From 9655bfd51b373df127005cbc92d04bc0d0242fdc Mon Sep 17 00:00:00 2001
From: abda <abda@dtu.dk>
Date: Tue, 13 Oct 2020 09:52:56 +0200
Subject: [PATCH] Upload New File
---
volread.py | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
create mode 100644 volread.py
diff --git a/volread.py b/volread.py
new file mode 100644
index 0000000..0878df6
--- /dev/null
+++ b/volread.py
@@ -0,0 +1,50 @@
+"""
+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
+
+
+
--
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