Pixel Extraction - input several product files - extracts values from only 1 file

I would like to batch export pixel values.

I used Pixel Extraction (Raster->Export->Extract Pixel Values) with several product files. The product files are VI calculated from S2-2A products with applied mask. The product files are from the same area (same coordinates). The Extraction stats that it is successful but in the result file only the values from the first product are extracted. When I remove the first file from the input list of Pixel Extraction and Extract again. Again, only the values from the new first file are extracted.
There is not any error in the log file.

Is this a bug or do I do something wrong?

I could imagine that this related to the multi-resolution characteristics of Sentinel-2. I guess you haven’t resampled the L2A products after the sen2cor processing, right?
I would suggest that you resample the products to a common resolution, safe the result to DIMAP or NetCDf4 (to save disk space). Then try again the pixel extraction.

The products that I try to Pixel Extract have 1 band (calculated VI), the same resolution and saved in DIMAP format.

They are obtained by:
I downloaded 2A products (did not use sen2cor myself), then in a graph file for all my images (2A products from different dates) executed: 1. resampled, 2. created mask to exclude the clouds 3. Imported mask for my test area 4. Calculate VI 5. Apply the mask of the test area on the VI images.

And then I tried (with Pixel Extraction) for all my images to export the values of the resulted Vis images of my area of interest

May I ask you to provide two of the files where you want to extract the pixels from?
Then I can try to replicated this issue.
I’ll send you a PM tell you where you can upload the data.

Hello all,
I have temporal set of data(S2). I have performed several vegetation indices on those data, i also had some field data with the help of which i extracted the indices values(how the value has changed temporally). Now, i want to know(extract) all those pixels present in the image that show same sort of temporal change in the indices value.