From 2c6e78195bfc6e074303c5f513629b7c2c3eaf79 Mon Sep 17 00:00:00 2001
From: Omer Faruk Gulban <farukgulban@gmail.com>
Date: Tue, 12 Jul 2022 17:04:21 +0200
Subject: [PATCH] Fix nibabel `.get_data` warnings

---
 pydeface/__main__.py | 10 ++++++----
 pydeface/utils.py    |  9 +++++----
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/pydeface/__main__.py b/pydeface/__main__.py
index bb4e182..e9695da 100644
--- a/pydeface/__main__.py
+++ b/pydeface/__main__.py
@@ -99,12 +99,14 @@ def main():
         print("Defacing mask also applied to:")
         for applyfile in args.applyto:
             applyfile_img = load(applyfile)
+            applyfile_data = np.asarray(applyfile_img.dataobj)
+            warped_mask_data = np.asarray(warped_mask_img.dataobj)
             try:
-                outdata = applyfile_img.get_data() * warped_mask_img.get_data()
+                outdata = applyfile_data * warped_mask_data
             except ValueError:
-                tmpdata = np.stack([warped_mask_img.get_data()] *
-                           applyfile_img.get_data().shape[-1], axis=-1)
-                outdata = applyfile_img.get_data() * tmpdata
+                tmpdata = np.stack(warped_mask_data * applyfile_data.shape[-1],
+                                   axis=-1)
+                outdata = applyfile_data * tmpdata
             applyfile_img = Nifti1Image(outdata, applyfile_img.affine,
                                         applyfile_img.header)
             outfile = pdu.output_checks(applyfile, force=args.force)
diff --git a/pydeface/utils.py b/pydeface/utils.py
index 10e4fff..b99eb37 100644
--- a/pydeface/utils.py
+++ b/pydeface/utils.py
@@ -113,13 +113,14 @@ def deface_image(infile=None, outfile=None, facemask=None,
 
     # multiply mask by infile and save
     infile_img = load(infile)
+    infile_data = np.asarray(infile_img.dataobj)
     warped_mask_img = load(warped_mask)
+    warped_mask_data = np.asarray(warped_mask_img.dataobj)
     try:
-        outdata = infile_img.get_data().squeeze() * warped_mask_img.get_data()
+        outdata = infile_data.squeeze() * warped_mask_data
     except ValueError:
-        tmpdata = np.stack([warped_mask_img.get_data()] *
-                           infile_img.get_data().shape[-1], axis=-1)
-        outdata = infile_img.get_data() * tmpdata
+        tmpdata = np.stack(warped_mask_data * infile_img.shape[-1], axis=-1)
+        outdata = infile_data * tmpdata
 
     masked_brain = Nifti1Image(outdata, infile_img.affine, infile_img.header)
     masked_brain.to_filename(outfile)