Nifti1 -> Nifti2

vviewer/loadImage.py

@@ -11,7 +11,7 @@ import numpy as np
 from nibabel import load
 from nibabel.affines import apply_affine
 from nibabel.volumeutils import shape_zoom_affine
-from nibabel import Nifti1Image
+from nibabel import Nifti2Image
 
 import pyqtgraph as pg
 
@@ -55,13 +55,13 @@ def loadImageFromNifti(fileobject, pref, f_type):
     if f_type != 0:
         color_cm = True
     try:
-        image = Nifti1Image(fileobject.get_data(), fileobject.affine)
+        image = Nifti2Image(fileobject.get_data(), fileobject.affine)
         hdr = fileobject.header
     except RuntimeError:
             print("Cannot load Nifti object!")
 
     if len(image.get_data().shape) == 2:
-       image = Nifti1Image(np.atleast_3d(image.get_data()), image.affine)
+       image = Nifti2Image(np.atleast_3d(image.get_data()), image.affine)
     if len(image.get_data().shape) == 3:
         img = Image3D.Image3D(image=image, color=color_cm)
     elif len(image.get_data().shape) == 4:
@@ -106,14 +106,14 @@ def loadImageFromFile(filename, pref, f_type):
     if (filetype=='.nii' or filetype=='.gz'):
         try:
             temp_img = load(filename)
-            image = Nifti1Image(temp_img.get_data(), temp_img.affine)
+            image = Nifti2Image(temp_img.get_data(), temp_img.affine)
             hdr = temp_img.header
         except RuntimeError:
             print("Cannot load .nii or nii.gz file given!")
     elif (filetype=='.hdr' or filetype=='.img'):
         try:
             temp_img = load(filename)
-            image = Nifti1Image(temp_img.get_data(), temp_img.affine)
+            image = Nifti2Image(temp_img.get_data(), temp_img.affine)
             image.dataobj[np.isnan(image.dataobj)] = 0
             hdr = temp_img.header
         except RuntimeError:
@@ -138,7 +138,7 @@ def loadImageFromFile(filename, pref, f_type):
                 # if affine is still build incorrectly, use identity
                 if np.linalg.det(affine[0:2, 0:2]) == 0:
                     affine = np.identity(4)
-                image = Nifti1Image(img_data.astype(np.float32), affine)
+                image = Nifti2Image(img_data.astype(np.float32), affine)
             else: # version 2 .v file
                 # sform, or qform, and if not, then fall-back affine
                 if sform_code != 0:
@@ -148,7 +148,7 @@ def loadImageFromFile(filename, pref, f_type):
                     affine = qform_affine
                 else:
                     affine = shape_zoom_affine(img_data.shape, pixdim[1:4], False)
-                image = Nifti1Image(img_data.astype(np.float32), affine)
+                image = Nifti2Image(img_data.astype(np.float32), affine)
                 if sform_code != 0:
                     image.set_sform(sform)
                 if qform_code != 0:
@@ -161,11 +161,11 @@ def loadImageFromFile(filename, pref, f_type):
     if np.isnan(image.get_data()).any():
         notnan = image.get_data()
         notnan[np.isnan(image.get_data())] = 0
-        image = Nifti1Image(notnan, image.affine)
+        image = Nifti2Image(notnan, image.affine)
 
     # allow 2d-images here:
     if len(image.get_data().shape) == 2:
-       image = Nifti1Image(np.atleast_3d(image.get_data()), image.affine)
+       image = Nifti2Image(np.atleast_3d(image.get_data()), image.affine)
 
     if len(image.get_data().shape) == 3:
         img = Image3D.Image3D(image=image, color=color_cm)