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DAMASK_EICMD
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now more flexible, works for synthetic data and user selected data

This commit is contained in:
Martin Diehl 2016-11-06 22:57:34 +01:00
parent e57fd8e01a
commit 8179a703fb
1 changed files with 38 additions and 28 deletions
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64
processing/misc/DREAM3D_toTable.py
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@ -14,14 +14,28 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
Convert DREAM3D file to ASCIItable
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [dream3dfile[s]]', description = """
Convert DREAM3D file to ASCIItable. Works for 3D datasets, but, hey, its not called DREAM2D ;)
""", version = scriptID)
parser.add_option('-d','--data',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'data to extract from DREAM3D file')
parser.add_option('-c','--container',
dest = 'container', metavar = 'string',
help = 'root container(group) in which data is stored [%default]')
parser.set_defaults(container="ImageDataContainer",
)
(options, filenames) = parser.parse_args()
rootDir ='DataContainers/ImageDataContainer'
if options.data is None:
parser.error('No data selected')
rootDir ='DataContainers/'+options.container
# --- loop over input files -------------------------------------------------------------------------
@ -36,33 +50,29 @@ for name in filenames:
damask.util.report(scriptName,name)
inFile = h5py.File(name, 'r')
grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
try:
grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
except:
damask.util.croak('Group {} not found'.format(options.container))
table.close(dismiss = True)
continue
# --- read comments --------------------------------------------------------------------------------
coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T
coords = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
+ inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
+ inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
table.data = np.hstack( (coords,
inFile[rootDir+'/CellData/EulerAngles'][...].reshape(grid.prod(),3),
inFile[rootDir+'/CellData/Phases'][...].reshape(grid.prod(),1),
inFile[rootDir+'/CellData/Confidence Index'][...].reshape(grid.prod(),1),
inFile[rootDir+'/CellData/Fit'][...].reshape(grid.prod(),1),
inFile[rootDir+'/CellData/Image Quality'][...].reshape(grid.prod(),1)))
labels = ['1_pos','2_pos','3_pos',
'1_Euler','2_Euler','3_Euler',
'PhaseID','CI','Fit','IQ']
try:
table.data = np.hstack((table.data, inFile[rootDir+'/CellData/FeatureIds'][...].reshape(grid.prod(),1)))
labels.append(['FeatureID'])
except Exception:
pass
table.data = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
+ inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
+ inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
labels = ['1_pos','2_pos','3_pos']
for data in options.data:
try:
l = np.prod(inFile[rootDir+'/CellData/'+data].shape[3:])
labels+=['{}_{}'.format(i+1,data.replace(' ','')) for i in range(l)] if l >1 else [data.replace(' ','')]
except KeyError:
damask.util.croak('Data {} not found'.format(data))
pass
table.data = np.hstack((table.data,
inFile[rootDir+'/CellData/'+data][...].reshape(grid.prod(),l)))
# ------------------------------------------ assemble header ---------------------------------------
table.labels_clear()
@ -70,5 +80,5 @@ for name in filenames:
table.head_write()
# ------------------------------------------ finalize output ---------------------------------------
table.data_writeArray() #(fmt='%e2.2')
table.data_writeArray()
table.close()