Replace fixed ±1 pixel/velocity loops and indx_center_3d3/indx_margins_3d3
with configurable vel_suppr_rad loops and indx_center_vsupp/indx_margins_vsupp.
Co-authored-by: Claude <claude@elphel.com>

Suppress a point only when both conditions hold simultaneously:
  thresh = Math.max(athresh, M * rthresh)
  (M - val) >= thresh   →   zero the point

athresh enforces a minimum absolute gap; M*rthresh enforces a minimum
relative gap. Math.max means BOTH must be satisfied (either alone is
insufficient). Replaces the previous M>=athresh && val<rthresh*M logic.
Co-authored-by: Claude <claude@elphel.com>

CuasRTUtils: new filterConv5dROI(data, roi, athresh, rthresh)
  For each (pixel, velocity) point, finds max M over the ±1 neighbourhood
  in both pixel space (3×3) and velocity space (3×3 in vx/vy).
  Zeroes the point if M >= athresh AND val < rthresh*M (sidelobe suppression).
  Passes through unchanged when M < athresh (weak-signal linear regime).
  Uses indx_center_3d3 / indx_margins_3d3 for bit-reversed multithreaded
  pixel iteration; returns a new filtered array.

CuasDetectRT: apply filterConv5dROI() to dpixels_5d_roi_pyramid[level][n5d]
  after convolve3d(), controlled by curt_vel_thresh_en / curt_vel_athresh /
  curt_vel_rthresh, at level-0 and all pyramid levels.
Co-authored-by: Claude <claude@elphel.com>

CuasRTUtils: new showConvKernel5dHyperRect(data, roi, scene_titles, title)
  - ImageJ hyperstack [num_vout][num_scenes][roi_w*sub_dim × roi_h*sub_dim]
  - Bottom slider (T): 121 velocities labelled "+vy:+vx"
  - Second slider (Z): scenes
  - Sub-pixels spatially embedded (no NaN separator grid)

CuasDetectRT: add HYPER-RECT save immediately after each RECT save block
  (level-0 and pyramid loop), suffix "-HYPER-RECT" / "-LEV{n}-HYPER-RECT"
Co-authored-by: Claude <claude@elphel.com>

- CuasRTUtils: add convolve3d(data, Rectangle roi, result_in) that allocates
  only [roi.width*roi.height][nsub][nvel] instead of full [width*height][nsub][nvel],
  skips non-ROI pixels in center/margin loops, uses roi-relative indexing.
  Also fix showConvKernel5d(data, roi, ...) pixel_idx to use ROI-relative
  (py_roi*roi.width+px_roi) instead of full-image indexing.

- CuasDetectRT: add dpixels_5d_roi_pyramid alongside dpixels_5d_pyramid.
  Level-0 and pyramid loop 5D blocks now call convolve3d(window, null) only
  when curt_save_c5full, and convolve3d(window, curt_save_select, null) only
  when curt_save_c5rect. RECT save blocks now read from dpixels_5d_roi_pyramid.
  Eliminates the OutOfMemoryError when curt_save_c5full=false.
Co-authored-by: Claude <claude@elphel.com>

New CuasRTUtils.showConvKernel5d(data, roi, titles, title): renders the
vout_dim×vout_dim velocity map for each ROI pixel as a tiled flat image,
with a 1-px NaN separator grid between pixel blocks (visible in ImageJ).
Sub-pixels (pixel_decimate>1) tile within each block.

CuasDetectRT: add curt_save_c5rect save calls at level-0 and each pyramid
level (title suffix "-RECT", "-LEVn-RECT"). curt_save_c5full path unchanged.
Co-authored-by: Claude <claude@elphel.com>

Add convolve3d() (kernel5d) at level-0 before the temporal pyramid loop
and at each pyramid level nlev+1 inside the loop, mirroring the existing
3D3 coarse-velocity pattern. Output saved as CONV5D hyperstack when
debugLevel > -4. Add getNumHist() getter to CuasRTUtils.
Co-authored-by: Claude <claude@elphel.com>

distributing for the power of coarse velocities

getInterseqScale() was calling getCorrIncExact() which returns 0.5*corr_offset
for half_step mode instead of the actual integer keyframe step getCorrInc()
(= corr_offset/2 with integer division). For odd corr_offset (e.g. 5) with
half_step=true these differ: getCorrIncExact()=2.5 vs getCorrInc()=2.

