Vjylku

I'm using Earth Engine to preprocess and download some NDVI data. I used a region of interest to clip the imagery to a geometry, and values from the Summary QA layer to mask out pixels that were of poor quality. However, when I export imagery to my drive account, download, and open in R, the areas that were masked have pixel values set to 0. I want those pixels to be set to NA's instead. A repeatable example:

// Generate Region of Interest

var ROI = ee.FeatureCollection('TIGER/2016/Counties')

  .filter(ee.Filter.eq('NAME', 'Waldo'));



// Create clipping function

var clipper = function(image){

  return image.clip(ROI);

};



// Create a QA mask function

var masker = function(image){ 

  var mask1 = image.select('SummaryQA').lte(1);

  var mask2 = image.select('SummaryQA').gte(0);

  return image.updateMask(mask1).updateMask(mask2);

};



// Compile the data

var dataset = ee.ImageCollection('MODIS/006/MOD13Q1')

                  .filter(ee.Filter.date('2018-01-01', '2018-12-31'))

                  .map(clipper);

print("MOD13Q1 Image Collection", dataset);



// Select just NDVI for repeatable code

var ndvi = dataset.map(masker).select('NDVI');

print("MOD13Q1 NDVI Collection",ndvi);





// PREPARE DATA FOR EXPORT

// Tyler Erickson provided the stacking function

// https://gis.stackexchange.com/a/254778/67264

var stackCollection = function(collection) {

  var first = ee.Image(collection.first()).select([]);



  // Write a function that appends a band to an image.

  var appendBands = function(image, previous) {

      var dateString = ee.Date(image.get('system:time_start')).format('yyyy-MM-dd');

      return ee.Image(previous).addBands(image.rename(dateString));

  };

  return ee.Image(collection.iterate(appendBands, first));

};

var ndvi_img = stackCollection(ndvi);



// Export the data

Export.image.toDrive({

  image: ndvi_img,

  description: 'MOD13Q1_comp_NDVI',

  scale: 250,

  region: ROI,

  fileFormat: 'GeoTIFF',

  formatOptions: {

    cloudOptimized: true

  }

});

If you take the product from Export.image.toDrive() and read it into R using...

library(raster)

NDVI = stack("/PATH/TO/MOD13Q1_comp_NDVI.tif")

plot(NDVI[[10]])

...you will find that areas outside the AOI, and areas that were masked, have values of 0, rather than NA. Is there a way to export imagery from Earth Engine with masked areas set to NA, or some other obvious non-standard value? I'd be fine with masked areas set to -99999 because they can get set to NA after the fact.

I looked into using the defaultValue argument described here but when I include that in the formatOptions an error is returned indicating that it isn't a valid argument ("defaultValue" is not a valid option, the image format "GEO_TIFF""may have the following options: cloudOptimized, fileDimensions").