trodi 0.2.4

Label interferogram pixels or images as outliers

trodi

Label outliers on a stack of interferograms, either at the pixel level, or SAR-scene level.

Installation

Recommended to have a conda environment set up.

pip install trodi

Note that you need to install GDAL if you are not using simple binary files with a ROI_PAC ".rsc" file describing the dimensions:

conda install gdal
# Or if you are using mamba for quicker installation (https://github.com/mamba-org/mamba), mamba install gdal

To make an editable installation

git clone https://github.com/scottstanie/trodi
cd trodi
pip install -e .

If you're using a conda environment

conda install --file requirements.txt
# mamba install --file requirements.txt
pip install -e .

Usage

If you have a set of unwrapped interferograms (".unw" files) in a folder called "igrams",

$ trodi --search-path igrams 
[03/04 22:37:15] [INFO core.py] Searching for igrams in igrams/ with extention .unw
[03/04 22:37:15] [INFO core.py] Found 9 igrams, 5 unique SAR dates
[03/04 22:37:15] [INFO utils.py] Making dimensions and variables
[03/04 22:37:15] [INFO utils.py] Writing dummy data for igrams
[03/04 22:37:15] [INFO core.py] Averaging 4 igrams for 2015-02-08 (1 out of 5)
[03/04 22:37:15] [INFO core.py] Averaging 4 igrams for 2015-03-28 (2 out of 5)
[03/04 22:37:15] [INFO core.py] Averaging 3 igrams for 2015-04-09 (3 out of 5)
[03/04 22:37:15] [INFO core.py] Averaging 3 igrams for 2015-05-27 (4 out of 5)
[03/04 22:37:15] [INFO core.py] Averaging 4 igrams for 2015-06-20 (5 out of 5)
[03/04 22:37:16] [INFO logger.py] Total elapsed time for create_averages : 0.02 minutes (1.26 seconds)
[03/04 22:37:17] [INFO core.py] Computing 5 sigma outlier labels at scene level.
[03/04 22:37:17] [INFO core.py] Saving outlier labels to labels_scene.nc:/labels
[03/04 22:37:17] [INFO core.py] Saving data to labels_scene.nc:/data
[03/04 22:37:17] [INFO core.py] Saving threshold to labels_scene.nc:/threshold

To get pixel-level labels:

$ trodi --level pixel --outfile labels_pixel.nc 

With the labels recorded, we can read these in Python with xarray, (or h5py, or a NetCDF reader):

import xarray as xr
>>> ds = xr.open_dataset("labels.nc")
>>> ds
<xarray.Dataset>
Dimensions:    (date: 5)
Coordinates:
  * date       (date) datetime64[ns] 2015-02-08 2015-03-28 ... 2015-06-20
Data variables:
    labels     (date) bool ...
    data       (date) float32 ...
    threshold  float32 ...

>>> print(ds['labels'])
<xarray.DataArray 'labels' (date: 5)>
array([False, False, False, False,  True])
Coordinates:
  * date     (date) datetime64[ns] 2015-02-08 2015-03-28 ... 2015-06-20

The labels dataset gives a True for any SAR dates determined to be significantly noisier than the other acquisitions.

In MATLAB, you can read the results using ncread:

>> ncread('labels_scene.nc', 'labels')
ans =
  5×1 int8 column vector
   0
   0
   0
   0
   1

>> ncread('labels_scene.nc', 'threshold')
ans =
    0.8059

We see that for this dummy example, the threshold was 0.8059 on the average interferograms.

You can check the average_ifgs.nc file on the labeled dates to see what the estimated atmosphere is.

Example on real dataset

You can also test this out on an example dataset provided by MintPy and ARIA.

Area: San Francisco Bay, California, USA Data: Sentinel-1 A/B descending track 42 during May 2015 - March 2020 (114 acquisitoins; Zenodo) Size: ~2.7 GB

wget https://zenodo.org/record/4265413/files/SanFranSenDT42.tar.xz
tar -xvJf SanFranSenDT42.tar.xz
cd SanFranSenDT42

The unwrapped interferograms are in the unwrappedPhase folder. They are provided as binary files with VRT files to load using GDAL (so you need to have GDAL installed, e.g. mamba install gdal) where the first band is the phase.

Note that there is a watermask provided, but it uses "0"s to indicate where the water is. We'll add the --mask-is-zero option to flip that to numpy masking conventions.

$ trodi --search-path unwrappedPhase/ --ext .vrt --band 1  --max-temporal 250 --mask-files mask/watermask.msk --mask-is-zero
[07/07 10:30:27] [INFO core.py] Searching for igrams in unwrappedPhase/ with extention .vrt
[07/07 10:30:27] [INFO core.py] Found 505 igrams, 114 unique SAR dates
[07/07 10:30:27] [INFO utils.py] Making dimensions and variables
[07/07 10:30:27] [INFO utils.py] Writing dummy data for average_ifgs
[07/07 10:30:27] [INFO core.py] Averaging 3 igrams for 2015-05-12 (1 out of 114)
...

You can check the average_ifgs.nc file for each day's noise estimate:

See trodi --help for full option list.