Export yearly median MODIS/061/MOD13Q1-based products using Google Earth Engine

Question

I am trying to export yearly median MODIS-based NDVI products at 250m spatial resolution. I am using the 16 day MODIS/061/MOD13Q1 product. I have found this code which I am following.

The yearly median NDVI image I produced looks like this:

Because I have very little knowledge in Google Earth Engine, I wanted to ask if the code to generate yearly median MODIS/061/MOD13Q1 product (free of cloud, cloud shadows and bad quality pixels) is correct.

I am asking this, because the areas highlighted in red are water bodies and, as far as I know, water bodies should have negative NDVI values. As you can see from the picture, the NDVI range of my image has no negative values (0.0066-0.7318).

Here is the code:

var table = ee.FeatureCollection("users/nikostziokas/mumbai_7767");

var maskEmptyPixels = function(image) {
  var withObs = image.select('NDVI').gt(0);
  return image.updateMask(withObs); 
  };
  
var maskClouds = function(image) {
  var QA = image.select('SummaryQA');
  var bitMask = 1 << 10;
  return image.updateMask(QA.bitwiseAnd(bitMask).eq(0));
}; 

var table_bounds = function(image){
 return image.clip(table); 
};

var collection = ee.ImageCollection("MODIS/061/MOD13Q1")
               .filterDate('2018-01-01', '2018-12-31')
                .filterBounds(table).select('NDVI','SummaryQA')
                .map(maskEmptyPixels);
                
var evicollection = collection.map(table_bounds);

var totalObsCount = evicollection
        .select('NDVI')
        .count();
        
var collectionCloudMasked = evicollection.map(maskClouds);

var clearObsCount = collectionCloudMasked
        .select('NDVI')
        .count()
        .unmask(0);
        
Map.setCenter(35.94,-0.37,8);

Map.addLayer(
    collectionCloudMasked.median(),
    {bands: ['NDVI'],
     gain: 0.07,
     gamma: 1.4
    },
    'median of masked collection'
);
  
print(collectionCloudMasked);
  
//Calculate the median for each band (B2 to B7), multiply by scale factor
//(0.0001), and clip to country polygon
var median1 = collectionCloudMasked.select('NDVI')
.reduce(ee.Reducer.median())
.multiply(0.0001)
.clip(table);

Export.image.toDrive({
image: median1,
description: 'ndvi',
scale: 250, //100 for Band10
maxPixels: 1000000000000,
region: table,
crs: 'EPSG: 7767', 
folder: 'Landsat-5'});

Answer 1

By removing the maskEmptyPixels function, the water bodies have negative NDVI values.