From b63d2eafe83277396d02a58610413520c8cbce68 Mon Sep 17 00:00:00 2001
From: Philip	Eisenlohr <eisenlohr@egr.msu.edu>
Date: Tue, 26 Nov 2013 20:19:27 +0000
Subject: [PATCH] new scripts for:

-generating vtk point cloud from x,y,z ASCIItable data
-adding scalar values and color tuples from ASCIItable to vtk point cloud
-permuting data in ASCIItable columns (used to shuffle ordered grain indices)
---
 processing/post/permuteData.py           | 125 ++++++++++++++++++
 processing/post/vtk_addPointcloudData.py | 155 +++++++++++++++++++++++
 processing/post/vtk_pointcloud.py        | 116 +++++++++++++++++
 processing/setup/symLink_Processing.py   |   3 +
 4 files changed, 399 insertions(+)
 create mode 100755 processing/post/permuteData.py
 create mode 100755 processing/post/vtk_addPointcloudData.py
 create mode 100755 processing/post/vtk_pointcloud.py

diff --git a/processing/post/permuteData.py b/processing/post/permuteData.py
new file mode 100755
index 000000000..95b0b1926
--- /dev/null
+++ b/processing/post/permuteData.py
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+
+import os,re,sys,math,numpy,string
+import damask
+from collections import defaultdict
+from optparse import OptionParser, Option
+
+scriptID = '$Id$'
+scriptName = scriptID.split()[1]
+
+# -----------------------------
+class extendableOption(Option):
+# -----------------------------
+# used for definition of new option parser action 'extend', which enables to take multiple option arguments
+# taken from online tutorial http://docs.python.org/library/optparse.html
+  
+  ACTIONS = Option.ACTIONS + ("extend",)
+  STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
+  TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
+  ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
+
+  def take_action(self, action, dest, opt, value, values, parser):
+    if action == "extend":
+      lvalue = value.split(",")
+      values.ensure_value(dest, []).extend(lvalue)
+    else:
+      Option.take_action(self, action, dest, opt, value, values, parser)
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
+Permute all values in given column(s).
+
+""" + string.replace(scriptID,'\n','\\n')
+)
+
+parser.add_option('-l','--label',   dest='label', action='extend', type='string',
+                                    help='heading(s) of column to permute',
+                                    metavar='<label>')
+
+parser.set_defaults(label = [])
+
+(options,filenames) = parser.parse_args()
+
+if len(options.label)== 0:
+  parser.error('no data column specified...')
+
+datainfo = {                                                               # list of requested labels per datatype
+             'scalar':     {'len':1,
+                            'label':[]},
+           }
+
+if options.label != None: datainfo['scalar']['label'] += options.label
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+if filenames == []:
+  files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
+else:
+  for name in filenames:
+    if os.path.exists(name):
+      files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
+
+#--- loop over input files ------------------------------------------------------------------------
+for file in files:
+  if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
+  else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
+
+  table = damask.ASCIItable(file['input'],file['output'],False)             # make unbuffered ASCII_table
+  table.head_read()                                                         # read ASCII header info
+  table.info_append(string.replace(scriptName,'\n','\\n') + \
+                    '\t' + ' '.join(sys.argv[1:]))
+
+# --------------- figure out columns to process
+  active = defaultdict(list)
+  column = defaultdict(dict)
+
+  for datatype,info in datainfo.items():
+    for label in info['label']:
+      foundIt = False
+      for key in ['1_'+label,label]:
+        if key in table.labels:
+          foundIt = True
+          active[datatype].append(label)
+          column[datatype][label] = table.labels.index(key)                   # remember columns of requested data
+      if not foundIt:
+        file['croak'].write('column %s not found...\n'%label)
+       
+# ------------------------------------------ assemble header ---------------------------------------  
+
+  table.head_write()
+
+# ------------------------------------------ process data ---------------------------------------  
+
+  permutation = {}
+  theColumns = table.data_asArray([column['scalar'][label] for label in active['scalar']])
+  print 'shape:',theColumns.shape
+  for i,label in enumerate(active['scalar']):
+    unique = list(set(theColumns[:,i]))
+    permutated = numpy.random.permutation(unique)
