streamlined geom-info reporting; added --float option to some scripts; hardened against NaN; "microstructures" now reports uniques not max

processing/pre/geom_canvas.py

@@ -35,7 +35,7 @@ parser.add_option('-f',
                   type = 'float', metavar = 'float',
                   help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
 parser.add_option('--float',
-                  dest = 'real',
+                  dest = 'float',
                   action = 'store_true',
                   help = 'use float input')
 parser.add_option('--blank',
@@ -45,13 +45,13 @@ parser.add_option('--blank',
 
 parser.set_defaults(grid = ['0','0','0'],
                     offset = (0,0,0),
-                    fill = 0,
+                    fill = 0.0,
-                    real = False,
+                    float = False,
                    )
 
 (options, filenames) = parser.parse_args()
 
-datatype = 'f' if options.real else 'i'
+datatype = 'f' if options.float else 'i'
 options.grid = ['1','1','1'] if options.blank and options.grid == ['0','0','0'] else options.grid
 options.fill = 1 if options.blank and options.fill == 0 else options.fill
 
@@ -107,7 +107,7 @@ for name in filenames:
   newInfo['grid'] = np.where(newInfo['grid'] > 0, newInfo['grid'],info['grid'])
 
   microstructure_cropped = np.zeros(newInfo['grid'],datatype)
-  microstructure_cropped.fill(options.fill if options.real or options.fill > 0 else microstructure.max()+1)
+  microstructure_cropped.fill(options.fill if options.float or options.fill > 0 else np.nanmax(microstructure)+1)
   
   if not options.blank:
     xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+newInfo['grid'][0],info['grid'][0]))
@@ -130,7 +130,7 @@ for name in filenames:
   newInfo['size']   = info['size']/info['grid']*newInfo['grid'] if np.all(info['grid'] > 0) else newInfo['grid']
   newInfo['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \
                               else newInfo['size']/newInfo['grid'])*options.offset
-  newInfo['microstructures'] = microstructure_cropped.max()
+  newInfo['microstructures'] = len(np.unique(microstructure_cropped))
 
 # --- report ---------------------------------------------------------------------------------------
 
@@ -172,7 +172,7 @@ for name in filenames:
 
 # --- write microstructure information ------------------------------------------------------------
 
-  format = '%g' if options.real else '%{}i'.format(int(math.floor(math.log10(microstructure_cropped.max())+1)))
+  format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure_cropped))+1)))
   table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
   table.data_writeArray(format,delimiter=' ')
     

processing/pre/geom_clean.py

@@ -50,13 +50,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -73,7 +67,7 @@ for name in filenames:
 # --- do work ------------------------------------------------------------------------------------
 
   microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_')
-  newInfo = {'microstructures': microstructure.max()}
+  newInfo = {'microstructures': len(np.unique(microstructure))}
 
 # --- report ---------------------------------------------------------------------------------------
   if (    newInfo['microstructures'] != info['microstructures']):
@@ -91,9 +85,9 @@ for name in filenames:
 
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
   table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+  table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
 
 # --- output finalization --------------------------------------------------------------------------
 

processing/pre/geom_fromMinimalSurface.py

@@ -90,12 +90,7 @@ for name in filenames:
 
 #--- report ---------------------------------------------------------------------------------------
 
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
+  damask.util.report_geom(info)
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')

processing/pre/geom_fromTable.py

@@ -192,12 +192,7 @@ for name in filenames:
           'homogenization':  options.homogenization,
          }
 
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
+  damask.util.report_geom(info)
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
     
 # --- write header ---------------------------------------------------------------------------------
 
@@ -230,7 +225,7 @@ for name in filenames:
 # --- write microstructure information ------------------------------------------------------------
 
   table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
+  table.data_writeArray('%{}i'.format(formatwidth),delimiter=' ')
   
 #--- output finalization --------------------------------------------------------------------------
 

processing/pre/geom_grainGrowth.py

@@ -69,13 +69,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -200,8 +194,7 @@ for name in filenames:
         newID += 1
         microstructure = np.where(microstructure == microstructureID, newID, microstructure)
 
-  newInfo = {'microstructures': 0,}
+  newInfo = {'microstructures': len(np.unique(microstructure)),}
-  newInfo['microstructures'] = microstructure.max()
 
 # --- report --------------------------------------------------------------------------------------
 
@@ -226,7 +219,7 @@ for name in filenames:
 
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
   table.data = microstructure[::1 if info['grid'][0]>1 else 2,
                               ::1 if info['grid'][1]>1 else 2,
                               ::1 if info['grid'][2]>1 else 2,].\

processing/pre/geom_mirror.py

@@ -23,6 +23,13 @@ parser.add_option('-d','--direction',
                   dest = 'directions',
                   action = 'extend', metavar = '<string LIST>',
                   help = "directions in which to mirror {'x','y','z'}")
+parser.add_option('--float',
+                  dest = 'float',
+                  action = 'store_true',
+                  help = 'use float input')
+
+parser.set_defaults(float = False,
+                   )
 
