Merge branch 'development' into geom-fully-out-of-place

.gitlab-ci.yml

@@ -25,6 +25,7 @@ before_script:
     fi
   - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
       do sleep 5m;
+      echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
     done
   - source $DAMASKROOT/env/DAMASK.sh
   - cd $DAMASKROOT/PRIVATE/testing
@@ -87,6 +88,7 @@ checkout:
     - echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue
     - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
         do sleep 5m;
+        echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
       done
   script:
     - mkdir -p $DAMASKROOT

PRIVATE

@@ -1 +1 @@
-Subproject commit 555f3e01f2b5cf43ade1bd48423b890adca21771
+Subproject commit fa2885da8604c3ac46f64670393f04678dd1f45b

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-233-g190f8a82
+v3.0.0-alpha-275-g7801f527f

processing/legacy/addAPS34IDEstrainCoords.py

@@ -42,11 +42,10 @@ rot_to_TSL = damask.Rotation.from_axis_angle([-1,0,0,.75*np.pi])
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    
+
     coord      = - table.get(options.frame)
     coord[:,2] += table.get(options.depth)[:,0]
 
-    table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))
+    table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))\
-
+         .save((sys.stdout if name is None else name),legacy=True)
-    table.to_file(sys.stdout if name is None else name)

processing/legacy/addCumulative.py

@@ -39,10 +39,10 @@ if options.labels is None:
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     for label in options.labels:
-        table.add('cum_{}({})'.format('prod'     if options.product else 'sum',label),
+        table = table.add('cum_{}({})'.format('prod'     if options.product else 'sum',label),
-                  np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
+                          np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
-                  scriptID+' '+' '.join(sys.argv[1:]))
+                          scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name),legacy=True)

processing/post/DADF5_postResults.py

@@ -38,8 +38,8 @@ for filename in options.filenames:
     N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
     N_digits = 5 # hack to keep test intact
     for inc in damask.util.show_progress(results.iterate('increments'),len(results.increments)):
-        table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
+        table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})\
-        table = table.add('pos',coords.reshape(-1,3))
+                      .add('pos',coords.reshape(-1,3))
 
         results.pick('materialpoints',False)
         results.pick('constituents',  True)
@@ -60,4 +60,4 @@ for filename in options.filenames:
             os.mkdir(dirname,0o755)
         file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
                                          inc[3:].zfill(N_digits))
-        table.to_file(os.path.join(dirname,file_out))
+        table.save(os.path.join(dirname,file_out),legacy=True)

processing/post/addCompatibilityMismatch.py

@@ -172,7 +172,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
   grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
   F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
@@ -191,4 +191,4 @@ for name in filenames:
                       volumeMismatch.reshape(-1,1,order='F'),
                       scriptID+' '+' '.join(sys.argv[1:]))
 
-  table.to_file(sys.stdout if name is None else name)
+  table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addCurl.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addDerivative.py

@@ -14,9 +14,9 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 def derivative(coordinates,what):
-  
+
   result = np.empty_like(what)
-  
+
   # use differentiation by interpolation
   # as described in http://www2.math.umd.edu/~dlevy/classes/amsc466/lecture-notes/differentiation-chap.pdf
 
@@ -31,7 +31,7 @@ def derivative(coordinates,what):
                    (coordinates[0] - coordinates[1])
   result[-1,:]   = (what[-1,:] - what[-2,:]) / \
                    (coordinates[-1] - coordinates[-2])
-  
+
   return result
 
 
@@ -65,10 +65,10 @@ if options.labels is None:
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     for label in options.labels:
         table = table.add('d({})/d({})'.format(label,options.coordinates),
                           derivative(table.get(options.coordinates),table.get(label)),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addDisplacement.py

@@ -47,25 +47,25 @@ parser.set_defaults(f   = 'f',
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
     if options.nodal:
-        table = damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'),
+        damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'),
                      {'pos':(3,)})\
               .add('avg({}).{}'.format(options.f,options.pos),
                    damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'),
                    scriptID+' '+' '.join(sys.argv[1:]))\
               .add('fluct({}).{}'.format(options.f,options.pos),
                    damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
-                    scriptID+' '+' '.join(sys.argv[1:]))
+                    scriptID+' '+' '.join(sys.argv[1:]))\
-        table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
+               .save((sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt'), legacy=True)
     else:
-        table = table.add('avg({}).{}'.format(options.f,options.pos),
+        table.add('avg({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))\
              .add('fluct({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
-                  scriptID+' '+' '.join(sys.argv[1:]))
+                  scriptID+' '+' '.join(sys.argv[1:]))\
-        table.to_file(sys.stdout if name is None else name)
+             .save((sys.stdout if name is None else name), legacy=True)

processing/post/addDivergence.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addEuclideanDistance.py

@@ -142,7 +142,7 @@ for i,feature in enumerate(features):
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     neighborhood = neighborhoods[options.neighborhood]
@@ -158,7 +158,7 @@ for name in filenames:
         diffToNeighbor[:,:,:,i] = ndimage.convolve(microstructure,stencil)                          # compare ID at each point...
                                                                                                     # ...to every one in the specified neighborhood
                                                                                                     # for same IDs at both locations ==> 0
-  
+
     diffToNeighbor = np.sort(diffToNeighbor)                                                        # sort diff such that number of changes in diff (steps)...
                                                                                                     # ...reflects number of unique neighbors
     uniques = np.where(diffToNeighbor[1:-1,1:-1,1:-1,0] != 0, 1,0)                                  # initialize unique value counter (exclude myself [= 0])
@@ -184,4 +184,4 @@ for name in filenames:
                           distance[i,:],
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addGaussian.py

@@ -63,7 +63,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     damask.grid_filters.coord0_check(table.get(options.pos))
 
     for label in options.labels:
@@ -73,4 +73,4 @@ for name in filenames:
                                                           mode = 'wrap' if options.periodic else 'nearest'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addGradient.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addOrientations.py

@@ -110,7 +110,7 @@ R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degree
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     if   options.eulers is not None:
         label = options.eulers
@@ -147,4 +147,4 @@ for name in filenames:
     if 'axisangle' in options.output:
         table = table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addSchmidfactors.py

@@ -175,7 +175,7 @@ labels = ['S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]'
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     o = damask.Rotation.from_quaternion(table.get(options.quaternion))
 
@@ -189,4 +189,4 @@ for name in filenames:
     for i,label in enumerate(labels):
         table = table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/filterTable.py

@@ -27,7 +27,7 @@ def sortingList(labels,whitelistitems):
     else:
       indices.append(0)
       names.append(label)
-      
+
   return [indices,names,whitelistitems]
 
 
@@ -72,11 +72,11 @@ for name in filenames:
     continue
   damask.util.report(scriptName,name)
 
-# ------------------------------------------ assemble info ---------------------------------------  
+# ------------------------------------------ assemble info ---------------------------------------
 
   table.head_read()
 
-# ------------------------------------------ process data ---------------------------------------  
+# ------------------------------------------ process data ---------------------------------------
 
   specials = { \
                '_row_': 0,
@@ -103,12 +103,12 @@ for name in filenames:
             else np.lexsort(sortingList(labels,whitelistitem))                                      # reorder if unique, i.e. no "-1" in whitelistitem
   else:
     order = range(len(labels))                                                                      # maintain original order of labels
-  
+
 # --------------------------------------- evaluate condition ---------------------------------------
   if options.condition is not None:
     condition = options.condition                                                                   # copy per file, since might be altered inline
     breaker = False
-  
+
     for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))):              # find three groups
       idx = table.label_index(column)
       dim = table.label_dimension(column)
@@ -123,11 +123,11 @@ for name in filenames:
                                                         's#':'str'}[marker],idx)                      # take float or string value of data column
         elif dim > 1:                                                                                 # multidimensional input (vector, tensor, etc.)
           replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim)                 # use (flat) array representation
-       
+
         condition = condition.replace('#'+all+'#',replacement)
-    
+
     if breaker: continue                                                                              # found mistake in condition evaluation --> next file
-  
+
 # ------------------------------------------ assemble header ---------------------------------------
 
   table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
@@ -138,7 +138,7 @@ for name in filenames:
 # ------------------------------------------ process and output data ------------------------------------------
 
   positions = np.array(positions)[order]
-  
+
   atOnce = options.condition is None
   if atOnce:                                                                                          # read full array and filter columns
     try:

processing/post/permuteData.py

@@ -47,7 +47,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file
     rng = np.random.default_rng(randomSeed)
@@ -58,4 +58,4 @@ for name in filenames:
         rng.shuffle(uniques)
         table = table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/pre/geom_fromDREAM3D.py

@@ -154,4 +154,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom',format='ASCII',pack=False)
+  geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)

processing/pre/geom_fromMinimalSurface.py

@@ -89,4 +89,4 @@ geom=damask.Geom(microstructure,options.size,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+geom.save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/geom_fromOsteonGeometry.py

@@ -142,4 +142,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    homogenization=options.homogenization,comments=header)
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+geom.save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/geom_fromTable.py

@@ -68,7 +68,7 @@ if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)])                           # x fast, y slow
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
@@ -105,5 +105,4 @@ for name in filenames:
                        homogenization=options.homogenization,comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
+    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
-                 format='ASCII',pack=False)

processing/pre/geom_fromVoronoiTessellation.py

@@ -171,7 +171,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     size   = np.ones(3)
     origin = np.zeros(3)
@@ -228,5 +228,4 @@ for name in filenames:
                        homogenization=options.homogenization,comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
+    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
-                 format='ASCII',pack=False)

processing/pre/geom_grainGrowth.py

@@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid_original = geom.grid
   damask.util.croak(geom)
@@ -169,7 +169,7 @@ for name in filenames:
     # undo any changes involving immutable microstructures
     microstructure = np.where(immutable, microstructure_original,microstructure)
 
-  geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
+  geom = geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+  geom.save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/hybridIA_linODFsampling.py

@@ -31,7 +31,7 @@ def binAsBins(bin,intervals):
   bins[1] = (bin//intervals[2]) % intervals[1]
   bins[2] = bin % intervals[2]
   return bins
-  
+
 def binsAsBin(bins,intervals):
   """Implode 3D bins into compound bin."""
   return (bins[0]*intervals[1] + bins[1])*intervals[2] + bins[2]
@@ -95,7 +95,7 @@ def directInversion (ODF,nSamples):
                                                                                         float(nInvSamples)/nOptSamples-1.0,
                                                                                         scale,nSamples))
   repetition = [None]*ODF['nBins']                                                                  # preallocate and clear
-    
+
   for bin in range(ODF['nBins']):                                                                   # loop over bins
     repetition[bin] = int(round(ODF['dV_V'][bin]*scale))                                            # calc repetition
 
@@ -105,7 +105,7 @@ def directInversion (ODF,nSamples):
   for bin in range(ODF['nBins']):
     set[i:i+repetition[bin]] = [bin]*repetition[bin]                                                # fill set with bin, i.e. orientation
     i += repetition[bin]                                                                            # advance set counter
-  
+
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
@@ -117,7 +117,7 @@ def directInversion (ODF,nSamples):
     orientations[j] = np.degrees(Eulers)
     reconstructedODF[bin] += unitInc
     set[ex] = set[j]                                                                                # exchange orientations
-  
+
   return orientations, reconstructedODF
 
 
@@ -130,7 +130,7 @@ def MonteCarloEulers (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   for j in range(nSamples):
     MC = maxdV_V*2.0
     bin = 0
@@ -153,7 +153,7 @@ def MonteCarloBins (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   for j in range(nSamples):
     MC = maxdV_V*2.0
     bin = 0
@@ -173,14 +173,14 @@ def TothVanHoutteSTAT (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   selectors = [random.random() for i in range(nSamples)]
   selectors.sort()
   indexSelector = 0
-  
+
   cumdV_V = 0.0
   countSamples = 0
-  
+
   for bin in range(ODF['nBins']) :
     cumdV_V += ODF['dV_V'][bin]
     while indexSelector < nSamples and selectors[indexSelector] < cumdV_V:
@@ -191,7 +191,7 @@ def TothVanHoutteSTAT (ODF,nSamples):
       indexSelector += 1
 
   damask.util.croak('created set of %i when asked to deliver %i'%(countSamples,nSamples))
-  
+
   return orientations, reconstructedODF
 
