Access to the GLOBEC NEP Satellite SST and SeaWiFS Archives

(US West Coast and Gulf of Alaska)

Access to Global Altimeter SSH Data

 

Below we describe two ways to access the GLOBEC SST (surface temperature) and ocean color (chlorophyll pigment concentration) data in the NE Pacific; we also describe access to  global altimeter SSH (surface height) data. The web archive and IDL widgets for SST and ocean color only access data in the NE Pacific. The IDL widget for SSH allows access to global data. If you are only interested in the altimeter SSH data, the widget access is described at the end of this document, but it would help to read the more detailed description about the SST widget first, since the altimeter widget works similarly and is not described in as much detail. The altimeter data are available through the widget, but are not yet (10-11-07)  on the archive. Altimeter field for the California Current, with improved coverage next to the coast, will be place on the archive in the future.

 

There are two ways for those with COAS accounts to look at and retrieve the AVHRR SST and SeaWiFS pigment concentration images in the GLOBEC NEP Satellite Data Archive maintained by Ted Strub, Eric Beals and Corinne James: (1) Using the Archive website now maintained by Eric Beals; and (2) Using "widgets" produced by Corinne James using IDL (no knowledge of IDL is required). Those without a COAS account can use the Archive web site but not the widget, unless they request an account specifically for this purpose from Ted Strub. Each of these tools has a slightly different purpose. Both allow access only to the SST and pigment concentration data archived at COAS in the NE Pacific Ocean: in the California Current from Baja California to southern Alaska; and in the Gulf of Alaska between B.C. and the Aleutian Islands. The widget allows access to global altimeter SSH data.

 

WEB SITE: (http://coho.coas.oregonstate.edu). This is actually an alias, but should continue to work, no matter where the web site actually goes.

 

The web site allows anyone to pick a specific region (one of several large, fixed regions) and year and choose images from a list for that year. Each image can be seen well enough to estimate whether it is cloud-free enough to warrant getting the file (using anonymous ftp). One chooses a specific region, then a specific year. A list of all files for the year is displayed, with file names that indicate year-day. Clicking on a given file displays it. Another button produces an identical list and allows you to ftp the files you want.

 

WIDGET: (login to coho.coas.oregonstate.edu using your college account or an account set up by Eric Beals for non-COAS users). This widget accesses the same data and makes a "warmest pixel" composite of SST (AVHRR) or an average of all “cloud-free” pixels for pigment concentration (CHL, from SeaWiFS) for all images within a specified period, within a subset region. It then allows you to look at single SST or CHL images from within that period, note the clearest, and choose single or subset groups of the images in that period to use to reform the composite (SST) or average (CHL). For SSH, it grids all of the alongtrack data in the region and time period you specify to make a single map of gridded SSH. It allows you to change or roll the palette to bring out the features of interest and then to output the viewed image as a postscript image file or the actual data values as a byte array of temperatures, pigment concentrations or SSH. These are stored in your home directory on the COAS system. The postscript files can then be printed or ftp’d to another system. The data files can be imported to other analysis tools (Matlab, IDL, etc.).

 

The use of these two tools is described in more detail below.

 

WEB SITE

The Archive web site allows anyone to look at the available AVHRR and SeaWiFS

images. The AVHRR archive extends back in time to1992 and will extend through 2004. The SeaWiFS site begins in fall 1997 and extends to within several months of the present, except during periods of reprocessing. The website allows you to look for clear images for several regions and use anonymous FTP to get the files (single SST and pigment images). You then use your own software (most use Matlab) to subset and display them.

 

Go to   http://coho.coas.oregonstate.edu

 

AVHRR

Read the AAREADME... file for details on the actual 1-km and 3-km AVHRR files, how to ftp them outside of the web site, what they represent, etc. - it's long but has all the details for the AVHRR files. You may only need to read the parts pertaining to one of the regions (north, south and central in the Calif Current, east and west in the Gulf of Alaska). There are also links to an older archive of channel 4 (11 micrometer) AVHRR SST in several smaller regions. These were collected in the ONR EBC project and should eventually be removed.

 

There is also a page for 9-km Pathfinder AVHRR data (“weekly” 9-day “warmest pixel” composites, centered every week, and monthly warmest pixel composites made from those), extending back to 1985 and covering the very large-scale NE Pacific east of about 170W. Scroll down to the first section of the home page and you can click on the Pathfinder data. There is also a comparison of selected Pathfinder images that show the El Nino effects on the California Current during 1997-98.