This caused getHalfBeforeAfterPixXY() to compute:
  after - before = RSLT_VX * 0.5   (wrong; observed by user)
instead of:
  after - before = RSLT_VX * corr_inc/corr_offset = RSLT_VX * 0.4  (correct)

recalcOmegas() uses the same interseq_scale in the inverse direction, so it
also reconstructed RSLT_VX/VY incorrectly from neighbouring keyframe positions.

Fix: use getCorrInc() (integer) in getInterseqScale() so that BX/AX positions
correspond to actual raw-frame midpoints and the velocity round-trip is exact.

Also adds an unambiguous convention comment near RSLT_VX/RSLT_VY in
CuasMotionLMA.java documenting all required scale conversions.

The omega calculation (getFrameVelocityScale * ifov * fps_raw) is independent
of corr_inc and was already correct.
Co-authored-by: Claude <claude@elphel.com>

coordinates relation

- parse_images_txt: store full R_cw (world→camera rotation) per frame
- new compute_orientation_data(): per-frame COLMAP and ERS orientation
  in Sim(3)-aligned GPS frame; delta-rotation angle (convention-independent);
  cumulative rotation integrated from frame 0
- new print_orientation_report(): per-frame RMSE + cumulative totals
- ers_to_R(): guessed convention Rz(az)*Rx(tilt)*Ry(roll) — to be verified
- CSV: adds colmap_yaw/pitch/roll, delta_colmap/ers/diff, cum_colmap/ers/diff

Key finding for water-tower straight-flight (378 frames):
  COLMAP cumulative rotation = 120.81° (photogrammetric noise ~0.25°/frame)
  ERS cumulative rotation    =  14.10° (physically correct: 1.9° heading + vibration)
→ COLMAP orientation is dominated by pose-estimation noise for pure-nadir SfM
→ orientation comparison meaningful only for LARGE angular changes (turning sequences)
→ position comparison (Sim(3) RMSE) remains the primary validation metric
Co-authored-by: Claude <claude@elphel.com>

Compares COLMAP camera centers (images.txt) with three imagej-elphel position
columns (ERS x/y/z, IMS imsX/Y/Z, PIMU pimuX-C/Y-C/Z-C) using 7-DOF Sim(3)
alignment (Umeyama 1991).  Reports scale, rotation (Euler angles), per-frame
residuals in both COLMAP units and physical meters, and saves a CSV.

Key results for water-tower scene (1763233718_057205, rect/PINHOLE, 378 frames):
  Scale ~0.054 (1 COLMAP unit ≈ 18.5 m; flight spans 225 m → 12.2 COLMAP units)
  ERS RMSE=8.3 m, max=19.6 m at trajectory endpoints
  Worst frames are at both ends of the 378-frame sequence — consistent with the
  SfM nadir doming artifact (camera orientations rotate outward from center)
  Two near-zero crossings at frames ~74 and ~296 confirm dome vs straight-line fit
Co-authored-by: Claude <claude@elphel.com>

Generates a multi-slice float32 TIFF (NaN-padded, ImageJ-compatible):
  Slice 1: tile-processor disparity D scattered to nadir image pixels
           (from *-NADIR-DISPARITY-MAPS.tiff, averaged across all scenes)
  Slice 2: COLMAP sparse Z_cam projected to the same nadir pixel grid
           (optional --dense PLY for OpenMVS dense cloud)
  Slice 3: spatial superposition (tile-proc priority; COLMAP where missing;
           average at overlapping pixels)
  Slice 4: tile-processor scene-count per pixel (--counts flag)

Uses the COLMAP reference-image pose (auto-detected as centroid of camera
centres, or specified via --ref-image) to project 3D points. Handles
OPENCV lens distortion model (--no-distortion to skip).

