verify LT-1 stack compatibility with ISCE2 stack tooling
validate MintPy input and output expectations
record runnable command templates
collect conclusions that should later be promoted into docs/ or backend services
maintain the current SBAS product contract before backend embedding

Structure

notes/
- experiment notes, pitfalls, conclusions
configs/
- sample templates, parameter files, manifest drafts
scripts/
- throwaway or semi-stable experiment scripts
scratch/
- local temporary workspace placeholder only

Rules

do not commit raw SAR scenes
do not commit large DEM or orbit datasets
do not commit large intermediate outputs
keep production code changes out of this folder unless the goal is to prototype file layout or commands
when an experiment becomes stable, move the result back into the formal backend or docs/

Suggested first experiments

Check whether LT-1/LUTAN1 scenes can be ingested by official ISCE2 stack tooling.
Determine whether MintPy can consume the generated stack layout without extra conversion.
Record the minimal command chain needed for one small AOI smoke test.
Draft the first psinsar manifest and product directory convention.

Current scripts

backend/app/isce2_pipeline/lt1_input_resolver.py
- shared LT-1 input helper reused by D-InSAR and stack experiments
- centralizes DEM resolution, orbit-pool resolution, and LT-1 precise-orbit XML generation
scripts/scan_lt1_stack_candidates.py
- scan LT-1 single-scene folders and build a stack candidate manifest
scripts/build_lt1_stack_prep.py
- consume a selected stack manifest
- resolve orbit pool and DEM
- generate a dry-run scratch/... workspace for stripmapStack --nofocus
- write the current adapter contract and a preflight run script
scripts/materialize_lt1_stack_scenes.py
- consume scratch/.../stack_input_manifest.json
- materialize one or more LT-1 acquisitions into SLC/YYYYMMDD/
- write YYYYMMDD.slc, YYYYMMDD.slc.xml, and data
scripts/install_isce2_stack_runtime_ubuntu2404.sh
- install known WSL isce2 runtime dependencies
- default pip mirror is Tsinghua
scripts/install_mintpy_runtime_ubuntu2404.sh
- create or update a dedicated WSL mintpy conda environment
- default conda channels use Tsinghua mirror URLs
scripts/install_mintpy_into_cloned_isce2_env_ubuntu2404.sh
- clone the working WSL isce2 env into a dedicated unified-env target such as isce2_mintpy
- install MintPy into that clone with Tsinghua mirror channels
scripts/run_mintpy_unified_env_ubuntu2404.sh
- run MintPy commands directly inside the cloned unified env
scripts/run_mintpy_sbas_unified_env_smoketest_ubuntu2404.sh
- run the current LT-1 SBAS smoke test in the cloned unified env
- reuses the same strict-mask and patched-launcher helpers as the bridge route
scripts/run_mintpy_with_isce_ubuntu2404.sh
- run MintPy commands in the dedicated mintpy env
- bridge only the top-level WSL isce package into the mintpy env
- avoids pulling conflicting h5py / numeric packages from the isce2 env
scripts/create_mintpy_all_ifgram_mask.py
- build a strict maskAllValid.h5 from inputs/ifgramStack.h5
- keep only pixels valid in all interferograms before SBAS inversion
scripts/run_smallbaselineApp_patched.py
- repo-local launcher for MintPy smallbaselineApp
- applies a local workaround for the MintPy 1.6.2 single-pixel partial-network inversion bug
scripts/run_mintpy_sbas_smoketest_ubuntu2404.sh
- run the current LT-1 SBAS smoke test in three steps:
  - load_data
  - strict-mask generation
  - modify_network -> velocity
scripts/export_mintpy_publish_products_ubuntu2404.sh
- geocode MintPy outputs into latitude/longitude grids
- convert selected outputs into GeoTIFF
- build a publish-style bundle with manifest.json, assets/, preview/, and metadata/
- defaults to the bridge runner but now also supports MINTPY_RUNNER=... override
scripts/export_mintpy_publish_products_unified_env_ubuntu2404.sh
- run the same publish export logic through the cloned unified env runner
scripts/export_conda_env_snapshot_ubuntu2404.sh
- export one WSL conda environment into reproducible snapshot files
- writes no_builds.yml, explicit.txt, conda_list.txt, and runtime_versions.txt
scripts/export_phase4_env_snapshots_ubuntu2404.sh
- export both isce2 and isce2_mintpy_v1 snapshots for the current phase-4 record
scripts/build_mintpy_publish_bundle.py
- generate preview/velocity_preview.png
- summarize quality masks
- write the publish-style manifest.json
scripts/prepare_lt1_stack_dem.py
- clip a stack-local DEM window from the source DEM
- store it under scratch/.../inputs/dem/
- avoid global-DEM bbox problems during createWaterMask
scripts/run_generated_stack_runfile_ubuntu2404.sh
- execute one generated run_XX_* file under Ubuntu-24.04
- standardize PATH, PYTHONPATH, and log output
scripts/create_synthetic_watermask.py
- create a local all-land geom_reference/waterMask.rdr
- used only when run_01_reference cannot download SWBD from Earthdata

