def test_dtype_with_object(self):
"Test using an explicit dtype with an object"
assert_equal(True, False)
from datetime import date
import time
data = """ 1; 2001-01-01
2; 2002-01-31 """
ndtype = [('idx', int), ('code', np.object)]
func = lambda s: strptime(s.strip(), "%Y-%m-%d")
converters = {1: func}
test = textadapter.genfromtxt(StringIO(data),
delimiter=";",
dtype=ndtype,
converters=converters)
control = np.array([(1, datetime(2001, 1, 1)),
(2, datetime(2002, 1, 31))],
dtype=ndtype)
assert_equal(test, control)
#
ndtype = [('nest', [('idx', int), ('code', np.object)])]
try:
test = textadapter.genfromtxt(StringIO(data),
delimiter=";",
dtype=ndtype,
converters=converters)
except NotImplementedError:
errmsg = "Nested dtype involving objects should be supported."
raise AssertionError(errmsg)
def test_user_filling_values(self):
"Test with missing and filling values"
ctrl = np.array([(0, 3), (4, -999)], dtype=[('a', int), ('b', int)])
data = "N/A, 2, 3\n4, ,???"
kwargs = dict(delimiter=",",
dtype=int,
names="a,b,c",
missing_values={
0: "N/A",
'b': " ",
2: "???"
},
filling_values={
0: 0,
'b': 0,
2: -999
})
test = textadapter.genfromtxt(StringIO(data), **kwargs)
ctrl = np.array([(0, 2, 3), (4, 0, -999)],
dtype=[(_, int) for _ in "abc"])
assert_equal(test, ctrl)
test = textadapter.genfromtxt(StringIO(data),
usecols=(0, -1),
**kwargs)
ctrl = np.array([(0, 3), (4, -999)], dtype=[(_, int) for _ in "ac"])
assert_equal(test, ctrl)
def test_commented_header(self):
"Check that names can be retrieved even if the line is commented out."
data = StringIO("""
#gender age weight
M 21 72.100000
F 35 58.330000
M 33 21.99
""")
# The # is part of the first name and should be deleted automatically.
test = textadapter.genfromtxt(data, names=True, dtype=None)
ctrl = np.array(
[('M', 21, 72.1), ('F', 35, 58.33), ('M', 33, 21.99)],
# JNB: changed test because textadapter defaults to object string
# instead of fixed length string, and unsigned long int
# instead of int.
dtype=[('gender', 'O'), ('age', 'u8'), ('weight', 'f8')])
#dtype=[('gender', '|S1'), ('age', int), ('weight', float)])
assert_equal(test, ctrl)
# Ditto, but we should get rid of the first element
data = StringIO("""
# gender age weight
M 21 72.100000
F 35 58.330000
M 33 21.99
""")
test = textadapter.genfromtxt(data, names=True, dtype=None)
assert_equal(test, ctrl)
def test_replace_space(self):
"Test the 'replace_space' option"
txt = "A.A, B (B), C:C\n1, 2, 3.14"
# Test default: replace ' ' by '_' and delete non-alphanum chars
test = textadapter.genfromtxt(StringIO(txt),
delimiter=",",
names=True,
dtype=None)
ctrl_dtype = [("AA", int), ("B_B", int), ("CC", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
# Test: no replace, no delete
test = textadapter.genfromtxt(StringIO(txt),
delimiter=",",
names=True,
dtype=None,
replace_space='',
deletechars='')
ctrl_dtype = [("A.A", int), ("B (B)", int), ("C:C", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
# Test: no delete (spaces are replaced by _)
test = textadapter.genfromtxt(StringIO(txt),
delimiter=",",
names=True,
dtype=None,
deletechars='')
ctrl_dtype = [("A.A", int), ("B_(B)", int), ("C:C", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
def test_skip_footer_with_invalid(self):
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
basestr = '1 1\n2 2\n3 3\n4 4\n5 \n6 \n7 \n'
warnings.filterwarnings("ignore")
# Footer too small to get rid of all invalid values
assert_raises(ValueError,
textadapter.genfromtxt,
StringIO(basestr),
skip_footer=1)
a = textadapter.genfromtxt(StringIO(basestr),
skip_footer=1,
invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [2., 2.], [3., 3.], [4., 4.]]))
