Coregistrating more than two Sentinel-1 SLC IW products

Handling multiple polarizations in backgeocoding has been solved. Where do you get the nulls errors?

You were totally right, I think I was using the same graph xml that I started with for a coherence estimation… It was still strange though - once I managed to coregister all images using backgeocoding (two scenes at a time) I found a lot of banding issues that appeared to be related to phase, which I solved by skipping that step and using create-stack ->cross correlation -> warp after multilooking.

A reason for the null errors was that I was testing on my local machine, with a limit of around 10gb of vmem, and that is why I was splitting up the polarisations.

Sorry for the slow reply,


Hi All,

I need to prepare the time-series of interferograms for creating the DEMs. The goal is the vegetation height estimation using S1 SLC images. This task is not very easy.
My boss says that I have to coregister all the 6 images in one stack, split them and create pairs of the interferograms from that. I chose the last date’s image as master and I can coregistrate all the 6 images in one stack … and here my problems start.

  1. If I split them, I have 4 images. Master (the last date) and image from the very first date lost. Ok, I think I have to coregister (or create stack) for pairs which I would choose from these 4 images, but neither coregister, not create stack are able to help me. Coregister shows an error, create stack works, but I can’t create interferogram after it. It doesn’t show any message, just don’t create anything.
  2. I tried to go further with the monster stack. I created the ifg from it, did topo phase removal, Goldstein filter. On this stage I can’t split the stack because of “NodeId error”. So, I exported this to SNAPHU, did unwrapping, but it SNAPHU does work only on the master image. Despite I was able to import it back I can’t obtain any information for my slave images.
  3. I tried to delete images and metadata from my stack manually. It doesn’t work. In any case, I receive results for my master image only.
  4. I tried to work with pairs only. If I would have the same master for each pair I would have the results only for the date of the master image. If I would work with pairs having images from each date as masters I can obtain results for different dates, but my boss told me that is unproper way of working because such pairs would coregistered to the different master and therefore would be uncompareable to each other.
    So, I need to take all the coregistered images from the monster stack somehow, prepare new stack and recieve results for all my dates. I would really appreciate any suggestions. Thanks!

Hi guys, could I ask what the lessons learned are? I’m trying to coregister a year of SLC data (let’s say 30 scenes for each relative orbit). Isn’t there any option to take one master, and coregister at once all remaining 29 scenes to this master? I read here that you need to coregister each scene separately to that master; is that still the general workflow?
And even so, can you specify directly which scene to use as master? It looks like, if I try this, the software determines itself which image will be master and which one will be slave.
Would be easier to build a giant stack and coregister everything at once against one master…

Hi Kristof,

On one side, I would suggest to coregister one by one, as this option is more attractive when you try to do operational works, let’s say you need to coregister a new scene each 6 days. Or when you decide to continue your work by adding one more year of data. On the other side creating giant stacks requires also more powerful computing environments to work.

Depending of the application the selection of master image can matters or not much. For interferometric application it matters, but for amplitude analysis it is not that much relevant. You could select first image as master, and use all the other ones as slave.

This is only my personal point of view, as I said it depends on the desired application.

From a computational perspective one should do one co-registration at a time, sequentially (in batch). Generating monster-graphs uses huge amounts of memory and accessing many files at the same time makes I/O much more inefficient.

@mdelgado and @mengdahl, thanks to both of you for the swift replies. I’m creating time series of coherences, so not sure based on what I should choose the master image.
Although processing power is not too much of an issue here, I agree with your advice and I’ll process each scene separately against the master. With regard to that, I use S1-TOPS coregistration tool. The tool has two “read” functions, but it doesn’t talk explicitly about master and slave. Do I have to assume that the first read will always be the master, and the second one the slave?

In addition, as I’ ve been reading earlier in this thread, it’s still necessary to do the complete coregistration for each subswath separately, and merging them again afterwards?

And finally, let’s say you want to process into different products: coherence, Sigma0 amplitude and Gamma0 amplitude. Coregistration is beneficial for all these products. When is generally a good time? My first thought:

SLC -> TOPRSAR-Split -> Apply precise orbit -> back-geocoding -> write to coregistered image

That output file can then be used for:

-> thermal noise removal -> calibration -> debursting -> multilooking -> TC -> output Sigma0
-> thermal noise removal -> calibration -> debursting -> TF -> multilooking -> TC -> output Gamma0
-> coherence estimation -> multilooking -> TC -> output coherence

Or do I make a mistake somewhere?

Hi @kristofvt,

If you plan to use coherences better not get the master as the first image as mentioned on my last post, as coherence decorrelates with time.

Master is the Read 1 and slave Read 2.

I have put available some scripts that could help you to do so, you only need to change the xml to use in one of the steps. Not sure you needed. It can be found in the thread: Snap2stamps package: a free tool to automate the SNAP-StaMPS Workflow .
If you may want me to help you to customise the processing for your particular case, contact me.

Regarding the procedure you mentioned, at first sight it seems fine to me.

I hope this helps.

From my point of view, you could avoid the merging afterwards, as the coherence must be computed at subswath level and there is not a real need to merge them. From my point of view it is a personal decision as you can work perfectly at subswath level.

Great! I’ll definitely have a look at those resources. So if you’d plan to look at coherence time series, what’s the best way? If you coregister each image pair separately, that would yield highest coherences, but coregistration of all the different coherence images would not be perfect… If you choose one master and use that for coregistration along the entire series, there’s the temporal decorrelation problem?