Reproducible Flow

Generate or refresh the sample stack workspace with build_lt1_stack_prep.py.
Materialize the LT-1 acquisitions with materialize_lt1_stack_scenes.py.
Clip a stack-local DEM window with prepare_lt1_stack_dem.py.
In Ubuntu-24.04, run scripts/install_isce2_stack_runtime_ubuntu2404.sh.
Regenerate the stack workspace so it picks the local DEM.
Run the generated wrapper through the validated chain:
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_01_reference
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_02_focus_split
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_03_geo2rdr_coarseResamp
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_04_refineSecondaryTiming
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_05_invertMisreg
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_06_fineResamp
- scripts/run_generated_stack_runfile_ubuntu2404.sh <scratch_root_wsl> run_07_grid_baseline
- if Earthdata credentials are missing, the wrapper now auto-generates a synthetic all-land waterMask.rdr from shadowMask.rdr and treats run_01_reference as recovered
In Ubuntu-24.04, run scripts/install_mintpy_runtime_ubuntu2404.sh before the first MintPy validation.
In Ubuntu-24.04, run scripts/run_mintpy_with_isce_ubuntu2404.sh prep_isce.py ... for the first MintPy metadata preparation on stripmapStack outputs.
In Ubuntu-24.04, run:
- scripts/run_mintpy_sbas_smoketest_ubuntu2404.sh <cfg_wsl> <mintpy_work_dir_wsl>
Review:

notes/PHASE2_MINTPY_SBAS_SMOKETEST.md

In Ubuntu-24.04, run:

scripts/export_mintpy_publish_products_ubuntu2404.sh <mintpy_work_dir_wsl> <publish_dir_wsl>

Review:

notes/PHASE3_PUBLISH_EXPORT_SMOKETEST.md

Record findings under notes/ before promoting anything into backend code.

Product Contract

Formal product guidance now lives in:

docs/ISCE2_SBAS_PRODUCT_SPEC.md

Current practical rule:

runtime success is proven by radar-coordinate timeseries.h5 and velocity.h5
publish success is proven by a geocoded bundle under publish/.../
system embedding should treat manifest.json as the publish entrypoint
true time-series capability should be judged against assets/geo_timeseries.h5, not only assets/velocity.tif

Unified-Environment Track

The bridge route remains the validated baseline.

A separate unified-environment experiment is now staged in:

notes/PHASE4_UNIFIED_ENV_EXPERIMENT.md
notes/PHASE4_UNIFIED_ENV_DECISION.md

Current practical rule:

the unified env has now completed the same SBAS smoke test chain and publish export in experiment scope
the unified env is now the preferred SBAS experiment runtime
do not replace or mutate the current isce2 env used by D-InSAR production
do not replace the bridge route as the default fallback until the comparison note is fully written
current successful unified env:
- /home/administrator/miniconda3/envs/isce2_mintpy_v1
current successful unified SBAS work dir:
- scratch/lt1a_strip1_hh_descending_e123p3_n46p1/stack_work/mintpy_sbas_unified_v1
current successful unified publish dir:
- scratch/lt1a_strip1_hh_descending_e123p3_n46p1/publish/mintpy_sbas_unified_v1

Current Offline Assumption

the LT-1 sample experiment already has local SAR scenes, local orbit XML, and a local DEM
the remaining optional online dependency is the SWBD water mask normally fetched by createWaterMask.py
for this experiment track, do not download SWBD
continue with the local synthetic all-land waterMask.rdr fallback until the stack route is otherwise stable
current validated MintPy boundary is radar-coordinate timeseries.h5 plus velocity.h5
current validated publish boundary is a geocoded experiment bundle under publish/.../