Missing Scripts

[antonydellavecchia]

I am running into issues when trying to run the triplet pipeline script, seems like the following three additional scripts are missing
clip_raster_by_shp.py
trim_ndv.py
dem_mask.py

[ShashankBice]

Hi Antony,
These scripts are from other repos, which you would need to include in path after installing them. If you used the environment.yml file for installing the environment, you would see src/ folder in your local skysat_stereo git directory. In there, you would find pygeotools and demcoreg folders, paths to those should be added to your ~/.bashrc. I will clear this in the install instructions.
Let me know how the experiments go, which should help me in tuning the scripts better for diverse use-cases/topography.

Thanks,
Shashank

[dshean]

At some point, we should rewrite these steps using geopandas and rasterio, and eliminate the pygeotools dependency.

[antonydellavecchia]

ah i see, so i added some hotfixes to add python to the front of the run cmd when executing a script that was in the scripts folder, which i already thought was kind of funking that it wasn't working for me without that hotfix. So do you just make all of these scripts + the pygeotools scripts executables? is there a way to get around this using python modules somehow?

[Bea07]

Dear team,
I am facing a missing script as well skysat_overlap_parallel.py, in order to run the second step of triplets pipeline (skysat_preprocess.py line 25). Am I missing some files or dependencies too?
any suggestions are very much appreciated
Thank you

[ShashankBice]

Hi @antonydellavecchia,
Sorry for getting back on this so late, we got stuffed into an impromptu high priority project when you originally raised this, and it fell into the cracks. I am aware of the adhoc subprocess calls occuring in the wrapper script, and I will be updating these to fully python apis in the coming weeks. I will let you know once I have them done, slowly taking time off from some other grad school projects :)

[ShashankBice]

Hi @Bea07,
Sorry I misinterpreted your question :( . The help message here needs to be updated. You should be using the skysat_overlap.py script for this purpose, as indicated here in the wrapper script. This will write out a overlap_stereo_only.pkl file like this, which you can pass to the preprocess script as mentioned here.

A good nudge to create better documentation, and thanks for pointing it out David :)

Thanks
Shashank