checked Unix command piping conformity -- seems to now work:
seeds_fromRandom | geom_fromVoronoiTessellation | geom_grainGrowth | geom_unpack | geom_pack However, grainGrowth functionality seems broken...
This commit is contained in:
Philip Eisenlohr
parent
f66c0727d0
commit
ccb950f3d8
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@ -15,14 +15,15 @@ class ASCIItable():
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def __init__(self,
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fileIn = sys.stdin,
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fileOut = sys.stdout,
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buffered = True,
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labels = True):
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buffered = False, # flush writes
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labels = True): # assume table has labels
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self.__IO__ = {'in': fileIn,
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'out':fileOut,
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'output':[],
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'buffered':buffered,
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'labels':labels,
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'validReadSize': 0,
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'readBuffer': [], # buffer to hold non-advancing reads
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'dataStart': 0,
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}
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self.info = []
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@ -100,7 +101,8 @@ class ASCIItable():
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pass
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if self.__IO__['validReadSize'] == 0: # in case no valid data length is known
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self.__IO__['validReadSize'] = len(self.__IO__['in'].readline().split()) # assume constant data width from first line
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self.data_read(advance = False)
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self.__IO__['validReadSize'] = len(self.data) # assume constant data width from first line
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# ------------------------------------------------------------------
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def head_write(self):
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@ -123,7 +125,7 @@ class ASCIItable():
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def labels_append(self,
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what):
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'''
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add item or list to existing set of labels
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add item or list to existing set of labels (and switch on labeling)
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'''
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if not isinstance(what, (str, unicode)):
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try:
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@ -137,6 +139,9 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def labels_clear(self):
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'''
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delete existing labels and switch to no labeling
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'''
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self.labels = []
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self.__IO__['labels'] = False
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@ -183,6 +188,9 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def info_clear(self):
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'''
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delete any info block
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'''
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self.info = []
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# ------------------------------------------------------------------
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@ -190,13 +198,28 @@ class ASCIItable():
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self.__IO__['in'].seek(self.__IO__['dataStart'])
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# ------------------------------------------------------------------
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def data_skipLines(self,lines):
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for i in range(lines):
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self.__IO__['in'].readline()
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def data_skipLines(self,count):
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'''
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wind forward by count number of lines
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'''
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for i in xrange(count):
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alive = self.data_read()
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return alive
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# ------------------------------------------------------------------
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def data_read(self):
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line = self.__IO__['in'].readline() # get next data row
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def data_read(self,advance = True):
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'''
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read next line (possibly buffered) and parse it into data array
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'''
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if len(self.__IO__['readBuffer']) > 0:
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line = self.__IO__['readBuffer'].pop(0) # take buffered content
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else:
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line = self.__IO__['in'].readline() # get next data row from file
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if not advance:
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self.__IO__['readBuffer'].append(line) # keep line just read in buffer
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if self.__IO__['labels']:
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items = line.split()[:self.__IO__['validReadSize']] # use up to valid size (label count)
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self.data = items if len(items) == self.__IO__['validReadSize'] else [] # take if correct number of entries
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@ -207,8 +230,11 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_readLine(self,line):
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'''
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seek beginning of data and wind forward to selected line
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'''
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self.__IO__['in'].seek(self.__IO__['dataStart'])
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for i in range(line-1):
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for i in xrange(line-1):
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self.__IO__['in'].readline()
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self.data_read()
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@ -223,15 +249,21 @@ class ASCIItable():
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if labels == []: indices = range(self.__IO__['validReadSize']) # use all columns
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else: indices = self.labels_index(labels) # use specified columns
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self.data_rewind()
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try:
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self.data_rewind() # try to wind back to start of data
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except:
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pass # assume/hope we are at data start already...
