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Fix subidx to enable computing the NoRMCorre template frame from subset of movie frames #1133

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Fix subidx to enable computing the NoRMCorre template frame from subset of movie frames #1133

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8662025
fix subidx to compute motion correction template from a movie slice
ludovicbellier Apr 26, 2023
eb35738
Merge pull request #1 from inscopix/subidx
ludovicbellier Apr 28, 2023
4aebaae
Update README.md
EricThomson Jun 30, 2023
17cd8e2
Merge pull request #1125 from EricThomson/main
EricThomson Jun 30, 2023
24f5efc
Merge branch 'flatironinstitute:main' into master
ludovicbellier Jul 6, 2023
164f496
refocus PR on subidx
ludovicbellier Jul 7, 2023
a08a067
Merge branch 'dev' into master
ludovicbellier Jul 7, 2023
88d1b48
isxd reading ability
ludovicbellier Oct 11, 2023
e4eea82
Revert "isxd reading ability"
ludovicbellier Oct 11, 2023
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16 changes: 16 additions & 0 deletions caiman/base/movies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1604,6 +1604,22 @@ def rgb2gray(rgb):
elif extension == '.sima':
raise Exception("movies.py:load(): FATAL: sima support was removed in 1.9.8")

elif extension == '.isxd':
import isx
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mov = isx.Movie.read(file_name)
T = mov.timing.num_samples
dims = mov.spacing.num_pixels
fr = 1e6 / mov.timing.period.to_usecs()

idx_frames = np.arange(T)
if subindices is not None:
idx_frames = idx_frames[subindices]
T = len(idx_frames)

input_arr = np.zeros([T] + list(dims), dtype=outtype)
for idx in range(T):
input_arr[idx, :, :] = mov.get_frame_data(idx)

else:
raise Exception('Unknown file type')
else:
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1 change: 1 addition & 0 deletions caiman/motion_correction.py
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Expand Up @@ -2101,6 +2101,7 @@ def high_pass_filter_space(img_orig, gSig_filt=None, freq=None, order=None):
return cm.movie(np.array([cv2.idft(cv2.dft(img, flags=cv2.DFT_COMPLEX_OUTPUT) *
H[..., None])[..., 0] for img in img_orig]) / (rows*cols))


def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=None, newstrides=None, upsample_factor_grid=4,
upsample_factor_fft=10, show_movie=False, max_deviation_rigid=2, add_to_movie=0, shifts_opencv=False, gSig_filt=None,
use_cuda=False, border_nan=True):
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