#
a = textadapter.genfromtxt(StringIO(basestr), skip_footer=3)
assert_equal(a, np.array([[1., 1.], [2., 2.], [3., 3.], [4., 4.]]))
#
basestr = '1 1\n2 \n3 3\n4 4\n5 \n6 6\n7 7\n'
a = textadapter.genfromtxt(StringIO(basestr),
skip_footer=1,
invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [3., 3.], [4., 4.], [6., 6.]]))
a = textadapter.genfromtxt(StringIO(basestr),
skip_footer=3,
invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [3., 3.], [4., 4.]]))
finally:
warn_ctx.__exit__()
def test_usecols_with_named_columns(self):
"Test usecols with named columns"
ctrl = np.array([(1, 3), (4, 6)], dtype=[('a', float), ('c', float)])
data = "1 2 3\n4 5 6"
kwargs = dict(names="a, b, c")
test = textadapter.genfromtxt(StringIO(data),
usecols=(0, -1),
**kwargs)
assert_equal(test, ctrl)
test = textadapter.genfromtxt(StringIO(data),
usecols=('a', 'c'),
**kwargs)
assert_equal(test, ctrl)
def test_gft_using_generator(self):
def count():
for i in range(10):
yield "%d" % i
res = textadapter.genfromtxt(count())
assert_array_equal(res, np.arange(10))
def test_usecols_as_css(self):
"Test giving usecols with a comma-separated string"
data = "1 2 3\n4 5 6"
test = textadapter.genfromtxt(StringIO(data),
names="a, b, c",
usecols="a, c")
ctrl = np.array([(1, 3), (4, 6)], dtype=[(_, float) for _ in "ac"])
assert_equal(test, ctrl)
def test_tricky_converter_bug1666(self):
"Test some corner case"
assert_equal(True, False)
s = StringIO('q1,2\nq3,4')
cnv = lambda s: float(s[1:])
test = textadapter.genfromtxt(s, delimiter=',', converters={0: cnv})
control = np.array([[1., 2.], [3., 4.]])
assert_equal(test, control)
def test_with_masked_column_uniform(self):
"Test masked column"
data = StringIO('1 2 3\n4 5 6\n')
test = textadapter.genfromtxt(data,
dtype=None,
missing_values='2,5',
usemask=True)
control = ma.array([[1, 2, 3], [4, 5, 6]], mask=[[0, 1, 0], [0, 1, 0]])
assert_equal(test, control)
def test_names_auto_completion(self):
"Make sure that names are properly completed"
data = "1 2 3\n 4 5 6"
test = textadapter.genfromtxt(StringIO(data),
dtype=(int, float, int),
names="a")
ctrl = np.array([(1, 2, 3), (4, 5, 6)],
dtype=[('a', int), ('f1', float), ('f2', int)])
assert_equal(test, ctrl)
def test_skip_footer(self):
data = ["# %i" % i for i in range(1, 6)]
data.append("A, B, C")
data.extend(["%i,%3.1f,%03s" % (i, i, i) for i in range(51)])
data[-1] = "99,99"
kwargs = dict(delimiter=",", names=True, skip_header=5, skip_footer=10)
test = textadapter.genfromtxt(StringIO("\n".join(data)), **kwargs)
ctrl = np.array([("%f" % i, "%f" % i, "%f" % i) for i in range(41)],
dtype=[(_, float) for _ in "ABC"])
assert_equal(test, ctrl)
def test_with_masked_column_various(self):
"Test masked column"
data = StringIO('True 2 3\nFalse 5 6\n')
test = textadapter.genfromtxt(data,
dtype=None,
missing_values='2,5',
usemask=True)
control = ma.array([(1, 2, 3), (0, 5, 6)],
mask=[(0, 1, 0), (0, 1, 0)],
dtype=[('f0', bool), ('f1', bool), ('f2', int)])
assert_equal(test, control)
def test_userconverters_with_explicit_dtype(self):
"Test user_converters w/ explicit (standard) dtype"
data = StringIO('skip,skip,2001-01-01,1.0,skip')
test = textadapter.genfromtxt(data,
delimiter=",",
names=None,
dtype=float,
usecols=(2, 3),
converters={2: bytes})
control = np.array([('2001-01-01', 1.)],
dtype=[('', '|S10'), ('', float)])
assert_equal(test, control)
def test_missing_with_tabs(self):
"Test w/ a delimiter tab"
txt = "1\t2\t3\n\t2\t\n1\t\t3"
test = textadapter.genfromtxt(
StringIO(txt),
delimiter="\t",
usemask=True,
)
ctrl_d = np.array([(1, 2, 3), (np.nan, 2, np.nan), (1, np.nan, 3)], )
ctrl_m = np.array([(0, 0, 0), (1, 0, 1), (0, 1, 0)], dtype=bool)
assert_equal(test.data, ctrl_d)
assert_equal(test.mask, ctrl_m)
def test_empty_file(self):
"Test that an empty file raises the proper warning."
