functionality now provided by more general “geom_fromImage”

2015-08-07 22:16:40 +00:00 · 2015-08-07 22:16:40 +00:00 · bbeb210708
parent 9729c03c00
commit bbeb210708
1 changed files with 0 additions and 99 deletions
--- a/processing/pre/geom_fromTIFF.py
+++ b/processing/pre/geom_fromTIFF.py
@ -1,99 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: UTF-8 no BOM -*-
-
-import os,sys,math,string
-import numpy as np
-from optparse import OptionParser
-from PIL import Image
-import damask
-
-scriptID   = string.replace('$Id$','\n','\\n')
-scriptName = os.path.splitext(scriptID.split()[1])[0]
-
-#--------------------------------------------------------------------------------------------------
-#                                MAIN
-#--------------------------------------------------------------------------------------------------
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
-
-Generate geometry description and from stacked 8bit tiff images. No orientation info is used.
-Microstructure index is based on gray scale value (1...256).
-
-""", version = scriptID)
-
-parser.add_option('--homogenization',      dest='homogenization', type='int', metavar = 'int',
-                  help='homogenization index for <microstructure> configuration [%default]')
-              
-parser.set_defaults(homogenization = 1)
-
-(options,filenames) = parser.parse_args()
-
-
-#--- setup file handles ---------------------------------------------------------------------------
-files = []
-for name in filenames:
-  if os.path.exists(name):
-    files.append({'name':name,
-                  'input':open(name),
-                  'output':open(name+'_tmp','w'),
-                  'croak':sys.stdout,
-                  })
-
-#--- loop over input files ------------------------------------------------------------------------
-for file in files:
-  file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
-
-  info = {
-          'grid':   np.ones (3,'i'),
-          'size':   np.zeros(3,'d'),
-          'origin': np.zeros(3,'d'),
-          'microstructures': 0,
-          'homogenization':  options.homogenization,
-         }
-
-  ImageFile=Image.open(file['input'])
-  i=0
-  a=[]
-  while True:
-    try:
-      ImageFile.seek(i)
-      a.append(np.array(ImageFile.transpose(Image.FLIP_TOP_BOTTOM)))
-      i+=1
-    except EOFError:
-      break
-# http://docs.scipy.org/doc/scipy/reference/ndimage.html
-# http://scipy-lectures.github.io/advanced/image_processing/
-  imarray=np.asarray(a)
-  info['grid'] = np.array(imarray.shape)[::-1]
-  info['size'] = np.array(imarray.shape,'d')[::-1]
-  info['microstructures']=len(np.unique(imarray))
-#--- report ---------------------------------------------------------------------------------------
-  file['croak'].write('grid     a b c:  %s\n'%(' x '.join(map(str,info['grid']))) +
-                      'size     x y z:  %s\n'%(' x '.join(map(str,info['size']))) +
-                      'origin   x y z:  %s\n'%(' : '.join(map(str,info['origin']))) +
-                      'homogenization:  %i\n'%info['homogenization'] +
-                      'microstructures: %i\n\n'%info['microstructures'])
-
-  if np.any(info['grid'] < 1):
-    file['croak'].write('invalid grid a b c.\n')
-    continue
-  if np.any(info['size'] <= 0.0):
-    file['croak'].write('invalid size x y z.\n')
-    continue
-
-
-#--- write data -----------------------------------------------------------------------------------
-  header = [' '.join([scriptID] + sys.argv[1:]),
-            "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2]),
-            "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2]),
-            "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2]),
-            "microstructures\t%i"%info['microstructures'],
-            "homogenization\t%i"%info['homogenization'],
-            ]
-  file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n')
-  np.savetxt(file['output'],imarray.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]),
-                            fmt='%0'+str(1+int(math.log10(np.amax(imarray))))+'d')
-  
-#--- output finalization -------------------------------------------------------------------------- 
-  if file['name'] != 'STDIN':
-    file['output'].close()
-    os.rename(file['name']+'_tmp', os.path.splitext(file['name'])[0] +'.geom')