nb=0 #1172
nb=0 #1172
Conversation
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Sounds very cool -- thanks! Will review in the next day. |
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| Y_resf = np.dot(Y, f.T) | ||
| b = np.maximum(Y_resf, 0) / (np.linalg.norm(f)**2) | ||
| if Y.shape[-1] < 30000: |
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We may want to consider making this threshold overridable or at least less magical
| else: | ||
| print('estimating f') | ||
| f = 0 | ||
| for xxx in np.where(not_px)[0]: |
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Can we give this variable a better name?
| @@ -197,7 +197,8 @@ def update_temporal_components(Y, A, b, Cin, fin, bl=None, c1=None, g=None, sn=N | |||
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| A = scipy.sparse.hstack((A, b)).tocsc() | |||
| S = np.zeros(np.shape(Cin)) | |||
| Cin = np.vstack((Cin, fin)) | |||
| if fin is not None: | |||
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Could you add a comment explaining how this works?
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Generally looks good |
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Since the selem keyword was deprecated at scikit learn, and we still have it, it might be nice to define what it means in this function: e.g., in the docs for it maybe just mention it stands for 'structuring element'
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you mean skimage? I remember playing with this years ago, it means something like the "where stuff is multiplier" =S
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this explains selem, the structuring element https://scikit-image.org/docs/stable/auto_examples/applications/plot_morphology.html
| if Y.shape[-1] < 30000: | ||
| f = Y[not_px, :].mean(0) | ||
| else: | ||
| print('estimating f') |
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There are a few print statements in here -- in final draft convert to logger info or debug statements?
Description
Enable to run CNMF without background components (nb=0) for cases when the background has already been removed in a pre-processing step using other means. Fixes #1068. (and a deprecation mentioned in #1130)
Type of change
Has your PR been tested?
Yes
python caimanmanager.py testand
python caimanmanager.py demotest