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Handle upcoming minor deprecations #1306

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merged 2 commits into from
Mar 31, 2024
Merged

Handle upcoming minor deprecations #1306

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0629765
handle grey_dilation import update
EricThomson Mar 22, 2024
fa38f06
get_colormap api updated before deprecation
EricThomson Mar 22, 2024
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2 changes: 1 addition & 1 deletion caiman/source_extraction/cnmf/spatial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -841,7 +841,7 @@ def determine_search_location(A, dims, method='ellipse', min_size=3, max_size=8,
Exception 'You cannot pass empty (all zeros) components!'
"""

from scipy.ndimage.morphology import grey_dilation
from scipy.ndimage import grey_dilation

# we initialize the values
if len(dims) == 2:
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6 changes: 3 additions & 3 deletions caiman/utils/visualization.py
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Expand Up @@ -154,7 +154,7 @@ def nb_view_patches(Yr, A, C, b, f, d1, d2, YrA=None, image_neurons=None, thr=0.
name of colormap (e.g. 'viridis') used to plot image_neurons
"""

colormap = matplotlib.cm.get_cmap(cmap)
colormap = matplotlib.colormaps.get_cmap(cmap)
grayp = [matplotlib.colors.rgb2hex(m) for m in colormap(np.arange(colormap.N))]
nr, T = C.shape
nA2 = np.ravel(np.power(A, 2).sum(0)) if isinstance(A, np.ndarray) else np.ravel(A.power(2).sum(0))
Expand Down Expand Up @@ -516,7 +516,7 @@ def nb_view_patches3d(Y_r, A, C, dims, image_type='mean', Yr=None,
A = csc_matrix(A)[index_permut, :]
dims = tuple(np.array(dims)[order[:3]])
d1, d2, d3 = dims
colormap = matplotlib.cm.get_cmap(cmap)
colormap = matplotlib.colormaps.get_cmap(cmap)
grayp = [matplotlib.colors.rgb2hex(m) for m in colormap(np.arange(colormap.N))]
nr, T = C.shape

Expand Down Expand Up @@ -780,7 +780,7 @@ def nb_imshow(image, cmap='jet'):
"""
Interactive equivalent of imshow for ipython notebook
"""
colormap = matplotlib.cm.get_cmap(cmap) # choose any matplotlib colormap here
colormap = matplotlib.colormaps.get_cmap(cmap) # choose any matplotlib colormap here
grayp = [matplotlib.colors.rgb2hex(m) for m in colormap(np.arange(colormap.N))]
xr = Range1d(start=0, end=image.shape[1])
yr = Range1d(start=image.shape[0], end=0)
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