From 8869bec608d0e4d16c8d4f0d6e93c742eb419639 Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Tue, 1 Oct 2024 01:26:09 -0400 Subject: [PATCH 1/6] update docstring --- caiman/source_extraction/cnmf/cnmf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index 05ce34a6d..fb4c6b912 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/caiman/source_extraction/cnmf/cnmf.py @@ -109,8 +109,8 @@ def __init__(self, n_processes, k=5, gSig=[4, 4], gSiz=None, merge_thresh=0.8, p p: int order of the autoregressive process used to estimate deconvolution - Ain: ndarray - if know, it is the initial estimate of spatial filters + Ain: np.ndarray + if know, it is the initial estimate of spatial filters, shape is [n_pixels, n_components] ssub: int downsampleing factor in space From 0c513655690eb9a6ee8fa8d7216046d9930f9ffa Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Tue, 1 Oct 2024 01:26:54 -0400 Subject: [PATCH 2/6] Update cnmf.py --- caiman/source_extraction/cnmf/cnmf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index fb4c6b912..37af175e6 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/caiman/source_extraction/cnmf/cnmf.py @@ -110,7 +110,7 @@ def __init__(self, n_processes, k=5, gSig=[4, 4], gSiz=None, merge_thresh=0.8, p order of the autoregressive process used to estimate deconvolution Ain: np.ndarray - if know, it is the initial estimate of spatial filters, shape is [n_pixels, n_components] + if know, it is the initial estimate of spatial filters, array must be 'F' order of shape: [n_pixels, n_components] ssub: int downsampleing factor in space From 7512651de65c2cf2b06f420e5839239e5ff157d0 Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Tue, 1 Oct 2024 01:29:14 -0400 Subject: [PATCH 3/6] Update estimates.py --- caiman/source_extraction/cnmf/estimates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/caiman/source_extraction/cnmf/estimates.py b/caiman/source_extraction/cnmf/estimates.py index d32a1ce23..79b79557a 100644 --- a/caiman/source_extraction/cnmf/estimates.py +++ b/caiman/source_extraction/cnmf/estimates.py @@ -36,7 +36,8 @@ def __init__(self, A=None, b=None, C=None, f=None, R=None, dims=None): Args: A: scipy.sparse.csc_matrix (dimensions: # of pixels x # components) - set of spatial footprints. Each footprint is represented in a column of A, flattened with order = 'F' + set of spatial footprints. Each footprint is represented in a column of A, flattened with order = 'F'. + Must be a np.ndarray of type `bool` is used for manual seeded initialization. C: np.ndarray (dimensions: # of components x # of timesteps) set of temporal traces (each row of C corresponds to a trace) From 9c15cc5b9d4bcb7bfb12eacae50ad1eb3563b202 Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Tue, 1 Oct 2024 01:29:48 -0400 Subject: [PATCH 4/6] Update cnmf.py --- caiman/source_extraction/cnmf/cnmf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index 37af175e6..b2016bbf8 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/caiman/source_extraction/cnmf/cnmf.py @@ -110,7 +110,7 @@ def __init__(self, n_processes, k=5, gSig=[4, 4], gSiz=None, merge_thresh=0.8, p order of the autoregressive process used to estimate deconvolution Ain: np.ndarray - if know, it is the initial estimate of spatial filters, array must be 'F' order of shape: [n_pixels, n_components] + if know, it is the initial estimate of spatial filters, array must be of type `bool` in 'F' order of shape: [n_pixels, n_components] ssub: int downsampleing factor in space From 7d74927c31183ab78b11ecc90f1fe25035ad8a97 Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Fri, 11 Oct 2024 19:20:10 -0400 Subject: [PATCH 5/6] Update cnmf.py --- caiman/source_extraction/cnmf/cnmf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index b2016bbf8..c8f8d6bdc 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/caiman/source_extraction/cnmf/cnmf.py @@ -110,7 +110,7 @@ def __init__(self, n_processes, k=5, gSig=[4, 4], gSiz=None, merge_thresh=0.8, p order of the autoregressive process used to estimate deconvolution Ain: np.ndarray - if know, it is the initial estimate of spatial filters, array must be of type `bool` in 'F' order of shape: [n_pixels, n_components] + if known, it is the initial estimate of spatial filters. Array must be of type `bool` in 'F' order of shape: [n_pixels, n_components] ssub: int downsampleing factor in space From cf0dd626e82b00b8a10a5333eb6cbf7691ef4f8b Mon Sep 17 00:00:00 2001 From: Kushal Kolar Date: Fri, 11 Oct 2024 19:21:02 -0400 Subject: [PATCH 6/6] Update estimates.py --- caiman/source_extraction/cnmf/estimates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caiman/source_extraction/cnmf/estimates.py b/caiman/source_extraction/cnmf/estimates.py index 79b79557a..d92945a21 100644 --- a/caiman/source_extraction/cnmf/estimates.py +++ b/caiman/source_extraction/cnmf/estimates.py @@ -37,7 +37,7 @@ def __init__(self, A=None, b=None, C=None, f=None, R=None, dims=None): Args: A: scipy.sparse.csc_matrix (dimensions: # of pixels x # components) set of spatial footprints. Each footprint is represented in a column of A, flattened with order = 'F'. - Must be a np.ndarray of type `bool` is used for manual seeded initialization. + Must be a np.ndarray of type `bool` if used for manual seeded initialization. C: np.ndarray (dimensions: # of components x # of timesteps) set of temporal traces (each row of C corresponds to a trace)