removed code doubling

lib/damask/test/test.py

@@ -227,15 +227,8 @@ class Test():
 
   def execute_inCurrentDir(self,cmd,streamIn=None):
 
-    initialPath=os.getcwd()
-    os.chdir(self.dirCurrent())
     logging.info(cmd)
-    process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
+    out,error = damask.util.execute(cmd,streamIn,self.dirCurrent())
-    if streamIn != None:
-      out,error = process.communicate(streamIn.read())
-    else:
-      out,error = process.communicate()
-    os.chdir(initialPath)
 
     logging.info(error)
     logging.debug(out)

lib/damask/util.py

@@ -1,9 +1,9 @@
 # -*- coding: UTF-8 no BOM -*-
 
 # damask utility functions
-import sys,time,random,threading
+import sys,time,random,threading,os,subprocess,shlex
 import numpy as np
-from optparse import OptionParser, Option
+from optparse import Option
 
 # -----------------------------
 def croak(what,
@@ -398,3 +398,20 @@ def curve_fit_bound(f, xdata, ydata, p0=None, sigma=None, bounds=None, **kw):
         return popt, pcov, infodict, errmsg, ier
     else:
         return popt, pcov
+
+        
+def execute(cmd,streamIn=None,wd='./'):
+  '''
+    executes a command in given directory and returns stdout and stderr for optional stdin
+  '''
+  initialPath=os.getcwd()
+  os.chdir(wd)
+  process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
+  if streamIn != None:
+    out,error = process.communicate(streamIn.read())
+  else:
+    out,error = process.communicate()
+  os.chdir(initialPath)
+
+  return out,error
+

processing/misc/yieldSurface.py

@@ -9,7 +9,7 @@ import damask
 from damask.util import leastsqBound
 
 scriptID   = string.replace('$Id$','\n','\\n')
-scriptName = scriptID.split()[1][:-3]
+scriptName = os.path.splitext(scriptID.split()[1])[0]
 
 def runFit(exponent, eqStress, dimension, criterion):
   global s, threads, myFit
@@ -48,21 +48,6 @@ def runFit(exponent, eqStress, dimension, criterion):
     threads[i].join()
   print fitResidual
 
-def execute(cmd,streamIn=None,wd='./'):
-  '''
-    executes a command in given directory and returns stdout and stderr for optional stdin
-  '''
-  initialPath=os.getcwd()
-  os.chdir(wd)
-  process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
-  if streamIn != None:
-    out,error = process.communicate(streamIn.read())
-  else:
-    out,error = process.communicate()
-  os.chdir(initialPath)
-
-  return out,error
-
 def principalStresses(sigmas):
   '''
     computes principal stresses (i.e. eigenvalues) for a set of Cauchy stresses.
@@ -163,16 +148,6 @@ def sym6to33(sigma6):
   sigma33[2,0] = sigma6[5]; sigma33[0,2] = sigma6[5]
   return sigma33
 
-def array2tuple(array):
-  '''transform numpy.array into tuple'''
-  try:
-    return tuple(array2tuple(i) for i in array)
-  except TypeError:
-    return array
-def get_weight(ndim):
-#more to do
-  return np.ones(ndim)
-
 
 class Criteria(object):
   '''
@@ -1243,7 +1218,7 @@ def doSim(delay,thread):
   if not os.path.isfile('%s_%i.spectralOut'%(options.geometry,loadNo)):
     print('starting simulation %s from %s'%(loadNo,thread))
     s.release()
-    execute('DAMASK_spectral -g %s -l %i'%(options.geometry,loadNo))
+    damask.util.execute('DAMASK_spectral -g %s -l %i'%(options.geometry,loadNo))
   else: s.release()
    
   s.acquire()
@@ -1251,12 +1226,12 @@ def doSim(delay,thread):
     print('starting post processing for sim %i from %s'%(loadNo,thread))
     s.release()
     try:
-      execute('postResults --cr f,p --co totalshear %s_%i.spectralOut'%(options.geometry,loadNo))
+      damask.util.execute('postResults --cr f,p --co totalshear %s_%i.spectralOut'%(options.geometry,loadNo))
     except:
-      execute('postResults --cr f,p %s_%i.spectralOut'%(options.geometry,loadNo))
+      damask.util.execute('postResults --cr f,p %s_%i.spectralOut'%(options.geometry,loadNo))
-    execute('addCauchy ./postProc/%s_%i.txt'%(options.geometry,loadNo))
+    damask.util.execute('addCauchy ./postProc/%s_%i.txt'%(options.geometry,loadNo))
-    execute('addStrainTensors -l -v ./postProc/%s_%i.txt'%(options.geometry,loadNo))
+    damask.util.execute('addStrainTensors -l -v ./postProc/%s_%i.txt'%(options.geometry,loadNo))
-    execute('addMises -s Cauchy -e ln(V) ./postProc/%s_%i.txt'%(options.geometry,loadNo))
+    damask.util.execute('addMises -s Cauchy -e ln(V) ./postProc/%s_%i.txt'%(options.geometry,loadNo))
   else: s.release()
 
   s.acquire()
@@ -1264,7 +1239,7 @@ def doSim(delay,thread):
   print('reading values for sim %i from %s'%(loadNo,thread))
   s.release()
 
-  refFile = open('./postProc/%s_%i.txt'%(options.geometry,loadNo))
+  refFile = './postProc/%s_%i.txt'%(options.geometry,loadNo)
   table = damask.ASCIItable(refFile)
   table.head_read()
   if options.fitting =='equivalentStrain':

processing/pre/seeds_fromDistribution.py

@@ -14,21 +14,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 mismatch = None
 currentSeedsName = None
 
-def execute(cmd,streamIn=None,dir='./'):
-  '''
-    executes a command in given directory and returns stdout and stderr for optional stdin
-  ''' 
-  initialPath=os.getcwd()
-  os.chdir(dir)
-  process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
-  if streamIn != None:
-    out,error = process.communicate(streamIn.read())
-  else:
-    out,error = process.communicate()
-  os.chdir(initialPath)
-
-  return out,error
-
 #---------------------------------------------------------------------------------------------------
 class myThread (threading.Thread):
 #---------------------------------------------------------------------------------------------------
@@ -113,7 +98,7 @@ class myThread (threading.Thread):
       perturbedGeomVFile.close()
       perturbedGeomVFile = StringIO()
       perturbedSeedsVFile.reset()
-      perturbedGeomVFile.write(execute('geom_fromVoronoiTessellation '+
+      perturbedGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
                      ' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0])
       perturbedGeomVFile.reset()
 
@@ -257,7 +242,7 @@ if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'):
   with open(os.path.splitext(options.seedFile)[0]+'.seeds') as initialSeedFile:
     for line in initialSeedFile: bestSeedsVFile.write(line)
 else:
-  bestSeedsVFile.write(execute('seeds_fromRandom'+\
+  bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
                                 ' -g '+' '.join(map(str, options.grid))+\
                                 ' -r %i'%options.randomSeed+\
                                 ' -N '+str(nMicrostructures))[0])
@@ -266,7 +251,7 @@ bestSeedsUpdate = time.time()
 # ----------- tessellate initial seed file to get and evaluate geom file
 bestSeedsVFile.reset()
 initialGeomVFile = StringIO()
-initialGeomVFile.write(execute('geom_fromVoronoiTessellation '+
+initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
                                ' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0])
 initialGeomVFile.reset()
 initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)