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Make sima run on python 3 and numpy 1.26 #257

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4 changes: 2 additions & 2 deletions sima/__init__.py
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Expand Up @@ -6,7 +6,7 @@
from sima.imaging import ImagingDataset
from sima.sequence import Sequence

from numpy.testing import Tester
test = Tester().test
import numpy.testing as testing
test = testing.test

__version__ = '1.3.2'
4 changes: 2 additions & 2 deletions sima/motion/__init__.py
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@@ -1,6 +1,6 @@
from __future__ import absolute_import
from numpy.testing import Tester
test = Tester().test
import numpy.testing as testing
test = testing.test

from .motion import MotionEstimationStrategy, ResonantCorrection
from .frame_align import PlaneTranslation2D, VolumeTranslation
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4 changes: 2 additions & 2 deletions sima/motion/_motion.pyx
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Expand Up @@ -9,8 +9,8 @@ import cython
import numpy as np
cimport numpy as np

INT_TYPE = np.int
FLOAT_TYPE = np.float
INT_TYPE = int
FLOAT_TYPE = float
ctypedef np.int_t INT_TYPE_t
ctypedef np.float_t FLOAT_TYPE_t

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6 changes: 3 additions & 3 deletions sima/segment/_opca.pyx
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Expand Up @@ -11,8 +11,8 @@ cimport numpy as np

# from sima.misc import pairwise

INT_TYPE = np.int
FLOAT_TYPE = np.float
INT_TYPE = int
FLOAT_TYPE = float
ctypedef np.int_t INT_TYPE_t
ctypedef np.float_t FLOAT_TYPE_t

Expand All @@ -38,7 +38,7 @@ def _fast_ocorr(dataset, np.ndarray[INT_TYPE_t, ndim=2] pixel_pairs, channel=0):
X = np.nan_to_num(frames[0][channel] - time_avg)
Y = np.nan_to_num(frames[1][channel] - time_avg)
if not frame_idx % 100:
print frame_idx
print(frame_idx)
ostdevs += X * Y
for pair_idx in range(num_pairs):
a0 = pixel_pairs[pair_idx, 0]
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