Ocean Biogeochemistry Lab
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Ocean Biogeochemistry Lab |
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For more specific information about these programs also see the SeaDAS Seadisp Program-Level Documentation at the SeaDAS homepage.
Data for Blotches/Histograms/etc...:
We'll be working with images in SEADAS today. You can use the following AVHRR files:
199707h09ma-gdm.hdf
199712h09ma-gdm.hdf
You've worked with these before, and they're available on Icy at /home/eess141/AVHRR/. Copy them over to your own folder on /disk3/eess141/ (you can make an AVHRR sub-directory), rather than working from the home directory. Or if you prefer, you can use your own favorite SeaWiFS or MODIS/Aqua image, downloaded from the Ocean Color website. You can store your downloaded image(s) in your own folder (on /disk3/eess141/).
Load using seadas:
SeaDAS Main Menu, -> 'Display'
Click the Sea surface temperature button to load SST band.
Working with Blotches
[ Displayed Image Window -> Functions -> Annotate/blotch ]
Often you do not want to do statistics on an image as a whole (see histograms),
but want to focus on a smaller area of interest, or want to compare
2 or more 'provinces' or 'zones' in the image. This can be done with the
Annotate/Blotch function (find it under the Functions menu of the Display
window).
With Annotate/Blotch you can draw blotches of various shapes; freestyle (polygon), ellipse and rectangular. Also note that you can add text or arrows on your image. Might be useful when you want to point out some interesting features on your fully processed image.
Example: Suppose you want to analyze the area of higher temperature in the middle of the Gulf of Mexico (see image). This feature might be an eddy or something. Using the Anntotate/Blotch function you can mark this area easily with the freestyle object (see figure). Just click and hold and then outline the feature on the image. The blotch is defined as the area marked by the color you choose (red is the default). So you will have to Fill the area Solid (by clicking next to the 'Solid' button, in the 'Fill' category), otherwise SeaDAS thinks that the blotch is only the colored outline itself.
You can change the shape or move the blotch by dragging the white squares at each corner, or the middle square, respectively. Managing blotches is a little bit tricky sometimes. It's easy to delete them accidentally. If you see the white squares, the blotch will be deleted if you select another object (Rectangular, Ellipse, etc.). Save them by pressing the Save button.
Multiple blotches can be drawn on the same image. If the area of interest is not contiguous (i.e., cannot be drawn with one blotch), you want to use the same color. If you want to have two separate areas of interest for separate analyses, use a different color for the second blotch.
Often you want to do the same analysis on more then just this one image. So you have to save the current blotches to an object file so you can load it later on another image. Saving to file is different than just pressing the Save button on the Annotate window. (The latter Save function is only to prevent the blotch you have just drawn from being deleted/replaced when you want to add another one). The key when using saved (to file) blotches on multiple images is that all the images must have the same projection and size as the original one. If not, the blotches will be misaligned. To save a blotch as an 'object', select File --> Save As. Blotch files should be saved to your personal directory on /disk3/eess141/. To load a previously saved blotch select File --> Load.
One can also add text using the Annotate/blotch function. For this check the circle next to 'ABC', Type the desired text in the text window; then click on the image to add it. The size, alignment, and font can be changed from the menu. Also, the text can me moved using the white squares. The text can be saved in the same way as the blotches.
Histograms
[ Displayed Image Window -> Functions -> Histogram ]
Some simple statistics of your image can be calculated using the histogram function.
On the display window of interest select 'histogram'. A new window will
pop up. If you are interested in analyzing the statistics within a blotch, select 'blotch' instead of 'Full Image' (be sure to select the correct color of the blotch of interest). Select the Data Min and
Max carefully. Whole numbers are easiest to understand. The number of bins
(intervals) shouldn't be too high or too low. Some experimenting might be
necessary. If, for example, the maximum temperature value is 28.3500
degrees, you might select 30 as your max. As min you can use -2 (close to the freezing temperature of seawater) or the actual min (rounded).
If you make the bin size 1 (degree C) the resulting histogram will be easy
to analyze (it will display the number of pixels with a temperature
of 0-1, 1-2, 2-3, ..., 29-30). Click 'Plot' and the result pops up (see
figure). In the legend you can read
the min, max, median, mean, etc. You can output (save) the histogram either
as an image (eg. postscript or .png, by selecting Output on
the histogram plot) or as data by saving it to a text (ascii) file (select
Output Data on the Histogram Settings window). The ascii file you
can download/ftp to your PC/Mac for further analysis, plotting in Excel for
example.
