From f220a4470d36210447862080971c5b36146a539a Mon Sep 17 00:00:00 2001
From: jmsgrogan <grogan@maths.ox.ac.uk>
Date: Thu, 28 Sep 2017 10:47:15 +0100
Subject: [PATCH] Add output generation for histograms.

---
 src/stack3d/formats/unet.py | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/stack3d/formats/unet.py b/src/stack3d/formats/unet.py
index e339746..28dcedc 100644
--- a/src/stack3d/formats/unet.py
+++ b/src/stack3d/formats/unet.py
@@ -104,6 +104,7 @@ def skeleton_to_csv(skeleton, output_path):
     f.write("P0 - x, P0 - y, P0 - z, P1 - x, P1 - y, P1 - z, diameter")
 
     for _, _, branch in skeleton.skeleton_branch_iter():
+        print ('length', branch.length)
         for idx, p1 in enumerate(branch.points):
             if idx > 0:
                 p0 = branch.points[idx-1]
@@ -111,6 +112,21 @@ def skeleton_to_csv(skeleton, output_path):
                 p1_s = str(p1.x) + "," + str(p1.y) + "," + str(p1.z)
                 f.write(p0_s + "," + p1_s + "," + str(branch.diameter) + "\n")
     f.close()
+    
+def skeleton_lengths(skeleton, output_path):
+
+    """
+    Convert the skeleton's network description to csv format
+    """
+
+#     if os.path.isabs(output_path) and not os.path.exists(output_path):
+#         os.makedirs(output_path)
+
+    f = open(output_path, "w")
+
+    for _, _, branch in skeleton.skeleton_branch_iter():
+        f.write(str(branch.length) + "," + str(branch.diameter) + "\n")
+    f.close()
 
 
 if __name__ == "__main__":
@@ -129,8 +145,10 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     skeleton = load_skeleton(args.input)
+    print(skeleton.pix_dim)
     if "csv" in args.format:
-        skeleton_to_csv(skeleton, args.output)
+        skeleton_lengths(skeleton, args.output)
+        #skeleton_to_csv(skeleton, args.output)
     elif "mat" in args.format:
         skeleton_to_matlab(skeleton, args.field, args.output)
     
\ No newline at end of file