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volread.py

+"""
+Created on Tue Oct 13 2020
+
+@author: Anders Bjorholm Dahl
+abda@dtu.dk
+"""
+import numpy as np
+import io
+
+def readvol(file_name):
+    """
+    Todo: Test this function on images of uint8, uint16, and when dimensions are 
+    not all the same.
+    
+    Parameters
+    ----------
+    file_name : Sting
+        name of .vol and .vgi files without extension
+
+    Returns
+    -------
+    V : numpy array (float32, uint8, or uint16)
+        3D volume.
+
+    """
+    vgi_name = file_name + '.vgi'
+    f = io.open(vgi_name, 'r')
+    t = f.read()
+    f.close()
+    elem = []
+    dt = ''
+    for l in t.splitlines():
+        if(l.startswith('Size = ')):
+            elem = [int(n) for n in l.split() if n.isdigit()]
+        if(l.startswith('Datatype = float')):
+            dt = np.float32
+        elif(l.startswith('Datatype = uint8')):
+            dt = np.uint8
+        elif(l.startswith('Datatype = uint16')):
+            dt = np.uint16
+
+    vol_name = file_name + '.vol'
+    V = np.fromfile(vol_name, dtype = dt, count = elem[0]*elem[1]*elem[2])
+    V = np.reshape(V, (elem[2], elem[0], elem[1]))
+    V = V.transpose((0,2,1))
+
+    return V
+
+
+