Add layer masking, profile tool, theme toggle, buffer visualization, and prepare-disp-s1 fixes#23
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mgovorcin wants to merge 4 commits intoopera-adt:mainfrom
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Add layer masking, profile tool, theme toggle, buffer visualization, and prepare-disp-s1 fixes#23mgovorcin wants to merge 4 commits intoopera-adt:mainfrom
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…setup-dolphin fixes
## GUI changes
### New components
- **MeasureTool**: click-to-measure polyline tool on the map with cumulative
distance display; toggled from the sidebar footer.
- **ProfileTool**: draw a line/polyline on the map and extract a raster value
profile along it; persistent line while the button is active; draggable
vertex adjustment; profile chart shown/hidden from the sidebar footer.
- **RefPointChart**: floating chart showing time series of all pixels within
the reference-point buffer (median + random samples ± 1σ fill); labels
match the main time-series x-axis timestamps.
- **Histogram**: value-distribution histogram for the current time step,
shown in the sidebar under "Value Distribution".
### Sidebar additions
- **Point Picking ON/OFF** pill (footer) — disables map-click point picking
to prevent conflicts with Measure/Profile tools.
- **Re-referencing ON/OFF** pill (footer) — enables/disables spatial
re-referencing for all datasets and charts.
- **Show/Hide Profile** button (footer) — toggles the profile chart panel.
- **Show/Hide Ref Buffer Chart** button (footer, visible when buffer is ON).
- **Reference Buffer** section — ON/OFF toggle + radius slider; when ON the
median within the radius is used for re-referencing instead of a single
pixel; updates tile shift and time-series simultaneously.
- **Layer Masking** section — replaces fixed coherence/phase-similarity/
inversion-residual sliders with a flexible multi-mask UI: pick any loaded
raster group, choose ≥ or ≤ mode, set a 0–1 normalised threshold (scaled
server-side to the layer's actual data range); add/remove multiple masks
that are combined with AND logic; custom GeoTIFF upload preserved.
- **Colormap panel** — added Grays and Jet options; colormap now persists
per-dataset in localStorage and is restored on dataset switch.
- **Value Distribution** section — inline histogram with p2/p98 and p16/p84
percentile markers.
### Time-series chart improvements
- Multi-point time series with per-point colour-coded lines.
- Legend label colour changed to white for readability.
- Masking thresholds (layer masks) applied to all API calls.
- Reference buffer radius passed to /multi_point for median re-referencing.
- Trend lines and residuals toggleable.
### Map display
- Tile shift (re-referencing) uses buffer median when Reference Buffer is ON.
- Ref values re-fetched automatically when buffer toggle or radius changes,
and on ref-marker drag-end.
- Layer masks sent as JSON to both COG and MD tile endpoints.
## Backend masking
- Replace fixed coherence/phase-similarity/inversion-residual params with a
generic layer_masks list [{dataset, threshold, mode}] in /multi_point,
/buffer_timeseries, InputDependency (COG tiles), XarrayPathDependency (MD).
- Threshold normalised 0–1 and scaled to each layer's actual data range;
per-variable range cached at startup to avoid repeated nanmin/nanmax.
## Reference buffer re-referencing
- _get_ref_median(): computes nanmedian within circular buffer in MD mode;
falls back to single pixel when buffer_m=0 or COG mode.
- Tile shift and time-series both use buffer median when buffer is ON.
- Buffer median re-aligned to full-length index array (NaN for missing steps).
## Float16 / GDAL type-15 support (readers.py)
- RasterReader.from_file: catches KeyError when rasterio does not recognise
the GDAL dtype (Float16 = type 15, new in GDAL 3.7+); falls back to GDAL
directly for shape/transform/nodata, treats dtype as float32.
- RasterReader.bounds: same fallback using rasterio.transform.array_bounds.
## setup-dolphin fixes (cli.py)
- _glob() validates each file is openable (skips truly unreadable files,
includes Float16 files via KeyError catch).
- _glob_first() tries alternate glob patterns in order.
- velocity and Filtered velocity use _glob() instead of bare string literals.
- Groups with empty file_list silently skipped before RasterGroup().
- Temporal coherence and Phase cosine similarity fall back to broader globs
to handle date-range-suffixed filenames (e.g. similarity_20251025_20260117).
