From f6e703148ccee605631f0cd54e13533ac93a4bc0 Mon Sep 17 00:00:00 2001 From: Oren Amsalem Date: Fri, 11 Apr 2025 11:07:40 -0400 Subject: [PATCH 1/3] suppress division warning Same as here https://github.com/JaneliaSciComp/bigstream/blob/6e91bfb822c417bfde621b1ffd4caf9b056e3d60/bigstream/distributed_align.py#L311 --- bigstream/piecewise_align.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bigstream/piecewise_align.py b/bigstream/piecewise_align.py index 66b7c5c..814c22d 100644 --- a/bigstream/piecewise_align.py +++ b/bigstream/piecewise_align.py @@ -375,7 +375,8 @@ def align_single_block(indices, static_transform_list): missing_weights[region] += weights[neighbor_region] # rebalance the weights - weights = weights / (1 - missing_weights) + with np.errstate(divide='ignore', invalid='ignore'): + weights = weights / (1 - missing_weights) weights[np.isnan(weights)] = 0. # edges of blocks are 0/0 weights = weights.astype(np.float32) From fb8d7d03b6106666f6d51dfe112b7afe3e6bcee5 Mon Sep 17 00:00:00 2001 From: Oren Amsalem Date: Fri, 11 Apr 2025 17:08:35 -0400 Subject: [PATCH 2/3] python3.12 --- bigstream/transform.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bigstream/transform.py b/bigstream/transform.py index 8557ffc..fd31d7c 100644 --- a/bigstream/transform.py +++ b/bigstream/transform.py @@ -230,7 +230,12 @@ def apply_transform_to_coordinates( # interpolate position field at coordinates, reformat, return ndims = transform.shape[-1] interp = lambda x: map_coordinates(x, coordinates, mode='nearest') - dX = np.array([interp(transform[..., i]) for i in range(ndims)]).transpose() + dX = [] + for i in range(ndims): + if transform[..., i]: + dX.append(interp(transform[..., i])) + else: + dx.append(interp([0]) coordinates = coordinates.transpose() * spacing + dX if origin is not None: coordinates += origin From 9fcf5c65d632c8254f78b6faa250cee9d2691803 Mon Sep 17 00:00:00 2001 From: Oren Amsalem Date: Fri, 11 Apr 2025 19:03:00 -0400 Subject: [PATCH 3/3] Update transform.py --- bigstream/transform.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bigstream/transform.py b/bigstream/transform.py index fd31d7c..4f8b9d4 100644 --- a/bigstream/transform.py +++ b/bigstream/transform.py @@ -231,11 +231,11 @@ def apply_transform_to_coordinates( ndims = transform.shape[-1] interp = lambda x: map_coordinates(x, coordinates, mode='nearest') dX = [] - for i in range(ndims): + for i in range(ndims): if transform[..., i]: dX.append(interp(transform[..., i])) else: - dx.append(interp([0]) + dX.append(interp([0]) coordinates = coordinates.transpose() * spacing + dX if origin is not None: coordinates += origin