 (options, filenames) = parser.parse_args()
 
@@ -32,6 +39,8 @@ if not set(options.directions).issubset(validDirections):
   invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
   parser.error('invalid directions {}. '.format(*invalidDirections))
 
+datatype = 'f' if options.float else 'i'
+
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
@@ -39,7 +48,8 @@ if filenames == []: filenames = [None]
 for name in filenames:
   try:
     table = damask.ASCIItable(name = name,
-                              buffered = False, labeled = False)
+                              buffered = False,
+                              labeled = False)
   except: continue
   damask.util.report(scriptName,name)
 
@@ -47,13 +57,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-                     'homogenization:  %i'%info['homogenization'],
-                     'microstructures: %i'%info['microstructures'],
-                    ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -65,7 +69,7 @@ for name in filenames:
 
 # --- read data ------------------------------------------------------------------------------------
 
-  microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F')          # read microstructure
+  microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F')  # read microstructure
 
   if 'z' in options.directions:
     microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
@@ -107,9 +111,9 @@ for name in filenames:
 
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
   table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+  table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
 
 # --- output finalization --------------------------------------------------------------------------
 

processing/pre/geom_pack.py

@@ -35,13 +35,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
  
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')

processing/pre/geom_renumber.py

@@ -35,13 +35,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -93,7 +87,7 @@ for name in filenames:
 
 # --- write microstructure information -----------------------------------------------------------
 
-  format = '%{}i'.format(int(math.floor(math.log10(newInfo['microstructures'])+1)))
+  format = '%{}i'.format(int(math.floor(math.log10(np.nanmax(renumbered))+1)))
   table.data = renumbered.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
   table.data_writeArray(format,delimiter = ' ')
 

processing/pre/geom_rescale.py

@@ -31,14 +31,21 @@ parser.add_option('-r', '--renumber',
                   dest = 'renumber',
                   action = 'store_true',
                   help = 'renumber microstructure indices from 1..N [%default]')
+parser.add_option('--float',
+                  dest = 'float',
+                  action = 'store_true',
+                  help = 'use float input')
 
 parser.set_defaults(renumber = False,
                     grid = ['0','0','0'],
                     size  = ['0.0','0.0','0.0'],
+                    float = False,
                    )
 
 (options, filenames) = parser.parse_args()
 
+datatype = 'f' if options.float else 'i'
+
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
@@ -46,7 +53,8 @@ if filenames == []: filenames = [None]
 for name in filenames:
   try:
     table = damask.ASCIItable(name = name,
-                              buffered = False, labeled = False)
+                              buffered = False,
+                              labeled = False)
   except: continue
   damask.util.report(scriptName,name)
 
@@ -54,13 +62,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -72,7 +74,7 @@ for name in filenames:
 
 # --- read data ------------------------------------------------------------------------------------
 
-  microstructure = table.microstructure_read(info['grid'])                                          # read microstructure
+  microstructure = table.microstructure_read(info['grid'],datatype)                                   # read microstructure
 
 # --- do work ------------------------------------------------------------------------------------
  
@@ -113,7 +115,7 @@ for name in filenames:
         newID += 1
         microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape)
 
-  newInfo['microstructures'] = microstructure.max()
+  newInfo['microstructures'] = len(np.unique(microstructure))
 
 # --- report ---------------------------------------------------------------------------------------
 
@@ -152,9 +154,9 @@ for name in filenames:
   
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
   table.data = microstructure.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+  table.data_writeArray(format,delimiter=' ')
     
 # --- output finalization --------------------------------------------------------------------------
 

processing/pre/geom_rotate.py

@@ -43,9 +43,15 @@ parser.add_option('-f', '--fill',
                   dest = 'fill',
                   type = 'int', metavar = 'int',
                   help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]')
+parser.add_option('--float',
+                  dest = 'float',
+                  action = 'store_true',
+                  help = 'use float input')
 
 parser.set_defaults(degrees = False,
-                    fill = 0)
+                    fill = 0,
+                    float = False,
+                   )
 
 (options, filenames) = parser.parse_args()
 
@@ -61,6 +67,8 @@ if options.matrix is not None:
 if options.eulers is not None:
   eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
 
+datatype = 'f' if options.float else 'i'
+
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
@@ -77,13 +85,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -95,9 +97,9 @@ for name in filenames:
 
 # --- read data ------------------------------------------------------------------------------------
 
-  microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F')                    # read microstructure
+  microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F')                  # read microstructure
 
-  newGrainID = options.fill if options.fill != 0 else microstructure.max()+1
+  newGrainID = options.fill if options.fill != 0 else np.nanmax(microstructure)+1
   microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
   microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X
   microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
@@ -107,19 +109,18 @@ for name in filenames:
   newInfo = {
              'size':   microstructure.shape*info['size']/info['grid'],
              'grid':   microstructure.shape,
-             'microstructures': microstructure.max(),
+             'microstructures': len(np.unique(microstructure)),
             }
 
