Merge branch 'add-stitched-similarity' of github.com:scottstanie/dolp…

…hin into add-stitched-similarity

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: "v4.6.0"
+ rev: "v5.0.0"
  hooks:
  # https://github.com/pre-commit/pre-commit-hooks/issues/718
  # - id: check-added-large-files # Fails with git v1.8.3
@@ -20,13 +20,13 @@ repos:
  - id: trailing-whitespace
 
  - repo: https://github.com/psf/black
- rev: "24.8.0"
+ rev: "24.10.0"
  hooks:
  - id: black
  args: [--preview]
 
  - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.6.8
+ rev: v0.6.9
  hooks:
  - id: ruff
  args: [--fix, --exit-non-zero-on-fix, --show-fixes]

src/dolphin/phase_link/_core.py

@@ -401,9 +401,9 @@ def process_coherence_matrices(
  """
  rows, cols, n, _ = C_arrays.shape
 
+ evd_eig_vals, evd_eig_vecs = eigh_largest_stack(C_arrays * jnp.abs(C_arrays))
  if use_evd:
  # EVD
- evd_eig_vals, evd_eig_vecs = eigh_largest_stack(C_arrays)
  eig_vals, eig_vecs = evd_eig_vals, evd_eig_vecs
  estimator = jnp.zeros(eig_vals.shape, dtype=bool)
  else:
@@ -449,7 +449,6 @@ def process_coherence_matrices(
  inv_has_nans_3d = jnp.tile(inv_has_nans[:, :, None], (1, 1, n))
 
  # For EVD, or places where inverting |Gamma| failed: fall back to computing EVD
- evd_eig_vals, evd_eig_vecs = eigh_largest_stack(C_arrays)
  eig_vecs = lax.select(
  inv_has_nans_3d,
  # Run this on True: EVD, since we failed to invert:

src/dolphin/workflows/wrapped_phase.py

@@ -170,6 +170,7 @@ def run(
  slc_vrt_stack=vrt_stack,
  output_folder=pl_path,
  ministack_size=cfg.phase_linking.ministack_size,
+ output_reference_idx=cfg.phase_linking.output_reference_idx,
  new_compressed_reference_idx=new_compressed_slc_reference_idx,
  half_window=cfg.phase_linking.half_window.model_dump(),
  strides=strides,