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DAMASK_EICMD
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Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

This commit is contained in:
Chuanlai Liu 2016-11-07 09:10:39 +01:00
parent 551b4369a1 0653383c95
commit 6d91ce866e
5 changed files with 43 additions and 33 deletions
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4
DAMASK_env.csh
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@ -25,11 +25,11 @@ endif
# this seems to make sense for the stack size
if ( `which free` != "free: Command not found." ) then
set freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
set stack=`expr $freeMem / $DAMASK_NUM_THREADS / 2`
set heap=` expr $freeMem / 2`
set stack=`expr $freeMem / $DAMASK_NUM_THREADS / 2`
# http://superuser.com/questions/220059/what-parameters-has-ulimit
limit stacksize $stack # maximum stack size (kB)
limit datasize $heap # maximum heap size (kB)
limit stacksize $stack # maximum stack size (kB)
endif
if ( `limit | grep memoryuse` != "" ) then
limit memoryuse unlimited # maximum physical memory size

2
DAMASK_env.sh
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@ -40,8 +40,8 @@ FREE=$(which free 2>/dev/null)
if [ "x$FREE" != "x" ]; then
freeMem=$(free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}')
# http://superuser.com/questions/220059/what-parameters-has-ulimit
ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2) 2>/dev/null # maximum stack size (kB)
ulimit -d $(expr $freeMem / 2) 2>/dev/null # maximum heap size (kB)
ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2) 2>/dev/null # maximum stack size (kB)
fi
ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -m unlimited 2>/dev/null # maximum physical memory size

2
DAMASK_env.zsh
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@ -28,8 +28,8 @@ if [ "`which free 2>/dev/null`" != "free not found" ]; then
freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
# http://superuser.com/questions/220059/what-parameters-has-ulimit
#ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB)
ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB)
ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB)
fi
ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -m unlimited 2>/dev/null # maximum physical memory size

2
VERSION
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@ -1 +1 @@
v2.0.1-294-g2fa4e48
v2.0.1-298-g8179a70

66
processing/misc/DREAM3D_toTable.py
View File

@ -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
coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T
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()