 
@@ -233,8 +233,8 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   damask.util.report(scriptName,name)
-  
+
-  table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   randomSeed = int(os.urandom(4).hex(),16)  if options.randomSeed is None else options.randomSeed  # random seed per file
   random.seed(randomSeed)
@@ -253,7 +253,7 @@ for name in filenames:
   if eulers.shape[0] != ODF['nBins']:
     damask.util.croak('expecting %i values but got %i'%(ODF['nBins'],eulers.shape[0]))
     continue
-  
+
 # ----- build binnedODF array and normalize ------------------------------------------------------
   sumdV_V = 0.0
   ODF['dV_V'] = [None]*ODF['nBins']
@@ -267,7 +267,7 @@ for name in filenames:
     if ODF['dV_V'][b] > 0.0:
       sumdV_V += ODF['dV_V'][b]
       ODF['nNonZero'] += 1
-  
+
   for b in range(ODF['nBins']):
     ODF['dV_V'][b] /= sumdV_V                                                            # normalize dV/V
 
@@ -277,19 +277,19 @@ for name in filenames:
                'Volume integral of ODF: %12.11f\n'%sumdV_V,
                'Reference Integral: %12.11f\n'%(ODF['limit'][0]*ODF['limit'][2]*(1-math.cos(ODF['limit'][1]))),
                ])
-                                                     
+
   Functions = {'IA': 'directInversion', 'STAT': 'TothVanHoutteSTAT', 'MC': 'MonteCarloBins'}
   method = Functions[options.algorithm]
 
   Orientations, ReconstructedODF = (globals()[method])(ODF,options.number)
-  
+
 # calculate accuracy of sample
   squaredDiff     = {'orig':0.0,method:0.0}
   squaredRelDiff  = {'orig':0.0,method:0.0}
   mutualProd      = {'orig':0.0,method:0.0}
   indivSum        = {'orig':0.0,method:0.0}
   indivSquaredSum = {'orig':0.0,method:0.0}
-  
+
   for bin in range(ODF['nBins']):
     squaredDiff[method] += (ODF['dV_V'][bin] - ReconstructedODF[bin])**2
     if ODF['dV_V'][bin] > 0.0:
@@ -299,7 +299,7 @@ for name in filenames:
     indivSquaredSum[method] += ReconstructedODF[bin]**2
   indivSum['orig'] += ODF['dV_V'][bin]
   indivSquaredSum['orig'] += ODF['dV_V'][bin]**2
-  
+
   damask.util.croak(['sqrt(N*)RMSD of ODFs:\t %12.11f'% math.sqrt(options.number*squaredDiff[method]),
                'RMSrD of ODFs:\t %12.11f'%math.sqrt(squaredRelDiff[method]),
                'rMSD of ODFs:\t %12.11f'%(squaredDiff[method]/indivSquaredSum['orig']),
@@ -311,10 +311,10 @@ for name in filenames:
                         (ODF['nNonZero']*math.sqrt((indivSquaredSum['orig']/ODF['nNonZero']-(indivSum['orig']/ODF['nNonZero'])**2)*\
                         (indivSquaredSum[method]/ODF['nNonZero']-(indivSum[method]/ODF['nNonZero'])**2)))),
               ])
-  
+
   if method == 'IA' and options.number < ODF['nNonZero']:
     strOpt = '(%i)'%ODF['nNonZero']
-  
+
   formatwidth = 1+int(math.log10(options.number))
 
   materialConfig = [
@@ -324,12 +324,12 @@ for name in filenames:
       '<microstructure>',
       '#-------------------#',
       ]
-  
+
   for i,ID in enumerate(range(options.number)):
     materialConfig += ['[Grain%s]'%(str(ID+1).zfill(formatwidth)),
                       '(constituent)   phase %i   texture %s   fraction 1.0'%(options.phase,str(ID+1).rjust(formatwidth)),
                      ]
-  
+
   materialConfig += [
       '#-------------------#',
       '<texture>',
@@ -338,12 +338,12 @@ for name in filenames:
 
   for ID in range(options.number):
     eulers = Orientations[ID]
-  
+
     materialConfig += ['[Grain%s]'%(str(ID+1).zfill(formatwidth)),
                      '(gauss)   phi1 {}   Phi {}   phi2 {}   scatter 0.0   fraction 1.0'.format(*eulers),
                      ]
 
-#--- output finalization -------------------------------------------------------------------------- 
+#--- output finalization --------------------------------------------------------------------------
 
   with (open(os.path.splitext(name)[0]+'_'+method+'_'+str(options.number)+'_material.config','w')) as outfile:
     outfile.write('\n'.join(materialConfig)+'\n')

processing/pre/mentat_spectralBox.py

@@ -130,10 +130,10 @@ def geometry():
 
 
 #-------------------------------------------------------------------------------------------------
-def initial_conditions(microstructures):
+def initial_conditions(materials):
   elements = []
   element = 0
-  for id in microstructures:
+  for id in materials:
     element += 1
     if len(elements) < id:
       for i in range(id-len(elements)):
@@ -153,7 +153,7 @@ def initial_conditions(microstructures):
   for grain,elementList in enumerate(elements):
     cmds.append([\
             "*new_icond",
-            "*icond_name microstructure_%i"%(grain+1),
+            "*icond_name material_%i"%(grain+1),
             "*icond_type state_variable",
             "*icond_param_value state_var_id 2",
             "*icond_dof_value var %i"%(grain+1),
@@ -196,15 +196,15 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    microstructure = geom.microstructure.flatten(order='F')
+    materials = geom.materials.flatten(order='F')
 
     cmds = [\
       init(),
       mesh(geom.grid,geom.size),
       material(),
       geometry(),
-      initial_conditions(microstructure),
+      initial_conditions(materials),
       '*identify_sets',
       '*show_model',
       '*redraw',

processing/pre/seeds_fromDistribution.py

@@ -78,7 +78,7 @@ class myThread (threading.Thread):
       perturbedSeedsVFile = StringIO()
       myBestSeedsVFile.seek(0)
 
-      perturbedSeedsTable = damask.Table.from_ASCII(myBestSeedsVFile)
+      perturbedSeedsTable = damask.Table.load(myBestSeedsVFile)
       coords = perturbedSeedsTable.get('pos')
       i = 0
       for ms,coord in enumerate(coords):
@@ -89,8 +89,7 @@ class myThread (threading.Thread):
           coords[i]=newCoords
           direction[i]*=2.
           i+= 1
-      perturbedSeedsTable.set('pos',coords)
+      perturbedSeedsTable.set('pos',coords).save(perturbedSeedsVFile,legacy=True)
-      perturbedSeedsTable.to_file(perturbedSeedsVFile)
 
 #--- do tesselation with perturbed seed file ------------------------------------------------------
       perturbedGeomVFile.close()
@@ -101,7 +100,7 @@ class myThread (threading.Thread):
       perturbedGeomVFile.seek(0)
 
 #--- evaluate current seeds file ------------------------------------------------------------------
-      perturbedGeom = damask.Geom.from_file(perturbedGeomVFile)
+      perturbedGeom = damask.Geom.load_ASCII(perturbedGeomVFile)
       myNmicrostructures = len(np.unique(perturbedGeom.microstructure))
       currentData=np.bincount(perturbedGeom.microstructure.ravel())[1:]/points
       currentError=[]
@@ -213,14 +212,14 @@ if options.randomSeed is None:
   options.randomSeed = int(os.urandom(4).hex(),16)
 damask.util.croak(options.randomSeed)
 delta = options.scale/np.array(options.grid)
-baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
+baseFile = os.path.splitext(os.path.basename(options.seedFile))[0]
 points = np.array(options.grid).prod().astype('float')
 
 # ----------- calculate target distribution and bin edges
-targetGeom = damask.Geom.from_file(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
+targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
 nMicrostructures = len(np.unique(targetGeom.microstructure))
 targetVolFrac = np.bincount(targetGeom.microstructure.flatten())/targetGeom.grid.prod().astype(np.float)
-target=[]
+target = []
 for i in range(1,nMicrostructures+1):
   targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
   target.append({'histogram':targetHist,'bins':targetBins})
@@ -243,7 +242,7 @@ initialGeomVFile = StringIO()
 initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
                                ' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
 initialGeomVFile.seek(0)
-initialGeom = damask.Geom.from_file(initialGeomVFile)
+initialGeom = damask.Geom.load_ASCII(initialGeomVFile)
 
 if len(np.unique(targetGeom.microstructure)) != nMicrostructures:
   damask.util.croak('error. Microstructure count mismatch')
@@ -273,8 +272,8 @@ sys.stdout.flush()
 initialGeomVFile.close()
 
 # start mulithreaded monte carlo simulation
-threads=[]
+threads = []
-s=threading.Semaphore(1)
+s = threading.Semaphore(1)
 
 for i in range(options.threads):
   threads.append(myThread(i))

processing/pre/seeds_fromGeom.py

@@ -17,7 +17,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #--------------------------------------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
-Create seed file taking microstructure indices from given geom file.
+Create seed file taking material indices from given geom file.
 Indices can be black-listed or white-listed.
 
 """, version = scriptID)
@@ -46,12 +46,12 @@ options.blacklist = [int(i) for i in options.blacklist]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    microstructure = geom.microstructure.reshape((-1,1),order='F')
+    materials = geom.materials.reshape((-1,1),order='F')
 
-    mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist else \
+    mask = np.logical_and(np.in1d(materials,options.whitelist,invert=False) if options.whitelist else \
                           np.full(geom.grid.prod(),True,dtype=bool),
-                          np.in1d(microstructure,options.blacklist,invert=True)  if options.blacklist else \
+                          np.in1d(materials,options.blacklist,invert=True)  if options.blacklist else \
                           np.full(geom.grid.prod(),True,dtype=bool))
 
     seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F')
@@ -63,6 +63,6 @@ for name in filenames:
                 'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
                 'homogenization\t{}'.format(geom.homogenization)]
 
-    table = damask.Table(seeds[mask],{'pos':(3,)},comments)
+    damask.Table(seeds[mask],{'pos':(3,)},comments)\
-    table = table.add('microstructure',microstructure[mask])
+          .add('material',materials[mask].astype(int))\
-    table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds')
+          .save(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds',legacy=True)

processing/pre/seeds_fromPokes.py

@@ -52,7 +52,7 @@ options.box = np.array(options.box).reshape(3,2)
 
 for name in filenames:
     damask.util.report(scriptName,name)
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     offset =(np.amin(options.box, axis=1)*geom.grid/geom.size).astype(int)
     box    = np.amax(options.box, axis=1) \
@@ -91,6 +91,6 @@ for name in filenames:
                 'homogenization\t{}'.format(geom.homogenization)]
 
     table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
-    table.set('microstructure',table.get('microstructure').astype(np.int))
+    table.set('microstructure',table.get('microstructure').astype(np.int))\
-    table.to_file(sys.stdout if name is None else \
+         .save(sys.stdout if name is None else \
-                  os.path.splitext(name)[0]+f'_poked_{options.N}.seeds')
+                     os.path.splitext(name)[0]+f'_poked_{options.N}.seeds',legacy=True)

processing/pre/seeds_fromRandom.py

@@ -154,12 +154,12 @@ for name in filenames:
                 'randomSeed\t{}'.format(options.randomSeed),
                ]
 
-    table = damask.Table(np.hstack((seeds,eulers)),{'pos':(3,),'euler':(3,)},comments)
+    table = damask.Table(np.hstack((seeds,eulers)),{'pos':(3,),'euler':(3,)},comments)\
-    table = table.add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int))
+                  .add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int))
 
     if options.weights:
         weights = np.random.uniform(low = 0, high = options.max, size = options.N) if options.max > 0.0 \
              else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)
         table = table.add('weight',weights)
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save(sys.stdout if name is None else name,legacy=True)

python/damask/__init__.py

@@ -18,6 +18,7 @@ from ._lattice     import Symmetry, Lattice# noqa
 from ._orientation import Orientation      # noqa
 from ._result      import Result           # noqa
 from ._geom        import Geom             # noqa
+from ._material    import Material         # noqa
 from .             import solver           # noqa
 
 # deprecated

python/damask/_colormap.py

@@ -235,100 +235,128 @@ class Colormap(mpl.colors.ListedColormap):
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
-    def to_file(self,fname=None,format='ParaView'):
+
+    def save_paraview(self,fname=None):
         """
-        Export colormap to file for use in external programs.
+        Write colormap to JSON file for Paraview.
 
