def read(self, filename):
hklfile = file(filename, "r")
## TODO OPT: Use lineiter = iter(hklfile) instead of iter(lines).
## Then it's not necessary to create an array of lines.
lines = hklfile.readlines()
lineiter = iter(lines)
line = lineiter.next()
while not line.startswith('XCells'):
line = lineiter.next()
xcells = string.atoi(string.split(line)[1])
line = lineiter.next()
ycells = string.atoi(string.split(line)[1])
line = lineiter.next()
xstep = string.atof(string.split(line)[1])
line = lineiter.next()
ystep = string.atof(string.split(line)[1])
line = lineiter.next()
od = orientmapdata.OrientMap(
primitives.iPoint(xcells, ycells),
primitives.Point(xcells * xstep, ycells * ystep))
while not string.split(line)[0] == 'Phase':
line = lineiter.next()
prog = progress.getProgress(os.path.basename(filename),
progress.DEFINITE)
try:
count = 0
npts = xcells * ycells
for line in lineiter:
vals = string.split(line)
phase = vals[0]
x = string.atof(vals[1])
y = string.atof(vals[2])
angles = map(string.atof, vals[5:8])
mad = string.atof(vals[8]) # mean angular deviation
ij = primitives.iPoint(int(round(x / xstep)),
ycells - 1 - int(round(y / ystep)))
try:
self.phaselists[phase].append(ij)
except KeyError:
self.phaselists[phase] = [ij]
self.set_angle(
od, ij,
corientation.COrientBunge(*map(math.radians, angles)))
prog.setFraction(float(count) / npts)
prog.setMessage("%d/%d orientations" % (count, npts))
count += 1
if pbar.stopped():
return None
finally:
prog.finish()
return od
def _bunge_to_base(bunge_reg, vlist=None):
args = vlist or bunge_reg.getParamValues() # (phi1, theta, phi2)
return corient_to_base(corientation.COrientBunge(*map(math.radians, args)))
def __init__(self, position, angletuple, phasename):
self.position = position
self.angle = corientation.COrientBunge(*angletuple)
self.phasename = phasename
def __init__(self, phi1, theta, phi2):
self.phi1 = phi1
self.theta = theta
self.phi2 = phi2
self.corient = corientation.COrientBunge(
*map(math.radians, (phi1, theta, phi2)))
def readfile(self, filename, prog, z=0):
tslfile = file(filename, "r")
prog.setMessage("Reading " + filename)
count = 1 # line counter
lines = tslfile.readlines()
nlines = len(lines)
data = utils.ReservableList(nlines)
angletype = None
for line in lines:
if line[0] == '#':
if line.startswith("Column 1-3", 2):
if "radians" in line:
angletype = "radians"
else:
angletype = "degrees"
debug.fmsg("Angles are in %s." % angletype)
else: # line[0] != '#'
substrings = line.split()
if len(substrings) < 5:
raise ooferror.ErrUserError(
"Too few numbers in line %d of %s" % (count, filename))
values = map(float, substrings[:5])
if angletype == "radians":
angles = values[:3]
elif angletype == "degrees":
angles = map(math.radians, values[:3])
else:
raise ooferror.ErrDataFileError(
"Angle type not specified in TSL data file")
orientation = corientation.COrientBunge(*angles)
if config.dimension() == 2:
point = primitives.Point(values[3], values[4])
elif config.dimension() == 3:
point = primitives.Point(values[3], values[4], z)
data.append(
DataPoint(
point, # position
angles,
' '.join(substrings[10:]))) # phase name
count += 1 # count actual file lines, comments and all
prog.setMessage("read %d/%d lines" % (count, nlines))
prog.setFraction(float(count) / nlines)
npts = len(data)
debug.fmsg("read %d lines, %d data points" % (count, npts))
# We don't yet know if the points are on a rectangular or a
# hexagonal lattice, so split the data up into rows.
# getrows() is a generator, but we need an actual list so that
# we can index into it.
rows = list(getrows(data))
if len(rows) < 2:
raise ooferror.ErrUserError(
"Orientation map data has too few rows.")
if rows[0][0].position[0] != rows[1][0].position[0]:
# Must be a hexagonal lattice. Throw out every other row.
reporter.warn(
"Converting hexagonal lattice to rectangular by discarding alternate rows."
)
rows = rows[::2] # discard odd numbered rows
return rows, npts