+    permutation[label] = dict(zip(unique,permutated))
+
+  table.data_rewind()
+  while table.data_read():                                                  # read next data line of ASCII table
+    
+    for datatype,labels in active.items():                                  # loop over vector,tensor
+      for label in labels:                                                  # loop over all requested stiffnesses
+        for c in xrange(column[datatype][label],
+                        column[datatype][label]+datainfo[datatype]['len']):
+          table.data[c] = permutation[label][float(table.data[c])]       # apply permutation
+    
+    table.data_write()                                                      # output processed line
+
+# ------------------------------------------ output result ---------------------------------------  
+
+  table.output_flush()                                                      # just in case of buffered ASCII table
+
+  if file['name'] != 'STDIN':
+    file['input'].close()                                                   # close input ASCII table
+    file['output'].close()                                                  # close output ASCII table
+    os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new
diff --git a/processing/post/vtk_addPointcloudData.py b/processing/post/vtk_addPointcloudData.py
new file mode 100755
index 000000000..219f0f8d4
--- /dev/null
+++ b/processing/post/vtk_addPointcloudData.py
@@ -0,0 +1,155 @@
+#!/usr/bin/env python
+
+import os,sys,string,re,numpy,vtk
+import damask
+from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+
+scriptID = '$Id$'
+scriptName = scriptID.split()[1]
+
+#--------------------------------------------------------------------------------------------------
+class extendedOption(Option):
+#--------------------------------------------------------------------------------------------------
+# used for definition of new option parser action 'extend', which enables to take multiple option arguments
+# taken from online tutorial http://docs.python.org/library/optparse.html
+    
+    ACTIONS = Option.ACTIONS + ("extend",)
+    STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
+    TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
+    ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
+
+    def take_action(self, action, dest, opt, value, values, parser):
+        if action == "extend":
+            lvalue = value.split(",")
+            values.ensure_value(dest, []).extend(lvalue)
+        else:
+            Option.take_action(self, action, dest, opt, value, values, parser)
+
+
+parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
+Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).
+""" + string.replace(scriptID,'\n','\\n')
+)
+
+parser.add_option('-v', '--vtk',   dest='vtk', type='string', \
+                  help = 'VTK file name')
+parser.add_option('-s', '--scalar',   dest='scalar', action='extend', \
+                  help = 'scalar values')
+parser.add_option('-c', '--color',   dest='color', action='extend', \
+                  help = 'RGB color tuples')
+
+parser.set_defaults(scalar = [])
+parser.set_defaults(color = [])
+
+(options, filenames) = parser.parse_args()
+
+datainfo = {                                                               # list of requested labels per datatype
+             'scalar':     {'len':1,
+                            'label':[]},
+             'color':      {'len':3,
+                            'label':[]},
+           }
+
+if not os.path.exists(options.vtk):
+  options.error('VTK file does not exist'); sys.exit()
+
+reader = vtk.vtkXMLPolyDataReader()
+reader.SetFileName(options.vtk)
+reader.Update()
+Npoints = reader.GetNumberOfPoints()
+Ncells = reader.GetNumberOfCells()
+Nvertices = reader.GetNumberOfVerts()
+Polydata = reader.GetOutput()
+
+if Npoints != Ncells or Npoints != Nvertices:
+  options.error('Number of points, cells, and vertices in VTK differ from each other'); sys.exit()
+if options.scalar != None:  datainfo['scalar']['label'] += options.scalar
+if options.color  != None:  datainfo['color']['label']  += options.color
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+if filenames == []:
+  files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
+else:
+  for name in filenames:
+    if os.path.exists(name):
+      files.append({'name':name, 'input':open(name), 'output':sys.stderr, 'croak':sys.stderr})
+
+#--- loop over input files ------------------------------------------------------------------------
+for file in files:
+  if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
+  else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
+
+  table = damask.ASCIItable(file['input'],file['output'],False)             # make unbuffered ASCII_table
