I haven’t seen anyone on the forums reliably use PyRate. The instructions are incomplete and there are a lot of bugs to fix and manual fixes that you need to do.
I’ve been experimenting with a SNAP workflow but it is currently incomplete. For some reason, it doesn’t generate one of the coherence files so the PyRate process fails. I created a Github issue with the PyRate authors to discuss it earlier this week.
If anyone is interested, I shared the full steps I’ve done in the Github issue. I used the suggestions by @SebBuchelt (SNAP forum link ).
See the issue report here:
opened 07:06PM - 11 Jan 22 UTC
**Describe the bug**
SNAP workflow is incomplete and doesn't represent GAMMA fo… rmat properly. Some discussion on SNAP forums [here](https://forum.step.esa.int/t/output-name-errors-when-saving-snap-files-for-pyrate/28849). I've been using your repo's [gamma test data](https://github.com/GeoscienceAustralia/PyRate/tree/master/tests/test_data/gamma) as a reference as well as the discussion in the forum.
For now, I'm testing PyRate on Google Colab due to current storage limitations with my Windows workstation. I process the SLC data on my Windows machine then upload the processed data to a Colab instance. PyRate on Colab seems to have compiled correctly. I run `python3 -m pytest tests/test_timeseries.py` and it shows it passes the tests.
I'm testing with a very small dataset (3 images total) just so it's quicker to upload to Colab and debug. After much tinkering I only got as far as `prepifg`. It cannot generate one of the coherence files even though I can see the input `.coh` file and it is in the `coh_list` file which I inputted in the conf file. `pyrate prepifg` subsequently fails because it cannot find the missing `.coh` file.
I'm wondering if I can get some insight into how to fix this? I hope to create and share a SNAP workflow for PyRate.
Cheers.
**To Reproduce**
*SNAP PROCESSING*
1. Apply Orbit
2. TOPSAR Split
3. Backgeocoding
4. Interferogram
5. Deburst
6. Topophase Removal
7. Multilook
8. Filter
9. SNAPHU Export
10. Unwrapping
11. SNAPHU Import
12. Terrain Correction
13. Save DEM as GAMMA; Save Unw phase, coherence as GAMMA for PyRate
*ADDITIONAL FIXING THAT I NEEDED TO DO*
I have a Python script that automates the following items:
14. Rename Unw Phase `.rslc` file to `{reference_date}-{secondary_date}.unw`
15. Rename coherence `.rslc` file to `{reference_date}-{secondary_date}.coh`
15. Add datum and ellipsoid data to DEM.par file
16. Add missing data to slc header files. There is only frequency, incident_angle, and date.
17. Add missing data to DEM header file. Including origin coords, pixel spacing in decimal degrees, crs information.
**Expected behavior**
Use SNAP to export as "Gamma for PyRate" format and then use with PyRate with no problems.
**Screenshots**
Input data for Pyrate using a custom workflow:
**Desktop (please complete the following information):**
- OS (PyRate): Ubuntu 18.04.5 LTS (Google Colab)
- OS (SNAP): Windows 8
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
**Additional context**
Log for conv2tif:
```
18:49:33 main:105 2715 INFO 0/0 Verbosity set to INFO.
18:49:33 shared:1400 2715 INFO 0/0 Running 'conv2tif' step in serial
18:49:33 conv2tif:78 2715 INFO 0/0 Converting input interferograms to geotiff
18:49:33 conv2tif:87 2715 INFO 0/0 Running geotiff conversion in serial
18:49:33 conv2tif:115 2715 WARNING 0/0 Full-res geotiff already exists in out/interferogram_dir/20210607-20210619_unw.tif! Returning existing geotiff!
18:49:33 conv2tif:115 2715 WARNING 0/0 Full-res geotiff already exists in out/interferogram_dir/20210619-20210701_unw.tif! Returning existing geotiff!
18:49:33 conv2tif:115 2715 WARNING 0/0 Full-res geotiff already exists in out/coherence_dir/20210619-20210701_coh.tif! Returning existing geotiff!
18:49:33 conv2tif:115 2715 WARNING 0/0 Full-res geotiff already exists in out/geometry_dir/elevation_rslc.tif! Returning existing geotiff!
18:49:33 conv2tif:69 2715 INFO 0/0 Finished 'conv2tif' step
```
Log for prepifg
```
18:49:35 main:105 2730 INFO 0/0 Verbosity set to INFO.
18:49:35 shared:1400 2730 INFO 0/0 Running 'prepifg' step in serial
18:49:35 gdal_python:247 2730 INFO 0/0 Writing geotiff: out/interferogram_dir/20210607-20210619_ifg.tif
18:49:35 gdal_python:247 2730 INFO 0/0 Writing geotiff: out/interferogram_dir/20210619-20210701_ifg.tif
18:49:36 gdal_python:247 2730 INFO 0/0 Writing geotiff: out/geometry_dir/dem.tif
Traceback (most recent call last):
File "/usr/local/bin/pyrate", line 33, in <module>
sys.exit(load_entry_point('Py-Rate==0.6.0', 'console_scripts', 'pyrate')())
File "/usr/local/lib/python3.7/dist-packages/pyrate/main.py", line 111, in main
prepifg.main(params)
File "/usr/local/lib/python3.7/dist-packages/pyrate/prepifg.py", line 102, in main
do_prepifg(process_ifgs_paths, exts, params)
File "/usr/local/lib/python3.7/dist-packages/pyrate/prepifg.py", line 172, in do_prepifg
_prepifg_multiprocessing(m_path, exts, params)
File "/usr/local/lib/python3.7/dist-packages/pyrate/prepifg.py", line 304, in _prepifg_multiprocessing
coherence_thresh=coherence_thresh)
File "/usr/local/lib/python3.7/dist-packages/pyrate/core/prepifg_helper.py", line 199, in prepare_ifg
out_driver_type=driver_type, hdr=header, coherence_path=coherence_path, coherence_thresh=coherence_thresh
File "/usr/local/lib/python3.7/dist-packages/pyrate/core/gdal_python.py", line 194, in crop_resample_average
src_ds, src_ds_mem = _setup_source(input_tif)
File "/usr/local/lib/python3.7/dist-packages/pyrate/core/gdal_python.py", line 329, in _setup_source
src_ds = gdal.Open(input_tif)
File "/usr/local/lib/python3.7/dist-packages/osgeo/gdal.py", line 3019, in Open
return _gdal.Open(*args)
RuntimeError: out/coherence_dir/20210607-20210619_coh.tif: No such file or directory
```
2 Likes