Creating Cloud free images out of a MOD09A1 MODIS image in GEE?

Question

How can I mask clouds in a MODIS\MOD09A1 images in GEE? I know I should do sth with the "Bitmask for QA", but how?

var myImgCln = ee.ImageCollection("MODIS/006/MOD09A1")
    .filterMetadata(???

Answer 1

I haven't actually worked with MODIS, but it looks like most other image collections in EE. The images contains a QA band, StateQA, with data about clouds/shadow/etc. The catalog contains a description of which bits contains which information:

Bits 0-1: Cloud state
    0: Clear
    1: Cloudy
    2: Mixed
    3: Not set, assumed clear
Bit 2: Cloud shadow
    0: No
    1: Yes
Bits 3-5: Land/water flag
    0: Shallow ocean
    1: Land
    2: Ocean coastlines and lake shorelines
    3: Shallow inland water
    4: Ephemeral water
    5: Deep inland water
    6: Continental/moderate ocean
    7: Deep ocean
Bits 6-7: Aerosol quantity
    0: Climatology
    1: Low
    2: Average
    3: High
Bits 8-9: Cirrus detected
    0: None
    1: Small
    2: Average
    3: High
Bit 10: Internal cloud algorithm flag
    0: No cloud
    1: Cloud
Bit 11: Internal fire algorithm flag
    0: No fire
    1: Fire
Bit 12: MOD35 snow/ice flag
    0: No
    1: Yes
Bit 13: Pixel is adjacent to cloud
    0: No
    1: Yes
Bit 14: BRDF correction performed data
    0: No
    1: Yes
Bit 15: Internal snow mask
    0: No snow
    1: Snow

The below code uses a little utility function to extract the values for a range of bits. A mask with "Deep inland water" would be bitwiseExtract(image, 3, 5).eq(5).

var image = ee.ImageCollection("MODIS/006/MOD09A1").first()
var qa = image.select('StateQA')
var cloudState = bitwiseExtract(qa, 0, 1) 
var cloudShadowState = bitwiseExtract(qa, 2)
var cirrusState = bitwiseExtract(qa, 8, 9)
var mask = cloudState.eq(0) // Clear
  .and(cloudShadowState.eq(0)) // No cloud shadow
  .and(cirrusState.eq(0)) // No cirrus
var maskedImage = image.updateMask(mask)  

Map.addLayer(image, {min: 0, max: 6000}, 'unmasked', false)
Map.addLayer(maskedImage, {min: 0, max: 6000}, 'masked')

/**
 * Utility to extract bitmask values. 
 * Look up the bit-ranges in the catalog.
 * 
 * value - ee.Number or ee.Image to extract from.
 * fromBit - int or ee.Number with the first bit.
 * toBit - int or ee.Number with the last bit (inclusive). 
 *         Defaults to fromBit.
 */
function bitwiseExtract(value, fromBit, toBit) {
  if (toBit === undefined) toBit = fromBit
  var maskSize = ee.Number(1).add(toBit).subtract(fromBit)
  var mask = ee.Number(1).leftShift(maskSize).subtract(1)
  return value.rightShift(fromBit).bitwiseAnd(mask)
}

https://code.earthengine.google.com/06804ee80db139b931c2aa6329fa4c8b