Skip to content

Skipmissing before starting the inner loop #76

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
felixcremer wants to merge 4 commits into
base: main
Choose a base branch
from
Open

Skipmissing before starting the inner loop #76

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
5de8eb5
Skipmissing before starting the inner loop
Feb 14, 2025
6bca6f1
Add check for number of significant change pixels on main run
Feb 14, 2025
738673c
Remove unnecessary show statements
Feb 14, 2025
2c2a750
Remove folder with legacy versions of the input from default kwarg
Feb 14, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 2 additions & 6 deletions src/main.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ function main(;
polarisation="VH",
orbit="*",
threshold=3.0,
folders=["V01R01", "V0M2R4", "V1M0R1", "V1M1R1", "V1M1R2"]
folders=[ "V0M2R4", "V1M1R1", "V1M1R2"]
)
if isdir(indir) && isempty(indir)
error("Input directory $indir must not be empty")
Expand All @@ -84,24 +84,20 @@ function main(;

filenamelist = [glob("$(sub)/*$(continent)*20M/$(tilefolder)/*$(polarisation)_$(orbit)*.tif", indir) for sub in folders]
allfilenames = collect(Iterators.flatten(filenamelist))
@show allfilenames

relorbits = unique([split(basename(x), "_")[5][2:end] for x in allfilenames])
@show relorbits
for relorbit in relorbits
for y in years

filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
@time cube = gdalcube(filenames)

path = joinpath(YAXDefaults.workdir[], "$(tilefolder)_rqatrend_$(polarisation)_$(relorbit)_thresh_$(threshold)_year_$(y)")
@show path
ispath(path * ".done") && continue
ispath(path * "_zerotimesteps.done") && continue

tcube = cube[Time=Date(y - 1, 7, 1) .. Date(y + 1, 7, 1)]
@show size(cube)
@show size(tcube)

if size(tcube, 3) == 0
touch(path * "_zerotimesteps.done")
continue
Expand Down
2 changes: 1 addition & 1 deletion src/rqatrend.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ Compute the RQA trend metric for the non-missing time steps of xin, and save it
`thresh` specifies the epsilon threshold of the Recurrence Plot computation
"""
function rqatrend(pix_trend, pix, thresh=2)
pix_trend .= rqatrend_impl(pix; thresh)
pix_trend .= rqatrend_impl(collect(skipmissing(pix)); thresh)
end


Expand Down
8 changes: 7 additions & 1 deletion test/testdata.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,14 +1,15 @@

@testitem "testdata julia_main" begin
import Pkg: Artifacts.@artifact_str, ensure_artifact_installed
using YAXArrays, Zarr

ensure_artifact_installed("rqatestdata", "Artifacts.toml")
testdatapath = joinpath(artifact"rqatestdata", "RQADeforestationTestData-2.0")

testdir = "tmp/testdata"
rm(testdir, recursive=true, force=true)
mkpath(testdir)
outdir = "$testdir/out.zarr"
outdir = "$testdir/out"
indir = "$testdir/in"
cp(testdatapath, indir)

Expand All @@ -18,10 +19,15 @@
"--continent", "EU",
"--in-dir", indir,
"--out-dir", outdir,
"--years", "2021"
])
# test normal execution
RQADeforestation.julia_main()
# test short cut implementation using cache files
RQADeforestation.julia_main()

outpath = joinpath(outdir, "E051N018T3_rqatrend_VH_022_thresh_3.0_year_2021.zarr")
c = Cube(outpath)
@test count(c .< -1.28) > 200
copy!(ARGS, OLD_ARGS)
end
Loading