A multilayer mask overlay combines a set of single-color bitmask overlays. A multilayer mask uses data values from a quality variable to color each pixel whose bit is set to 1 with a different color.

We'll start by opening the VIIRS chlorophyll data file example_viirs_chlor_flags_oct_2022.hdf in CDAT and loading the chlor_a and l2_flags variables, then zoom into Hawaii:

CDAT window showing chlorophyll data in Hawaii

The l2_flags variable holds quality information that we'll use to mask the chlorophyll data, using individual bits in a 32-bit integer. For simplicity we'll show an example using the first 8 bits as follows:

Click the Mask button in the toolbar, and then Multilayer bitmask.
An overlay properties window will appear — select l2_flags as the mask variable, leave the mask size as 8-bits, and then replace the layer labels as follows:
- Bit 1 → ATMFAIL
- Bit 2 → LAND
- Bit 3 → LOWLWCORR
- Bit 4 → HIGLINT
- Bit 5 → HILT
- Bit 6 → HISATZEN
- Bit 7 → COASTZ
- Bit 8 → LANDADJ
Click OK to finish creating the overlay.
Select the new Multilayer 1 overlay in the list and click the Edit button.

You should now see the following:

CDAT window showing chlorophyll data in Hawaii with multilayer bitmask overlay properties

We can now turn on and off each bitmask layer to see which pixels it masks. Make sure the Auto-apply is checked to see each change to the overlay as you make it. The main bitmask layers that you'll see in this view will be the LAND, COASTZ, and LANDADJ bits. Zoom out while keeping the overlay properties window open to see the HISATZEN and LOWLWCORR bits.

Bonus exercises:

Click the Info button in the toolbar to look at the raw metadata for the l2_flags variable and see what the various flag bits contain. This metadata shows only the flag_masks and flag_meanings attributes, and not the corresponding bit numbers. You can use the Wang et al., VIIRS Ocean Color ATBD, Version 1.0, June 2017 as the documentation for all the flag bits (see the table on page 39, and note the bit numbering start at 0).
Try changing the mask size to 32-bits to see all the flags. Turn on bit 21 to see the moderate sunglint contamination mask.
Try clicking the Show All and Hide All buttons and see what they do.
See the Saving and Loading Overlay Groups exercises — there you'll find a bonus exercise for loading a pre-made overlay group with labels for all 32 bits of the l2_flags variable.