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
warnings.filterwarnings("ignore",
message="genfromtxt: Empty input file:")
data = StringIO()
test = textadapter.genfromtxt(data)
assert_equal(test, np.array([]))
finally:
warn_ctx.__exit__()
def test_names_with_usecols_bug1636(self):
"Make sure we pick up the right names w/ usecols"
data = "A,B,C,D,E\n0,1,2,3,4\n0,1,2,3,4\n0,1,2,3,4"
ctrl_names = ("A", "C", "E")
test = textadapter.genfromtxt(StringIO(data),
dtype=(int, int, int),
delimiter=",",
usecols=(0, 2, 4),
names=True)
assert_equal(test.dtype.names, ctrl_names)
#
test = textadapter.genfromtxt(StringIO(data),
dtype=(int, int, int),
delimiter=",",
usecols=("A", "C", "E"),
names=True)
assert_equal(test.dtype.names, ctrl_names)
#
test = textadapter.genfromtxt(StringIO(data),
dtype=int,
delimiter=",",
usecols=("A", "C", "E"),
names=True)
assert_equal(test.dtype.names, ctrl_names)
def test_gft_using_filename(self):
# Test that we can load data from a filename as well as a file object
wanted = np.arange(6).reshape((2, 3))
if sys.version_info[0] >= 3:
# python 3k is known to fail for '\r'
linesep = ('\n', '\r\n')
else:
linesep = ('\n', '\r\n', '\r')
for sep in linesep:
data = '0 1 2' + sep + '3 4 5'
f, name = mkstemp()
# We can't use NamedTemporaryFile on windows, because we cannot
# reopen the file.
try:
os.write(f, asbytes(data))
assert_array_equal(textadapter.genfromtxt(name), wanted)
finally:
os.close(f)
os.unlink(name)
def readMesh(fileLoc, fileName, LOFEM=False):
'''
Takes in the file location and file name and it then generates a dictionary structure from those files for the mesh.
Input: fileLoc = a string of the loaction of file on your computer
fileName = a string of the name of the file assuming they are all equal for .mesh, .kocks, and .grain
Outpute: mesh = a dictionary that contains the following fields in it:
name = file location
eqv = any equivalence nodes currently this is an empty nest
grains = what grain each element corresponds to
con = connectivity of the mesh for each element
crd = coordinates of each node
surfaceNodes = surface nodes of the mesh
kocks = kocks angles for each grain
phases = phase number of each element
'''
surfaceNodes = []
con = []
crd = []
eqv = []
name = fileLoc
meshLoc = fileLoc + fileName + '.mesh'
grainLoc = fileLoc + fileName + '.grain'
kockLoc = fileLoc + fileName + '.kocks'
grains = []
phases = []
kocks = []
mesh = {}
mesh['name'] = name
mesh['eqv'] = []
with open(meshLoc) as f:
# data = f.readlines()
for line in f:
words = line.split()
# print(words)
lenWords = len(words)
if not words:
continue
if lenWords == 4:
nums = wordParser(words)
crd.append(nums[1:4])
if lenWords == 7:
nums = wordParser(words)
surfaceNodes.append(nums[0:7])
if lenWords == 11:
nums = wordParser(words)
con.append(nums[1:11])
grains = np.genfromtxt(grainLoc, usecols=(0), skip_header=1, skip_footer=0)
ugrains = np.unique(grains)
phases = np.genfromtxt(grainLoc, usecols=(1), skip_header=1, skip_footer=0)
kocks = np.genfromtxt(kockLoc,
usecols=(0, 1, 2),
skip_header=2,
skip_footer=1)
if not kocks.shape[0] == ugrains.shape[0]:
kocks = np.genfromtxt(kockLoc,
usecols=(0, 1, 2),
skip_header=2,
skip_footer=0)
mesh['con'] = np.require(np.asarray(con, order='F',
dtype=np.int32).transpose(),
requirements=['F'])
mesh['crd'] = np.require(np.asarray(crd, order='F').transpose(),
requirements=['F'])
