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DAMASK_EICMD
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use 4 space indentation

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chen 2016-10-14 12:06:09 -04:00
parent 87b857d307
commit 1f01dce862
1 changed files with 49 additions and 44 deletions
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93
processing/post/ascii2hdf5.py
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@ -33,44 +33,44 @@ scriptID = ' '.join([scriptName,damask.version])
# ----- helper function ----- # # ----- helper function ----- #
def get_rectMshVectors(xyz_array, posNum): def get_rectMshVectors(xyz_array, posNum):
"""take in a xyz array from rectangular mesh and figure out Vx, Vy, Vz""" """take in a xyz array from rectangular mesh and figure out Vx, Vy, Vz"""
# need some improvement, and only works for rectangular grid # need some improvement, and only works for rectangular grid
v = sorted(list(set(xyz_array[:, posNum]))) v = sorted(list(set(xyz_array[:, posNum])))
v_interval = (v[2]+v[1])/2.0 - (v[1]+v[0])/2.0 v_interval = (v[2]+v[1])/2.0 - (v[1]+v[0])/2.0
v_start = (v[1]+v[0])/2.0 - v_interval v_start = (v[1]+v[0])/2.0 - v_interval
v_end = (v[-1]+v[-2])/2.0 + v_interval v_end = (v[-1]+v[-2])/2.0 + v_interval
V = np.linspace(v_start, v_end, len(v)+1) V = np.linspace(v_start, v_end, len(v)+1)
return V return V
# ----- MAIN ---- # # ----- MAIN ---- #
desp_msg = "Convert DAMASK ascii table to HDF5 file" desp_msg = "Convert DAMASK ascii table to HDF5 file"
parser = OptionParser(option_class=damask.extendableOption, parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]', usage='%prog options [file[s]]',
description = desp_msg, description = desp_msg,
version = scriptID) version = scriptID)
parser.add_option('-D', '--DefinitionFile', parser.add_option('-D', '--DefinitionFile',
dest = 'storage definition file', dest = 'storage definition file',
type = 'string', type = 'string',
metavar = 'string', metavar = 'string',
help = 'definition file for H5 data storage') help = 'definition file for H5 data storage')
parser.add_option('-p', parser.add_option('-p',
'--pos', '--position', '--pos', '--position',
dest = 'pos', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.set_defaults(DefinitionFile='default', parser.set_defaults(DefinitionFile='default',
pos='pos') pos='pos')
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
filename = filenames[0] filename = filenames[0]
if options.DefinitionFile == 'default': if options.DefinitionFile == 'default':
defFile = None defFile = None
else: else:
defFile = options.DefinitionFile defFile = options.DefinitionFile
# ----- read in data using DAMASK ASCII table class ----- # # ----- read in data using DAMASK ASCII table class ----- #
asciiTable = damask.ASCIItable(name=filename, buffered=False) asciiTable = damask.ASCIItable(name=filename, buffered=False)
@ -96,9 +96,9 @@ mshGridDim = [len(Vx)-1, len(Vy)-1, len(Vz)-1]
# force remove existing HDF5 file # force remove existing HDF5 file
h5fName = filename.replace(".txt", ".h5") h5fName = filename.replace(".txt", ".h5")
try: try:
os.remove(h5fName) os.remove(h5fName)
except OSError: except OSError:
pass pass
h5f = damask.H5Table(h5fName, h5f = damask.H5Table(h5fName,
new_file=True, new_file=True,
dsXMLFile=defFile) dsXMLFile=defFile)
@ -112,24 +112,29 @@ h5f.add_data("Vz", Vz)
# add the rest of data from table # add the rest of data from table
labelsProcessed = ['inc'] labelsProcessed = ['inc']
for fi in xrange(len(labels)): for fi in xrange(len(labels)):
featureName = labels[fi] featureName = labels[fi]
# remove trouble maker "("" and ")" from label/feature name # remove trouble maker "("" and ")" from label/feature name
if "(" in featureName: featureName = featureName.replace("(", "") if "(" in featureName:
if ")" in featureName: featureName = featureName.replace(")", "") featureName = featureName.replace("(", "")
# skip increment and duplicated columns in the ASCII table if ")" in featureName:
if featureName in labelsProcessed: continue featureName = featureName.replace(")", "")
# skip increment and duplicated columns in the ASCII table
if featureName in labelsProcessed:
continue
featureIdx = labels_idx[fi] featureIdx = labels_idx[fi]
featureDim = featuresDim[fi] featureDim = featuresDim[fi]
# grab the data hook # grab the data hook
dataset = fullTable[:, featureIdx:featureIdx+featureDim] dataset = fullTable[:, featureIdx:featureIdx+featureDim]
# mapping 2D data onto a 3D rectangular mesh to get 4D data # mapping 2D data onto a 3D rectangular mesh to get 4D data
# WARNING: In paraview, the data for a recmesh is mapped as: # WARNING: In paraview, the data for a recmesh is mapped as:
# --> len(z), len(y), len(x), size(data) # --> len(z), len(y), len(x), size(data)
# dataset = dataset.reshape((mshGridDim[0], mshGridDim[1], mshGridDim[2], # dataset = dataset.reshape((mshGridDim[0],
# dataset.shape[1])) # mshGridDim[1],
# write out data # mshGridDim[2],
print "adding {}...".format(featureName) # dataset.shape[1]))
h5f.add_data(featureName, dataset) # write out data
# write down the processed label print "adding {}...".format(featureName)
labelsProcessed.append(featureName) h5f.add_data(featureName, dataset)
# write down the processed label
labelsProcessed.append(featureName)