         Parameters
         ----------
         fname : file, str, or pathlib.Path, optional.
             Filename to store results. If not given, the filename will
-            consist of the name of the colormap and an extension that
+            consist of the name of the colormap and extension '.json'.
-            depends on the file format.
-        format : {'ParaView', 'ASCII', 'GOM', 'gmsh'}, optional
-            File format, defaults to 'ParaView'. Available formats are:
-            - ParaView: JSON file, extension '.json'.
-            - ASCII: Plain text file, extension '.txt'.
-            - GOM: Aramis GOM (DIC), extension '.legend'.
-            - Gmsh: Gmsh FEM mesh-generator, extension '.msh'.
 
         """
         if fname is not None:
             try:
-                f = open(fname,'w')
+                fhandle = open(fname,'w')
             except TypeError:
-                f = fname
+                fhandle = fname
         else:
-            f = None
+            fhandle = None
 
-        if format.lower() == 'paraview':
-            Colormap._export_paraview(self,f)
-        elif format.lower() == 'ascii':
-            Colormap._export_ASCII(self,f)
-        elif format.lower() == 'gom':
-            Colormap._export_GOM(self,f)
-        elif format.lower() == 'gmsh':
-            Colormap._export_gmsh(self,f)
-        else:
-            raise ValueError('Unknown output format: {format}.')
-
-    @staticmethod
-    def _export_paraview(colormap,fhandle=None):
-        """Write colormap to JSON file for Paraview."""
         colors = []
-        for i,c in enumerate(np.round(colormap.colors,6).tolist()):
+        for i,c in enumerate(np.round(self.colors,6).tolist()):
             colors+=[i]+c
 
         out = [{
                 'Creator':util.execution_stamp('Colormap'),
                 'ColorSpace':'RGB',
-                'Name':colormap.name,
+                'Name':self.name,
                 'DefaultMap':True,
                 'RGBPoints':colors
                }]
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.json', 'w') as f:
+            with open(self.name.replace(' ','_')+'.json', 'w') as f:
                 json.dump(out, f,indent=4)
         else:
             json.dump(out,fhandle,indent=4)
 
-    @staticmethod
+
-    def _export_ASCII(colormap,fhandle=None):
+    def save_ASCII(self,fname=None):
-        """Write colormap to ASCII table."""
+        """
-        labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
+        Write colormap to ASCII table.
-        t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.txt'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
+
+        labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
+        t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
 
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
+            with open(self.name.replace(' ','_')+'.txt', 'w') as f:
-                t.to_file(f,new_style=True)
+                t.save(f)
         else:
-            t.to_file(fhandle,new_style=True)
+            t.save(fhandle)
 
-    @staticmethod
+
-    def _export_GOM(colormap,fhandle=None):
+    def save_GOM(self,fname=None):
-        """Write colormap to GOM Aramis compatible format."""
+        """
+        Write colormap to GOM Aramis compatible format.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.legend'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
         # ToDo: test in GOM
-        GOM_str = f'1 1 {colormap.name.replace(" ","_")} 9 {colormap.name.replace(" ","_")} ' \
+        GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
                 +  '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
-                + f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(colormap.colors)}' \
+                + f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(self.colors)}' \
-                + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((colormap.colors*255).astype(int))]) \
+                + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
                 + '\n'
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.legend', 'w') as f:
+            with open(self.name.replace(' ','_')+'.legend', 'w') as f:
                 f.write(GOM_str)
         else:
             fhandle.write(GOM_str)
 
 
-    @staticmethod
+    def save_gmsh(self,fname=None):
-    def _export_gmsh(colormap,fhandle=None):
+        """
-        """Write colormap to Gmsh compatible format."""
+        Write colormap to Gmsh compatible format.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.msh'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
         # ToDo: test in gmsh
         gmsh_str = 'View.ColorTable = {\n' \
-                 +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in colormap.colors[:,:3]*255]) \
+                 +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
                  +'\n}\n'
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.msh', 'w') as f:
+            with open(self.name.replace(' ','_')+'.msh', 'w') as f:
                 f.write(gmsh_str)
         else:
             fhandle.write(gmsh_str)

python/damask/_geom.py

@@ -1,7 +1,5 @@
-import sys
 import copy
-import multiprocessing
+import multiprocessing as mp
-from io import StringIO
 from functools import partial
 
 import numpy as np
@@ -60,11 +58,11 @@ class Geom:
     def __repr__(self):
         """Basic information on geometry definition."""
         return util.srepr([
-               f'grid     a b c:     {util.srepr(self.grid,  " x ")}',
+               f'grid     a b c:  {util.srepr(self.grid,  " x ")}',
-               f'size     x y z:     {util.srepr(self.size,  " x ")}',
+               f'size     x y z:  {util.srepr(self.size,  " x ")}',
-               f'origin   x y z:     {util.srepr(self.origin,"   ")}',
+               f'origin   x y z:  {util.srepr(self.origin,"   ")}',
-               f'# materialpoints:   {self.N_materials}',
+               f'# materials:     {self.N_materials}',
-               f'max materialpoint:  {np.nanmax(self.materials)}',
+               f'max material:    {np.nanmax(self.materials)}',
               ])
 
 
@@ -102,12 +100,12 @@ class Geom:
             message.append(util.emph(  f'origin   x y z:     {util.srepr( self.origin,"   ")}'))
 
         if other.N_materials != self.N_materials:
-            message.append(util.delete(f'# materialpoints:   {other.N_materials}'))
+            message.append(util.delete(f'# materials:        {other.N_materials}'))
-            message.append(util.emph(  f'# materialpoints:   { self.N_materials}'))
+            message.append(util.emph(  f'# materials:        { self.N_materials}'))
 
         if np.nanmax(other.materials) != np.nanmax(self.materials):
-            message.append(util.delete(f'max materialpoint:  {np.nanmax(other.materials)}'))
+            message.append(util.delete(f'max material:       {np.nanmax(other.materials)}'))
-            message.append(util.emph(  f'max materialpoint:  {np.nanmax( self.materials)}'))
+            message.append(util.emph(  f'max material:       {np.nanmax( self.materials)}'))
 
         return util.return_message(message)
 
@@ -123,7 +121,7 @@ class Geom:
 
 
     @staticmethod
-    def from_file(fname):
+    def load_ASCII(fname):
         """
         Read a geom file.
 
@@ -187,7 +185,7 @@ class Geom:
 
 
     @staticmethod
-    def from_vtr(fname):
+    def load(fname):
         """
         Read a VTK rectilinear grid.
 
@@ -198,13 +196,13 @@ class Geom:
             Valid extension is .vtr, it will be appended if not given.
 
         """
-        v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
+        v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
         comments = v.get_comments()
         grid = np.array(v.vtk_data.GetDimensions())-1
         bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
         size = bbox[1] - bbox[0]
 
-        return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0],comments=comments)
+        return Geom(v.get('material').reshape(grid,order='F'),size,bbox[0],comments=comments)
 
 
     @staticmethod
@@ -241,7 +239,7 @@ class Geom:
             seeds_p   = seeds
             coords    = grid_filters.cell_coord0(grid,size).reshape(-1,3)
 
-        pool = multiprocessing.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
+        pool = mp.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
         result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
         pool.close()
         pool.join()
@@ -286,131 +284,102 @@ class Geom:
                    )
 
 
-    def to_file(self,fname,format='vtr',pack=None):
+    def save_ASCII(self,fname,compress=None):
         """
         Writes a geom file.
 
         Parameters
         ----------
         fname : str or file handle
-            Geometry file to write.
+            Geometry file to write with extension '.geom'.
-        format : {'vtr', 'ASCII'}, optional
+        compress : bool, optional
-            File format, defaults to 'vtr'. Available formats are:
+            Compress geometry with 'x of y' and 'a to b'.
-            - vtr: VTK rectilinear grid file, extension '.vtr'.
-            - ASCII: Plain text file, extension '.geom'.
-        pack : bool, optional
-            Compress ASCII geometry with 'x of y' and 'a to b'.
 
         """
-        def _to_ASCII(geom,fname,pack=None):
+        header =  [f'{len(self.comments)+4} header'] + self.comments \
-            """
+                + ['grid   a {} b {} c {}'.format(*self.grid),
-            Writes a geom file.
+                   'size   x {} y {} z {}'.format(*self.size),
+                   'origin x {} y {} z {}'.format(*self.origin),
+                   'homogenization 1',
+                  ]
 
-            Parameters
+        grid = self.grid
-            ----------
-            geom : Geom object
-                Geometry to write.
-            fname : str or file handle
-                Geometry file to write.
-            pack : bool, optional
-                Compress geometry with 'x of y' and 'a to b'.
 
-            """
+        if compress is None:
-            header =  [f'{len(geom.comments)+4} header'] + geom.comments \
+            plain = grid.prod()/self.N_materials < 250
-                     +[ 'grid   a {} b {} c {}'.format(*geom.grid),
-                        'size   x {} y {} z {}'.format(*geom.size),
-                        'origin x {} y {} z {}'.format(*geom.origin),
-                        'homogenization 1',
-                       ]
-
-            grid = geom.grid
-
-            if pack is None:
-                plain = grid.prod()/geom.N_materials < 250
-            else:
-                plain = not pack
-
-            if plain:
-                format_string = '%g' if geom.materials.dtype in np.sctypes['float'] else \
-                                '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(geom.materials)))))
-                np.savetxt(fname,
-                           geom.materials.reshape([grid[0],np.prod(grid[1:])],order='F').T,
-                           header='\n'.join(header), fmt=format_string, comments='')
-            else:
-                try:
-                    f = open(fname,'w')
-                except TypeError:
-                    f = fname
-
-                compressType = None
-                former = start = -1
-                reps = 0
-                for current in geom.materials.flatten('F'):
-                    if abs(current - former) == 1 and (start - current) == reps*(former - current):
-                        compressType = 'to'
-                        reps += 1
-                    elif current == former and start == former:
-                        compressType = 'of'
-                        reps += 1
-                    else:
-                        if   compressType is None:
-                            f.write('\n'.join(header)+'\n')
-                        elif compressType == '.':
-                            f.write(f'{former}\n')
-                        elif compressType == 'to':
-                            f.write(f'{start} to {former}\n')
-                        elif compressType == 'of':
-                            f.write(f'{reps} of {former}\n')
-
-                        compressType = '.'
-                        start = current
-                        reps = 1
-
-                    former = current
-
-                if compressType == '.':
-                    f.write(f'{former}\n')
-                elif compressType == 'to':
-                    f.write(f'{start} to {former}\n')
-                elif compressType == 'of':
-                    f.write(f'{reps} of {former}\n')
-
-
-        def _to_vtr(geom,fname=None):
-            """
-            Generates vtk rectilinear grid.
-
-            Parameters
-            ----------
-            geom : Geom object
-                Geometry to write.
-            fname : str, optional
-                Filename to write. If no file is given, a string is returned.
-                Valid extension is .vtr, it will be appended if not given.
-
-            """
-            v = VTK.from_rectilinearGrid(geom.grid,geom.size,geom.origin)
-            v.add(geom.materials.flatten(order='F'),'materialpoint')
-            v.add_comments(geom.comments)
-
-            if fname:
-                v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
-            else:
-                sys.stdout.write(v.__repr__())
-
-        if format.lower() == 'ascii':
-            return _to_ASCII(self,fname,pack)
-        elif format.lower() == 'vtr':
-            return _to_vtr(self,fname)
         else:
-            raise TypeError(f'Unknown format {format}.')
+            plain = not compress
 