mesh['surfaceNodes'] = np.require(np.asarray(surfaceNodes,
order='F',
dtype=np.int32).transpose(),
requirements=['F'])
mesh['grains'] = np.asfortranarray(grains.transpose(), dtype=np.int32)
mesh['kocks'] = util.mat2d_row_order(np.asfortranarray(kocks.transpose()))
mesh['phases'] = np.asfortranarray(phases.transpose(), dtype=np.int8)
if (LOFEM):
crd_meshLoc = fileLoc + fileName + '.cmesh'
crd_grainLoc = fileLoc + fileName + '.cgrain'
cgrains = ta.genfromtxt(crd_grainLoc, usecols=(0))
cphases = ta.genfromtxt(crd_grainLoc, usecols=(1))
ccon = ta.genfromtxt(crd_meshLoc, skip_header=1)
mesh['crd_con'] = np.asfortranarray(ccon.transpose(),
dtype=np.int32) - 1
mesh['crd_grains'] = np.asfortranarray(cgrains.transpose(),
dtype=np.int32)
mesh['crd_phases'] = np.asfortranarray(cphases.transpose(),
dtype=np.int8)
return mesh
def readGrainData(fileLoc, grainNum, frames=None, grData=None):
'''
Reads in the grain data that you are interested in. It can read the
specific rod, gammadot, and gamma files.
Input: fileLoc = a string of the file location
grainNum = an integer of the grain number
frames = what frames you are interested in, default value is all of them
lofemData = what data files you want to look at, default value is:
ang, gamma, gammadot
Output: data a dictionary that contains an ndarray of all the values
read in the above file.
rod_0: a float array of the original orientation at
each nodal point of the grain.
rod: a float array of the orientation at each nodal point
of the grain through each frame.
gamma: a float array of the integrated gammadot at each nodal
point of the grain through each frame.
gdot: a float array of the gammadot at each nodal point
of the grain through each frame.
'''
flDflt = False
frDflt = False
data = {}
if grData is None:
grData = ['ang', 'gamma', 'gdot']
flDflt = True
if frames is None:
strgrnum = np.char.mod('%4.4d', np.atleast_1d(grainNum))[0]
if grData[0] == 'ang':
fend = '.rod'
else:
fend = '.data'
file = fileLoc + 'gr_' + grData[0] + strgrnum + fend
nFrames = findComments(file)
if grData[0] == 'ang':
nFrames = nFrames - 1
frames = np.arange(1, nFrames + 1)
frDflt = True
else:
nFrames = np.size(frames)
frames = np.asarray(frames) + 1
for fName in grData:
print(fName)
tFrames = []
if fName == 'ang':
tnf = nFrames + 1
tFrames = frames.copy()
fend = 'rod'
if (not frDflt):
tFrames = np.concatenate(([1], tFrames))
else:
tnf = nFrames
tFrames = frames.copy()
fend = 'data'
tmp = []
strgrnum = np.char.mod('%4.4d', np.atleast_1d(grainNum))[0]
fLoc = fileLoc + 'gr_' + fName + strgrnum + '.' + fend
if frDflt:
tmp = ta.genfromtxt(fLoc, comments='%')
else:
tmp = selectFrameTxt(fLoc, tFrames, comments='%')
vec = np.atleast_2d(tmp).shape
if vec[0] == 1:
vec = (vec[1], vec[0])
temp = np.reshape(np.ravel(tmp),
(tnf, np.int32(vec[0] / tnf), vec[1])).T
if fName == 'ang':
data['angs_0'] = np.atleast_3d(temp[:, :, 0])
data['angs'] = np.atleast_3d(temp[:, :, 1::1])
else:
data[fName] = np.atleast_3d(temp)
return data
def readLOFEMData(fileLoc,
nProc,
nstps=None,
nelems=None,
ncrds=None,
nqpts=15,
frames=None,
lofemData=None,
restart=False):
'''
Reads in the data files that you are interested in across all the processors
and only for the frames that you are interested in as well
Input: fileLoc = a string of the file location
nProc = an integer of the number of processors used in the simulation
