS files or download your tiles manually. The awesome pyModis scripts allow you to download directly from a USGS server, which at least for me was almost always faster than the LP-DAAC connection the two other solutions before used. However up so far both the MODISTools and MODIS package have processed the original MODIS tiles (which ship in hdf4 container format) for you. Using this solution you have to access the hdf4 files yourself and extract the layers you are interested in.
Here is an example how to download a whole hdf4 container using the modis_download.py script Just query modis_download.py -h if you are unsure about the command line parameters.
# Custom command. You could build your own using a loop and paste f <- paste0("modis_download.py -r -p MOD13Q1.005 -t ",tile," -e ","2014-05-01"," -f ","2014-05-30"," tmp/","h21v09") # Call the python script system(f) # Then go into your defined download folder (tmp/ in our case) # Now we are dealing with the original hdf4 files. # The MODIS package in R has some processing options to get a hdf4 layer into a raster object using gdal as a backbone library(MODIS) lay <- "MOD13Q1.A2014145.h21v09.005.2014162035037.hdf" # One of the raw 16days MODIS tiles we downloaded mod <- getSds(lay,method="gdal") # Get the layer names and gdal links # Load the layers from the hdf file. Directly apply scaling factor ndvi <- raster(mod$SDS4gdal) * 0.0001 evi <- raster(mod$SDS4gdal) * 0.0001 reliability <- raster(mod$SDS4gdal) s <- stack(ndvi,evi,reliability) #Now extract the coordinates values extract(s,sp)
There you go. Everything presented here was executed on a Linux Debian machine and I have no clue if it works for you Windows or MAC users. Try it out. Hope everyone got some inspiration how to process MODIS data in R ;)
The Sun is shining, birds are singing and most scientists have nothing better to do than jetting around the globe to attend conferences. Yes, it is summer indeed. Here is some advertising for the 2014 Tropical Ecology – Early Carer Meeting of the British Ecological Society. This year the fun is happening in York. As many people seem to be on vacation the deadline for abstracts has been extended to the 14th of July. See the attached Documents ( BES-TEG 2014 Flyer ,BES_TEG Key speakers ) for more information. I will be there as well… .
The British Ecology Society – Tropical Ecology Group (BES-TEG) are organizing a 7th early career meeting scheduled to take place at the University of York, on the 14th and 15th of August 2014. Day one will focus on Ecology and Ecosystem Processes while day two will focus on Practical Applications and Links to Policy; such as conservation, livelihood, policy and development. All early-career researchers, both PhD and Post-Docs, are welcome to present their tropical ecology related research as a poster and/or oral presentation. The deadline for abstract submission has been extended to Monday the 14th of July 2014.
Please find attached the flyer and conference document for detailed information.
It would be appreciated if this flyer circulates within your department. Students are encouraged to come to York for what should be a really interesting few days in August.
An event website has been set up for registration
The start of this year was marked by the publication of two new global datasets for environmental analysis. My impression is that both of those datasets will be of increasing importance in ecological analysis in the future (even though their value for conservation biology has been actively criticized, see Tropek et al. 2014). Thus there is a need to assess the accuracy of their forest loss detection over time and if they are consistent.
The first dataset is the already famous Global Forest Map published by Hansen et al. (2013) in Science end of last year. The temporal span of their dataset goes back from the year 2000 up to the year 2012 and by using only Landsat data in a temporal time-series analysis they got a pretty decent high-resolution land-cover product. Although the resolution of the Hansen dataset is great (30m global average coming from Landsat) Hansen et al. decided to only publish the year 2000 baseline with the forest cover. They provide us with aggregated loss, gain and loss per year layers though, but nevertheless the user has no option to reproduce a similar product for the year 2012.
The other dataset is the combined published result from a 4 year long monitoring by the japanese satellite ALOS-PALSAR. They decided to release a global forest cover map at a 50m spatial resolution, which in contrast to Hansen can be acquired for the whole time-frame of the ALOS-PALSAR mission. It thus has a temporal coverage of the whole globe from the year 2007 until 2010. The data can be acquired on their homepage after getting an account. The ALOS PALSAR data has a nice temporal span and can be downloaded for multiple years, thus in theory allowing to make temporal comparisons and predictions about future land-use trends. However I am a bit concerned about the accuracy of their classifications as I have found multiple errors already in the area I am working in.
Because I am interested in using the ALOS PALSAR dataset in my analysis (how often do you get a nice spatial-temporal dataset of forest cover) I made a comparison between the forest loss detected in my area of interest for both datasets. It should be noted that is a comparison between different satellite sensors as well and not only by classification algorithms. So we are not comparing products from the same data source.
So what is the plan for our comparison:
- We downloaded the whole ALOS PALSAR layers for all years covered of the area around Kilimanjaro in northern Tanzania (N00, E035). We then extracted only the forest cover (Value == 1) and calculate the difference between years to acquire the forest loss for the year 2008,2009 and 2010 respectively.