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self.data = numpy.loadtxt(self.__IO__['in'], usecols=indices)
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if len(self.data.shape) < 2: # single column
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if len(self.data.shape) < 2: # single column
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self.data = self.data.reshape(self.data.shape[0],1)
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return self.data.shape
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# ------------------------------------------------------------------
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def data_write(self, delimiter='\t'):
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if len(self.data) == 0: return
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def data_write(self,delimiter = '\t'):
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'''
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write current data array and report alive output back
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'''
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if len(self.data) == 0: return True
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if isinstance(self.data[0],list):
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return self.output_write([delimiter.join(map(str,items)) for items in self.data])
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@ -239,12 +271,12 @@ class ASCIItable():
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return self.output_write(delimiter.join(map(str,self.data)))
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# ------------------------------------------------------------------
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def data_writeArray(self,format='%g',delimiter = '\t'):
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def data_writeArray(self,format = '%g',delimiter = '\t'):
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import numpy
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'''
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write whole numpy array data
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'''
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return numpy.savetxt(self.__IO__['out'], self.data, fmt=format, delimiter=delimiter)
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return numpy.savetxt(self.__IO__['out'],self.data,fmt = format,delimiter = delimiter)
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# ------------------------------------------------------------------
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def data_append(self,
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@ -119,25 +119,25 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'])
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theTable = damask.ASCIItable(file['input'],file['output'],buffered = False)
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theTable.head_read()
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labels = ['x','y','z']
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index = 0
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if numpy.all(theTable.labels_index(['phi1','Phi','phi2'])) != -1:
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hasEulers = True
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hasEulers = numpy.all(theTable.labels_index(['phi1','Phi','phi2'])) != -1
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hasGrains = theTable.labels_index('microstructure') != -1
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if hasEulers:
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labels += ['phi1','Phi','phi2']
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index += 3
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else:
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hasEulers = False
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eulerCol = index
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if theTable.labels_index('microstructure') != -1:
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hasGrains = True
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if hasGrains:
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labels += ['microstructure']
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index += 1
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else:
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hasGrains = False
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grainCol = index
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theTable.data_readArray(labels)
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@ -257,7 +257,6 @@ for file in files:
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = 1+int(math.log10(newInfo['microstructures']))
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@ -90,7 +90,7 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
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theTable.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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@ -137,8 +137,8 @@ for file in files:
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(numpy.prod([2 if i == 1 else i for i in info['grid']]),'i') # 2D structures do not work
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i = 0
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theTable.data_rewind()
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while theTable.data_read():
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while theTable.data_read(): # read next data line of ASCII table
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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@ -179,15 +179,15 @@ for file in files:
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for i in range(3):
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for j in range(3):
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for k in range(3):
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boundary = numpy.maximum(boundary,\
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interfacialEnergy(microstructure,microExt[i:microstructure.shape[0]+i,\
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j:microstructure.shape[1]+j,\
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k:microstructure.shape[2]+k]))
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index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances=False,return_indices=True)
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boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary!=0.,\
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structure=struc,\
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iterations=2*options.d-1),\
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boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),\
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boundary = numpy.maximum(boundary,
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interfacialEnergy(microstructure,microExt[i:microstructure.shape[0]+i,
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j:microstructure.shape[1]+j,
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k:microstructure.shape[2]+k]))
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index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances = False,return_indices = True)
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boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary != 0.,
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structure = struc,
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iterations = 2*options.d-1),
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boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),
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0.))*gauss)
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index = ndimage.morphology.distance_transform_edt(boundary >= 0.5,return_distances=False,return_indices=True)
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microstructure = microstructure[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape)
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@ -211,7 +211,6 @@ for file in files:
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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@ -76,7 +76,7 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
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theTable.head_read()
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@ -130,7 +130,6 @@ for file in files:
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"microstructures\t%i"%(info['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write packed microstructure information -----------------------------------------------------
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type = ''
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@ -138,8 +137,8 @@ for file in files:
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start = -1
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reps = 0
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theTable.data_rewind()
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while theTable.data_read():
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outputAlive = True
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while outputAlive and theTable.data_read(): # read next data line of ASCII table
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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@ -155,28 +154,36 @@ for file in files:
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type = 'of'
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reps += 1
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else:
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theTable.data = {
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'' : [],
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'.' : [str(former)],
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'to': ['%i to %i'%(former-reps+1,former)],
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'of': ['%i of %i'%(reps,former)],
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}[type]
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theTable.data_write(delimiter=' ')
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if type == '':
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theTable.data = []
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elif type == '.':
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theTable.data = [str(former)]
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elif type == 'to':
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theTable.data = ['%i to %i'%(former-reps+1,former)]
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elif type == 'of':
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theTable.data = ['%i of %i'%(reps,former)]
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outputAlive = theTable.data_write(delimiter = ' ') # output processed line
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type = '.'
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start = current
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reps = 1
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former = current
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theTable.data = {
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'.' : [str(former)],
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'to': ['%i to %i'%(former-reps+1,former)],
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'of': ['%i of %i'%(reps,former)],
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}[type]
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theTable.data_write(delimiter=' ')
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theTable.output_flush()
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outputAlive = theTable.data_write(delimiter = ' ') # output processed line
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and theTable.output_flush() # just in case of buffered ASCII table
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['input'].close()
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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file['input'].close() # close input ASCII table
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file['output'].close() # close input ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -81,7 +81,7 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
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theTable.head_read()
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@ -126,8 +126,8 @@ for file in files:
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i')
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i = 0
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theTable.data_rewind()
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while theTable.data_read():
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while theTable.data_read(): # read next data line of ASCII table
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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@ -151,7 +151,6 @@ for file in files:
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"microstructures\t%i"%(info['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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@ -163,6 +162,6 @@ for file in files:
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['input'].close()
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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file['input'].close() # close input ASCII table
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file['output'].close() # close input ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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