-    def as_ASCII(self,pack=False):
+        if plain:
-        """Format geometry as human-readable ASCII."""
+            format_string = '%g' if self.materials.dtype in np.sctypes['float'] else \
-        f = StringIO()
+                            '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.materials)))))
-        self.to_file(f,'ASCII',pack)
+            np.savetxt(fname,
-        f.seek(0)
+                       self.materials.reshape([grid[0],np.prod(grid[1:])],order='F').T,
-        return ''.join(f.readlines())
+                       header='\n'.join(header), fmt=format_string, comments='')
+        else:
+            try:
+                f = open(fname,'w')
+            except TypeError:
+                f = fname
+
+            compressType = None
+            former = start = -1
+            reps = 0
+            for current in self.materials.flatten('F'):
+                if abs(current - former) == 1 and (start - current) == reps*(former - current):
+                    compressType = 'to'
+                    reps += 1
+                elif current == former and start == former:
+                    compressType = 'of'
+                    reps += 1
+                else:
+                    if   compressType is None:
+                        f.write('\n'.join(header)+'\n')
+                    elif compressType == '.':
+                        f.write(f'{former}\n')
+                    elif compressType == 'to':
+                        f.write(f'{start} to {former}\n')
+                    elif compressType == 'of':
+                        f.write(f'{reps} of {former}\n')
+
+                    compressType = '.'
+                    start = current
+                    reps = 1
+
+                former = current
+
+            if compressType == '.':
+                f.write(f'{former}\n')
+            elif compressType == 'to':
+                f.write(f'{start} to {former}\n')
+            elif compressType == 'of':
+                f.write(f'{reps} of {former}\n')
+
+
+    def save(self,fname,compress=True):
+        """
+        Generates vtk rectilinear grid.
+
+        Parameters
+        ----------
+        fname : str, optional
+            Filename to write. If no file is given, a string is returned.
+            Valid extension is .vtr, it will be appended if not given.
+        compress : bool, optional
+            Compress with zlib algorithm. Defaults to True.
+
+        """
+        v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
+        v.add(self.materials.flatten(order='F'),'material')
+        v.add_comments(self.comments)
+
+        v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
+
+
+    def show(self):
+        """Show on screen."""
+        v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
+        v.show()
 
 
     def add_primitive(self,dimension,center,exponent,

python/damask/_material.py

@@ -0,0 +1,193 @@
+from io import StringIO
+import copy
+
+import yaml
+import numpy as np
+
+from . import Lattice
+from . import Rotation
+
+class NiceDumper(yaml.SafeDumper):
+    """Make YAML readable for humans."""
+
+    def write_line_break(self, data=None):
+        super().write_line_break(data)
+
+        if len(self.indents) == 1:
+            super().write_line_break()
+
+    def increase_indent(self, flow=False, indentless=False):
+        return super().increase_indent(flow, False)
+
+
+class Material(dict):
+    """Material configuration."""
+
+    def __repr__(self):
+        """Show as in file."""
+        output = StringIO()
+        self.save(output)
+        output.seek(0)
+        return ''.join(output.readlines())
+
+    @staticmethod
+    def load(fname):
+        """Load from yaml file."""
+        try:
+            fhandle = open(fname)
+        except TypeError:
+            fhandle = fname
+        return Material(yaml.safe_load(fhandle))
+
+    def save(self,fname='material.yaml'):
+        """
+        Save to yaml file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for reading.
+
+        """
+        try:
+            fhandle = open(fname,'w')
+        except TypeError:
+            fhandle = fname
+        fhandle.write(yaml.dump(dict(self),width=256,default_flow_style=None,Dumper=NiceDumper))
+
+
+    @property
+    def is_complete(self):
+        """Check for completeness."""
+        ok = True
+        for top_level in ['homogenization','phase','microstructure']:
+            # ToDo: With python 3.8 as prerequisite we can shorten with :=
+            ok &= top_level in self
+            if top_level not in self: print(f'{top_level} entry missing')
+
+        if ok:
+           ok &= len(self['microstructure']) > 0
+           if len(self['microstructure']) < 1: print('Incomplete microstructure definition')
+
+        if ok:
+            homogenization = set()
+            phase          = set()
+            for i,v in enumerate(self['microstructure']):
+                if 'homogenization' in v:
+                    homogenization.add(v['homogenization'])
+                else:
+                    print(f'No homogenization specified in microstructure {i}')
+                    ok = False
+
+                if 'constituents' in v:
+                    for ii,vv in enumerate(v['constituents']):
+                        if 'orientation' not in vv:
+                            print('No orientation specified in constituent {ii} of microstructure {i}')
+                            ok = False
+                        if 'phase' in vv:
+                            phase.add(vv['phase'])
+                        else:
+                            print(f'No phase specified in constituent {ii} of microstructure {i}')
+                            ok = False
+
+            for k,v in self['phase'].items():
+                if 'lattice' not in v:
+                    print(f'No lattice specified in phase {k}')
+                    ok = False
+
+            #for k,v in self['homogenization'].items():
+            #    if 'N_constituents' not in v:
+            #        print(f'No. of constituents not specified in homogenization {k}'}
+            #        ok = False
+
+            if phase - set(self['phase']):
+                print(f'Phase(s) {phase-set(self["phase"])} missing')
+                ok = False
+            if homogenization - set(self['homogenization']):
+                print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
+                ok = False
+
+        return ok
+
+
+    @property
+    def is_valid(self):
+        """Check for valid file layout."""
+        ok = True
+
+        if 'phase' in self:
+            for k,v in self['phase'].items():
+                if 'lattice' in v:
+                    try:
+                        Lattice(v['lattice'])
+                    except KeyError:
+                        s = v['lattice']
+                        print(f"Invalid lattice: '{s}' in phase '{k}'")
+                        ok = False
+
+        if 'microstructure' in self:
+            for i,v in enumerate(self['microstructure']):
+                if 'constituents' in v:
+                    f = 0.0
+                    for c in v['constituents']:
+                        f+= float(c['fraction'])
+                        if 'orientation' in c:
+                            try:
+                                Rotation.from_quaternion(c['orientation'])
+                            except ValueError:
+                                o = c['orientation']
+                                print(f"Invalid orientation: '{o}' in microstructure '{i}'")
+                                ok = False
+                    if not np.isclose(f,1.0):
+                        print(f"Invalid total fraction '{f}' in microstructure '{i}'")
+                        ok = False
+
+        return ok
+
+
+    def microstructure_rename_phase(self,mapping,ID=None,constituent=None):
+        """
+        Change phase name in microstructure.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected microstructure IDs.
+        constituent: list of ints, optional
+            Limit renaming to selected constituents.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['microstructure']):
+            if ID and i not in ID: continue
+            for c in m['constituents']:
+                if constituent is not None and c not in constituent: continue
+                try:
+                    c['phase'] = mapping[c['phase']]
+                except KeyError:
+                    continue
+        return dup
+
+
+    def microstructure_rename_homogenization(self,mapping,ID=None):
+        """
+        Change homogenization name in microstructure.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected homogenization IDs.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['microstructure']):
+            if ID and i not in ID: continue
+            try:
+                m['homogenization'] = mapping[m['homogenization']]
+            except KeyError:
+                continue
+        return dup

python/damask/_result.py

@@ -1100,7 +1100,7 @@ class Result:
         pool.join()
 
 
-    def write_XDMF(self):
+    def save_XDMF(self):
         """
         Write XDMF file to directly visualize data in DADF5 file.
 
@@ -1196,7 +1196,7 @@ class Result:
             f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
 
 
-    def to_vtk(self,labels=[],mode='cell'):
+    def save_vtk(self,labels=[],mode='cell'):
         """
         Export to vtk cell/point data.
 
@@ -1268,4 +1268,4 @@ class Result:
             u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
             v.add(u,'u')
 
-            v.to_file(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')
+            v.save(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')

python/damask/_table.py

@@ -27,8 +27,11 @@ class Table:
         self.comments = [] if comments_ is None else [c for c in comments_]
         self.data = pd.DataFrame(data=data)
         self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
-        self._label_condensed()
+        self._label_uniform()
 
+    def __repr__(self):
+        """Brief overview."""
+        return util.srepr(self.comments)+'\n'+self.data.__repr__()
 
     def __copy__(self):
         """Copy Table."""
@@ -39,7 +42,7 @@ class Table:
         return self.__copy__()
 
 
-    def _label_flat(self):
+    def _label_discrete(self):
         """Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
         labels = []
         for label,shape in self.shapes.items():
@@ -48,8 +51,8 @@ class Table:
         self.data.columns = labels
 
 
-    def _label_condensed(self):
+    def _label_uniform(self):
-        """Label data condensed, e.g. 1_v 2_v 3_v ==> v v v."""
+        """Label data uniformly, e.g. 1_v 2_v 3_v ==> v v v."""
         labels = []
         for label,shape in self.shapes.items():
             labels += [label] * int(np.prod(shape))
@@ -64,12 +67,15 @@ class Table:
 
 
     @staticmethod
-    def from_ASCII(fname):
+    def load(fname):
         """
-        Create table from ASCII file.
+        Load ASCII table file.
 
-        The first line can indicate the number of subsequent header lines as 'n header',
+        In legacy style, the first line indicates the number of
-        alternatively first line is the header and comments are marked by '#' ('new style').
+        subsequent header lines as "N header", with the last header line being
+        interpreted as column labels.
+        Alternatively, initial comments are marked by '#', with the first non-comment line
+        containing the column labels.
         Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
         Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
 
@@ -119,9 +125,9 @@ class Table:
         return Table(data,shapes,comments)
 
     @staticmethod
-    def from_ang(fname):
+    def load_ang(fname):
         """
-        Create table from TSL ang file.
+        Load ang file.
 
         A valid TSL ang file needs to contains the following columns:
         * Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
@@ -289,9 +295,9 @@ class Table:
 
         """
         dup = self.copy()
-        dup._label_flat()
+        dup._label_discrete()
         dup.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
-        dup._label_condensed()
+        dup._label_uniform()
         dup.comments.append(f'sorted {"ascending" if ascending else "descending"} by {labels}')
         return dup
 
@@ -338,59 +344,38 @@ class Table:
             return dup
 
 
-    def to_file(self,fname,format='ASCII',new_style=False):
+    def save(self,fname,legacy=False):
         """
-        Store as plain text file.
+        Save as plain text file.
 
         Parameters
         ----------
         fname : file, str, or pathlib.Path
             Filename or file for writing.
-        format : {ASCII'}, optional
+        legacy : Boolean, optional
-            File format, defaults to 'ASCII'. Available formats are:
+            Write table in legacy style, indicating header lines by "N header"
-            - ASCII: Plain text file, extension '.txt'.
+            in contrast to using comment sign ('#') at beginning of lines.
-        new_style : Boolean, optional
-            Write table in new style, indicating header lines by comment sign ('#') only.
 
         """
-        def _to_ASCII(table,fname,new_style=False):
+        seen = set()
-            """
+        labels = []
-            Store as plain text file.
+        for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
+            if self.shapes[l] == (1,):
+                labels.append(f'{l}')
+            elif len(self.shapes[l]) == 1:
+                labels += [f'{i+1}_{l}' \
+                          for i in range(self.shapes[l][0])]
+            else:
+                labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
+                          for i in range(np.prod(self.shapes[l]))]
 
-            Parameters
+        header = ([f'{len(self.comments)+1} header'] + self.comments) if legacy else \
-            ----------
+                  [f'# {comment}' for comment in self.comments]
-            table : Table object
-                Table to write.
-            fname : file, str, or pathlib.Path
-                Filename or file for writing.
-            new_style : Boolean, optional
-                Write table in new style, indicating header lines by comment sign ('#') only.
 
-            """
+        try:
-            seen = set()
+            fhandle = open(fname,'w')
-            labels = []
+        except TypeError:
-            for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
+            fhandle = fname
-                if table.shapes[l] == (1,):
-                    labels.append(f'{l}')
-                elif len(table.shapes[l]) == 1:
-                    labels += [f'{i+1}_{l}' \
-                              for i in range(table.shapes[l][0])]
-                else:
-                    labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
-                              for i in range(np.prod(table.shapes[l]))]
 
-            header = [f'# {comment}' for comment in table.comments] if new_style else \
+        for line in header + [' '.join(labels)]: fhandle.write(line+'\n')
-                     [f'{len(table.comments)+1} header'] + table.comments
+        self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)
-
-            try:
-                f = open(fname,'w')
-            except TypeError:
-                f = fname
-
-            for line in header + [' '.join(labels)]: f.write(line+'\n')
-            table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
-
-        if format.lower() == 'ascii':
-            return _to_ASCII(self,fname,new_style)
-        else:
-            raise TypeError(f'Unknown format {format}.')

python/damask/_test.py

@@ -228,7 +228,7 @@ class Test:
 
   def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
 
-    source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
+    source = os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
     if len(targetfiles) == 0: targetfiles = sourcefiles
     for i,f in enumerate(sourcefiles):
       try:
@@ -287,30 +287,30 @@ class Test:
 
     import numpy as np
     logging.info('\n '.join(['comparing',File1,File2]))
-    table = damask.Table.from_ASCII(File1)
+    table = damask.Table.load(File1)
-    len1=len(table.comments)+2
+    len1 = len(table.comments)+2
-    table = damask.Table.from_ASCII(File2)
+    table = damask.Table.load(File2)
-    len2=len(table.comments)+2
+    len2 = len(table.comments)+2
 
     refArray = np.nan_to_num(np.genfromtxt(File1,missing_values='n/a',skip_header = len1,autostrip=True))
     curArray = np.nan_to_num(np.genfromtxt(File2,missing_values='n/a',skip_header = len2,autostrip=True))
 
     if len(curArray) == len(refArray):
       refArrayNonZero = refArray[refArray.nonzero()]
-      curArray = curArray[refArray.nonzero()]
+      curArray        = curArray[refArray.nonzero()]
-      max_err=np.max(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
+      max_err = np.   max(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
-      max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
+      max_loc = np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
       refArrayNonZero = refArrayNonZero[curArray.nonzero()]
-      curArray = curArray[curArray.nonzero()]
+      curArray        = curArray[curArray.nonzero()]
       print(f' ********\n * maximum relative error {max_err} between {refArrayNonZero[max_loc]} and {curArray[max_loc]}\n ********')
       return max_err
     else:
-       raise Exception('mismatch in array size to compare')
+       raise Exception(f'mismatch in array sizes ({len(refArray)} and {len(curArray)}) to compare')
 
 
   def compare_ArrayRefCur(self,ref,cur=''):
 