 

To view the higher resolution AVHRR SST images in one area (say the northern Calif Current, which includes approximately SF to the Queen Charlotte Islands), go to the web site, scroll down to "1-3 km AVHRR images" and click on that. You will be given a choice of regions and shown maps of those regions. Take a minute to look at those regions, and their subregions labeled A, B, C and D. These are used in the name of the files. Click on the region you want (North, South or Central Ch4 for the California Current region; East, East Ch4, West or West Ch4 for the Gulf of Alaska). The North and South regions for the California Current divide at around Monterey-San Francisco, with overlap between the North and South regions. They use “Pathfinder-like” algorithms to estimate absolute SST. The “Central Ch4” region covers most of the California Current with 3km pixels, using Channel 4 (11 microns) only (the least noisy channel), so the SST values are less accurate, but the gradients and features are less noisy. The East and West regions of the Alaska Gyre are, likewise, absolute SST, while the East Ch4 and West Ch4 are the less noisy channel 4 radiance temperatures.

 

After you choose a region, select a specific year and click “Go”. You will see a list of files for the whole year, arranged chronologically. The file names are of the form, nYYDDDHH_TTTT_nxx.gbc.Z, where the “n” stands for the northern regions (it will be “s” for the southern region and “c” for the central region, “w” for the western GOA and “e” for the eastern GOA). The YYDDDHH stands for the year, year-day (1-366), hour Zulu (GMT). The nXX will give the NOAA satellite number (n12 for NOAA 12). The “_TTTT” is an attempt to use the automatic cloud mask to estimate the tenths of clear cloud cover in each of 4 subregions of the image. The subregions are those we asked you to note above, on the opening page for the AVHRR high resolution data. NOTE — CLOUD MASKS DO NOT WORK VERY WELL FOR AVHRR. This is not the fault of those processing the data; it is simply a statement of the present lack of skill of operational cloud masks. Using this “TTTT” part of the name as an indicator of possible cloud-free regions is an option that will sometimes save time (look for the highest numbers, like “9999” (never found) or “7535” (more realistic). With this web page, the cloud mask is applied to all images except the Ch4 versions, so you won’t realize that there is good data under the white cloud mask unless you look at the Ch4 images or use the widget (below). The southern region gives 1km resolution in a region from about SF to below Baja Calif. Both northern and southern regions give SST as (approximate) “absolute temperature,” using algorithms like the Pathfinder non-linear algorithms (read the link to SST processing on the main page for further details). The central region is 3km channel 4 (11 micrometer) SST, covering the entire region from Baja California to British Columbia. The two Gulf of Alaska Regions are 1km resolution “Pathfinder” absolute SST, with equivalent regions covered by channel 4 radiance temperatures. By 1km we mean something like 1.4km .

 

This browser is a good way to quickly go through the available images for a region and period, write down the file names for the best ones, then go back to the top of the list and click on the ftp link shown there to “(don’t click on the name to the left; the name changes for each region; click on the name at the top of the list). You will see a similar file list. Choose those that you want and transfer them to someplace where you can analyze them. You get the entire file for each image (3-4MB), so be prepared to receive a large volume of data and then to subset the files and analyze them using your own software.

 

SeaWiFS

Separate links are available for the SeaWiFS surface pigment concentrations files,  made available by Andy Thomas (U. Maine, Orono). There are separate viewers for individual daily images and for 8-day composites. The data are 4km GAC data from NASA. Unlike the AVHRR files, which are plain byte arrays, these are HDF files, as required by NASA. Links to Andy’s web site provide the details of the data area definitions, suggestions for software that can help display the data, and examples of MATLAB and IDL code that read the files. To actually use the data, you should be an official SeaWiFS Investigator and the intial text fields give you a URL and you can click it to fill out the form needed to become an official SeaWiFS Investigator. The browser for the SeaWiFS data of 1-day fields works just like the AVHRR browser, allowing you to view and ftp the files. The browser for the SeaWiFS 8-day composites allows you to view the fields. To access the actual composite data files, you will need to contact Andrew Thomas (email given at the site).



 

WIDGETS FOR SATELLITE SST, PIGMENT AND SSH

 

Instructions for the view/composite widgets for the archived GLOBEC AVHRR and SeaWiFS files - for users with COAS computer access.

 

These IDL "widgets" were originally constructed by Corinne James to allow the GLOBEC NEP AVHRR files to be subset, displayed, composited and saved as postscript image files or byte arrays for use in other programs. They can be used from any workstation running an X-Window that can telnet to the workstation called coho.coas.oregonstate.edu. If you have a COAS login and password, that should allow you to telnet and login. Others should ask Ted Strub, Corinne James or Eric Beals for an account (this can take several days).

 

To run the widget on a SUN workstation, you must choose the “Common Desktop Environment” or CDE when you logon (choose this under “options” “session”).

 

On unix or linux workstations, first make your workstation able to display from

a remote workstation.

 

In UNIX

"xhost +"

or

"xhost coho"

 

On PC’s (I assume also MACs) you need to be in an X-window environment. We use software called “hummingbird” on PC’s.

