python3 compatible

hope that the new bar causes less trouble than the background message

lib/damask/util.py

@@ -132,6 +132,30 @@ class extendableOption(Option):
     else:
       Option.take_action(self, action, dest, opt, value, values, parser)
 
+# Print iterations progress
+# from https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
+def print_progress(iteration, total, prefix='', suffix='', decimals=1, bar_length=100):
+    """
+    Call in a loop to create terminal progress bar
+    @params:
+        iteration   - Required  : current iteration (Int)
+        total       - Required  : total iterations (Int)
+        prefix      - Optional  : prefix string (Str)
+        suffix      - Optional  : suffix string (Str)
+        decimals    - Optional  : positive number of decimals in percent complete (Int)
+        bar_length  - Optional  : character length of bar (Int)
+    """
+    str_format = "{0:." + str(decimals) + "f}"
+    percents = str_format.format(100 * (iteration / float(total)))
+    filled_length = int(round(bar_length * iteration / float(total)))
+    bar = '█' * filled_length + '-' * (bar_length - filled_length)
+
+    sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
+
+    if iteration == total:
+        sys.stdout.write('\n')
+sys.stdout.flush()
+
 # -----------------------------
 class backgroundMessage(threading.Thread):
   """Reporting with animation to indicate progress"""

processing/post/addGrainID.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,time,copy
@@ -78,7 +78,7 @@ for name in filenames:
     errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
   if not np.all(table.label_dimension(options.quaternion) == 4):
     errors.append('input "{}" does not have dimension 4.'.format(options.quaternion))
-  else:  column = table.label_index(label)
+  else:  column = table.label_index(options.quaternion)
 
   if remarks != []: damask.util.croak(remarks)
   if errors  != []:
@@ -93,26 +93,15 @@ for name in filenames:
                                                options.disorientation))                        # report orientation source and disorientation
   table.head_write()
 
-# ------------------------------------------ process data ------------------------------------------
-
 # ------------------------------------------ build KD tree -----------------------------------------
 
   table.data_readArray(options.pos)                                                                 # read position vectors
   grainID = -np.ones(len(table.data),dtype=int)
-
-# --- start background messaging
-
-  bg = damask.util.backgroundMessage()
-  bg.start()
-
-  start = tick = time.clock()
-  bg.set_message('building KD tree...')
+  Npoints = table.data.shape[0]
   kdtree = spatial.KDTree(copy.deepcopy(table.data))
 
 # ------------------------------------------ assign grain IDs --------------------------------------
 
-  tick = time.clock()
-
   orientations = []                                                                                 # quaternions found for grain
   memberCounts = []                                                                                 # number of voxels in grain
   p = 0                                                                                             # point counter
@@ -123,13 +112,10 @@ for name in filenames:
   table.data_rewind()
   while table.data_read():                                                                          # read next data line of ASCII table
 
-    if p > 0 and p % 1000 == 0:
+    if Npoints > 100 and p%(Npoints//100) == 0:                                                     # report in 1% steps if possible and avoid modulo by zero
+      damask.util.print_progress(iteration=p,total=Npoints)
 
-      time_delta = (time.clock()-tick) * (len(grainID) - p) / p
-      bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...'\
-            %(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),np.count_nonzero(memberCounts)))
-
-    o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])),
+    o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))),
                            symmetry   = options.symmetry).reduced()
 
     matched        = False
@@ -180,8 +166,6 @@ for name in filenames:
     outputAlive = table.data_write()                                                                # output processed line
     p += 1
 
-  bg.set_message('done after {} seconds'.format(time.clock()-start))
-
 # ------------------------------------------ output finalization -----------------------------------  
 
   table.close()                                                                                     # close ASCII tables