Merge pull request #24 from hjmjohnson/fix-test-warnings

Fix test warnings
pnlbwh · Jul 18, 2022 · ec40c7e · ec40c7e
2 parents 48f94ce + 3b60325
commit ec40c7e
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Showing 4 changed files with 13 additions and 13 deletions.
diff --git a/conversion/grad_avg.py b/conversion/grad_avg.py
@@ -25,7 +25,7 @@ def grad_avg(imgFile, outFile, bvalFile= None, bvecFile= None):
         bvecs= read_bvecs(bvecFile)
 
         img= nib.load(imgFile)
-        data = img.get_data()
+        data = img.get_fdata()
         if len(data.shape)!=4:
             raise AttributeError('Not a valid dwi, check dimension')
 

diff --git a/conversion/grad_remove.py b/conversion/grad_remove.py
@@ -26,7 +26,7 @@ def grad_remove(imgFile, outFile, qc_bad_indices= [], interval= [], bvalFile= No
         grad_axis= 3
 
         img= nib.load(imgFile)
-        data = img.get_data()
+        data = img.get_fdata()
         if len(data.shape)!=4:
             raise AttributeError('Not a valid dwi, check dimension')
 

diff --git a/conversion/nifti_write.py b/conversion/nifti_write.py
@@ -74,7 +74,7 @@ def nifti_write(inImg, prefix= None):
         volume_axes.remove(grad_axis)
         rotation= hdr['space directions'][volume_axes,:3]
 
-        xfrm_nhdr= np.matrix(np.vstack((np.hstack((rotation.T, np.reshape(translation,(3,1)))),[0,0,0,1])))
+        xfrm_nhdr= np.array(np.vstack((np.hstack((rotation.T, np.reshape(translation,(3,1)))),[0,0,0,1])))
 
         # put the gradients along last axis
         if grad_axis!=3:
@@ -87,7 +87,7 @@ def nifti_write(inImg, prefix= None):
             f_vec= open(prefix+'.bvec', 'w')
             b_max = float(hdr['DWMRI_b-value'])
 
-            mf= np.matrix(np.vstack((np.hstack((hdr['measurement frame'],
+            mf= np.array(np.vstack((np.hstack((hdr['measurement frame'],
                                                 [[0],[0],[0]])),[0,0,0,1])))
             for ind in range(hdr['sizes'][grad_axis]):
                 bvec = [float(num) for num in hdr[f'DWMRI_gradient_{ind:04}'].split()]
@@ -97,7 +97,7 @@ def nifti_write(inImg, prefix= None):
                 bvec.append(1)
                 # bvecINijk= RAS2IJK @ SPACE2RAS @ mf @ np.matrix(bvec).T
                 # simplified below
-                bvecINijk= xfrm_nhdr.T @ mf @ np.matrix(bvec).T
+                bvecINijk= xfrm_nhdr.T @ mf @ np.array(bvec).T
 
                 L_2= np.linalg.norm(bvecINijk[:3])
                 if L_2:

diff --git a/conversion/tests/test_file_conversion.py b/conversion/tests/test_file_conversion.py
@@ -1,9 +1,6 @@
 import os
-import sys
 
-# sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
-
-from numpy import testing
+from numpy import testing, array
 from conversion.tests.util import *
 from nrrd import read
 from nibabel import load
@@ -21,14 +18,14 @@ def test_nrrd2nifti(self):
 
         # load converted output
         converted_nifti= load(PREFIX+'.nii.gz')
-        converted_nifti_data= converted_nifti.get_data()
+        converted_nifti_data= converted_nifti.get_fdata()
         converted_nifti_affine= converted_nifti.affine
         converted_nifti_bvals= conversion.read_bvals(PREFIX+'.bval')
         converted_nifti_bvecs = conversion.read_bvecs(PREFIX+'.bvec')
 
         # load converted reference
         converted_nifti= load(CONVERTED_NIFTI)
-        reference_nifti_data= converted_nifti.get_data()
+        reference_nifti_data= converted_nifti.get_fdata()
         reference_nifti_affine= converted_nifti.affine
         reference_nifti_bvals= conversion.read_bvals(CONVERTED_BVAL)
         reference_nifti_bvecs = conversion.read_bvecs(CONVERTED_BVEC)
@@ -37,8 +34,11 @@ def test_nrrd2nifti(self):
         testing.assert_array_equal(reference_nifti_data, converted_nifti_data)
         testing.assert_array_equal(reference_nifti_affine, converted_nifti_affine)
         testing.assert_array_equal(reference_nifti_bvals, converted_nifti_bvals)
-        testing.assert_array_equal(reference_nifti_bvecs, converted_nifti_bvecs)
-
+        for bvec_idx in range(0,len(reference_nifti_bvecs)):
+            reference_bvec = array(reference_nifti_bvecs[bvec_idx])
+            converted_bvec = array(converted_nifti_bvecs[bvec_idx])
+            testing.assert_array_almost_equal_nulp(reference_bvec,
+                                                   converted_bvec, 1)
 
     def test_nifti2nrrd(self):