 

If your X-window software is not set up to connect to “coho” automatically, you probably have to use something like ssh or telnet

"ssh coho.coas.oregonstate.edu"  or

"telnet coho.coas.oregonstate.edu"

(then log on with your COAS login and password)

 

Once connected to coho, you must use “setenv” to tell coho to set the display to point to your local display:

"setenv DISPLAY computer_namw:0" (EXAMPLE: "setenv DISPLAY bettyb:0" for workstation bettyb)

 

then start the SST viewer with

"source /home/pisco/usr4/corinne/viewer" for the AVHRR data

 

or

"source /home/pisco/usr4/corinne/swview" for the SeaWiFS data

 

or

source   /home/pisco/usr5/corinne/grid” for the SSH data

 

 

AVHRR Widget

The "viewer" is designed to make "warmest pixel composites" from the archived SST files that occur in a specified period in specified spatial sub-regions of the original image domain. The final composites can be saved as a byte array or as a postscript file of the displayed color image. The viewer allows you to change and roll palettes before making the postscript file of the displayed image. The cloud masks are not used in this widget, unlike the archive web site viewer (above), where the cloud masks are always used. 

 

At the top of the viewer you have the choice of which regions to use as the

source of the image data ("Original Image Area"). You can choose "North"

"Central" or "South" for the same regions of the Calif Current described above for the web site and shown on our web page at http://coho.coas.oregonstate.edu (click on 1-3km AVHRR). The north and south regions have 1.4 km pixels (absolute temperature) splitting the Calif C. coverage around central Calif, while the "Central" region covers the entire CCS region, Baja to Canada with 3 km pixels - these are channel 4 radiance temperatures only, not absolute temperature, but they show the SST patterns using the channel with least noise. The other two regions are GOA West and GOA East. When you click one of these Original Areas it shows you the lat/long boundaries of that area. You then choose a Composite Area - the subregion you want to see, which must fit within the Original Image Area. Each Original Area has a default Composite Area. The default for the North region is the GLOBEC CCS field study region, 41N-46.5N out to 127W. You can change these. Below these boxes, you can change the date range for the initial composite you want to form. The viewer will form the "warmest pixel composite" for all images within this date range. Choosing the warmest pixel from all possible images at each pixel location eliminates many cloudy pixels, since they are colder, but it also smears features that move and favors one image over another if there are systematic offsets in temperature between images from day and night (there are) and from different sensors (there are) and different look angles (there are). For this reason (and because it takes a fair amount of time to uncompress each image and form a composite, you don't usually want to composite images from more than 3-10 days. Then you can use the viewer to view each of the images that went into that composite and to form new composites of just some or one of the images in the date range. The default date range is set to "yesterday and today". After choosing the date range, click "CONTINUE" to form the initial composite. If you only want to look at a single image, you still have to first form a composite of all images from that day, then choose the single image you want to see and make a new “composite” of just that image.

 

When you click on "CONTINUE," the viewer uncompresses the files within the date range, forms the composite and displays it in the two windows that appear. The left window is displayed at a fixed size for the pixels (small regions are displayed in a small window, big regions may require scrolling to see different parts), while the right window remains at a given spatial size on the screen (so small regions are blown up, large regions are reduced to fit in the window).

 

The numbers to the left of the windows show the Lat/Lon boundaries and date range chosen (changing them on this page has no effect, they are just for information). To change these ranges, you must click "New Date and Area Range" to go back to the previous window. The other buttons allow you to roll the palette, change to a different palette, change the coast color, save the composite image in the left window as a byte array or save a postscript file of the composite image in the left window exactly as it looks in the window (after adjusting palettes).

 

The color bar at the bottom left shows the temperature range and the current

palette. You may need to move your cursor over the image or the color bar to activate the colors. The arrows allow you to "roll" the palette. The "Palette" button allows you to choose a new palette. Click on "Palette" and it will produce a separate palette bar, with arrows, above the fixed one. Click on the "Palette" button on this bar and you will see a choice of three different types of palettes, IDL, DSP ASCII and DSP Native Palettes. The default is a slow AVHRR palette in the DSP Native palettes. To see other choices, click on "DSP Native Palettes", then choose the file "cj.pal", which is a collection of palettes from Corinne James. Choose the "f avhrr" to try the faster AVHRR palette. There are many choices. Click done on the two Palette boxes. Then click the arrows on the upper palette box to roll the palette. If the images don't change, move the cursor over an image, click somewhere in the image and select "palette" again and roll the palette. You can roll the palette using the low (permanent) palette arrows, but it does not update the image until the curser is moved over the actual palette bar or the image (i.e., until it is moved over some piece of color that the palette controls).

 

After the initial composite is formed (it takes some time to uncompress a large number of files, a bar shows the progress), a message appears on your screen explaining the controls available. To get rid of this message, click "Done with Xcompos Info" at the top.

