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Do driftcorrect on rectangular ROI #4

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Do driftcorrect on rectangular ROI #4

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dc967d2
Update registration.py
thagusta Feb 17, 2022
024ad4c
Update 2 - Driftcorrection.py
thagusta Feb 17, 2022
79909b7
Add files via upload
thagusta Feb 17, 2022
907a80a
Napari-example rectangular ROI
thagusta Feb 17, 2022
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8 changes: 7 additions & 1 deletion 2 - Driftcorrection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,8 +97,14 @@ def plot_stack(images, n, grid=False):
n=widgets.IntSlider(original.shape[0]//2, 0, original.shape[0]-1, 1, continuous_update=False)
)

# Get extent, by any means necessary. Example with center and square of fftsize
center = [dim//2 for dim in original.shape[1:]]
extent = (center[0]-fftsize, center[0]+fftsize, center[1]-fftsize, center[1]+fftsize)
fftsize = max(extent[1]-extent[0], extent[3]-extent[2]) //2 # used in calc half matrices

# Step 1 to 3 of the algorithm as described in section 4 of the paper.
sobel = crop_and_filter(original[Eslice,...].rechunk({0:dE}), sigma=3, finalsize=2*fftsize)
sobel = Reg.crop_and_filter_extent(original[Eslice, ...].rechunk({0: dE}), extent, sigma=sigma)
#sobel = crop_and_filter(original[Eslice,...].rechunk({0:dE}), sigma=3, finalsize=2*fftsize)
sobel = (sobel - sobel.mean(axis=(1,2), keepdims=True)) #.persist()
sobel

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