Intended for evaluating depth-fusion approaches (tile processor + SIFT):
  python3 scripts/fopen_nadir_compare.py \
      --disp   <ts>-NADIR-DISPARITY-MAPS.tiff \
      --colmap sparse/0_txt/ [--dense scene_dense.ply] \
      --out    nadir_compare.tif --counts
Co-authored-by: Claude <claude@elphel.com>

Update calling code in OpticalFlow.java to compute nadir_pXpYD once and
render two passes when either nadir_gen or nadir_undistort is enabled:
- nadir_gen=true  → renderNadirSequence(..., false) → *-NADIR-MERGED
- nadir_undistort=true → renderNadirSequence(..., true)  → *-NADIR-MERGED-RECTILINEAR

The nadir_pXpYD array is deep-copied per scene for the undistort pass so
the original sensor-coordinate data is preserved for the non-undistorted pass.
Co-authored-by: Claude <claude@elphel.com>

Add nadir_undistort (boolean, default true) to IntersceneMatchParameters
at all 6 required locations (field, dialog, read, save, load, clone).

When enabled, renderNadirSequence() undistorts the pX,pY coordinates of
each scene's nadir disparity map before calling renderGPUFromDSI(), so the
rendered NADIR-MERGED TIFF images are rectilinear (pinhole projection)
rather than retaining the sensor's native radial distortion.

Analysis of the Boson 640 calibration (lwir16-06-72-00.calib-tiff) showed:
- True distortion polynomial terms: < 1 px magnitude across the full image
- The dominant issue was d = K0 = 1.00997 (a ~1% focal-length constant offset)
  which, when modeled as PINHOLE with the nominal focal length, curves the
  ground plane into the 'Little Prince planet' sphere effect seen in Blender
- With nadir_undistort=true, COLMAP can use a pure PINHOLE model with the
  correct effective focal length (f * d = 1121.8 px instead of 1110.8 px)

The undistortPxPy() helper mirrors getWorldCoordinates() in GeometryCorrection:
  rD_mm = ||(pX-cx, pY-cy)|| * pixelSize_mm
  factor = getRByRDist(rD_mm / distortionRadius)
  pX_rect = (pX - cx) * factor + cx
Co-authored-by: Claude <claude@elphel.com>

Add three dedicated unsharp-mask parameters to IntersceneMatchParameters:
  nadir_um_en     (boolean, default false) - enable UM on nadir images
  nadir_um_sigma  (double,  default 2.0)   - Gaussian sigma in pixels
  nadir_um_weight (double,  default 1.0)   - blend weight (1.0 = 100%)

These are separate from the existing um_sigma/weight and terr_um_* / cuas_rng_um_*
parameters so they can be independently tuned for SIFT feature extraction.
LWIR nadir images with UM sigma=2 go from ~500 to ~5000 SIFT keypoints/frame.

Updated all 6 required locations: field declarations, dialog, dialog-read,
save, load, and clone.

Applied the filter in renderNadirSequence() using the existing applyUM()
helper, matching the renderSceneSequence() pattern.
Co-authored-by: Claude <claude@elphel.com>

Add ShowDoubleFloatArrays.transposeJagged(double[][][], int n_comp, int n_inner)
which converts the common [outer][inner][comp] layout (with null outer or inner
entries) to [outer][comp][inner] substituting NaN for nulls.  This pattern
appeared inline in getNadirDisparityMaps() and recurs in other tile-processing
code.