-    if cur =='': cur = ref
+    if cur == '': cur = ref
     refName = self.fileInReference(ref)
     curName = self.fileInCurrent(cur)
     return self.compare_Array(refName,curName)
@@ -331,7 +331,7 @@ class Test:
     logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
     if normHeadings == '': normHeadings = headings0
 
-# check if comparison is possible and determine lenght of columns
+# check if comparison is possible and determine length of columns
     if len(headings0) == len(headings1) == len(normHeadings):
       dataLength = len(headings0)
       length       = [1   for i in range(dataLength)]
@@ -399,10 +399,8 @@ class Test:
       if any(norm[i]) == 0.0 or absTol[i]:
         norm[i] = [1.0 for j in range(line0-len(skipLines))]
         absTol[i] = True
-        if perLine:
+        logging.warning(f'''{"At least one" if perLine else "Maximum"} norm of
-          logging.warning(f"At least one norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
+                            "{headings0[i]['label']}" in first table is 0.0, using absolute tolerance''')
-        else:
-          logging.warning(f"Maximum norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
 
     line1 = 0
     while table1.data_read():                                                  # read next data line of ASCII table
@@ -418,20 +416,18 @@ class Test:
 
     logging.info(' ********')
     for i in range(dataLength):
-      if absTol[i]:
+      logging.info(f''' * maximum {'absolute' if absTol[i] else 'relative'} error {maxError[i]}
-        logging.info(f" * maximum absolute error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
+                       between {headings0[i]['label']} and {headings1[i]['label']}''')
-      else:
-        logging.info(f" * maximum relative error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
     logging.info(' ********')
     return maxError
 
 
   def compare_TablesStatistically(self,
-                     files = [None,None],                                      # list of file names
+                                  files = [None,None],                                      # list of file names
-                     columns = [None],                                         # list of list of column labels (per file)
+                                  columns = [None],                                         # list of list of column labels (per file)
-                     meanTol = 1.0e-4,
+                                  meanTol = 1.0e-4,
-                     stdTol = 1.0e-6,
+                                  stdTol = 1.0e-6,
-                     preFilter = 1.0e-9):
+                                  preFilter = 1.0e-9):
     """
     Calculate statistics of tables.
 
@@ -440,9 +436,9 @@ class Test:
     if not (isinstance(files, Iterable) and not isinstance(files, str)):       # check whether list of files is requested
       files = [str(files)]
 
-    tables = [damask.Table.from_ASCII(filename) for filename in files]
+    tables = [damask.Table.load(filename) for filename in files]
     for table in tables:
-      table._label_flat()
+      table._label_discrete()
 
     columns += [columns[0]]*(len(files)-len(columns))                          # extend to same length as files
     columns = columns[:len(files)]                                             # truncate to same length as files
@@ -462,7 +458,7 @@ class Test:
 
     data = []
     for table,labels in zip(tables,columns):
-      table._label_condensed()
+      table._label_uniform()
       data.append(np.hstack(list(table.get(label) for label in labels)))
 
 
@@ -471,12 +467,11 @@ class Test:
       normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5
       normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
       mean = np.amax(np.abs(np.mean(normedDelta,0)))
-      std = np.amax(np.std(normedDelta,0))
+      std  = np.amax(np.std(normedDelta,0))
       logging.info(f'mean: {mean:f}')
       logging.info(f'std:  {std:f}')
 
-    return (mean<meanTol) & (std < stdTol)
+    return (mean < meanTol) & (std < stdTol)
-
 
 
   def compare_Tables(self,
@@ -491,7 +486,7 @@ class Test:
 
     if len(files) < 2: return True                                             # single table is always close to itself...
 
-    tables = [damask.Table.from_ASCII(filename) for filename in files]
+    tables = [damask.Table.load(filename) for filename in files]
 
     columns += [columns[0]]*(len(files)-len(columns))                          # extend to same length as files
     columns = columns[:len(files)]                                             # truncate to same length as files
@@ -580,7 +575,7 @@ class Test:
 
     if culprit == 0:
       count = len(self.variants) if self.options.select is None else len(self.options.select)
-      msg = 'Test passed.' if count == 1 else f'All {count} tests passed.'
+      msg = ('Test passed.' if count == 1 else f'All {count} tests passed.') + '\a\a\a'
     elif culprit == -1:
       msg = 'Warning: could not start test...'
       ret = 0

python/damask/_vtk.py

@@ -118,7 +118,7 @@ class VTK:
 
 
     @staticmethod
-    def from_file(fname,dataset_type=None):
+    def load(fname,dataset_type=None):
         """
         Create VTK from file.
 
@@ -168,7 +168,7 @@ class VTK:
     def _write(writer):
         """Wrapper for parallel writing."""
         writer.Write()
-    def to_file(self,fname,parallel=True,compress=True):
+    def save(self,fname,parallel=True,compress=True):
         """
         Write to file.
 
@@ -178,6 +178,8 @@ class VTK:
             Filename for writing.
         parallel : boolean, optional
             Write data in parallel background process. Defaults to True.
+        compress : bool, optional
+            Compress with zlib algorithm. Defaults to True.
 
         """
         if   isinstance(self.vtk_data,vtk.vtkRectilinearGrid):

python/damask/util.py

@@ -172,8 +172,9 @@ def scale_to_coprime(v):
     m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
     m = m//reduce(np.gcd,m)
 
-    if not np.allclose(v[v.nonzero()]/m[v.nonzero()],v[v.nonzero()][0]/m[m.nonzero()][0]):
+    with np.errstate(divide='ignore'):
-        raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
+        if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
+            raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
 
     return m
 

python/tests/reference/Geom/clean_2_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZwAAAA==eF7t0rcOgmAAhVEgNmyo2AuoWN//BR04EwsJcfzvcvabL47qxcFOJg177HPAIUdMOeaEU844Z8YFl1wx55obbrnjngceeeKZFxYseeWNd1Z88MkX3/zwy+Z/wf8YOqzX1uEPlgwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAagAAAA==eF7t0rkOglAARFExLrgCKuKuqLj8/w9acCoSY7B+05x+cqNOvSj4l92GPfY54JAxRxxzwilnnDNhyowLLrlizjULbrjljnseeOSJZ15Y8sob76z44JMvvtn8L9jObz2GDuv96vADk5QHBg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAGwAAAA==eF5jZIAAxlF6lB4AmmmUpogeDUfKaAD7jwDw
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAGQAAAA==eF5jZIAAxlF6lB4AmmmUHqUHkAYA/M8A8Q==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZwAAAA==eF7t0rcOgmAAhVEgNmyo2AuoWN//BR04EwsJcfzvcvabL47qxcFOJg177HPAIUdMOeaEU844Z8YFl1wx55obbrnjngceeeKZFxYseeWNd1Z88MkX3/zwy+Z/wf8YOqzX1uEPlgwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAagAAAA==eF7t0rkOglAARFExLrgCKuKuqLj8/w9acCoSY7B+05x+cqNOvSj4l92GPfY54JAxRxxzwilnnDNhyowLLrlizjULbrjljnseeOSJZ15Y8sob76z44JMvvtn8L9jObz2GDuv96vADk5QHBg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAIgAAAA==eF5jZIAAxlGaLJoJjSakntr6hzqN7v9RepSmJw0AC04A9Q==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAALwAAAA==eF5jZIAAxlGaLJoJjSakHpc+cvUTUkdrmlL3j9KU0dROF5TqH2iaVPcDAALOANU=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAcQAAAA==eF7t0rkOglAUBFAxKu6igvsKrv//gxYcm9fQGEPBNKe6yc1kolaZqPEndthljzH7HHDIEceccMoZE8654JIpM6645oZb7rjngUeeeOaFV+YseOOdDz754pthf+3Aqr7rdv9vw3+/NjssU7XDD0/8BuQ=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYQAAAA==eF7t0scVglAAAEHgqZgBA2ZExdR/gx6YCpDj38s0sEnUlgR7ccAhR0w55oRTzjjngktmzFlwxTU33LLkjnseeOSJZ15Y8cqaN975YMMnX3zzwy/j4F+GD9u6fvgD+gwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="2" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="2" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0rcSglAARFEHE0bAgBkE8///oAWnF8b2bXP6nRv1mkXBv+xzwCFHHDPmhFPOOOeCSyZMmXHFNTfcMueOex545IlnXliw5JUVa95454NPvvjmh79+DXYzdNisbYdfSqMHMg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAIAAAAA==eF5jZIAAxlF6lB4AmokAPdj1DzRNyP2jNH4aAMufANU=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAMAAAAA==eF5jYoAAJhw0IwEalz566aeUptT+oa6fUppS+4e6fkppSu0f6voppSm1HwBAngDh
       </DataArray>
     </CellData>

python/tests/reference/Material/material.yaml

@@ -0,0 +1,42 @@
+homogenization:
+  SX:
+    mech: {type: none}
+  Taylor:
+    mech: {type: isostrain, N_constituents: 2}
+
+microstructure:
+  - constituents:
+      - fraction: 1.0
+        orientation: [1.0, 0.0, 0.0, 0.0]
+        phase: Aluminum
+    homogenization: SX
+  - constituents:
+      - fraction: 1.0
+        orientation: [0.7936696712125002, -0.28765777461664166, -0.3436487135089419, 0.4113964260949434]
+        phase: Aluminum
+    homogenization: SX
+  - constituents:
+      - fraction: 1.0
+        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        phase: Aluminum
+    homogenization: SX
+  - homogenization: Taylor
+    constituents:
+      - fraction: .5
+        orientation: [0.28645844315788244, -0.022571491243423537, -0.467933059311115, -0.8357456192708106]
+        phase: Aluminum
+      - fraction: .5
+        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        phase: Steel
+
+phase:
+  Aluminum:
+    elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+    generic:
+      output: [F, P, Fe, Fp, Lp]
+    lattice: fcc
+  Steel:
+    elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
+    generic:
+      output: [F, P, Fe, Fp, Lp]
+    lattice: bcc

