nifti to numpy both way conversion scripts

Author: jaygshah

nii_to_npy.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# =============================================================================
+# Created By  : Jay Shah
+# Contact  : https://www.public.asu.edu/~jgshah1/
+# =============================================================================
+''' Module converts NIFTI(.nii) files to Numpy (.npy) format
+    Usage: python3 nii_to_npy.py choose_your_nii_folder/ folder_to_store_npy_files/ '''
+
+# =============================================================================
+# Imports
+# =============================================================================
+import nibabel as nib
+import numpy as np
+import glob, os, sys
+
+def nifti_to_numpy(file, input_folder, output_folder):
+
+	if not os.path.exists(output_folder):
+		os.mkdir(output_folder)
+
+	filename = str(file.split('/')[-1].split('.')[0])
+	print("Processing: ", filename)
+
+	img = nib.load(file)
+	img_arr = img.get_fdata()
+	img_arr = np.squeeze(img_arr)
+	# print(img_arr.shape)
+	np.save(output_folder+filename, img_arr)
+
+	# # to check npy file's shape to verify
+	# print(np.load(output_folder+filename+'.npy').shape)
+
+if __name__ == "__main__":
+    
+    in_folder = str(sys.argv[1])
+    out_folder = str(sys.argv[2])
+
+    for file in glob.glob(in_folder + '*.nii'):
+        data = nifti_to_numpy(file, in_folder, out_folder)
+    print("Numpy files saved to ", out_folder)

npy_to_nii.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# =============================================================================
+# Created By  : Jay Shah
+# Contact  : https://www.public.asu.edu/~jgshah1/
+# =============================================================================
+''' Module converts numpy files to NIFTI-format
+    also converts DPMs generated to NIFTI-format of size [181 x 217 x181] 
+    Usage: python3 npy_to_nii.py choose_your_npy_folder/ folder_to_store_nifti_files/ '''
+
+# =============================================================================
+# Imports
+# =============================================================================
+import nibabel as nib
+import numpy as np
+import glob, os, sys
+
+def probability_to_risk(raw):
+    x1, x2 = raw[0, :, :, :], raw[1, :, :, :]
+    risk = np.exp(x2) / (np.exp(x1) + np.exp(x2))
+    return risk
+
+def upsample(heat):
+    new_heat = np.zeros((46*4, 55*4, 46*4))
+    for start_idx1 in range(4):
+        for start_idx2 in range(4):
+            for start_idx3 in range(4):
+                new_heat[start_idx1::4, start_idx2::4, start_idx3::4] = heat
+    return new_heat[:181, :217, :181]
+
+def numpy_to_nifti(file, input_folder, output_folder):
+
+	if not os.path.exists(output_folder):
+		os.mkdir(output_folder)
+
+	filename = str(file.split('/')[-1].split('.')[0])
+	print("Processing: ", filename)
+
+	img = np.load(file)
+	img = np.squeeze(img)
+
+	# only if converting DPMs to NIFTI format
+	# else comment it out
+	img = upsample(probability_to_risk(img))
+
+	new_image = nib.Nifti1Image(img, affine=np.eye(4))
+	nib.save(new_image, out_folder+filename)
+
+
+if __name__ == "__main__":
+    
+    in_folder = str(sys.argv[1])
+    out_folder = str(sys.argv[2])
+
+    for file in glob.glob(in_folder + '*.npy'):
+        data = numpy_to_nifti(file, in_folder, out_folder)
+    print("NIFTI files saved to ", out_folder)
+