nel-lab
Windows CI runs are segfaulting
Not sure exactly what's going on but it seems to happen when tensorflow is being initialized. So maybe easier to just wait until tensorflow is no longer part of caiman, which is getting pretty close
Stack trace
Testing cnmf cnmf input_movie_path: 417d0c0b-f2bb-41df-8ded-ce51b96ee45e\417d0c0b-f2bb-41df-8ded-ce51b96ee45e-mcorr_els__d1_60_d2_80_d3_1_order_F_frames_2000.mmap Running a3d6d1f0-b0d6-404c-a3fc-9adca9e0e346 with local backend
Starting CNMF item:
algo cnmf
item_name test-cnmf
input_movie_path 417d0c0b-f2bb-41df-8ded-ce51b96ee45e\417d0c0b-...
params {'main': {'p': 2, 'nb': 1, 'rf': None, 'stride...
outputs None
added_time 2025-09-05T01:39:11
ran_time None
algo_duration None
comments None
uuid a3d6d1f0-b0d6-404c-a3fc-9adca9e0e346
Name: 1, dtype: object
With params:{'main': {'p': 2, 'nb': 1, 'rf': None, 'stride': 30, 'K': 10, 'gSig': [5, 5], 'ssub': 1, 'tsub': 1, 'method_init': 'greedy_roi', 'min_SNR': 2.5, 'rval_thr': 0.8, 'use_cnn': True, 'min_cnn_thr': 0.8, 'cnn_lowest': 0.1, 'decay_time': 1}, 'refit': True}
making memmap
C:\Miniconda\envs\mescore\lib\site-packages\caiman_init_.py:3: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
C:\Miniconda\envs\mescore\lib\site-packages\caiman_init_.py:3: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
C:\Miniconda\envs\mescore\lib\site-packages\caiman_init_.py:3: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
C:\Miniconda\envs\mescore\lib\site-packages\caiman\source_extraction\cnmf\deconvolution.py:1004: FutureWarning: Beginning in SciPy 1.17, multidimensional input will be treated as a batch, not raveled. To preserve the existing behavior and silence this warning, ravel arguments before passing them to toeplitz.
A = scipy.linalg.toeplitz(xc[lags + np.arange(lags)],
C:\Miniconda\envs\mescore\lib\site-packages\caiman\source_extraction\cnmf\deconvolution.py:1004: FutureWarning: Beginning in SciPy 1.17, multidimensional input will be treated as a batch, not raveled. To preserve the existing behavior and silence this warning, ravel arguments before passing them to toeplitz.
A = scipy.linalg.toeplitz(xc[lags + np.arange(lags)],
C:\Miniconda\envs\mescore\lib\site-packages\caiman\source_extraction\cnmf\deconvolution.py:1004: FutureWarning: Beginning in SciPy 1.17, multidimensional input will be treated as a batch, not raveled. To preserve the existing behavior and silence this warning, ravel arguments before passing them to toeplitz.
A = scipy.linalg.toeplitz(xc[lags + np.arange(lags)],
2025-09-05 01:39:27.018030: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Windows fatal exception: access violation
Thread 0x00000a00 (most recent call first): File "C:\Miniconda\envs\mescore\lib\multiprocessing\connection.py", line 310 in _recv_bytes File "C:\Miniconda\envs\mescore\lib\multiprocessing\connection.py", line 255 in recv File "C:\Miniconda\envs\mescore\lib\multiprocessing\pool.py", line 579 in _handle_results File "C:\Miniconda\envs\mescore\lib\threading.py", line 953 in run File "C:\Miniconda\envs\mescore\lib\threading.py", line 1016 in _bootstrap_inner File "C:\Miniconda\envs\mescore\lib\threading.py", line 973 in _bootstrap
Thread 0x00001764 (most recent call first): File "C:\Miniconda\envs\mescore\lib\multiprocessing\pool.py", line 531 in _handle_tasks File "C:\Miniconda\envs\mescore\lib\threading.py", line 953 in run File "C:\Miniconda\envs\mescore\lib\threading.py", line 1016 in _bootstrap_inner File "C:\Miniconda\envs\mescore\lib\threading.py", line 973 in _bootstrap
Thread 0x0000105c (most recent call first): File "C:\Miniconda\envs\mescore\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait File "C:\Miniconda\envs\mescore\lib\multiprocessing\connection.py", line 884 in wait File "C:\Miniconda\envs\mescore\lib\multiprocessing\pool.py", line 502 in _wait_for_updates File "C:\Miniconda\envs\mescore\lib\multiprocessing\pool.py", line 522 in _handle_workers File "C:\Miniconda\envs\mescore\lib\threading.py", line 953 in run File "C:\Miniconda\envs\mescore\lib\threading.py", line 1016 in _bootstrap_inner File "C:\Miniconda\envs\mescore\lib\threading.py", line 973 in _bootstrap
Thread 0x00001064 (most recent call first): File "C:\Miniconda\envs\mescore\lib\threading.py", line 324 in wait File "C:\Miniconda\envs\mescore\lib\threading.py", line 607 in wait File "C:\Miniconda\envs\mescore\lib\site-packages\tqdm_monitor.py", line 60 in run File "C:\Miniconda\envs\mescore\lib\threading.py", line 1016 in _bootstrap_inner File "C:\Miniconda\envs\mescore\lib\threading.py", line 973 in _bootstrap
Current thread 0x00001dd4 (most recent call first):
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\eager\context.py", line 622 in ensure_initialized
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\constant_op.py", line 101 in convert_to_eager_tensor
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\constant_op.py", line 304 in _constant_eager_impl
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\constant_op.py", line 279 in _constant_impl
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\constant_op.py", line 267 in constant
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\tensor_conversion_registry.py", line 48 in _default_conversion_function
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\framework\ops.py", line 1638 in convert_to_tensor
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\profiler\trace.py", line 183 in wrapped
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\ops\resource_variable_ops.py", line 1817 in _init_from_args
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\ops\resource_variable_ops.py", line 1659 in init
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\ops\variables.py", line 268 in call
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\util\traceback_utils.py", line 150 in error_handler
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\ops\variable_scope.py", line 2755 in default_variable_creator_v2
File "C:\Miniconda\envs\mescore\lib\site-packages\tensorflow\python\ops\variables.py", line 240 in
