Add explicit Z slice skipping

[msayr]

Motivation

• Users need a way to pre-specify Z slices to skip during Z alignment and rendering and the existing code logged low-confidence SIFT estimates but did not provide a CLI to skip slices ahead of time.
• The change implements an explicit, user-facing mechanism to mark slices as skipped in either project/global or stack-local coordinates so those slices are excluded from optical-flow computation, mesh relaxation influence and final rendering.

Description

• Added a project-level CLI --skip-slices to emalign.align_dataset_z and propagated those global indices into each stack's config before calling align_stack_z by extending execute_alignment and align_dataset_z signatures.
• Added stack-level CLI options --skip-slices-global and --skip-slices-local to emalign.scripts.align_stack_z and merged file/config values into the stack config.
• Normalized requested global/local indices to local TensorStore Z indices (normalized_skip_slices) and passed that list into compute_flow_dataset (as ignore_slices) and used it during rendering to skip and log user-skipped slices.
• Kept existing behavior for empty-slice skipping and flow cleaning; no changes were made to automatic SIFT-confidence-based skipping — SIFT valid_estimate continues to be logged while flow-cleaning thresholds remain controlled by flow_config parameters.

Testing

• Ran python -m py_compile emalign/scripts/align_stack_z.py emalign/align_dataset_z.py which succeeded.
• Ran git diff --check to validate whitespace/patch issues which returned clean.

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Handle skipped slices at the start of flow computation

When a new skip list contains the first slice that compute_flow_dataset will process (for example --skip-slices-local <local_z_min> on a stack with first_slice/reference_path, or <local_z_min + 1> on a root stack), this passes that z into _compute_flow's ignore path before any flow has been appended. That branch constructs the placeholder from flows[-1], so flows is empty and the run raises IndexError instead of completing the requested skip; seed the placeholder independently or advance past skipped starting slices before passing them as ignore_slices.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

Skip the initial reference slice before writing it

This check only runs in the rendering loop after root/disconnected stacks have already written their first non-empty slice in the first_slice is None and reference is None block and set start = z + 1. If the user requests skipping that first local/global slice, it is still rendered to the destination and used as the reference for subsequent flow, so --skip-slices* silently fails for the first slice of a root component; handle normalized_skip_slices before choosing/writing the initial reference slice.

Useful? React with 👍 / 👎.