revert back to original mask index functionality

CMakeLists.txt

@@ -13,13 +13,13 @@ find_package(Python 3.8
 find_package(nanobind CONFIG REQUIRED)
 
 # TODO: make this run only if ITK + ANTs are not already built
-if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-  execute_process(COMMAND cmd /c ${PROJECT_SOURCE_DIR}/scripts/configure_ITK.bat)
-  execute_process(COMMAND cmd /c ${PROJECT_SOURCE_DIR}/scripts/configure_ANTs.bat)
-else()
-  execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ITK.sh)
-  execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ANTs.sh)
-endif()
+#if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+#  execute_process(COMMAND cmd /c ${PROJECT_SOURCE_DIR}/scripts/configure_ITK.bat)
+#  execute_process(COMMAND cmd /c ${PROJECT_SOURCE_DIR}/scripts/configure_ANTs.bat)
+#else()
+#  execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ITK.sh)
+#  execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ANTs.sh)
+#endif()
 
 # ITK
 set(ITK_DIR "./itkbuild")

ants/core/ants_image.py

@@ -573,10 +573,9 @@ def __getitem__(self, idx):
             ])
 
         if isinstance(idx, ANTsImage):
-            arr = self.numpy()
-            other = idx.numpy()
-            arr[other == 0] = 0
-            return self.new_image_like(arr)
+            if not image_physical_space_consistency(self, idx):
+                raise ValueError('images do not occupy same physical space')
+            return self.numpy().__getitem__(idx.numpy().astype('bool'))
 
         ndim = len(idx)
         sizes = list(self.shape)

ants/core/ants_image_io.py

@@ -196,15 +196,11 @@ def make_image(
     -------
     ANTsImage
     """
-    if isinstance(voxval, iio.ANTsImage):
-        voxval = voxval.numpy()
-
     if isinstance(imagesize, iio.ANTsImage):
         img = imagesize.clone()
         sel = imagesize > 0
         if voxval.ndim > 1:
             voxval = voxval.flatten()
-            voxval = voxval[voxval > 0]
         if (len(voxval) == int((sel > 0).sum())) or (len(voxval) == 0):
             img[sel] = voxval
         else:
@@ -321,7 +317,7 @@ def images_to_matrix(image_list, mask=None, sigma=None, epsilon=0.5):
     def listfunc(x):
         if np.sum(np.array(x.shape) - np.array(mask.shape)) != 0:
             x = reg.resample_image_to_target(x, mask, 2)
-        return x.numpy()[mask.numpy().astype('bool')]
+        return x[mask]
 
     if mask is None:
         mask = utils.get_mask(image_list[0])
@@ -338,8 +334,7 @@ def listfunc(x):
                 utils.smooth_image(img, sigma, sigma_in_physical_coordinates=True)
             )
         else:
-            tmp_val = listfunc(img)
-            data_matrix[i, :] = tmp_val.flatten()
+            data_matrix[i, :] = listfunc(img)
     return data_matrix
 
 
@@ -651,4 +646,4 @@ def image_write(image, filename, ri=False):
         image.to_file(filename)
 
     if ri:
-        return image
+        return image

tests/test_core_ants_image_indexing.py

@@ -94,7 +94,7 @@ def test_2d_vector(self):
         img_v2 = img_v[:10,:10]
 
         self.assertTrue(ants.allclose(img2, ants.split_channels(img_v2)[0]))
-#
+
     def test_2d_vector_multi(self):
         img = ants.image_read(ants.get_data('r16'))
         img2 = img[:10,:10]

tests/test_core_ants_image_io.py

@@ -109,21 +109,20 @@ def test_make_image(self):
             self.assertTrue(ants.image_physical_space_consistency(img2,mask))
 
             # set with arr.ndim > 1
-            img2 = ants.make_image(mask, voxval=np.expand_dims(arr.numpy(),-1))
+            img2 = ants.make_image(mask, voxval=np.expand_dims(arr,-1))
             nptest.assert_allclose(img2.numpy(), (img*mask).numpy())
             self.assertTrue(ants.image_physical_space_consistency(img2,mask))
 
-            with self.assertRaises(Exception):
-                # wrong number of non-zero voxels
-                img3 = ants.make_image(img, voxval=np.random.randn((100)))
+            #with self.assertRaises(Exception):
+            #    # wrong number of non-zero voxels
+            #    img3 = ants.make_image(img, voxval=arr)
 
 
     def test_matrix_to_images(self):
         # def matrix_to_images(data_matrix, mask):
         for img in self.imgs:
             imgmask = ants.image_clone(  img > img.mean(), pixeltype = 'float' )
-            data = img[imgmask].numpy()
-            data = data[data > 0]
+            data = img[imgmask]
             dataflat = data.reshape(1,-1)
             mat = np.vstack([dataflat,dataflat]).astype('float32')
             imglist = ants.matrix_to_images(mat, imgmask)
@@ -348,4 +347,4 @@ def test_image_read_write(self):
 
 
 if __name__ == '__main__':
-    run_tests()
+    run_tests()