From f825e91bf11c84dae509f1c49ccdefe642a53a89 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Wed, 23 Aug 2017 14:08:11 -0400
Subject: [PATCH] script to straighten numbering in geom

---
 processing/pre/geom_renumber.py | 102 ++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100755 processing/pre/geom_renumber.py

diff --git a/processing/pre/geom_renumber.py b/processing/pre/geom_renumber.py
new file mode 100755
index 000000000..45dbe24ba
--- /dev/null
+++ b/processing/pre/geom_renumber.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,math
+import numpy as np
+import damask
+from optparse import OptionParser
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+#--------------------------------------------------------------------------------------------------
+#                                MAIN
+#--------------------------------------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
+renumber sorted microstructure indices to 1,...,N.
+
+""", version=scriptID)
+
+(options, filenames) = parser.parse_args()
+
+# --- loop over input files ----------------------------------------------------------------------
+
+if filenames == []: filenames = [None]
+
+for name in filenames:
+  try:    table = damask.ASCIItable(name = name,
+                                    buffered = False,
+                                    labeled = False)
+  except: continue
+  damask.util.report(scriptName,name)
+
+# --- interpret header ---------------------------------------------------------------------------
+
+  table.head_read()
+  info,extra_header = table.head_getGeom()
+
+  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
+               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
+               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
+               'homogenization:  %i'%info['homogenization'],
+               'microstructures: %i'%info['microstructures'],
+              ])
+
+  errors = []
+  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
+  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
+  if errors != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+
+# --- read data ----------------------------------------------------------------------------------
+
+  microstructure = table.microstructure_read(info['grid'])                                 # read microstructure
+
+# --- do work ------------------------------------------------------------------------------------
+
+  newInfo = {
+             'origin':  np.zeros(3,'d'),
+             'microstructures': 0,
+            }
+
+  grainIDs = np.unique(microstructure)
+  renumbered = np.copy(microstructure)
+  
+  for i, oldID in enumerate(grainIDs):
+    renumbered = np.where(microstructure == oldID, i+1, renumbered)
+
+  newInfo['microstructures'] = len(grainIDs)
+
+# --- report -------------------------------------------------------------------------------------
+
+  remarks = []
+  if (    newInfo['microstructures'] != info['microstructures']):
+    remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+  if remarks != []: damask.util.croak(remarks)
+
+# --- write header -------------------------------------------------------------------------------
+
+  table.labels_clear()
+  table.info_clear()
+  table.info_append(extra_header+[
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
+    "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
+    "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
+    "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=newInfo['origin']),
+    "homogenization\t{homog}".format(homog=info['homogenization']),
+    "microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
+    ])
+  table.head_write()
+
+# --- write microstructure information -----------------------------------------------------------
+
+  format = '%{}i'.format(int(math.floor(math.log10(len(grainIDs))+1)))
+  table.data = renumbered.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
+  table.data_writeArray(format,delimiter = ' ')
+
+# --- output finalization ------------------------------------------------------------------------
+
+  table.close()                                                                                   # close ASCII table