From 7924e119807c3f8295cd889272843380404c3899 Mon Sep 17 00:00:00 2001
From: Johannes Stelzer <johannes.stelzer@tuebingen.mpg.de>
Date: Thu, 23 Aug 2018 16:18:23 +0200
Subject: [PATCH] Nifti1 -> Nifti2
---
vviewer/loadImage.py | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/vviewer/loadImage.py b/vviewer/loadImage.py
index ffc32b1..18b159c 100644
--- a/vviewer/loadImage.py
+++ b/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)
--
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