 

The top dropdown bar ("Composite of X Images") under each window allows you to either view the composite or individual images in the window above it. Click the bar and then the names of files you want to see. The two windows can be used to compare different images that went into the composite (or one image with the composite). One procedure is to leave the composite in one of the two windows. Then click the top bar under the other window and sequentially go through the list of images, noting the clearest ones and the ones that appear to have formed the composite. Then go back and compute a new composite (using the lower list of files) and compare to the old composite. Make composites of the smallest number of images that allow you to see the features of interest (one image if possible).

 

The list of files at the bottom includes all of those found within the specified date range. A new subset of files can be selected from this list by holding down the "Control" key while clicking the files in the list. Then click "Reform Composite" to make the new composite. Using the dropdown list of files, you can click on a file and change the adjustment (offset in degrees C) that is added to all pixels of that file when forming the composite. At present we set default offsets based on buoy comparisons, but in fact the correct value for the offset depends on the look angle (how much atmosphere the satellite is looking through), even though the image has theoretically been corrected for atmospheric effects. It is tedious, but one can play with the offsets for clear parts of two images in order to make them look the same, then recomposite and the images will be more compatible. After setting a new offset, however, the composite doesn't change until you select the files below and click "Reform Composite". New composites can be formed from different groups of files in the right and left windows, to compare the effects of changing offsets, including different files, etc. A median filter is also used on the pixels and the width of this square filter can be changed.

 

Saving images (postscript files) or data (byte arrays): Images can only be saved from the left window. To save a byte array corresponding to the composite chosen in the Left Window, click "Save Image" in the lower left. To save a postscript file of the composite in the Left Window, click "PS file". You have the choice of making a postscript file that shows all of the individual images plus the composite or just the composite. The postscript file will look like the image in the Left Window, so you can roll or change the palette to highlight features, then save the postscript file. The save option refers to the Left Window only, the right window is just used for comparing images and composites. Individual images can be displayed and saved by specifying “Displayed Image only” or by simply selecting that one image and forming the "composite" of that image alone. You must specify the names for the saved images and postscript files. Note the path of the directory where it is placed (it should be your COAS home directory). You will need to ftp to move these files to other machines or systems.

 

SeaWiFS Widget

 

The SeaWiFS widget works just like the AVHRR widget, except that averages are formed for each pixel (not highest pigment composites), using all of the images in which that pixel is judged cloud free in the time series. The data are 4km daily images (only 1/day) and there are only two source regions – the complete California Current (Baja Calif to BC) and the Gulf of Alaska.

 

To start the SeaWiFS widget, telnet to coho.coas.oregonstate.edu, use the “setenv DISPLAY computername:0” command and then type

 

source /home/pisco/usr4/corinne/swview

 

SSH Widget

 

The SSH widget also works like the AVHRR widget, except that the data set is global and the widget grids the alongtrack SSH data to a grid of your choosing.

 

Read the “AVHRR Widget” instructions above to get the overall procedure.

 

Login into coho.coas.oregonstate.edu from a machine which is capable of displaying X windows (a unix box or a PC with hummingbird or similar X windows software installed). If you are using a SUN workstation, choose the CDE environment as you login).

 

Set the display variable on coho to point to your machine:

 

setenv DISPLAY XXX.XXX.XXX.XXX:0

 

where  XXX.XXX.XXX.XXX is the IP address of your machine. If this part is confusing to you, please ask someone you work with who is computer-saavy to help you.

 

 Then type:

source   /home/pisco/usr5/corinne/grid

 

to start the SSH IDL widget.

 

A window should be displayed on your screen which allows you to select a geographical area and a date.  This program will produce a 'snapshot' of altimeter data for the region specified, interpolated to the date you give. It works fine to just leave all the other defaults set as they are.

 

Once you click 'continue', you will get a new window which displays the data. There are 2 windows which can be manipulated independently so you can compare changes to the original display.  There may also be a third “IDL” window. You can eliminate that window or ignore it. Eliminating it should not end the X-window session, even though you are warned that it might.

 

There are options which let you change the way the data is displayed, by smoothing it, by contouring it, etc. You can also display the original alongtrack data over the gridded field so you get an idea of how much interpolation/extrapolation is taking place. There are also some controls

which allow you to redo that calculation with different parameters.

 

There are buttons on the left which allow you to make a postscript file of the field so you can print it. You can also save the data in a disk file either as a gridded field or in its original alongtrack arrangement.

 

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Questions can be asked of Eric Beals for the web site SST and color browser (beals@coas.oregonstate.edu), or Corinne James for the IDL widgets (corinne@coas.oregonstate.edu). Ted Strub (tstrub@coas.oregonstate.edu) can be contacted for general questions