frames = what frames you are interested in, default value is all of them
lofemData = what data files you want to look at, default value is:
.strain, .stress,.crss, .agamma
Output: data = a dictionary that contains a list/ndarray of all read in data files. If other files other than default are wanted than the keys for those
values will be the file location. The default files have the following key
values:
coord_0: a float array of original coordinates
hard_0: a float array of original crss_0/g_0 for each element
angs_0: a float array of original kocks angles for each element
vel_0: a float array of original velocity at each node
coord: a float array of deformed coordinates
hard: a float array of crss/g for each element
angs: a float array of evolved kocks angles for each element
stress: a float array of the crystal stress for each element
strain: a float array of the sample strain for each element
pldefrate: a float of the plastic deformation rate for each element
plstrain: a float ofp the plastic strain for each element
vel: a float array of the velocity at each node
'''
flDflt = False
frDflt = False
data = {}
proc = np.arange(nProc)
if lofemData is None:
lofemData = ['strain', 'stress', 'crss', 'agamma', 'ang']
flDflt = True
if frames is None:
if nstps is None:
fName = lofemData[0]
if fName == 'ang':
strgrnum = np.char.mod('%4.4d', np.atleast_1d(0))[0]
file = fileLoc + 'gr_' + fName + strgrnum + '.rod'
else:
file = fileLoc + 'lofem.' + fName + '.0'
nFrames = findComments(file)
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
if restart:
frames = np.arange(1, nFrames + 1)
else:
frames = np.arange(1, nFrames)
nFrames = nFrames - 1
else:
frames = np.arange(1, nFrames + 1)
frDflt = True
else:
if nstps is None:
fName = lofemData[0]
if fName == 'ang':
strgrnum = np.char.mod('%4.4d', np.atleast_1d(0))[0]
file = fileLoc + 'gr_' + fName + strgrnum + '.rod'
else:
file = fileLoc + 'lofem.' + fName + '.0'
nstps = findComments(file)
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
if not restart:
nstps = nstps - 1
# frames = np.arange(1, nstps + 1)
proc_elems, proc_crds = mpi_partioner(nProc, ncrds, nelems)
nFrames = np.size(frames)
frames = np.asarray(frames) + 1
for fName in lofemData:
print(fName)
tmp = []
tproc = []
temp = []
tFrames = []
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
tnf = nFrames + 1
if restart:
tnf = nFrames
tFrames = frames.copy()
if (not frDflt):
tFrames = np.concatenate(([1], tFrames))
else:
tnf = nFrames
tFrames = frames.copy()
npf = 0
for p in proc:
# print(p)
tmp = []
tmp1 = []
if fName == 'ang':
strgrnum = np.char.mod('%4.4d', np.atleast_1d(p))[0]
fLoc = fileLoc + 'gr_' + fName + strgrnum + '.rod'
else:
fLoc = fileLoc + 'lofem.' + fName + '.' + str(p)
if frDflt:
tmp = ta.genfromtxt(fLoc, comments='%')
else:
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'rod':
skipst = proc_crds[p] * (tFrames[0] - 1)
skipft = proc_crds[p] * (nstps - (tFrames[0]))
elif fName == 'agamma_q' or fName == 'gamma_q' or fName == 'gammadot_q':
skipst = proc_elems[p] * (tFrames[0] - 1) * nqpts
skipft = proc_elems[p] * tFrames[0] * nqpts
else:
skipst = proc_elems[p] * (tFrames[0] - 1)
skipft = proc_elems[p] * (nstps - (tFrames[0]))
nvals = skipft - skipst
nvals = skipft - skipst
tmp = np.genfromtxt(fLoc,
comments='%',
skip_header=skipst,
max_rows=nvals)
# tmp = selectFrameTxt(fLoc, tFrames, comments='%')
vec = np.atleast_2d(tmp).shape