- From the Google Engine app we downloaded the “loss per year” dataset and cropped it to our area of interest. Furthermore we are only interested in the aggregated Forest loss in the years 2008, 2009 and 2010 which we have available in the ALOS PALSAR dataset. We furthermore resampled the Hansen dataset up to 50m to match up with the ALOS PALSAR resolution.
I haven’t found a fancy way to display this simple comparison, so here comes just the result table. As predicted (if you look at it visually),the ALOS PALSAR algorithm overshots the amount of forest loss a lot.
|Hansen Forest Loss cells||262||304||529|
|ALOS PALSAR Forest Loss cells||26995||24970||16297|
|Equal cells in both||17||30||131|
So which one is right? I personally trust Hansens data a lot more. Especially because I found them to be pretty consistent in my area of study. For me the ALOS PALSAR data is not useable yet until the authors have figured out ways to improve their classification. It can be concluded that users should not forget that those Forest Cover products are ultimately just the result of a big un-supervised algorithm who doesn’t discriminate between right and wrong. Without validation and careful consideration of the observer you might end up having wrong results.
M. Shimada, O. Isoguchi, T. Tadono, and K. Isono, “PALSAR Radiometric and Geometric Calibration,” IEEE Trans. GRS, vol. 47, no. 12, pp.3915-3932, Dec 2009.
M. Shimada and T. Otaki, “Generating Continent-scale High-quality SAR Mosaic Datasets: Application to PALSAR Data for Global Monitoring,” IEEE JSTARS Special Issue on Kyoto and Carbon Initiative, vol. 3, Issue 4, 2010, pp.637-656.
Shimada, M.; Isoguchi, O.; Motooka, T.; Shiraishi, T.; Mukaida, A.; Okumura, H.; Otaki, T.; Itoh, T., “Generation of 10m resolution PALSAR and JERS-SAR mosaic and forest/non-forest maps for forest carbon tracking,” Geoscience and Remote Sensing Symposium (IGARSS), 2011 IEEE International , vol., no., pp.3510,3513, 24-29 July 2011
This is just a quick posting informing all the QGIS interested readers of this blog that I am about to release a new QGIS plugin. It’s name is QSDM (QGIS Species Distribution Modelling) and similar as with LecoS it is particular suited for the practicing ecologists out there. This time i had no plan and interest of coding a graphical interface and thus the whole plugin can only be executed from within the Processing Toolbox (QGIS version > 2.0 ). In my opinion this will be the future of most advanced QGIS plugins anyway.
So what is the idea? Basically QSDM is a plugin taking statistical models for species distribution modeling to QGIS. For now only the famous Maxent is enabled and working, but the ambitious plan is to enable other modeling techniques such as RandomForests and LogisticRegression as well if the user has the necessary libraries enabled.
You might ask what is the advantage of running Maxent from within QGIS? First, you can immediately see the output so it is nice for visual exploration. Second, the QSDM plugin helps you with the formating of your layers and occurrence files. For instance all input raster layers are automatically unified to a common resolution and exported as ESRI .asc files. You simply need to load in your layers and let the tool do the rest. For those of you who want more control (and I really insist that you want to), I also enabled functions to generate a custom parameter file for Maxent and enabled an option to start the Maxent GUI in a new process.
–> I recognize that the easiness of this tool might tempt more people to execute tools without really understanding what they do and how they work. Please be sure what you do and always (!!!) validate the outputs of the tools you use (this includes QSDM). For understanding Maxent parameters I highly recommend reading the attached literature list and this publication!
Other things i implemented in the initial release of QSDM
- Create Species Richness grid
- Creates a new raster containing Species Richness or Endemism of input occurence layer
- Calculate Niche Overlap Statistics
- Can calculate Schoener’s D or Warren’s I based on Hellinger distances for all input layers.
- Range Shift
- Shows the difference between two input prediction layers. For instance for current and likely future conditions.
- Data Transformations
- Makes quick transformations of input raster layers
More is planned, but this depends entirely on my inclination to do so, the time I have available and if it can be useful for my own research as well.
Please remember that the plugin is still experimental. So please don’t be angry if it doesn’t work for you. testing was conducted on QGIS 2.2 stable on my Debian Linux machine and it should hopefully work for Windows as well. But similar as with LecoS i have no opportunity to test the plugin on Mac OS based systems and I also don’t really intend to :-p. Sorry Apple.
- Steven J. Phillips, Robert P. Anderson and Robert E. Schapire, (2006) “Maximum entropy modeling of species geographic distributions” Ecological Modelling, Vol 190/3-4 pp 231-259
- Steven J. Phillips and Miroslav Dudik, (2008) “Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation.” Ecography, Vol 31, pp 161-175
- Jane Elith et al. (2011) “A statistical explanation of MaxEnt for ecologists” Diversity and Distributions, 17, 43–57 DOI: 10.1111/j.1472-4642.2010.00725.x