And regarding merging; it depends a bit. If the final coherence output of the subswaths is converted to geotiff and these subswaths are nicely aligned, I guess it’s indeed not needed. But what if there’s artefacts at the borders…

Hi @kristofvt
Well, probably this would need a deeper discussion, at it is quite specific.

Regarding master, a easy/fast solution is to get the master in the middle of the scene and coregister all the other images with this. If you plan to do short term coherence analysis, you can get separate pairs and verify afterwards that after doing the TerrainCorrection all images are aligned or not. From my experience in my area of interest the images were nicely aligned after the Terrain Correction.

There is still another solution, and If I am right, it is still not available within SNAP, is the multi-master interferogram. This is problably what you may need.

Regarding artefacts at the borders, they will probably be. Please check it as well. For the GRD you could apply the Border Noise Removal, but probably you will need to merge them. It will be interesting to see that if it may be requred or not. Maybe @lveci can say something more precise in this regard.

It looks like this issue is still open, in terms of creating a stack of S-1 interferograms coregistered to one master (what @Tomcater was attempting and I think what @mdelgado refers to as a multi-master interferogram?). I ran the python wrapper scripts from the snap2stamps package, which runs very nicely and smoothly (thanks). This creates a series of interferograms with one single master. I do not have access to Matlab or Gamma to continue with StaMPS, unfortunately.

Failing the ability to run back-geocoding/ESD on more than two images, I created a batch of back-geocoded/ESD registered image pairs, from a time-series (all in the same rel-orbit, location etc.), all with the same master (i.e. master-slaves as mst-slv1; mst-slv2; mst-slv3 etc.). I thought I could be clever and replace the .img and .hdr files such that data from slv1 in pair one becomes mst in pair two. I encountered some problems with the datatypes, so I converted slv1 data from flt32 to int16 and modified the .dim file.

I managed to ‘trick’ SNAP into generating an interferogram from slv1-slv2 in this way, but I end up with some very strange results (image below). On the left is the first mst-slv1 image, in the middle is slv1-slv2 and on the right slv2-slv3. I am almost certain that this is because the flat-earth phase removal is using the wrong metadata. However, on the second row are the interferograms without flat earth removal and the results are not as expected either. Do people have any suggestions for which parts of the metadata I need to adapt to overcome this, or am I overlooking some fundamental aspects of SNAP/S-1 data/InSAR that would make this a pointless exercise?
Thanks, James


You can use the Matlab 30-days trial license. It has all the toolboxes needed to run StaMPS.

For multi-master I mean the master image for which all slaves should be coregistered before doing interferograms among themselves. Slv1-Slv2 once done first Mst-Slv1 and Mst-Slv2.

I hope this helps

could it be that although the rasters are slave1 and slave2, the orbit information in the metadata (*.dim) could still result from the old pair (master and slave1) and this causes the ramps in the interferograms?

Thanks, that’s what I thought you meant by multi-master. I will try the 30-days trial license, good idea.

Thanks, I suspect that might be the cause. The next question is if it is feasible to switch the orbit information in the .dim file to the slave1 orbit information. The coregistered stack .dim file contains information that is produced from master/slave orbit calculations (e.g. baselines etc.) which may be necessary and overly complicated to replace. I will have a go and report back.

I discussed this quite extensively here: Interferogram averaging for DEM generation
You might want to have a look at it, mengdahl mentiones the role of the baseline here, and I tried some approaches but wasn’t successful.

Let us know if you find a way that works. Even if it involves much manual labor, this could be automated later by a python script, for example.

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I’m getting more sensible results from using a .dim file created by back-geocoding and ESD processing slv1 to slv2 (where they are named mst and slv1), and renaming the .data, .hdr and .img files to match it from the slv1 and slv2 files which had been coregistered to the first mst file. This means that a lot of extra processing needs to be done: for each image pair, except the first mst-slv1 pair, you need to generate an additional back-geocoded, ESD coregistered stack to obtain the necessary .dim file. The processing chain for a slv1 to slv2 interferogram coregistered to a different master is therefore, for three images [mst, slv1, slv2]:

  • Apply orbit files and select swath (TopSAR split), bursts and polarisation for each image
  • Produce back-geocoding and ESD stacks for
    –Mst and Slv1
    –Mst and Slv2
    –Slv1 and Slv2
  • from the Mst-Slv1 stack .data directory move the Slv1 q and i .img files to the Mst-Slv2 stack .data directory, replacing slv1 to mst in the filename, and converting from float32 to Int16 and byteswapping (for some reason gdal swaps the endianness when it writes in the ENVI format) - these are the commands I used, but with more appropriate filenames: -A slv1.img --A_band=1 --type=Int16 --format=ENVI --outfile=mst.img --calc=“round_(A,0)” --quiet --overwrite -A mst.img --A_band=1 --type=Int16 --format=ENVI --outfile=mst.img --calc=“ndarray.byteswap(A,inplace=True)” --quiet --overwrite

  • copy the .dim file from the slv1-slv2 coregistered stack to replace the mst-slv2 stack .dim file, and rename the mst-slv2 .data directory to the same name as the slv1-slv2 .data directory

Keep close track of directories and files as there is a lot of file and directory renaming going on, so it would be easy to get confused.


I had started to compare the .dim files from the mst-slv2 stack and the sl1-slv2 stack in order to parse which elements should be kept from each to preserve the correct image and orbit characteristics, when I realised the above might work. However, I imagine there are still some important metadata elements that have been lost, and if any of the images have a different size there will be complications.

interesting. Do the interferograms look better after the replacement of the dim file?