+  table.head_read()                                                         # read ASCII header info
+
+# --------------- figure out columns to process
+  active = {}
+  column = {}
+
+  array = {}
+  
+  for datatype,info in datainfo.items():
+    for label in info['label']:
+      foundIt = False
+      for key in ['1_'+label,label]:
+        if key in table.labels:
+          foundIt = True
+          if datatype not in active: active[datatype] = []
+          if datatype not in column: column[datatype] = {}
+          if datatype not in array:   array[datatype] = {}
+          active[datatype].append(label)
+          column[datatype][label] = table.labels.index(key)                   # remember columns of requested data
+          if datatype == 'scalar':
+            array[datatype][label] = vtk.vtkDoubleArray()
+            array[datatype][label].SetNumberOfComponents(1)
+            array[datatype][label].SetName(label)
+          elif datatype == 'color':
+            array[datatype][label] = vtk.vtkUnsignedCharArray()
+            array[datatype][label].SetNumberOfComponents(3)
+            array[datatype][label].SetName(label)
+      if not foundIt:
+        file['croak'].write('column %s not found...\n'%label)
+       
+# ------------------------------------------ process data ---------------------------------------  
+
+  while table.data_read():                                                  # read next data line of ASCII table
+    
+    for datatype,labels in active.items():                                  # loop over scalar,color
+      for label in labels:                                                  # loop over all requested items
+        theData = table.data[column[datatype][label]:\
+                             column[datatype][label]+datainfo[datatype]['len']]  # read strings
+        if datatype == 'color':
+          theData = map(lambda x: int(255.*float(x)),theData)
+          array[datatype][label].InsertNextTuple3(theData[0],theData[1],theData[2],)
+        elif datatype == 'scalar':
+          array[datatype][label].InsertNextValue(float(theData[0]))
+
+  file['input'].close()                                                   # close input ASCII table
+
+# ------------------------------------------ add data ---------------------------------------  
+
+  for datatype,labels in active.items():                                   # loop over scalar,color
+    if datatype == 'color':
+      Polydata.GetPointData().SetScalars(array[datatype][labels[0]])
+      Polydata.GetCellData().SetScalars(array[datatype][labels[0]])
+    for label in labels:                                                   # loop over all requested items
+      Polydata.GetPointData().AddArray(array[datatype][label])
+      Polydata.GetCellData().AddArray(array[datatype][label])
+
+  Polydata.Modified()
+  if vtk.VTK_MAJOR_VERSION <= 5:
+    Polydata.Update()
+
+# ------------------------------------------ output result ---------------------------------------  
+
+writer = vtk.vtkXMLPolyDataWriter()
+writer.SetDataModeToBinary()
+writer.SetCompressorTypeToZLib()
+writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtp')
+if vtk.VTK_MAJOR_VERSION <= 5:
+    writer.SetInput(Polydata)
+else:
+    writer.SetInputData(Polydata)
+writer.Write()
diff --git a/processing/post/vtk_pointcloud.py b/processing/post/vtk_pointcloud.py
new file mode 100755
index 000000000..0408cd875
--- /dev/null
+++ b/processing/post/vtk_pointcloud.py
@@ -0,0 +1,116 @@
+#!/usr/bin/env python
+
+import os,sys,string,re,numpy,vtk
+import damask
+from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+
+scriptID = '$Id$'
+scriptName = scriptID.split()[1]
+
+#--------------------------------------------------------------------------------------------------
+class extendedOption(Option):
+#--------------------------------------------------------------------------------------------------
+# used for definition of new option parser action 'extend', which enables to take multiple option arguments
+# taken from online tutorial http://docs.python.org/library/optparse.html
+    
+    ACTIONS = Option.ACTIONS + ("extend",)
+    STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
+    TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
+    ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
+
+    def take_action(self, action, dest, opt, value, values, parser):
+        if action == "extend":
+            lvalue = value.split(",")
+            values.ensure_value(dest, []).extend(lvalue)
+        else:
+            Option.take_action(self, action, dest, opt, value, values, parser)
+
+
+parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
+Add grain index based on similitude of crystal lattice orientation.