-
 # --- report ---------------------------------------------------------------------------------------
 
   remarks = []
   if (any(newInfo['grid']            != info['grid'])):
-    remarks.append('--> grid    a b c:  %s'%(' x '.join(map(str,newInfo['grid']))))
+    remarks.append('--> grid    a b c:  {}'.format(' x '.join(map(str,newInfo['grid']))))
   if (any(newInfo['size']            != info['size'])):
-    remarks.append('--> size    x y z:  %s'%(' x '.join(map(str,newInfo['size']))))
+    remarks.append('--> size    x y z:  {}'.format(' x '.join(map(str,newInfo['size']))))
   if (    newInfo['microstructures'] != info['microstructures']): 
-    remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+    remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
   if remarks != []: damask.util.croak(remarks)
 
 # --- write header ---------------------------------------------------------------------------------
@@ -138,9 +139,9 @@ for name in filenames:
 
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
   table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+  table.data_writeArray(format,delimiter=' ')
 
 # --- output finalization --------------------------------------------------------------------------
 

processing/pre/geom_toTable.py

@@ -20,15 +20,15 @@ Translate geom description into ASCIItable containing position and microstructur
 """, version = scriptID)
 
 parser.add_option('--float',
-                  dest = 'real',
+                  dest = 'float',
                   action = 'store_true',
                   help = 'use float input')
 
-parser.set_defaults(real = False,
+parser.set_defaults(float = False,
                    )
 (options, filenames) = parser.parse_args()
 
-datatype = 'f' if options.real else 'i'
+datatype = 'f' if options.float else 'i'
 
 # --- loop over input files -------------------------------------------------------------------------
 
@@ -47,13 +47,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
-                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: {}'.format(info['microstructures']),
-                    ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')

processing/pre/geom_translate.py

@@ -31,19 +31,19 @@ parser.add_option('-s', '--substitute',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'substitutions of microstructure indices from,to,from,to,...')
 parser.add_option('--float',
-                  dest = 'real',
+                  dest = 'float',
                   action = 'store_true',
                   help = 'use float input')
 
 parser.set_defaults(origin = (0.0,0.0,0.0),
                     microstructure = 0,
                     substitute = [],
-                    real = False,
+                    float = False,
                    )
 
 (options, filenames) = parser.parse_args()
 
-datatype = 'f' if options.real else 'i'
+datatype = 'f' if options.float else 'i'
 
 sub = {}
 for i in range(len(options.substitute)//2):                                                         # split substitution list into "from" -> "to"
@@ -64,13 +64,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -92,7 +86,7 @@ for name in filenames:
             }
 
   substituted = np.copy(microstructure)
-  for k, v in sub.items(): substituted[microstructure==k] = v                                   # substitute microstructure indices
+  for k, v in sub.items(): substituted[microstructure==k] = v                                       # substitute microstructure indices
 
   substituted += options.microstructure                                                             # shift microstructure indices
 
@@ -103,9 +97,9 @@ for name in filenames:
 
   remarks = []
   if (any(newInfo['origin']          != info['origin'])):
-    remarks.append('--> origin   x y z:  %s'%(' : '.join(map(str,newInfo['origin']))))
+    remarks.append('--> origin   x y z:  {}'.format(' : '.join(map(str,newInfo['origin']))))
   if (    newInfo['microstructures'] != info['microstructures']):
-    remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+    remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
   if remarks != []: damask.util.croak(remarks)
 
 # --- write header -------------------------------------------------------------------------------
@@ -124,7 +118,7 @@ for name in filenames:
 
 # --- write microstructure information -----------------------------------------------------------
 
-  format = '%g' if options.real else '%{}i'.format(int(math.floor(math.log10(microstructure.max())+1)))
+  format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(substituted))+1)))
   table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
   table.data_writeArray(format,delimiter = ' ')
 

processing/pre/geom_unpack.py

@@ -43,13 +43,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')

processing/pre/geom_vicinityOffset.py

@@ -73,13 +73,7 @@ for name in filenames:
 
   table.head_read()
   info,extra_header = table.head_getGeom()
-  
+  damask.util.report_geom(info)
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
-               'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
-               'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
-               'homogenization:  %i'%info['homogenization'],
-               'microstructures: %i'%info['microstructures'],
-              ])
 
   errors = []
   if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
@@ -108,7 +102,7 @@ for name in filenames:
                                                            extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
                             microstructure + options.offset,microstructure)
 
-  newInfo['microstructures'] = microstructure.max()
+  newInfo['microstructures'] = len(np.unique(microstructure))
 
 # --- report ---------------------------------------------------------------------------------------
 
@@ -131,9 +125,9 @@ for name in filenames:
   
 # --- write microstructure information ------------------------------------------------------------
 
-  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
   table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+  table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
     
 # --- output finalization --------------------------------------------------------------------------