if vec[0] == 1:
vec = (vec[1], vec[0])
npf += vec[0] / tnf
tmp1 = np.reshape(np.ravel(tmp),
(tnf, np.int32(vec[0] / tnf), vec[1])).T
tproc.append(tmp1)
temp = np.asarray(np.concatenate(tproc, axis=1))
# temp = tproc.reshape(vec[1], npf, tnf, order='F').copy()
# Multiple setup for the default data names have to be changed to keep comp saved
# First two if and if-else statements are for those that have default values
if fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'ang':
if fName == 'adx':
tName = 'coord'
elif fName == 'advel':
tName = 'vel'
elif fName == 'ang':
tName = 'angs'
else:
tName = 'crss'
if restart:
data[tName] = np.atleast_3d(temp)
else:
data[tName + '_0'] = np.atleast_3d(temp[:, :, 0])
data[tName] = np.atleast_3d(temp[:, :, 1::1])
elif fName == 'dpeff':
tName = 'pldefrate'
data[tName] = np.atleast_3d(temp)
elif fName == 'eqplstrain':
tName = 'plstrain'
data[tName] = np.atleast_3d(temp)
elif fName == 'agamma_q' or fName == 'gamma_q' or fName == 'gammadot_q':
nslip = temp.shape[0]
nqpts = 15
nelems = np.int32(temp.shape[1] / nqpts)
temp1d = np.ravel(temp)
temp4d = temp1d.reshape(nslip, nelems, nqpts, nFrames)
data[fName] = np.swapaxes(np.swapaxes(temp4d, 0, 2), 1, 2)
else:
data[fName] = np.atleast_3d(temp)
return data
#%%
r2d = 180 / np.pi
print('About to start processing data')
kor = 'rod'
ldata = fepxDM.readLOFEMData(fileLoc,
nproc,
lofemData=['strain', 'stress', 'crss'])
#print('Finished Reading LOFEM data')
print('Starting to read DISC data')
data = fepxDM.readData(fileLoc,
nproc,
fepxData=['adx', 'strain', 'stress', 'crss'],
restart=False) #, 'ang'])
print('Finished Reading DISC data')
#%%
misori = ta.genfromtxt(fileLoc + fBname + 'diff.emisori', comments='%')
dmisori = ta.genfromtxt(fileLoc + fBname + '_DISC.cmisori', comments='%')
gr_cmisori = ta.genfromtxt(fileLoc + fBname + '.cmisori', comments='%')
#alpha = ta.genfromtxt(fileLoc+fBname+'.alpha', comments='%')
dmisori = dmisori.reshape((nsteps, nels)).T * r2d
misori = misori.reshape((nsteps, nels)).T * r2d
#gr_cmisori = gr_misori.reshape((nsteps, nels)).T*r2d
#alpha = alpha.reshape((nsteps, nels)).T
print('Finished Reading in Misori, Gr Misori, and Alpha')
#%%
gconn = np.asarray([], dtype='float64')
gconn = np.atleast_2d(gconn)
gupts = np.asarray([], dtype=np.int32)
def test_integer_delimiter(self):
"Test using an integer for delimiter"
data = " 1 2 3\n 4 5 67\n890123 4"
test = textadapter.genfromtxt(StringIO(data), delimiter=3, dtype=int)
control = np.array([[1, 2, 3], [4, 5, 67], [890, 123, 4]])
assert_equal(test, control)
def readData(fileLoc, nProc, frames=None, fepxData=None, restart=False):
'''
Reads in the data files that you are interested in across all the processors
and only for the frames that you are interested in as well
Input: fileLoc = a string of the file location
nProc = an integer of the number of processors used in the simulation
frames = what frames you are interested in, default value is all of them
fepxData = what data files you want to look at, default value is:
.ang, .strain, .stress, .adx, .advel, .dpeff, .eqplstrain, .crss
Output: data = a dictionary that contains a list/ndarray of all read in data files. If other files other than default are wanted than the keys for those
values will be the file location. The default files have the following key
values:
coord_0: a float array of original coordinates
hard_0: a float array of original crss_0/g_0 for each element
angs_0: a float array of original kocks angles for each element
vel_0: a float array of original velocity at each node
coord: a float array of deformed coordinates
hard: a float array of crss/g for each element
angs: a float array of evolved kocks angles for each element
stress: a float array of the crystal stress for each element
strain: a float array of the sample strain for each element
pldefrate: a float of the plastic deformation rate for each element
plstrain: a float of the plastic strain for each element
vel: a float array of the velocity at each node
'''
flDflt = False
frDflt = False
data = {}
proc = np.arange(nProc)
if fepxData is None:
fepxData = [
'ang', 'strain', 'stress', 'adx', 'advel', 'dpeff', 'eqplstrain',
'crss'
]
flDflt = True
if frames is None:
fName = fepxData[0]
file = fileLoc + 'post.' + fName + '.0'
nFrames = findComments(file)
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
if restart:
frames = np.arange(1, nFrames + 1)
else:
frames = np.arange(1, nFrames)
nFrames = nFrames - 1
else:
frames = np.arange(1, nFrames + 1)
frDflt = True
else:
nFrames = np.size(frames)
frames = np.asarray(frames) + 1
for fName in fepxData:
print(fName)
tmp = []
tproc = []
temp = []
tFrames = []
if fName == 'ang' or fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
tnf = nFrames + 1
if restart:
tnf = nFrames
tFrames = frames.copy()
if (not frDflt):
tFrames = np.concatenate(([1], tFrames))
else:
tnf = nFrames
tFrames = frames.copy()
npf = 0
for p in proc:
# print(p)
tmp = []
tmp1 = []
fLoc = fileLoc + 'post.' + fName + '.' + str(p)
if frDflt:
tmp = ta.genfromtxt(fLoc, comments='%')
else:
tmp = selectFrameTxt(fLoc, tFrames, comments='%')
vec = np.atleast_2d(tmp).shape
if vec[0] == 1:
vec = (vec[1], vec[0])
npf += vec[0] / tnf
tmp1 = np.reshape(np.ravel(tmp),
(tnf, np.int32(vec[0] / tnf), vec[1])).T
tproc.append(tmp1)
temp = np.asarray(np.concatenate(tproc, axis=1))
# temp = tproc.reshape(vec[1], npf, tnf, order='F').copy()
# Multiple setup for the default data names have to be changed to keep comp saved
# First two if and if-else statements are for those that have default values
if fName == 'ang':
if restart:
data['angs'] = np.atleast_3d(temp[1:4, :, :])
else:
data['angs_0'] = np.atleast_3d(temp[1:4, :, 0])
data['angs'] = np.atleast_3d(temp[1:4, :, 1::1])
elif fName == 'adx' or fName == 'advel' or fName == 'crss' or fName == 'rod':
if fName == 'adx':
tName = 'coord'
elif fName == 'advel':
tName = 'vel'
elif fName == 'rod':
tName = 'rod'
else:
tName = 'crss'
if restart:
data[tName] = np.atleast_3d(temp)
else:
data[tName + '_0'] = np.atleast_3d(temp[:, :, 0])
data[tName] = np.atleast_3d(temp[:, :, 1::1])
elif fName == 'dpeff':
tName = 'pldefrate'
data[tName] = np.atleast_3d(temp)
elif fName == 'eqplstrain':
tName = 'plstrain'
data[tName] = np.atleast_3d(temp)
elif fName == 'stress_q':
nvec = temp.shape[0]
nqpts = 15
nelems = np.int32(temp.shape[1] / nqpts)
temp1d = np.ravel(temp)
temp4d = temp1d.reshape(nvec, nelems, nqpts, nFrames)
data[fName] = np.swapaxes(np.swapaxes(temp4d, 0, 2), 1, 2)
else:
data[fName] = np.atleast_3d(temp)
return data
def test_usecols_with_integer(self):
"Test usecols with an integer"
test = textadapter.genfromtxt(StringIO("1 2 3\n4 5 6"), usecols=0)
assert_equal(test, np.array([1., 4.]))