6.6 Comparing MERIS and AATSR data

In this final section, you will examine MERIS Level 2 chlorophyll data and interpret it in the light of the SST and SSHA data examined earlies The process is very similar to that used to open, mask and resample the AATSR data, so if in doubt about how to do something, refer back to section 6.1.

Opening and masking a MERIS L2 image

MERIS level 2 image files also contains flags indicating whether a pixel is cloud, land or sea. You can find more information about them in MERIS L2 Flags. The flags are used with the temperature data to select pixels containing valid SST measurements.

1. Open the MERIS image MER_RR__2PRBCM20040220~.N1.bz2 to displays the N1 file structure.

2. On the left hand side choose Bands, select the algal_data and the l2_flags bitmask, and open them connected.

3. Accept the defaults in the Extract and Redisplay dialog to open the full image.

4. The image also includes cloud and land data, so we will use a formula to mask these. Open mer2water.frm and examine its content. Make sure you understand how it works.

5. Apply the formula to the stack to create a new masked image. Save this as MER_2P_20040220m.dat.

6. Apply a palette, for example rainbow_minblack.pal.

7. Choose View > Coord from the menu bar to display the coordinates.

As you can see there several areas with scattered cloud in the MERIS image. The formula has masked those classed as 'cloud' during processing, but if you zoom in to one of these regions, for example around 49°E, 4°N, you will see that several pixels remain where the chlorophyll values are either too high or too low compared to the surrounding cloud free areas. This is caused by subpixel cloud, which was not sufficient for the pixel to be classified as cloud. However, they are clearly wrong, and must be removed before creating a composite.

In addition to the classification flags, MERIS L2 data also contains a number of quality flags, mostly raised during atmospheric correction. Use the table of MERIS flags from the side bar to look at these in more detail.

The confidence flag for the chlorophyll product is PCD_15. You can use a formula to mask pixels where this flag indicates that the chlorophyll data is suspect.

1. Open mer2water_not_pcd_15.frm and examine its content. Compare it to the earlier formula and note the differences. Make sure you know how it works.

2. Apply the formula to the stack of original algal_1 and l2_flags. Save the result as MER_2P_20040220m_15.dat.

3. Apply the same palette and Redisplay stretch as for the first masked image, and use View > Coords to set these.

4. Tile the two images side by side (minimise the stack and formulas and choose Window > tile vertical) so you can compare them.

Using TOA data to aid interpretation

It is often helpful to have the top of atmosphere (level 1) data available to aid interpretation, and understand the problems associated with anomalous chlorophyll values. The MERIS image MER_RR__1PRBCM20040220_~.N1.bz2 corresponds to the chlorophyll image you have just opened. To display the TOA data as a colour composite you have to:

1. Open the image and select the Bands folder in the left pane.

2. Open radiance_2, radiance_5 and radiance_7 as connected images. (These are the MERIS bands broadly corresponding to blue, green and red, respectively).

3. Tab to band 7 (red) and type 1 on the keyboard to change its location to @1. Find band 5 and change its location to @2.

4. From the menu bar select Image > Composite to display the colour image.

5. Select View from the menu bar and uncheck the colour bars (you don't need them).

6. Give the image an Autolinear or Equalize Redisplay stretch to display land and ocean more clearly.

7. Tile the image with the chlorophyll data and choose a Zoom that allows you to compare them.

Comparing the MERIS and AATSR composites

To speed up the creation of composite MERIS images for comparison between the chlorophyll and sea surface temperature data, a set of resampled chlorophyll images have been prepared for you. This may be turned into two composites, each of 9 images, which approximately match the time period of the corresponding weekly composites of AATSR data.

1. Open the Bilko set mer_2P_20040210_20040229.set, accepting the default Extract window, and make sure the Null value is set to 0 and the box is checked. (The mean formula requires the null values to be set to avoid the 0s being included in the mean value).

2. Open the formula mean_all.frm and modify it to select the first 9 images (i<=9). Apply it to the stack to create the first composite.

3. Open the formula View > Coordinates from the menu bar before saving the image with a suitable name.

4. Repeat to create a similar composite from the last 9 images in the set.

5. Give both images a suitable stretch, and apply the rainbow palette.

As you can see, the scattered cloud in the area gives the images a 'salt-and-pepper' appearance, even in these composites. You can reduce this and see the images better if you apply median filter. Here is how:

1. First open set the filter options to make sure they are what you want:

   • From the menu bar select Image > Filter > Options
   • When the Options dialog opens make sure the first 3 boxes are checked,
   • set the Type of the filtered image to Same as unfiltered,
   • set the Output Nulls t to Nan/Min, and
   • finally set the Null Threshold % to 30
     to fill the central pixel withe the filter output if more than 30% of the pixels in the window are valid.
   • Click OK to apply these options to any future filter operations.
     Note that you can also set these options in a formula document if you use this to apply a filter. See Bilko Help for how to do this.

2. The filter fills gaps based knowing where the Null values are, so check the Redisplay stretch to make sure Nulls are set to 0.

3. To apply the filter, you first need to select the region to filter, in this case the whole image: [CTRL+A] will select All.

4. From the menu bar select Image > Filter > Median , set the Filter Size to 3 rows by 3 columns, and click OK.

5. Save the filtered images with a suitable name, and adjust the stretch of each if you wish (e.g. Min=20, Max=200).

You are now ready to compare the MERIS and AATSR data from the two periods.

1. Open the two composite AATSR images you created in section 3, making sure the Null value is set.

2. Run a median filter with a window of 3 x 3 over each image.

3. Give the output a suitable stretch (e.g. Min=29700 and Max=30200), and apply the Modjet1 palette.

4. Tile the images so you can see each SST / Chlorophyll pair to compare them.

Next: Summary and Conclusions