Merge pull request #320 from christianbrodbeck/py310

Compatibility updates

Author: christianbrodbeck

surfer/io.py

@@ -7,7 +7,10 @@
 import gzip
 import numpy as np
 import nibabel as nib
-from nibabel.spatialimages import ImageFileError
+try:
+    from nibabel.spatialimages import ImageFileError  # removed in nibabel 5.1
+except ImportError:
+    from nibabel.filebasedimages import ImageFileError
 
 from .utils import verbose
 

surfer/tests/test_utils.py

@@ -73,15 +73,15 @@ def test_huge_cross():
 def test_create_color_lut():
     """Test various ways of making a colormap."""
     # Test valid lut
-    cmap_in = (np.random.rand(256, 4) * 255).astype(np.int)
+    cmap_in = (np.random.rand(256, 4) * 255).astype(int)
     cmap_out = utils.create_color_lut(cmap_in)
     assert_array_equal(cmap_in, cmap_out)
 
     # Test mostly valid lut
     cmap_in = cmap_in[:, :3]
     cmap_out = utils.create_color_lut(cmap_in)
     assert_array_equal(cmap_in, cmap_out[:, :3])
-    assert_array_equal(cmap_out[:, 3], np.ones(256, np.int) * 255)
+    assert_array_equal(cmap_out[:, 3], np.ones(256, int) * 255)
 
     # Test named matplotlib lut
     cmap_out = utils.create_color_lut("BuGn_r")

surfer/utils.py

@@ -1,4 +1,7 @@
-from collections import Sequence
+try:
+    from collections.abc import Sequence
+except ImportError:  # Py 2.7
+    from collections import Sequence
 from distutils.version import LooseVersion
 import logging
 import warnings
@@ -150,7 +153,7 @@ def load_curvature(self):
         """Load in curvature values from the ?h.curv file."""
         curv_path = op.join(self.data_path, "surf", "%s.curv" % self.hemi)
         self.curv = nib.freesurfer.read_morph_data(curv_path)
-        self.bin_curv = np.array(self.curv > 0, np.int)
+        self.bin_curv = np.array(self.curv > 0, int)
 
     def load_label(self, name):
         """Load in a Freesurfer .label file.
@@ -163,7 +166,7 @@ def load_label(self, name):
         """
         label = nib.freesurfer.read_label(op.join(self.data_path, 'label',
                                           '%s.%s.label' % (self.hemi, name)))
-        label_array = np.zeros(len(self.x), np.int)
+        label_array = np.zeros(len(self.x), int)
         label_array[label] = 1
         try:
             self.labels[name] = label_array
@@ -513,10 +516,10 @@ def create_color_lut(cmap, n_colors=256, center=None):
         if np.ndim(cmap) == 2:
             if cmap.shape[1] == 4:
                 # This looks likes a LUT that's ready to go
-                lut = cmap.astype(np.int)
+                lut = cmap.astype(int)
             elif cmap.shape[1] == 3:
                 # This looks like a LUT, but it's missing the alpha channel
-                alpha = np.ones(len(cmap), np.int) * 255
+                alpha = np.ones(len(cmap), int) * 255
                 lut = np.c_[cmap, alpha]
 
             return lut
@@ -548,7 +551,7 @@ def create_color_lut(cmap, n_colors=256, center=None):
             raise ValueError("Input %r was not valid for making a lut" % cmap)
 
     # Convert from a matplotlib colormap to a lut array
-    lut = (cmap(np.linspace(0, 1, n_colors)) * 255).astype(np.int)
+    lut = (cmap(np.linspace(0, 1, n_colors)) * 255).astype(int)
 
     return lut
 

surfer/viz.py

@@ -1457,7 +1457,7 @@ def _to_borders(self, label, hemi, borders, restrict_idx=None):
             n_vertices = label.size
             edges = utils.mesh_edges(self.geo[hemi].faces)
             border_edges = label[edges.row] != label[edges.col]
-            show = np.zeros(n_vertices, dtype=np.int)
+            show = np.zeros(n_vertices, dtype=int)
             keep_idx = np.unique(edges.row[border_edges])
             if isinstance(borders, int):
                 for _ in range(borders):