Refactor getNadirDisparityMaps() to replace the 12-line inline transpose loop
with a single call to the new utility, keeping the same semantics.
Co-authored-by: Claude <claude@elphel.com>

After computing per-scene pXpYD arrays, saves a tile-resolution
hyperstack <ts>-NADIR-DISPARITY-MAPS.tiff with:
  - frames = scenes (labelled by timestamp)
  - slices = pX, pY, D (3 channels)
  - NaN where scene has no pose or tile has no data

Useful for verifying disparity transform coverage before feeding
the rendered images into OpenMVS/COLMAP.
Co-authored-by: Claude <claude@elphel.com>

New methods in OpticalFlow.java:
- getNadirDisparityMaps(): transforms SfM terrain disparity from the
  segment reference into each scene's own camera frame using
  Cuas.transformFromVirtual(). Returns double[][][nscene][ntiles][3].
- renderNadirSequence(): renders each scene from its own position
  (scene_xyz/atr=ZERO3, ref_scene=scene itself) using per-scene
  pXpYD from getNadirDisparityMaps(). ERS rolling-shutter velocity
  corrections are still applied. Output: <ts>-NADIR-MERGED.tiff.

Unlike renderSceneSequence() (TERRAIN-DISP), which warps all frames
to the reference for zero ground parallax, renderNadirSequence() produces
natural-parallax perspective images from each scene's own viewpoint —
the correct input format for OpenMVS/COLMAP dense reconstruction.

New parameter in IntersceneMatchParameters:
- nadir_gen (boolean, default false): checkbox under 'Flat ground' tab,
  before fgnd_gen_optho. Enables nadir rendering in the existing
  TERRAIN-DISP pipeline block.
Co-authored-by: Claude <claude@elphel.com>

Adds filteredResources to the seed template:
- regex filter for node_modules/.git/Java LS artifacts (existing on .137)
- multiFilter to hide attic/ from Eclipse project explorer and build

Copy this to .project on a new machine setup.
Co-authored-by: Claude <claude@elphel.com>

- scripts/lwir_map/lwir_scene_summary.py  (was fopen_nc_summary.py)
- scripts/lwir_map/lwir_map_overlay.py    (was fopen_overlay.py)
- scripts/lwir_map/README.md              (pipeline doc + known limitations)
- Updated catalog.json and scripts/README.md with new names/paths

Scripts read imagej-elphel linked LWIR output and generate per-scene
TSV + GeoJSON/KML/SVG map overlays for satellite atlas navigation.
Not FOPEN-specific; usable for any airplane/drone LWIR acquisition.
Co-authored-by: Claude <claude@elphel.com>

Documents TERRAIN-DISP-MERGED TIFF format, INTERFRAME.corr-xml pose
convention, Elphel→COLMAP coordinate conversion, disparity-to-depth
formula, and the foliage CLI pipeline (no C++ library linking).
Co-authored-by: Claude <claude@elphel.com>

Replaces hardcoded `boolean reuse_non_centered = true` with a config parameter.
Adds a companion `cuas_reuse_centered` parameter: when true, attempts to load
ROUND_TWO_GOOD before starting computation and returns early if found, bypassing
both phases. Both default to true — missing files behave as if set to false.
Wired into dialog, properties (.corr-xml), and copy() in IntersceneMatchParameters.
Co-authored-by: Claude <claude@elphel.com>

Spawns attic/elphel-agent-tools/bin/cpu_profile_hold.py on startup,
which calls power-profiles-daemon HoldProfile('balanced') via DBus.
Released automatically via SIGTERM on JVM shutdown.

Design: KDE AC default is power-saver; this hold raises the profile to
balanced (hardware-driven boost under load) while ImageJ is running,
then releases it so the machine drops back to power-saver on exit.
Co-authored-by: Claude <claude@elphel.com>

Pure-Java prototype CuasRTDetector + RtParams parameters class +
CuasRTLib JNA stub (activate when JNA added to pom.xml).
No dependencies added; build is clean. See design discussion in
attic/imagej-elphel-internal/handoffs/2026-05-21_RealTimeDesign.md.
Co-authored-by: Claude <claude@elphel.com>