From a53973ac26e3e1ce280bd2d35a6ea4fe84981e07 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Fri, 23 Feb 2024 13:46:33 -0500 Subject: [PATCH 01/10] VERSION: 1.10.4 postrelease --- VERSION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/VERSION b/VERSION index 8b107faae..18b311420 100644 --- a/VERSION +++ b/VERSION @@ -1,2 +1 @@ -1.10.3 - +1.10.4 From e27ead4b6ccb1b9909426351a87c536b37a70b25 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Sun, 3 Mar 2024 23:17:50 -0500 Subject: [PATCH 02/10] Fix issue with dev release and last refactor of pathing --- caiman/base/movies.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caiman/base/movies.py b/caiman/base/movies.py index b0f9fec3d..e94ddd218 100644 --- a/caiman/base/movies.py +++ b/caiman/base/movies.py @@ -2261,7 +2261,7 @@ def get_file_size(file_name, var_name_hdf5:str='mov') -> tuple[tuple, Union[int, dims[0], dims[1] = pims_movie.frame_shape[0:2] elif extension == '.mmap': filename = os.path.split(file_name)[-1] - Yr, dims, T = load_memmap(os.path.join( + Yr, dims, T = caiman.mmapping.load_memmap(os.path.join( os.path.split(file_name)[0], filename)) elif extension in ('.h5', '.hdf5', '.nwb', 'n5', 'zarr'): # FIXME this doesn't match the logic in load() From 9f26fc6388fb259182fd80fcb14ff795ec12e78b Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 31 Jan 2024 15:44:46 -0500 Subject: [PATCH 03/10] Fix typo --- 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 866d117d6..caf82d906 100644 --- a/caiman/utils/utils.py +++ b/caiman/utils/utils.py @@ -649,7 +649,7 @@ def get_caiman_version() -> tuple[str, str]: # 'GITW') git rev-parse if caiman is built from "pip install -e ." and we are working # out of the checkout directory (the user may have since updated without reinstall) # 'RELF') A release file left in the process to cut a release. Should have a single line - # in it whick looks like "Version:1.4" + # in it which looks like "Version:1.4" # 'FILE') The date of some frequently changing files, which act as a very rough # approximation when no other methods are possible # From 83ce6ceea568d2bb6ee5f0af64e65993397e5dc3 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Mon, 4 Mar 2024 20:23:25 -0500 Subject: [PATCH 04/10] VERSION: post release to 1.10.5 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 18b311420..db77e0ee9 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.4 +1.10.5 From 9681c64f8f6575ad8b5a701ce1bc57d2a35ed920 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Tue, 2 Apr 2024 15:06:26 -0400 Subject: [PATCH 05/10] VERSION to 1.10.6 after release: main branch --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index db77e0ee9..7b4d9a4ff 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.5 +1.10.6 From 3cf859e2c5b3b77ed3780bee02c450330972009e Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Tue, 2 Apr 2024 22:31:10 -0400 Subject: [PATCH 06/10] VERSION to 1.10.7 after release --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 7b4d9a4ff..ccff224b7 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.6 +1.10.7 From d5cc46641b41fea673f14984cc22071b448a120c Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 3 Apr 2024 09:29:03 -0400 Subject: [PATCH 07/10] VERSION to 1.10.8 after release --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index ccff224b7..3cc3669ff 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.7 +1.10.8 From 1d6ee38e974e9adfdf916cf5e98517c6c5285e9d Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 3 Apr 2024 13:56:59 -0400 Subject: [PATCH 08/10] VERSION to 1.10.9 post release --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 3cc3669ff..b0dd75320 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.8 +1.10.9 From 9ea86c77cf7570fac2b631df3533743ae7a211e8 Mon Sep 17 00:00:00 2001 From: Pat Gunn Date: Wed, 3 Apr 2024 16:39:34 -0400 Subject: [PATCH 09/10] VERSION: 1.10.10 post-release --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index b0dd75320..2ee4474a1 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.10.9 +1.10.10 From fcaf2e01b149e7ceddaa00e4463fe7b79ade89ea Mon Sep 17 00:00:00 2001 From: pseudomanu <60672860+pseudomanu@users.noreply.github.com> Date: Wed, 10 Apr 2024 10:06:52 -0400 Subject: [PATCH 10/10] fixes inf values in components SNR --- caiman/source_extraction/cnmf/estimates.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/caiman/source_extraction/cnmf/estimates.py b/caiman/source_extraction/cnmf/estimates.py index c5889eb6e..f07df4e3b 100644 --- a/caiman/source_extraction/cnmf/estimates.py +++ b/caiman/source_extraction/cnmf/estimates.py @@ -1059,6 +1059,10 @@ def evaluate_components(self, imgs, params, dview=None): logging.warning('NaN values detected for trace SNR in {}'.format(np.where(np.isnan(SNR_comp))[0]) + '. Changing their value to 0.') SNR_comp = np.where(np.isnan(SNR_comp), 0, SNR_comp) + if np.any(np.isinf(SNR_comp)): + logging.warning('inf values detected for trace SNR in {}'.format(np.where(np.isinf(SNR_comp))[0]) + + '. Changing their value to 0.') + SNR_comp = np.where(np.isinf(SNR_comp), 0, SNR_comp) self.SNR_comp = SNR_comp self.r_values = r_values self.cnn_preds = cnn_preds