The default blotch color is red. If you made multiple blotches, or drew them in a different color, select the appropriate color to analyze for your histogram. The Non-Blotch selection will render a histogram of the full image excluding the blotch. Check the generated plot (and output data file) carefully if the number of points selected (shown at the bottom of the histogram plot) seems logical. Also, when you output data to a text file, the data of the last plotted histogram will be saved. For example, if you change the settings after you plotted a histogram, and click on Output Data the result will not be those of the changed settings but of the original histogram. So be sure to plot it first before you output the data.
Scatter Plots
[ Seadas Main Menu -> Utilities->Data visualization-> Scatter
Plots ]
To see if there is any relationship/correlation between two parameters displayed
in two different bands you can perform a scatterplot analysis. If you are using the given AVHRR files from July and December, try comparing one to the other in a scatterplot from your chosen region of the ocean. Does July or December have cooler SSTs? You can have
the histogram of the input image show on the side of the scatterplot as well. After you have
selected 'Image 1' and 'Image 2' you might have to modify the Data and/or
Axis range somewhat to exclude land/bad/missing data (see figure). You may want to choose
the 'Blotched area' instead of 'Full Image'. For this, one has to load the
saved blotches first from the annotate/blotch window.
Bathymetry Maps
[ Seadas Main Menu -> Utilities->Data visualization-> Generate Bathymetry Image ]
Often we want to know how deep an area of the ocean is (for example, when comparing coastal zones with off-shore waters). It is easy in SeaDAS to generate a bathymetry map with the same projection/size as your processed satellite image. Select 'Generate Bathymetry Image' under Functions (Seadisp Main Menu). Select the band number (see Band List Selection window) from where you want to retrieve the lat/lon limits, size, projection, etc., and click 'Okay' (see figure). The newly generated Bathymetry Image will show up as a new band in the Band List Selection window. Change to different color scheme if it's helpful. Also, adding the color bar might help.
Profiles (Ship Track)
[ Displayed Image Window -> Functions -> Ship Track ]
With the Ship Track function you can read and plot the pixel data along a line segment in the satellite image. You can load either a file with latitude and longitude values of your profile ('ship track') of interest using the 'Import Track Data' option. You can also define it on the image by clicking on the 'Modify Track Data' tab of the Ship Track Main Window.
To define a profile click on the 'Modify Track Data' tab. A cursor (yellow plus sign in the image) can be moved by dragging the 'normal' cursor in the black box ('virtual mousepad'). To mark the starting point, click 'Add a new point'. Then move to your endpoint and click on 'Add a new point' again. You can draw a line between the two points by setting 'Connect data points' to YES in the 'Track & Cursor Setup' options. More points can be added as well to your ship track.
Then go back to the 'Data Analysis & Plotting' tab and click on 'Image data along track' to generate a plot of the pixel values along that line. You can change the plot setup first by selecting 'Plot Setup' first. If you want the actual numbers to import to Excel for example, click on 'Output line segment data'.
FTP data to your directory: NCFTP and wget
FTP (file transfer program) allows you to transfer files between computers, for example from your computer to Icy and vice versa. Fetch is a FTP program that allows you to manually move files back and forth. You can download files from the Ocean Color website to your computer, then move them onto Icy using Fetch.To do so, open Fetch and it will prompt you for login (host: icy.stanford.edu and username: eess141). Enter the password and make sure you are securely connecting using 'SFTP'. Once logged in, 'get' will allow you to get a file from Icy to a specified folder on your computer, while 'put' allows you to put a file on Icy (in a specified directory) from your computer.
Another way to bring Ocean Color files to Icy is to quickly 'ftp' a file to your directory on Icy, using the command wget. For example, on NASA's oceancolor website, in the Level-3 Standard Mapped Images browser, right click (or control+click) on the link to a file, and select 'Copy Link'. Then on Icy, type: wget and paste the link. For example: wget http://oceancolor.gsfc.nasa.gov/cgi/getfile/A20080172008024.L3m_8D_CHLO_4.bz2. If the link contains '?sub=img' at the end you will need to delete those characters in order for wget to work. The file will automatically download right away to your current directory. Be sure not to put large numbers of files on the home directory -- use your directory on /disk3/eess141/.
