Merge pull request #587 from carterbox/warnings

MAI: Fix deprecation warnings from scipy

setup.cfg

@@ -43,7 +43,7 @@ install_requires =
     numexpr==2.*
     # numpy 1.22.4 breaks distribute_jobs
     # https://github.com/numpy/numpy/issues/21612
-    numpy>=1.12,!=1.22.4
+    numpy~=1.12,!=1.22.4
     pywavelets==1.*
     scikit-image~=0.17
     scipy==1.*

source/tomopy/misc/corr.py

@@ -53,7 +53,7 @@
                         unicode_literals)
 
 import numpy as np
-from scipy.ndimage import filters
+import scipy.ndimage
 import tomopy.util.mproc as mproc
 import tomopy.util.dtype as dtype
 import tomopy.util.extern as extern
@@ -154,7 +154,7 @@ def gaussian_filter(arr, sigma=3, order=0, axis=0, ncore=None):
         slc = [slice(None)] * arr.ndim
         for i in range(arr.shape[axis]):
             slc[axis] = i
-            e.submit(filters.gaussian_filter,
+            e.submit(scipy.ndimage.gaussian_filter,
                      arr[tuple(slc)],
                      sigma,
                      order=order,
@@ -192,7 +192,7 @@ def median_filter(arr, size=3, axis=0, ncore=None):
         slc = [slice(None)] * arr.ndim
         for i in range(arr.shape[axis]):
             slc[axis] = i
-            e.submit(filters.median_filter,
+            e.submit(scipy.ndimage.median_filter,
                      arr[tuple(slc)],
                      size=(size, size),
                      output=out[tuple(slc)])
@@ -470,7 +470,7 @@ def remove_outlier(arr, dif, size=3, axis=0, ncore=None, out=None):
         slc = [slice(None)] * arr.ndim
         for i in range(ncore):
             slc[axis] = chnk_slices[i]
-            e.submit(filters.median_filter,
+            e.submit(scipy.ndimage.median_filter,
                      arr[tuple(slc)],
                      size=filt_size,
                      output=tmp[tuple(slc)])
@@ -529,7 +529,7 @@ def remove_outlier1d(arr, dif, size=3, axis=0, ncore=None, out=None):
         slc = [slice(None)] * arr.ndim
         for i in range(ncore):
             slc[lar_axis] = chnk_slices[i]
-            e.submit(filters.median_filter,
+            e.submit(scipy.ndimage.median_filter,
                      arr[slc],
                      size=filt_size,
                      output=tmp[slc],

source/tomopy/recon/rotation.py

@@ -254,8 +254,8 @@ def find_center_vo(tomo, ind=None, smin=-50, smax=50, srad=6, step=0.25,
     # Denoising
     # There's a critical reason to use different window sizes
     # between coarse and fine search.
-    _tomo_cs = ndimage.filters.gaussian_filter(_tomo, (3, 1), mode='reflect')
-    _tomo_fs = ndimage.filters.gaussian_filter(_tomo, (2, 2), mode='reflect')
+    _tomo_cs = ndimage.gaussian_filter(_tomo, (3, 1), mode='reflect')
+    _tomo_fs = ndimage.gaussian_filter(_tomo, (2, 2), mode='reflect')
 
     # Coarse and fine searches for finding the rotation center.
     if _tomo.shape[0] * _tomo.shape[1] > 4e6:  # If data is large (>2kx2k)