python/tests/reference/Rotation/Visualize_hybridIA_sampling.ipynb

@@ -0,0 +1,276 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import damask\n",
+    "\n",
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "orientations,rODF = damask.Rotation.from_ODF('hybridIA_ODF.txt',\n",
+    "                                             2**14,\n",
+    "                                             degrees=True,\n",
+    "                                             reconstruct=True,\n",
+    "                                             fractions=True,\n",
+    "                                             seed=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "VTK = damask.VTK.from_rectilinearGrid([36,36,36],[90,90,90])\n",
+    "VTK.add(damask.Table.from_ASCII('hybridIA_ODF.txt').get('intensity'),'intensity')\n",
+    "VTK.add(rODF.flatten(order='F'),'rODF')\n",
+    "VTK.to_file('hybridIA_ODF.vtr')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Help on class VTK in module damask._vtk:\n",
+      "\n",
+      "class VTK(builtins.object)\n",
+      " |  VTK(geom)\n",
+      " |  \n",
+      " |  Spatial visualization (and potentially manipulation).\n",
+      " |  \n",
+      " |  High-level interface to VTK.\n",
+      " |  \n",
+      " |  Methods defined here:\n",
+      " |  \n",
+      " |  __init__(self, geom)\n",
+      " |      Set geometry and topology.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      geom : subclass of vtk.vtkDataSet\n",
+      " |          Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,\n",
+      " |          vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.\n",
+      " |  \n",
+      " |  __repr__(self)\n",
+      " |      ASCII representation of the VTK data.\n",
+      " |  \n",
+      " |  add(self, data, label=None)\n",
+      " |      Add data to either cells or points.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      data : numpy.ndarray\n",
+      " |          Data to add. First dimension need to match either\n",
+      " |          number of cells or number of points\n",
+      " |      label : str\n",
+      " |          Data label.\n",
+      " |  \n",
+      " |  add_comments(self, comments)\n",
+      " |      Add Comments.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      comments : str or list of str\n",
+      " |          Comments to add.\n",
+      " |  \n",
+      " |  get(self, label)\n",
+      " |      Get either cell or point data.\n",
+      " |      \n",
+      " |      Cell data takes precedence over point data, i.e. this\n",
+      " |      function assumes that labels are unique among cell and\n",
+      " |      point data.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      label : str\n",
+      " |          Data label.\n",
+      " |  \n",
+      " |  get_comments(self)\n",
+      " |      Return the comments.\n",
+      " |  \n",
+      " |  set_comments(self, comments)\n",
+      " |      Set Comments.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      comments : str or list of str\n",
+      " |          Comments.\n",
+      " |  \n",
+      " |  show(self)\n",
+      " |      Render.\n",
+      " |      \n",
+      " |      See http://compilatrix.com/article/vtk-1 for further ideas.\n",
+      " |  \n",
+      " |  write(self, fname, parallel=True)\n",
+      " |      Write to file.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      fname : str or pathlib.Path\n",
+      " |          Filename for writing.\n",
+      " |      parallel : boolean, optional\n",
+      " |          Write data in parallel background process. Defaults to True.\n",
+      " |  \n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Static methods defined here:\n",
+      " |  \n",
+      " |  from_file(fname, dataset_type=None)\n",
+      " |      Create VTK from file.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      fname : str or pathlib.Path\n",
+      " |          Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.\n",
+      " |      dataset_type : str, optional\n",
+      " |          Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,\n",
+      " |          vtkUnstructuredGrid, and vtkPolyData.\n",
+      " |  \n",
+      " |  from_polyData(points)\n",
+      " |      Create VTK of type vtk.polyData.\n",
+      " |      \n",
+      " |      This is the common type for point-wise data.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      points : numpy.ndarray of shape (:,3)\n",
+      " |          Spatial position of the points.\n",
+      " |  \n",
+      " |  from_rectilinearGrid(grid, size, origin=array([0., 0., 0.]))\n",
+      " |      Create VTK of type vtk.vtkRectilinearGrid.\n",
+      " |      \n",
+      " |      This is the common type for results from the grid solver.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      grid : numpy.ndarray of shape (3) of np.dtype = int\n",
+      " |          Number of cells.\n",
+      " |      size : numpy.ndarray of shape (3)\n",
+      " |          Physical length.\n",
+      " |      origin : numpy.ndarray of shape (3), optional\n",
+      " |          Spatial origin.\n",
+      " |  \n",
+      " |  from_unstructuredGrid(nodes, connectivity, cell_type)\n",
+      " |      Create VTK of type vtk.vtkUnstructuredGrid.\n",
+      " |      \n",
+      " |      This is the common type for results from FEM solvers.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      nodes : numpy.ndarray of shape (:,3)\n",
+      " |          Spatial position of the nodes.\n",
+      " |      connectivity : numpy.ndarray of np.dtype = int\n",
+      " |          Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.\n",
+      " |      cell_type : str\n",
+      " |          Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.\n",
+      " |  \n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Data descriptors defined here:\n",
+      " |  \n",
+      " |  __dict__\n",
+      " |      dictionary for instance variables (if defined)\n",
+      " |  \n",
+      " |  __weakref__\n",
+      " |      list of weak references to the object (if defined)\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "help(damask.VTK)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a,b=np.radians(([90,90],[45,45]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([1.57079633, 1.57079633])"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([0.78539816, 0.78539816])"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "b"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

python/tests/test_Colormap.py

@@ -75,41 +75,36 @@ class TestColormap:
             assert np.allclose(Colormap._xyz2msh(xyz),msh,atol=1.e-6,rtol=0)
 
 
-    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','Gmsh'])
+    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
     @pytest.mark.parametrize('model',['rgb','hsv','hsl','xyz','lab','msh'])
     def test_from_range(self,model,format,tmpdir):
         N = np.random.randint(2,256)
-        c = Colormap.from_range(np.random.rand(3),np.random.rand(3),model=model,N=N)
+        c = Colormap.from_range(np.random.rand(3),np.random.rand(3),model=model,N=N)    # noqa
-        c.to_file(tmpdir/'color_out',format=format)
+        eval(f'c.save_{format}(tmpdir/"color_out")')
 
-    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','Gmsh'])
+    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
     @pytest.mark.parametrize('name',['strain','gnuplot','Greys','PRGn','viridis'])
     def test_from_predefined(self,name,format,tmpdir):
         N = np.random.randint(2,256)
-        c = Colormap.from_predefined(name,N)
+        c = Colormap.from_predefined(name,N)                                            # noqa
         os.chdir(tmpdir)
-        c.to_file(format=format)
+        eval(f'c.save_{format}()')
 
     @pytest.mark.parametrize('format,name',[('ASCII','test.txt'),
                                             ('paraview','test.json'),
                                             ('GOM','test.legend'),
-                                            ('Gmsh','test.msh')
+                                            ('gmsh','test.msh')
                                            ])
     def test_write_filehandle(self,format,name,tmpdir):
-        c = Colormap.from_predefined('Dark2')
+        c = Colormap.from_predefined('Dark2')                                           # noqa
         fname = tmpdir/name
-        with open(fname,'w') as f:
+        with open(fname,'w') as f:                                                      # noqa
-            c.to_file(f,format=format)
+            eval(f'c.save_{format}(f)')
         for i in range(10):
             if fname.exists(): return
             time.sleep(.5)
         assert False
 
-    def test_write_invalid_format(self):
-        c = Colormap.from_predefined('Dark2')
-        with pytest.raises(ValueError):
-            c.to_file(format='invalid')
-
     @pytest.mark.parametrize('model',['rgb','hsv','hsl','lab','invalid'])
     def test_invalid_color(self,model):
         with pytest.raises(ValueError):
@@ -119,13 +114,13 @@ class TestColormap:
         c_1 = Colormap.from_predefined('stress')
         c_2 = c_1.reversed()
         assert (not np.allclose(c_1.colors,c_2.colors)) and \
-                np.allclose(c_1.colors,c_2.reversed().colors)
+                    np.allclose(c_1.colors,c_2.reversed().colors)
 
     def test_invert(self):
         c_1 = Colormap.from_predefined('strain')
         c_2 = ~c_1
-        assert (not np.allclose(c_1.colors,c_2.colors)) and \
+        assert (not np.allclose(c_1.colors,  c_2.colors)) and \
-                np.allclose(c_1.colors,(~c_2).colors)
+                    np.allclose(c_1.colors,(~c_2).colors)
 
     def test_add(self):
         c = Colormap.from_predefined('jet')
@@ -149,16 +144,16 @@ class TestColormap:
     @pytest.mark.parametrize('format,ext',[('ASCII','.txt'),
                                            ('paraview','.json'),
                                            ('GOM','.legend'),
-                                           ('Gmsh','.msh')
+                                           ('gmsh','.msh')
                                           ])
     def test_compare_reference(self,format,ext,tmpdir,reference_dir,update):
         name = 'binary'
-        c = Colormap.from_predefined(name)
+        c = Colormap.from_predefined(name)                                              # noqa
         if update:
             os.chdir(reference_dir)
-            c.to_file(format=format)
+            eval(f'c.save_{format}()')
         else:
             os.chdir(tmpdir)
-            c.to_file(format=format)
+            eval(f'c.save_{format}()')
             time.sleep(.5)
             assert filecmp.cmp(tmpdir/(name+ext),reference_dir/(name+ext))

python/tests/test_Geom.py

@@ -43,34 +43,26 @@ class TestGeom:
 
 
     def test_write_read_str(self,default,tmpdir):
-        default.to_file(str(tmpdir/'default.geom'),format='ASCII')
+        default.save_ASCII(str(tmpdir/'default.geom'))
-        new = Geom.from_file(str(tmpdir/'default.geom'))
+        new = Geom.load_ASCII(str(tmpdir/'default.geom'))
         assert geom_equal(default,new)
 
 
     def test_write_read_file(self,default,tmpdir):
         with open(tmpdir/'default.geom','w') as f:
-            default.to_file(f,format='ASCII',pack=True)
+            default.save_ASCII(f,compress=True)
         with open(tmpdir/'default.geom') as f:
-            new = Geom.from_file(f)
+            new = Geom.load_ASCII(f)
-        assert geom_equal(default,new)
-
-
-    def test_write_as_ASCII(self,default,tmpdir):
-        with open(tmpdir/'str.geom','w') as f:
-            f.write(default.as_ASCII())
-        with open(tmpdir/'str.geom') as f:
-            new = Geom.from_file(f)
         assert geom_equal(default,new)
 
 
     def test_read_write_vtr(self,default,tmpdir):
-        default.to_file(tmpdir/'default',format='vtr')
+        default.save(tmpdir/'default')
         for _ in range(10):
             time.sleep(.2)
             if os.path.exists(tmpdir/'default.vtr'): break
 
-        new = Geom.from_vtr(tmpdir/'default.vtr')
+        new = Geom.load(tmpdir/'default.vtr')
         assert geom_equal(new,default)
 
 
@@ -79,23 +71,23 @@ class TestGeom:
             f.write('this is not a valid header')
         with open('invalid_file','r') as f:
             with pytest.raises(TypeError):
-                Geom.from_file(f)
+                Geom.load_ASCII(f)
 
 
     def test_invalid_vtr(self,tmpdir):
         v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
-        v.to_file(tmpdir/'no_materialpoint.vtr')
+        v.save(tmpdir/'no_materialpoint.vtr')
         for _ in range(10):
             time.sleep(.2)
             if os.path.exists(tmpdir/'no_materialpoint.vtr'): break
         with pytest.raises(ValueError):
-            Geom.from_vtr(tmpdir/'no_materialpoint.vtr')
+            Geom.load(tmpdir/'no_materialpoint.vtr')
 
 
-    @pytest.mark.parametrize('pack',[True,False])
+    @pytest.mark.parametrize('compress',[True,False])
-    def test_pack(self,default,tmpdir,pack):
+    def test_compress(self,default,tmpdir,compress):
-        default.to_file(tmpdir/'default.geom',format='ASCII',pack=pack)
+        default.save_ASCII(tmpdir/'default.geom',compress=compress)
-        new = Geom.from_file(tmpdir/'default.geom')
+        new = Geom.load_ASCII(tmpdir/'default.geom')
         assert geom_equal(new,default)
 
 
@@ -125,11 +117,6 @@ class TestGeom:
             Geom(materials)
 
 
-    def test_invalid_write_format(self,default):
-        with pytest.raises(TypeError):
-            default.to_file(format='invalid')
-
-
     @pytest.mark.parametrize('directions,reflect',[
                                                    (['x'],        False),
                                                    (['x','y','z'],True),
@@ -141,8 +128,8 @@ class TestGeom:
         modified = default.mirror(directions,reflect)
         tag = f'directions={"-".join(directions)}_reflect={reflect}'
         reference = reference_dir/f'mirror_{tag}.geom'
-        if update: modified.to_file(reference)
+        if update: modified.save_ASCII(reference)
-        assert geom_equal(Geom.from_file(reference),
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
 
@@ -163,8 +150,8 @@ class TestGeom:
         modified = default.flip(directions)
         tag = f'directions={"-".join(directions)}'
         reference = reference_dir/f'flip_{tag}.geom'
-        if update: modified.to_file(reference)
+        if update: modified.save_ASCII(reference)
-        assert geom_equal(Geom.from_file(reference),
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
 
@@ -190,11 +177,11 @@ class TestGeom:
         current = default.clean(stencil,selection,periodic)
         reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
         if update and stencil > 1:
-            current.to_file(reference,format='vtr')
+            current.save(reference)
             for _ in range(10):
                 time.sleep(.2)
                 if os.path.exists(reference.with_suffix('.vtr')): break
-        assert geom_equal(Geom.from_vtr(reference) if stencil > 1 else default,
+        assert geom_equal(Geom.load(reference) if stencil > 1 else default,
                           current
                          )
 
@@ -212,8 +199,8 @@ class TestGeom:
         modified = default.scale(grid)
         tag = f'grid={util.srepr(grid,"-")}'
         reference = reference_dir/f'scale_{tag}.geom'
-        if update: modified.to_file(reference)
+        if update: modified.save_ASCII(reference)
-        assert geom_equal(Geom.from_file(reference),
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
 