## prepare_amplitude CLI command
- New bowser prepare-amplitude command: reads complex SLC GeoTIFFs, computes
20·log10(|z|), writes Cloud-Optimised GeoTIFF (float32, DEFLATE, 512×512).
- -m/--mask option: pre-loads combined_mask.tif once, applies per window.
- -j/--workers option (default 4): parallel processing via ThreadPoolExecutor.
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
…ute thresholds, custom colormaps - ProfileTool: remove redundant hide button; add radius (m) input with buffer corridor polygon on map; backend /profile returns centre/median/samples when radius > 0; chart renders median (bold) + random sample lines (faint) - MapContainer: RadiusCircles component draws dashed L.circle around TS points (bufferRadius) and reference marker (refBufferRadius) when enabled - Theme-aware charts: useThemeVersion() MutationObserver hook triggers useMemo rebuild of chartOptions on data-theme toggle; chart/profile panel backgrounds use var(--sb-surface) instead of hardcoded dark rgba - Colormaps: register cfastie_r / schwarzwald_r / rplumbo_r into rio_tiler's cmap.data *before* titiler imports so Literal validation accepts _r variants; fixes 422 when selecting these colormaps with inverted toggle active - Layer masks: threshold is now absolute (real data units); /dataset_range endpoint returns min/max/p2/p98; slider range and number input show actual values; backend _apply_layer_masks_md and InputDependency pass threshold directly without _scale_threshold normalization - Histogram: ±0 centering button (symmetric around zero) - CSS: mouseposition uses var(--sb-surface) + border for light theme; profile-panel uses var(--sb-surface); profile-radius-input styles added Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
… dir input
- _prepare_utils.py: fix S3 path bug — Path.resolve() on s3:// mangles the
double-slash (e.g. s3://bucket → /cwd/s3:/bucket), so the subsequent
.replace('s3://', '/vsis3/') never matched. Now detect s3:// first and
map directly to /vsis3/ without calling resolve(); local paths still go
through resolve() for portability.
TODO: verify /vsis3/ access works with the current AWS credentials/env when
input NetCDF files live in S3 — boto3/GDAL env vars (AWS_PROFILE,
AWS_DEFAULT_REGION) must be set before calling gdal.Translate on /vsis3/ paths.
- _prepare_utils.py: force Float32 output in gdal.Translate — Float64 VRTs
cause titiler to fail PNG tile rendering
- _prepare_utils.py: inline gdal.BuildOverviews() replacing removed
add_overviews() helper import
- _prepare_disp_s1.py: use .resolve() on glob results so VRT paths are
absolute (portable when bowser launched from a different cwd)
- cli.py: prepare-disp-s1 accepts directories as input; globs *.nc inside them
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
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Summary
New map tools
Sidebar / UI additions
/dataset_range); replaces fixed coherence/similarity/residual slidersuseThemeVersion()MutationObserver hook rebuilds Chart.js options on switchL.circlerings around TS points and reference marker when buffer is activeBackend
/profile: newradius/n_randomparams; returns{centre, median, samples}for buffer mode/dataset_range/{dataset_name}: min/max/p2/p98 for mask threshold UIlayer_maskslist replaces fixed masking params across tile and time-series endpoints; thresholds are absolute data-unit valuesreaders.py: patch rasteriodtype_fwdfor GDAL 3.12 Float16 (type code 15) at import timeutils.py: register cfastie/rplumbo/schwarzwald_rreversed variants intorio_tiler.cmap.databefore titiler imports — fixes 422 when invert toggle is activeprepare-disp-s1 CLI
Path.resolve()ons3://mangled the double-slash so/vsis3/mapping never matched; S3 inputs now mapped directly withoutresolve()— TODO: verify with a real S3 file that AWS env vars (AWS_PROFILE,AWS_DEFAULT_REGION) are setFloat32ingdal.Translate— Float64 VRTs break PNG tile rendering in titilergdal.BuildOverviews()replacing removedadd_overviews()helper.resolve()for absolute paths (portable across working dirs)*.ncinside themprepare-amplitudecommand: SLC complex GeoTIFF → 20·log10(|z|) Cloud-Optimised GeoTIFFTest plan
prepare-disp-s1with S3 NetCDF —/vsis3/VRT created correctlyCustom masking on-the-fly
