Access to the GLOBEC NEP Satellite SST and SeaWiFS
Archives
(US West Coast and
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
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
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
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
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
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
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 (
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.
--------
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