@@ -255,8 +242,8 @@ class TestGeom:
         modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
         tag = f'Eulers={util.srepr(Eulers,"-")}'
         reference = reference_dir/f'rotate_{tag}.geom'
-        if update: modified.to_file(reference)
+        if update: modified.save_ASCII(reference)
-        assert geom_equal(Geom.from_file(reference),
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
 

python/tests/test_Material.py

@@ -0,0 +1,61 @@
+import os
+
+import pytest
+
+from damask import Material
+
+@pytest.fixture
+def reference_dir(reference_dir_base):
+    """Directory containing reference results."""
+    return reference_dir_base/'Material'
+
+
+class TestMaterial:
+    
+    @pytest.mark.parametrize('fname',[None,'test.yaml'])
+    def test_load_save(self,reference_dir,tmp_path,fname):
+        reference = Material.load(reference_dir/'material.yaml')
+        os.chdir(tmp_path)
+        if fname is None:
+            reference.save()
+            new = Material.load('material.yaml')
+        else:
+            reference.save(fname)
+            new = Material.load(fname)
+        assert reference == new
+
+    def test_valid_complete(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        assert material_config.is_valid and material_config.is_complete
+
+    def test_invalid_lattice(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['phase']['Aluminum']['lattice']='fxc'
+        assert not material_config.is_valid
+    
+    def test_invalid_orientation(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['microstructure'][0]['constituents'][0]['orientation']=[0,0,0,0]
+        assert not material_config.is_valid
+    
+    def test_invalid_fraction(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['microstructure'][0]['constituents'][0]['fraction']=.9
+        assert not material_config.is_valid
+    
+
+    @pytest.mark.parametrize('item',['homogenization','phase','microstructure'])
+    def test_incomplete_missing(self,reference_dir,item):
+        material_config = Material.load(reference_dir/'material.yaml')
+        del material_config[item]
+        assert not material_config.is_complete
+    
+    def test_incomplete_wrong_phase(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        new = material_config.microstructure_rename_phase({'Steel':'FeNbC'})
+        assert not new.is_complete
+    
+    def test_incomplete_wrong_homogenization(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        new = material_config.microstructure_rename_homogenization({'Taylor':'isostrain'})
+        assert not new.is_complete

python/tests/test_Orientation.py

@@ -106,8 +106,8 @@ class TestOrientation:
             coords = np.array([(1,i+1) for i,x in enumerate(eu)])
             table = Table(eu,{'Eulers':(3,)})
             table = table.add('pos',coords)
-            table.to_ASCII(reference)
+            table.save(reference)
-        assert np.allclose(eu,Table.from_ASCII(reference).get('Eulers'))
+        assert np.allclose(eu,Table.load(reference).get('Eulers'))
 
     @pytest.mark.parametrize('lattice',Lattice.lattices)
     def test_disorientation360(self,lattice):
@@ -129,4 +129,3 @@ class TestOrientation:
         eqs = [r for r in R_1.equivalent]
         R_2 = Orientation.from_average(eqs)
         assert np.allclose(R_1.rotation.quaternion,R_2.rotation.quaternion)
-

python/tests/test_Result.py

@@ -339,8 +339,8 @@ class TestResult:
     @pytest.mark.parametrize('output',['F',[],['F','P']])
     def test_vtk(self,tmp_path,default,output):
         os.chdir(tmp_path)
-        default.to_vtk(output)
+        default.save_vtk(output)
 
     def test_XDMF(self,tmp_path,single_phase):
         os.chdir(tmp_path)
-        single_phase.write_XDMF()
+        single_phase.save_XDMF()

python/tests/test_Rotation.py

@@ -461,7 +461,7 @@ def mul(me, other):
         if other.shape == (3,):
             A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
             B = 2.0 * np.dot(me.quaternion[1:],other)
-            C = 2.0 * _P*me.quaternion[0]
+            C = 2.0 * _P *   me.quaternion[0]
 
             return A*other + B*me.quaternion[1:] + C * np.cross(me.quaternion[1:],other)
 
@@ -496,9 +496,8 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(rot.as_quaternion()[0],0.0,atol=atol):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
+                ok |= np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o),1.0), f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.norm(o),1.0)
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._om2qu,Rotation._qu2om),
                                                  (Rotation._om2eu,Rotation._eu2om),
@@ -512,8 +511,7 @@ class TestRotation:
             m = rot.as_matrix()
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.det(o),1.0)
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._eu2qu,Rotation._qu2eu),
                                                  (Rotation._eu2om,Rotation._om2eu),
@@ -531,9 +529,9 @@ class TestRotation:
             ok = ok or np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
             if np.isclose(m[1],0.0,atol=atol) or np.isclose(m[1],np.pi,atol=atol):
                 sum_phi = np.unwrap([m[0]+m[2],o[0]+o[2]])
-                ok = ok or np.isclose(sum_phi[0],sum_phi[1],atol=atol)
+                ok |= np.isclose(sum_phi[0],sum_phi[1],atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and (np.zeros(3)-1.e-9 <= o).all() \
-            assert ok and (np.zeros(3)-1.e-9 <= o).all() and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all()
+                      and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all(), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ax2qu,Rotation._qu2ax),
                                                  (Rotation._ax2om,Rotation._om2ax),
@@ -548,9 +546,8 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(m[3],np.pi,atol=atol):
-                ok = ok or np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
+                ok |= np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ro2qu,Rotation._qu2ro),
                                                  #(Rotation._ro2om,Rotation._om2ro),
@@ -566,8 +563,7 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(np.clip(m,None,cutoff),np.clip(o,None,cutoff),atol=atol)
             ok = ok or np.isclose(m[3],0.0,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0), f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0)
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ho2qu,Rotation._qu2ho),
                                                  (Rotation._ho2om,Rotation._om2ho),
@@ -581,8 +577,7 @@ class TestRotation:
             m = rot.as_homochoric()
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.linalg.norm(o) < _R1 + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.linalg.norm(o) < _R1 + 1.e-9
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._cu2qu,Rotation._qu2cu),
                                                  (Rotation._cu2om,Rotation._om2cu),
@@ -598,8 +593,7 @@ class TestRotation:
             ok = np.allclose(m,o,atol=atol)
             if np.count_nonzero(np.isclose(np.abs(o),np.pi**(2./3.)*.5)):
                 ok = ok or np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.max(np.abs(o)) < np.pi**(2./3.) * 0.5 + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.max(np.abs(o)) < np.pi**(2./3.) * 0.5 + 1.e-9
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._qu2om,qu2om),
                                                    (Rotation._qu2eu,qu2eu),
@@ -612,8 +606,7 @@ class TestRotation:
         vectorized(qu.reshape(qu.shape[0]//2,-1,4))
         co = vectorized(qu)
         for q,c in zip(qu,co):
-            print(q,c)
+            assert np.allclose(single(q),c) and np.allclose(single(q),vectorized(q)), f'{q},{c}'
-            assert np.allclose(single(q),c) and np.allclose(single(q),vectorized(q))
 
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._om2qu,om2qu),
@@ -625,8 +618,7 @@ class TestRotation:
         vectorized(om.reshape(om.shape[0]//2,-1,3,3))
         co = vectorized(om)
         for o,c in zip(om,co):
-            print(o,c)
+            assert np.allclose(single(o),c) and np.allclose(single(o),vectorized(o)), f'{o},{c}'
-            assert np.allclose(single(o),c) and np.allclose(single(o),vectorized(o))
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._eu2qu,eu2qu),
                                                    (Rotation._eu2om,eu2om),
@@ -638,8 +630,7 @@ class TestRotation:
         vectorized(eu.reshape(eu.shape[0]//2,-1,3))
         co = vectorized(eu)
         for e,c in zip(eu,co):
-            print(e,c)
+            assert np.allclose(single(e),c) and np.allclose(single(e),vectorized(e)), f'{e},{c}'
-            assert np.allclose(single(e),c) and np.allclose(single(e),vectorized(e))
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ax2qu,ax2qu),
                                                    (Rotation._ax2om,ax2om),
@@ -651,8 +642,7 @@ class TestRotation:
         vectorized(ax.reshape(ax.shape[0]//2,-1,4))
         co = vectorized(ax)
         for a,c in zip(ax,co):
-            print(a,c)
+            assert np.allclose(single(a),c) and np.allclose(single(a),vectorized(a)), f'{a},{c}'
-            assert np.allclose(single(a),c) and np.allclose(single(a),vectorized(a))
 
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ro2ax,ro2ax),
@@ -663,8 +653,7 @@ class TestRotation:
         vectorized(ro.reshape(ro.shape[0]//2,-1,4))
         co = vectorized(ro)
         for r,c in zip(ro,co):
-            print(r,c)
+            assert np.allclose(single(r),c) and np.allclose(single(r),vectorized(r)), f'{r},{c}'
-            assert np.allclose(single(r),c) and np.allclose(single(r),vectorized(r))
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ho2ax,ho2ax),
                                                    (Rotation._ho2cu,ho2cu)])
@@ -674,8 +663,7 @@ class TestRotation:
         vectorized(ho.reshape(ho.shape[0]//2,-1,3))
         co = vectorized(ho)
         for h,c in zip(ho,co):
-            print(h,c)
+            assert np.allclose(single(h),c) and np.allclose(single(h),vectorized(h)), f'{h},{c}'
-            assert np.allclose(single(h),c) and np.allclose(single(h),vectorized(h))
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._cu2ho,cu2ho)])
     def test_cubochoric_vectorization(self,set_of_rotations,vectorized,single):
@@ -684,8 +672,7 @@ class TestRotation:
         vectorized(cu.reshape(cu.shape[0]//2,-1,3))
         co = vectorized(cu)
         for u,c in zip(cu,co):
-            print(u,c)
+            assert np.allclose(single(u),c) and np.allclose(single(u),vectorized(u)), f'{u},{c}'
-            assert np.allclose(single(u),c) and np.allclose(single(u),vectorized(u))
 
     @pytest.mark.parametrize('func',[Rotation.from_axis_angle])
     def test_normalization_vectorization(self,func):
@@ -703,9 +690,8 @@ class TestRotation:
             o = Rotation.from_Eulers(rot.as_Eulers(degrees),degrees).as_quaternion()
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(rot.as_quaternion()[0],0.0,atol=atol):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
+                ok |= np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o),1.0), f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.norm(o),1.0)
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('normalize',[True,False])
@@ -717,12 +703,12 @@ class TestRotation:
             o = Rotation.from_axis_angle(rot.as_axis_angle(degrees)*c,degrees,normalize,P).as_Eulers()
             u = np.array([np.pi*2,np.pi,np.pi*2])
             ok = np.allclose(m,o,atol=atol)
-            ok = ok or np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
+            ok |= np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
             if np.isclose(m[1],0.0,atol=atol) or np.isclose(m[1],np.pi,atol=atol):
                 sum_phi = np.unwrap([m[0]+m[2],o[0]+o[2]])
-                ok = ok or np.isclose(sum_phi[0],sum_phi[1],atol=atol)
+                ok |= np.isclose(sum_phi[0],sum_phi[1],atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and (np.zeros(3)-1.e-9 <= o).all() \
-            assert ok and (np.zeros(3)-1.e-9 <= o).all() and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all()
+                      and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all(), f'{m},{o},{rot.as_quaternion()}'
 
     def test_matrix(self,set_of_rotations):
         for rot in set_of_rotations:
@@ -731,8 +717,8 @@ class TestRotation:
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(m[3],np.pi,atol=atol):
                 ok = ok or np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) \
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9
+                      and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('normalize',[True,False])
@@ -742,8 +728,7 @@ class TestRotation:
             m = rot.as_matrix()
             o = Rotation.from_Rodrigues(rot.as_Rodrigues()*c,normalize,P).as_matrix()
             ok = np.allclose(m,o,atol=atol)
-            print(m,o)
+            assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o}'
-            assert ok and np.isclose(np.linalg.det(o),1.0)
 
     @pytest.mark.parametrize('P',[1,-1])
     def test_homochoric(self,set_of_rotations,P):
@@ -753,8 +738,7 @@ class TestRotation:
             o = Rotation.from_homochoric(rot.as_homochoric()*P*-1,P).as_Rodrigues()
             ok = np.allclose(np.clip(m,None,cutoff),np.clip(o,None,cutoff),atol=atol)
             ok = ok or np.isclose(m[3],0.0,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0), f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0)
 
