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Preserve global Z offsets and support config groups in get_ordered_datasets #15

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Preserve global Z offsets and support config groups in get_ordered_datasets #15

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52 changes: 46 additions & 6 deletions emalign/align_z/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,8 @@ def get_ordered_datasets(config_paths, exclude=[]):
'''Open and order datastacks based on Z offset.

Args:
dataset_paths (list): List of paths to the datasets to open and order.
config_paths (list): List of paths to the config files containing datasets
to open and order. Nested lists are treated as a config group.
exclude (list, optional): List of strings to find in paths. If the string is found, the path will be ignored.

Returns:
Expand All @@ -85,6 +86,7 @@ def get_ordered_datasets(config_paths, exclude=[]):
offsets = []
previous_offset = 0
for config_group in config_groups:
group_datasets = []
group_offsets = []
z_shapes = []
for config_path in config_group:
Expand All @@ -103,14 +105,52 @@ def get_ordered_datasets(config_paths, exclude=[]):
dataset = open_store(ds, mode='r')
z_shapes.append(dataset.shape[0])

offset = get_store_attributes(dataset)['voxel_offset']
offset[0] += previous_offset # Shift this dataset by the previous dataset's offset
offset = list(get_store_attributes(dataset)['voxel_offset'])
group_datasets.append(dataset)
group_offsets.append(offset)
offsets.append(offset)
dataset_stores.append(dataset)

if not group_offsets:
continue

group_offsets = np.array(group_offsets, dtype=int)
group_z_start = group_offsets[:, 0]
group_z_end = group_z_start + np.array(z_shapes)

# Config groups are commonly either:
# 1. local stacks whose Z offsets should be concatenated after the
# previous group, or
# 2. stacks that already carry global Z offsets from an upstream prep.
#
# Older behavior always added previous_offset, which double-counted
# already-global offsets (e.g. stack2 offset 531 became 1062 after a
# 531-slice stack1). Treat a non-first group as already global when
# its raw Z range reaches the current global cursor; otherwise, shift it
# after the previous group.
group_is_already_global = (
previous_offset > 0 and (
group_z_start.min() >= previous_offset or
group_z_end.max() > previous_offset

@chatgpt-codex-connector chatgpt-codex-connector Bot Jun 29, 2026

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P1 Badge Stop treating long local groups as global

When a later config group uses local Z offsets starting at 0 but is longer than the previous group, group_z_end.max() > previous_offset is true, so the group is preserved instead of shifted after the prior stack. For example, two XY configs with local ranges [0, 100) and [0, 200) leave the second group at Z 0 because 200 > 100, causing it to sort before/overlap the first group and corrupting the Z alignment plan that previously concatenated such configs.

Useful? React with 👍 / 👎.

)
)
if group_is_already_global:
adjusted_offsets = group_offsets.copy()
logging.info(
'Preserving global Z offsets for config group %s; raw Z range '
'[%s, %s) already reaches current cursor %s.',
config_group,
int(group_z_start.min()),
int(group_z_end.max()),
int(previous_offset)
)
else:
adjusted_offsets = group_offsets.copy()
adjusted_offsets[:, 0] += previous_offset

offsets.extend(adjusted_offsets.tolist())
dataset_stores.extend(group_datasets)

# If configs are supposed to be consecutive stacks, the offsets should match that
previous_offset = np.array(group_offsets)[:,0].max() + z_shapes[np.array(group_offsets)[:,0].argmax()]
previous_offset = int(np.max(adjusted_offsets[:, 0] + np.array(z_shapes)))

offsets = np.array(offsets)

Expand Down