From dbd27dbc136f06a22c3b8628707068958313c36d Mon Sep 17 00:00:00 2001
From: Ethan Blackwood <ethanbblackwood@gmail.com>
Date: Wed, 15 May 2024 22:44:14 -0400
Subject: [PATCH 1/2] Clean up special cases for loading from HDF5 and fix None
handling
---
caiman/utils/utils.py | 27 +++++++++------------------
1 file changed, 9 insertions(+), 18 deletions(-)
diff --git a/caiman/utils/utils.py b/caiman/utils/utils.py
index caf82d906..3fe65ea44 100644
--- a/caiman/utils/utils.py
+++ b/caiman/utils/utils.py
@@ -561,25 +561,16 @@ def recursively_load_dict_contents_from_group(h5file:h5py.File, path:str) -> dic
for key, item in h5file[path].items():
if isinstance(item, h5py._hl.dataset.Dataset):
- val_set = np.nan
- if isinstance(item[()], str):
- if item[()] == 'NoneType':
- ans[key] = None
- else:
- ans[key] = item[()]
-
- elif key in ['dims', 'medw', 'sigma_smooth_snmf', 'dxy', 'max_shifts', 'strides', 'overlaps']:
- if isinstance(item[()], np.ndarray):
- ans[key] = tuple(item[()])
- else:
- ans[key] = item[()]
+ val = item[()]
+ if val == 'NoneType' or val == b'NoneType':
+ ans[key] = None
+ elif key in ['dims', 'medw', 'sigma_smooth_snmf',
+ 'dxy', 'max_shifts', 'strides', 'overlaps'] and isinstance(val, np.ndarray):
+ ans[key] = tuple(val)
+ elif isinstance(val, np.bool_): # sigh
+ ans[key] = bool(val)
else:
- if isinstance(item[()], np.bool_): # sigh
- ans[key] = bool(item[()])
- else:
- ans[key] = item[()]
- if isinstance(ans[key], bytes) and ans[key] == b'NoneType':
- ans[key] = None
+ ans[key] = item[()]
elif isinstance(item, h5py._hl.group.Group):
if key in ('A', 'W', 'Ab', 'downscale_matrix', 'upscale_matrix'):
From 09a8a0273a04d5d23516113b3f0fbf4618c2b9fe Mon Sep 17 00:00:00 2001
From: Ethan Blackwood <ethanbblackwood@gmail.com>
Date: Wed, 15 May 2024 22:51:49 -0400
Subject: [PATCH 2/2] Fix invalid comparison for non-scalars
---
caiman/utils/utils.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/caiman/utils/utils.py b/caiman/utils/utils.py
index 3fe65ea44..e0dd46f15 100644
--- a/caiman/utils/utils.py
+++ b/caiman/utils/utils.py
@@ -562,7 +562,7 @@ def recursively_load_dict_contents_from_group(h5file:h5py.File, path:str) -> dic
for key, item in h5file[path].items():
if isinstance(item, h5py._hl.dataset.Dataset):
val = item[()]
- if val == 'NoneType' or val == b'NoneType':
+ if isinstance(val, str) and val == 'NoneType' or isinstance(val, bytes) and val == b'NoneType':
ans[key] = None
elif key in ['dims', 'medw', 'sigma_smooth_snmf',
'dxy', 'max_shifts', 'strides', 'overlaps'] and isinstance(val, np.ndarray):