     @pytest.mark.parametrize('P',[1,-1])
     def test_cubochoric(self,set_of_rotations,P):
@@ -762,8 +746,7 @@ class TestRotation:
             m = rot.as_homochoric()
             o = Rotation.from_cubochoric(rot.as_cubochoric()*P*-1,P).as_homochoric()
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and np.linalg.norm(o) < (3.*np.pi/4.)**(1./3.) + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
-            assert ok and np.linalg.norm(o) < (3.*np.pi/4.)**(1./3.) + 1.e-9
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('accept_homomorph',[True,False])
@@ -774,9 +757,8 @@ class TestRotation:
             o = Rotation.from_quaternion(rot.as_quaternion()*c,accept_homomorph,P).as_cubochoric()
             ok = np.allclose(m,o,atol=atol)
             if np.count_nonzero(np.isclose(np.abs(o),np.pi**(2./3.)*.5)):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
+                ok |= np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
+            assert ok and o.max() < np.pi**(2./3.)*0.5+1.e-9, f'{m},{o},{rot.as_quaternion()}'
-            assert ok and o.max() < np.pi**(2./3.)*0.5+1.e-9
 
     @pytest.mark.parametrize('reciprocal',[True,False])
     def test_basis(self,set_of_rotations,reciprocal):
@@ -858,8 +840,7 @@ class TestRotation:
         for rot in set_of_rotations:
             v = rot.broadcast_to((5,)) @ data
             for i in range(data.shape[0]):
-                print(i-data[i])
+                assert np.allclose(mul(rot,data[i]),v[i]), f'{i-data[i]}'
-                assert np.allclose(mul(rot,data[i]),v[i])
 
 
     @pytest.mark.parametrize('data',[np.random.rand(3),
@@ -926,34 +907,39 @@ class TestRotation:
     @pytest.mark.parametrize('sigma',[5,10,15,20])
     @pytest.mark.parametrize('N',[1000,10000,100000])
     def test_spherical_component(self,N,sigma):
-        c = Rotation.from_random()
+        p = []
-        o = Rotation.from_spherical_component(c,sigma,N)
+        for run in range(5):
-        _, angles = c.misorientation(o).as_axis_angle(pair=True,degrees=True)
+            c = Rotation.from_random()
-        angles[::2] *= -1                                                                           # flip angle for every second to symmetrize distribution
+            o = Rotation.from_spherical_component(c,sigma,N)
+            _, angles = c.misorientation(o).as_axis_angle(pair=True,degrees=True)
+            angles[::2] *= -1                                                                       # flip angle for every second to symmetrize distribution
+
+            p.append(stats.normaltest(angles)[1])
 
-        p = stats.normaltest(angles)[1]
         sigma_out = np.std(angles)
-        print(f'\np: {p}, sigma ratio {sigma/sigma_out}')
+        p = np.average(p)
-        assert (.9 < sigma/sigma_out < 1.1) and p > 0.001
+        assert (.9 < sigma/sigma_out < 1.1) and p > 1e-2, f'{sigma/sigma_out},{p}'
 
 
     @pytest.mark.parametrize('sigma',[5,10,15,20])
     @pytest.mark.parametrize('N',[1000,10000,100000])
     def test_from_fiber_component(self,N,sigma):
-        """https://en.wikipedia.org/wiki/Full_width_at_half_maximum."""
+        p = []
-        alpha = np.random.random(2)*np.pi
+        for run in range(5):
-        beta  = np.random.random(2)*np.pi
+             alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
+             beta  = np.random.random()*2*np.pi,np.arccos(np.random.random())
 
-        f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
+             f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
-        f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
+             f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
-        ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
+             ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
-        n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True)                # rotation to align fiber axis in crystal and sample system
+             n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True)           # rotation to align fiber axis in crystal and sample system
 
-        o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
+             o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
-        angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
+             angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
-        dist   = np.array(angles) * (np.random.randint(0,2,N)*2-1)
+             dist   = np.array(angles) * (np.random.randint(0,2,N)*2-1)
+
+             p.append(stats.normaltest(dist)[1])
 
-        p = stats.normaltest(dist)[1]
         sigma_out = np.degrees(np.std(dist))
-        print(f'\np: {p}, sigma ratio {sigma/sigma_out}')
+        p = np.average(p)
-        assert (.9 < sigma/sigma_out < 1.1) and p > 0.001
+        assert (.9 < sigma/sigma_out < 1.1) and p > 1e-2, f'{sigma/sigma_out},{p}'

python/tests/test_Table.py

@@ -35,50 +35,50 @@ class TestTable:
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_write_read(self,default,tmpdir,mode):
-        default.to_file(tmpdir/'default.txt')
+        default.save(tmpdir/'default.txt')
         if   mode == 'path':
-            new = Table.from_ASCII(tmpdir/'default.txt')
+            new = Table.load(tmpdir/'default.txt')
         elif mode == 'str':
-            new = Table.from_ASCII(str(tmpdir/'default.txt'))
+            new = Table.load(str(tmpdir/'default.txt'))
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_read_file(self,default,tmpdir):
         with open(tmpdir/'default.txt','w') as f:
-            default.to_file(f)
+            default.save(f)
         with open(tmpdir/'default.txt') as f:
-            new = Table.from_ASCII(f)
+            new = Table.load(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
-    def test_write_read_new_style(self,default,tmpdir):
+    def test_write_read_legacy_style(self,default,tmpdir):
-        with open(tmpdir/'new_style.txt','w') as f:
+        with open(tmpdir/'legacy.txt','w') as f:
-            default.to_file(f,new_style=True)
+            default.save(f,legacy=True)
-        with open(tmpdir/'new_style.txt') as f:
+        with open(tmpdir/'legacy.txt') as f:
-            new = Table.from_ASCII(f)
+            new = Table.load(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_invalid_format(self,default,tmpdir):
         with pytest.raises(TypeError):
-            default.to_file(tmpdir/'shouldnotbethere.txt',format='invalid')
+            default.save(tmpdir/'shouldnotbethere.txt',format='invalid')
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_read_ang(self,reference_dir,mode):
         if   mode == 'path':
-            new = Table.from_ang(reference_dir/'simple.ang')
+            new = Table.load_ang(reference_dir/'simple.ang')
         elif mode == 'str':
-            new = Table.from_ang(str(reference_dir/'simple.ang'))
+            new = Table.load_ang(str(reference_dir/'simple.ang'))
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     def test_read_ang_file(self,reference_dir):
         f = open(reference_dir/'simple.ang')
-        new = Table.from_ang(f)
+        new = Table.load_ang(f)
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     @pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
     def test_read_strange(self,reference_dir,fname):
         with open(reference_dir/fname) as f:
-            Table.from_ASCII(f)
+            Table.load(f)
 
     def test_set(self,default):
         d = default.set('F',np.zeros((5,3,3)),'set to zero').get('F')
@@ -166,7 +166,7 @@ class TestTable:
         x = np.random.random((5,12))
         t = Table(x,{'F':(3,3),'v':(3,)},['random test data'])
         unsort = t.get('4_F')
-        sort = t.sort_by('4_F').get('4_F')
+        sort   = t.sort_by('4_F').get('4_F')
         assert np.all(np.sort(unsort,0)==sort)
 
     def test_sort_revert(self):
@@ -179,6 +179,6 @@ class TestTable:
         t = Table(np.array([[0,1,],[2,1,]]),
                   {'v':(2,)},
                   ['test data'])\
-                  .add('s',np.array(['b','a']))\
+            .add('s',np.array(['b','a']))\
-                  .sort_by('s')
+            .sort_by('s')
         assert np.all(t.get('1_v') == np.array([2,0]).reshape(2,1))

python/tests/test_VTK.py

@@ -32,22 +32,22 @@ class TestVTK:
         origin = np.random.random(3)
         v = VTK.from_rectilinearGrid(grid,size,origin)
         string = v.__repr__()
-        v.to_file(tmp_path/'rectilinearGrid',False)
+        v.save(tmp_path/'rectilinearGrid',False)
-        vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
+        vtr = VTK.load(tmp_path/'rectilinearGrid.vtr')
         with open(tmp_path/'rectilinearGrid.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
+        vtk = VTK.load(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
         assert(string == vtr.__repr__() == vtk.__repr__())
 
     def test_polyData(self,tmp_path):
         points = np.random.rand(100,3)
         v = VTK.from_polyData(points)
         string = v.__repr__()
-        v.to_file(tmp_path/'polyData',False)
+        v.save(tmp_path/'polyData',False)
-        vtp = VTK.from_file(tmp_path/'polyData.vtp')
+        vtp = VTK.load(tmp_path/'polyData.vtp')
         with open(tmp_path/'polyData.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'polyData.vtk','polyData')
+        vtk = VTK.load(tmp_path/'polyData.vtk','polyData')
         assert(string == vtp.__repr__() == vtk.__repr__())
 
     @pytest.mark.parametrize('cell_type,n',[
@@ -62,11 +62,11 @@ class TestVTK:
         connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
         v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
         string = v.__repr__()
-        v.to_file(tmp_path/'unstructuredGrid',False)
+        v.save(tmp_path/'unstructuredGrid',False)
-        vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
+        vtu = VTK.load(tmp_path/'unstructuredGrid.vtu')
         with open(tmp_path/'unstructuredGrid.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
+        vtk = VTK.load(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
         assert(string == vtu.__repr__() == vtk.__repr__())
 
 
@@ -75,8 +75,8 @@ class TestVTK:
         v = VTK.from_polyData(points)
         fname_s = tmp_path/'single.vtp'
         fname_p = tmp_path/'parallel.vtp'
-        v.to_file(fname_s,False)
+        v.save(fname_s,False)
-        v.to_file(fname_p,True)
+        v.save(fname_p,True)
         for i in range(10):
             if os.path.isfile(fname_p) and filecmp.cmp(fname_s,fname_p):
                 assert(True)
@@ -90,11 +90,11 @@ class TestVTK:
                                                   ('this_file_does_not_exist.vtx', None)])
     def test_invalid_dataset_type(self,name,dataset_type):
         with pytest.raises(TypeError):
-            VTK.from_file(name,dataset_type)
+            VTK.load(name,dataset_type)
 
     def test_invalid_extension_write(self,default):
         with pytest.raises(ValueError):
-            default.to_file('default.txt')
+            default.save('default.txt')
 
     def test_invalid_get(self,default):
         with pytest.raises(ValueError):
@@ -115,8 +115,8 @@ class TestVTK:
 
     def test_comments(self,tmp_path,default):
         default.add_comments(['this is a comment'])
-        default.to_file(tmp_path/'with_comments',parallel=False)
+        default.save(tmp_path/'with_comments',parallel=False)
-        new = VTK.from_file(tmp_path/'with_comments.vtr')
+        new = VTK.load(tmp_path/'with_comments.vtr')
         assert new.get_comments() == ['this is a comment']
 
     def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
@@ -124,9 +124,9 @@ class TestVTK:
         polyData = VTK.from_polyData(points)
         polyData.add(points,'coordinates')
         if update:
-             polyData.to_file(reference_dir/'polyData')
+             polyData.save(reference_dir/'polyData')
         else:
-             reference = VTK.from_file(reference_dir/'polyData.vtp')
+             reference = VTK.load(reference_dir/'polyData.vtp')
              assert polyData.__repr__() == reference.__repr__() and \
                     np.allclose(polyData.get('coordinates'),points)
 
@@ -139,8 +139,8 @@ class TestVTK:
         rectilinearGrid.add(c,'cell')
         rectilinearGrid.add(n,'node')
         if update:
-             rectilinearGrid.to_file(reference_dir/'rectilinearGrid')
+             rectilinearGrid.save(reference_dir/'rectilinearGrid')
         else:
-             reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
+             reference = VTK.load(reference_dir/'rectilinearGrid.vtr')
              assert rectilinearGrid.__repr__() == reference.__repr__() and \
                     np.allclose(rectilinearGrid.get('cell'),c)

python/tests/test_util.py

@@ -18,8 +18,8 @@ class TestUtil:
 
     @pytest.mark.parametrize('input,output',
                             [
-                            ([2,0],[1,0]),
+                            ([0,-2],[0,-1]),
-                            ([0.5,0.5],[1,1]),
+                            ([-0.5,0.5],[-1,1]),
                             ([1./2.,1./3.],[3,2]),
                             ([2./3.,1./2.,1./3.],[4,3,2]),
                             ])
@@ -30,4 +30,4 @@ class TestUtil:
 
     def test_lackofprecision(self):
         with pytest.raises(ValueError):
-            util.scale_to_coprime(np.array([1/3333,1,1]))
+            util.scale_to_coprime(np.array([1/333.333,1,1]))