+""" + string.replace(scriptID,'\n','\\n')
+)
+
+parser.add_option('-p', '--positions',   dest='pos', type='string', \
+                  help = 'coordinate label')
+
+parser.set_defaults(pos = 'pos')
+
+(options, filenames) = parser.parse_args()
+
+datainfo = {                                                               # list of requested labels per datatype
+             'vector':     {'len':3,
+                            'label':[]},
+           }
+
+if options.pos != None:  datainfo['vector']['label'] += [options.pos]
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+for name in filenames:
+  if os.path.exists(name):
+    files.append({'name':name, 'input':open(name), 'output':os.path.splitext(name)[0]+'.vtp', 'croak':sys.stderr})
+
+#--- loop over input files ------------------------------------------------------------------------
+for file in files:
+  if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
+  else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
+
+  table = damask.ASCIItable(file['input'],file['croak'],False)             # make unbuffered ASCII_table
+  table.head_read()                                                         # read ASCII header info
+
+# --------------- figure out columns to process
+  active = {}
+  column = {}
+  head = []
+
+  for datatype,info in datainfo.items():
+    for label in info['label']:
+      foundIt = False
+      for key in ['1_'+label,label]:
+        if key in table.labels:
+          foundIt = True
+          if datatype not in active: active[datatype] = []
+          if datatype not in column: column[datatype] = {}
+          active[datatype].append(label)
+          column[datatype][label] = table.labels.index(key)                 # remember columns of requested data
+      if not foundIt:
+        file['croak'].write('column %s not found...\n'%label)
+        break
+
+
+# ------------------------------------------ process data ---------------------------------------  
+
+  Polydata = vtk.vtkPolyData()
+  Points = vtk.vtkPoints()
+  Vertices = vtk.vtkCellArray()
+  pos = table.data_asArray(range(column['vector'][options.pos],\
+                                 column['vector'][options.pos]+datainfo['vector']['len']))
+
+  print range(column['vector'][options.pos],\
+                                 column['vector'][options.pos]+datainfo['vector']['len']),len(pos),pos[0]
+  for p in pos:
+    id = Points.InsertNextPoint(p)
+    Vertices.InsertNextCell(1)
+    Vertices.InsertCellPoint(id)
+
+  Polydata.SetPoints(Points)
+  Polydata.SetVerts(Vertices)
+  Polydata.Modified()
+  if vtk.VTK_MAJOR_VERSION <= 5:
+    Polydata.Update()
+ 
+# ------------------------------------------ output result ---------------------------------------  
+
+  writer = vtk.vtkXMLPolyDataWriter()
+  writer.SetDataModeToBinary()
+  writer.SetCompressorTypeToZLib()
+  writer.SetFileName(file['output'])
+  if vtk.VTK_MAJOR_VERSION <= 5:
+      writer.SetInput(Polydata)
+  else:
+      writer.SetInputData(Polydata)
+  writer.Write()
+
+  file['input'].close()                                                   # close input ASCII table
diff --git a/processing/setup/symLink_Processing.py b/processing/setup/symLink_Processing.py
index 51091d50f..a514fd7f4 100755
--- a/processing/setup/symLink_Processing.py
+++ b/processing/setup/symLink_Processing.py
@@ -36,6 +36,7 @@ bin_link = { \
                 ],
         'post' : [
                 '3Dvisualize.py',
+                'permuteData.py'
                 'addCalculation.py',
                 'addCauchy.py',
                 'addCompatibilityMismatch.py',
@@ -71,6 +72,8 @@ bin_link = { \
                 'tagLabel.py',
                 'vtk2ang.py',
                 'vtk_addData.py',
+                'vtk_pointcloud.py',
+                'vtk_addPointcloudData.py'
                 ],
             }