R cannot correctly read the extents of sentinel data but gis can

Question

I'm working with Sentinel-1 data and trying to use the raster package in r to read it. I got the following error. The raster seems not to be well georeferenced. The resolution and extent are not displayed correctly. Meanwhile, I reckon r also does not read the dimensions correctly. The matrix of 26503*16885 should be the dimensions of valid pixels only.

> library(raster)
> x = raster('s1a-iw-grd-vv-20180130t193923-20180130t193948-020388-022d67-001.tiff')
> x
class      : RasterLayer
dimensions : 16885, 26503, 447503155  (nrow, ncol, ncell)
resolution : 1, 1  (x, y)
extent     : 0, 26503, 0, 16885  (xmin, xmax, ymin, ymax)
crs        : +proj=longlat +datum=WGS84 +no_defs
source     : /scratch/os22/yy4778/SingleChannelAlgo_90m/sentinel/S1A_IW_GRDH_1SDV_20180130T193923_20180130T193948_020388_022D67_6CF9.SAFE/measurement/s1a-iw-grd-vv-20180130t193923-20180130t193948-020388-022d67-001.tiff
names      : s1a.iw.grd.vv.20180130t193923.20180130t193948.020388.022d67.001
values     : 0, 65535  (min, max)

When I use ArcGIS or QGIS to read it, it can be displayed correctly. It can be seen that the dimensions have been adjusted to 30344*20520 and the extent can be read correctly.

### Information from QGIS###

Name    s1a-iw-grd-vv-20180130t193923-20180130t193948-020388-022d67-001
Path    /g/data/fj4/users/yu/s1a-iw-grd-vv-20180130t193923-20180130t193948-020388-022d67-001.tiff
CRS EPSG:4326 - WGS 84 - Geographic
Extent  143.5295688650110151,-32.2190784216897512 : 146.6789677467667730,-30.0893109205815179
Unit    degrees
Width   30344
Height  20520
Data type   UInt16 - Sixteen bit unsigned integer
GDAL Driver Description GTiff
GDAL Driver Metadata    GeoTIFF
Dataset Description 
Compression 
Band 1  
STATISTICS_APPROXIMATE=YES
STATISTICS_MAXIMUM=1175
STATISTICS_MEAN=71.533019359901
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=68.573526261316
STATISTICS_VALID_PERCENT=100
More information    
Dimensions  X: 30344 Y: 20520 Bands: 1
Origin  143.53,-30.0893
Pixel Size  0.0001037898392352941792,-0.0001037898392352941792

A correct display by QGIS is attached as below.

Can I ask how should I use R to correctly read the data?

I have tried methods like gdal utils (e.g. gdal_translate) to set the four corners but does not work for this one.

The tiff data is available from: https://drive.google.com/file/d/1Ox6uOhQYSFMzO1Hut-CjAqjPu06_-y1o/view?usp=sharing

Answer 1

The problem has been fixed. Sentinel-1 GRD data are not georeferenced and need to be preprocessed before usage. This GitHub repository works for me.

https://github.com/ffilipponi/Sentinel-1_GRD_preprocessing

Once completing the preprocessing step using a tool called Sentinel Application Platform (SNAP), which can be executed in the command line, Sigma0_VH_db.img and Sigma0_VV_db.img will be generated. Both of them are readable in R and correctly georeferenced. I set the resolution as 20m so the dimensions of generated data differ from the one in QGIS.

> library(raster)
> x = raster('Sigma0_VV_db.img')
> x
class      : RasterLayer
dimensions : 11852, 17529, 207753708  (nrow, ncol, ncell)
resolution : 0.0001796631, 0.0001796631  (x, y)
extent     : 143.5296, 146.6789, -32.21875, -30.08939  (xmin, xmax, ymin, ymax)
crs        : +proj=longlat +ellps=WGS84 +no_defs
source     : /scratch/os22/yy4778/SingleChannelAlgo_90m/sentinel/S1A_IW_GRDH_1SDV_20180130T193923_20180130T193948_020388_022D67_6CF9.data/Sigma0_VV_db.img
names      : Sigma0_VV_db

A plot using R is as below.

> plot(x, zlim=c(-30,-10))