fix io tests

ANTsX · May 14, 2024 · 975a919 · 975a919
1 parent 84eefb0
commit 975a919
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Showing 3 changed files with 20 additions and 14 deletions.
diff --git a/CMakeLists.txt b/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")

diff --git a/ants/core/ants_image_io.py b/ants/core/ants_image_io.py
@@ -196,11 +196,15 @@ 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:
@@ -317,7 +321,7 @@ 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[mask]
+        return x.numpy()[mask.numpy().astype('bool')]
 
     if mask is None:
         mask = utils.get_mask(image_list[0])
@@ -334,7 +338,8 @@ def listfunc(x):
                 utils.smooth_image(img, sigma, sigma_in_physical_coordinates=True)
             )
         else:
-            data_matrix[i, :] = listfunc(img)
+            tmp_val = listfunc(img)
+            data_matrix[i, :] = tmp_val.flatten()
     return data_matrix
 
 

diff --git a/tests/test_core_ants_image_io.py b/tests/test_core_ants_image_io.py
@@ -109,20 +109,21 @@ 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,-1))
+            img2 = ants.make_image(mask, voxval=np.expand_dims(arr.numpy(),-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=arr)
+            with self.assertRaises(Exception):
+                # wrong number of non-zero voxels
+                img3 = ants.make_image(img, voxval=np.random.randn((100)))
 
 
     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]
+            data = img[imgmask].numpy()
+            data = data[data > 0]
             dataflat = data.reshape(1,-1)
             mat = np.vstack([dataflat,dataflat]).astype('float32')
             imglist = ants.matrix_to_images(mat, imgmask)