Prac%cal: Using the Giovanni tool to inves%gate variability in phytoplankton Stephanie Henson

Transcription

1 IOCCG Ocean Op+cs School 2014 Prac%cal: Using the Giovanni tool to inves%gate variability in phytoplankton Stephanie Henson

2 Introduc%on to the prac%cal Use a simple online tool to play with some +me series data We ll do one example together of crea+ng, downloading and analysing a +me series We ll run some simple code (Matlab/Scilab) to create: Climatology Anomalies A metric of peak chl +ming Then you ll have a chance to play with data from your own region At the end, I d like some students to show a plot or 2 and explain what they ve discovered

3 Introduc%on to the prac%cal Giovanni online data analysis tool h?p://disc.sci.gsfc.nasa.gov/giovanni I ve checked in Firefox and IE (I haven t checked Chrome) Some kind of sopware to open text files (Excel or similar) Programming: Scilab or Matlab

4 Introduc%on to the prac%cal Giovanni online data analysis tool h?p://disc.sci.gsfc.nasa.gov/giovanni Advantages: No need to download tons of data Useful as a first look, if you know exactly what data you want (+me period/loca+on) For more quan+ta+ve analysis s+ll need Matlab (or whatever your preferred sopware) No programming required Not just chlorophyll

5 Introduc%on to the prac%cal Disadvantages: Can be slow for large amounts of data Limited to maximum resolu+on of 8- day, 4km data for NASA satellites only (SeaWiFS and MODIS) Cannot extract +me series from irregularly shaped areas Can only use standard products So not necessarily suitable in Case 2 waters and anything op+cally complex (e.g. turbid) No inland waters

6 Choose the dataset

7 Choose the dataset We re going to use monthly data today because it s quicker, but note that 8- day data is also available

8 Select an area of interest Either draw a box or type in the la+tude/longitude co- ordinates

9 Select a parameter Tick the box for the relevant parameter

10 Select the %me period 2. Select Time series op+on 3. Go! 1. Set the +me period you re interested in

11 You ll probably get a warning about extrac%ng a large amount of data.

12 You ll probably get a warning about extrac%ng a large amount of data.

13 Wait. The online tool has to complete 7 steps to extract the data. You can check back to see how it s doing. Only when it s finished will you get the final figure

14 The output It s finished processing when you see the graph

15 Download the data Download the plot Download the +me series as a text file

16 Introduc%on to the prac%cal In today s prac+cal, we ll run through a couple of examples of using Giovanni together, then you can have a go with your own region of interest Hopefully we will have +me for some of you to show some interes+ng +me series results from your own region of interest

17 hcp://disc.sci.gsfc.nasa.gov/giovanni Choose Ocean Products, then Ocean Color Radiometry Online Visualiza+on and Analysis Monthly Data La+tude/longitude bounds: 39 to 51N and - 25 to - 11E Select MODIS- Aqua 9km Chlorophyll Date range: Jan 2003 to Dec 2013 Visualisa+on type: Time series

18 Monthly +me series, NE Atlan+c Don t close the Results tabs at the top! To go back to the menu select tab Home

19 Map of chl in June 2012 Same lat/lon bounds; select Begin Date and End Date to both be June 2012; Visualisa+on Type: Lat- Lon Map, Time- averaged

20 Map of chl anomaly in June 2012 Same lat/lon bounds; select Analysis Op+on: Anomaly; Begin Date and End Date to both be June 2012; Visualisa+on Type: Lat- Lon Map, Time- averaged Before you hit Go...Select Edit preferences ; set Color Bar Mode to Custom; Set min/max as - 2 to 2

21 Hovmoller plot of chl (la+tude vs +me) Same lat/lon bounds; select Analysis Op+on: Parameter; Begin Date and End Date to Jan 2003 and Dec 2012; Visualisa+on Type: La+tude- Time Hovmoller diagram

22 Download our +me series data Select Result #1 tab Select Download Data tab Under Time Series Rendering +ck the box next to ASC, click Download in Batch Save the file somewhere convenient Unzip/extract the text file Open it in Excel (or other spreadsheet sopware)

23 Import the data Unzip text file 7Zip is useful Start up Scilab (or Matlab) Highlight just the chl values, copy and paste into Scilab: - - > Chl1=[ (now paste in values) ]; Try plosng - - > figure;plot(chl1) In Matlab: File>Import data Make sure Number of text header lines is set to 9, then accept defaults. Your data will end up in variable data Following commands are iden+cal in Matlab, so use that if you prefer

24 Time series

25 // Define your +me step here it s monthly (so 12 per year) and our +me series is 132 steps long ct=1:12:132; // For each +me step (here each month) find all the Januarys, then all the Februarys etc. and average together for M=1:12 p=ct+(m- 1); A=Chl1(p); meanchl1(m)=nanmean(a); end //Now plot it... figure;plot(meanchl1) Create a climatology

26 Climatological chlorophyll

27 Create an anomaly +me series // replicate the climatology X +mes (here 11, because our +me series is 11 years long) to make it the same length as your full +me series mean_+me_series=repmat(meanchl1,11,1); In Matlab mean_+me_series=repmat(meanchl1,1,11) ; // now subtract the mean from the +me series anom_chl1=chl1- mean_+me_series; //try plosng it

28 Anomaly +me series

29 Calculate the peak (and +ming) Calculate the peak (and its +ming) for each year ct=1:12:132; for Y=1:11 // For each of 11 years T=Chl1(ct(Y):ct(Y)+11); // Extract one year at a +me [mx(y),mx_month(y)]=nanmax(t); // end figure;plot(mx) //save your work save( IOCCG )

30 Time series of annual peak chl value

31 Now it s your turn! How might you use +me series of ocean colour data in your work? What is the interes+ng science ques+on you might ask with +me series data? Now think about temporal scale, spa+al scales, parameters, type of informa+on/analysis/plots that will be useful to answer your ques+on...and go for it! Make a plot or 2 to show your results at the end of the session