def read(self, filepattern):
dirname = os.path.dirname(filepattern)
items = os.listdir(dirname)
escaped_pattern = string.replace(
re.escape(os.path.basename(filepattern)), "\\*", ".*?")
files = []
for item in items:
match = re.match(escaped_pattern, item)
if match != None:
span = match.span()
if span[0] == 0 and span[1] == len(item):
files.append(os.path.join(dirname, item))
prog = progress.getProgress(os.path.basename(filepattern),
progress.DEFINITE)
try:
# Look at the just the first file to get some info
z = 0
rows, npts = self.readfile(files[0], prog, z)
nx = len(rows[0])
ny = len(rows)
nz = len(files)
dx = rows[0][1].position[0] - rows[0][0].position[0]
dy = rows[1][0].position[1] - rows[0][0].position[1]
dz = 1
pxlsize = primitives.Point(dx, dy, dz)
size = rows[-1][-1].position + pxlsize
od = orientmapdata.OrientMap(primitives.iPoint(nx, ny, nz),
size)
count = 0
for row in rows:
count += 1
for datum in row:
self.addDatum(od, datum, pxlsize, ny, count, npts,
prog, nz)
# now look at the rest of the files
for file in files[1:]:
z = z + dz
rows, nrowpts = self.readfile(file, prog, z)
npts = npts + nrowpts
count = 0
for row in rows:
count += 1
if len(row) != nx:
raise ooferror.ErrUserError(
"Orientation map data appears to be incomplete"
)
for datum in row:
self.addDatum(od, datum, pxlsize, ny, count, npts,
prog, nz)
finally:
prog.finish()
return od
def read(self, filename):
prog = progress.getProgress(os.path.basename(filename),
progress.DEFINITE)
rows, npts = self.readfile(filename, prog)
try:
nx = len(rows[0])
ny = len(rows)
count = 0
for row in rows:
count += 1
if len(row) != nx:
raise ooferror.ErrUserError(
"Orientation map data appears to be incomplete")
# pixel size
dx = rows[0][1].position[0] - rows[0][0].position[0]
dy = rows[1][0].position[1] - rows[0][0].position[1]
pxlsize = primitives.Point(dx, dy)
# If we assume that the points are in the centers of the
# pixels, then the actual physical size is one pixel bigger
# than the range of the xy values.
size = rows[-1][-1].position + pxlsize
debug.fmsg("nx=", nx, "ny=", ny, "size=", size, "pxlsize=",
pxlsize)
if config.dimension() == 2:
od = orientmapdata.OrientMap(primitives.iPoint(nx, ny),
size)
else:
od = orientmapdata.OrientMap(primitives.iPoint(nx, ny, 1),
size)
count = 0
for row in rows:
for datum in row:
self.addDatum(od, datum, pxlsize, ny, count, npts,
prog)
finally:
prog.finish()
return od
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 _loadOrientationMap(menuitem, microstructure, filename, orientations):
# orientations is a list of 3-tuples representing ABG Euler
# angles.
mscontext = ooflib.common.microstructure.microStructures[microstructure]
ms = mscontext.getObject()
od = orientmapdata.OrientMap(ms.sizeInPixels(), ms.size())
reader = orientmapdata.OrientMapReader() # just to borrow its set_angle fn
count = 0
for pixel in ms.coords():
reader.set_angle(od, pixel,
corientation.COrientABG(*orientations[count]))
count += 1
orientmapdata.registerOrientMap(microstructure, od)
orientmapplugin = mscontext.getObject().getPlugIn('OrientationMap')
orientmapplugin.set_data(od, filename)
orientmapplugin.timestamp.increment()
orientmapdata.orientationmapNotify(ms)
def _read(self, datafile, prog):
# readData gets data from the file, but does no processing
data = self.readData(datafile, prog)
rows = list(getrows(data)) # sorts data
# The grid is hexagonal if the first two rows don't start at the same x.
if rows[0][0].position[0] != rows[1][0].position[0]:
# Throw out every other row.
reporter.warn("Converting hexagonal lattice to rectangular"
" by discarding alternate rows.")
rows = rows[::2] # discard odd numbered rows
# Check that all rows are the same length, and flip the
# coordinates if requested.
nx = len(rows[0])
ny = len(rows)
ymax = rows[-1][0].position[1]
ymin = rows[0][0].position[1]
xmax = rows[0][-1].position[0]
xmin = rows[0][0].position[0]
count = 0
for row in rows:
count += 1
if len(row) != nx:
raise ooferror.ErrUserError(
"Orientation map data appears to be incomplete.\n"
"len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))
for point in row:
if self.flip_x:
point.position[0] = xmax - point.position[0]
else:
point.position[0] = point.position[0] - xmin
if self.flip_y:
point.position[1] = ymax - point.position[1]
else:
point.position[1] = point.position[1] - ymin
# pixel size
dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
pxlsize = primitives.Point(dx, dy)
width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
# If we assume that the points are in the centers of the
# pixels, then the actual physical size is one pixel bigger
# than the range of the xy values.
size = primitives.Point(width, height) + pxlsize
npts = len(rows) * len(rows[0])
od = orientmapdata.OrientMap(primitives.iPoint(nx, ny),
size * self.scale_factor)
prog.setMessage("%d/%d orientations" % (0, npts))
count = 0
for row in rows:
for datum in row:
ij = primitives.iPoint(
int(round(datum.position[0] / pxlsize[0])),
int(round(datum.position[1] / pxlsize[1])))
for groupname in datum.groups:
try:
self.groupmembers[groupname].append(ij)
except KeyError:
self.groupmembers[groupname] = [ij]
if self.angle_units == 'Degrees':
offset = math.radians(self.angle_offset)
angleargs = datum.angletuple
else: # angle units are Radians
offset = self.angle_offset
# All Orientation subclasses that take angle args
# assume that they're in degrees. They have a
# static radians2Degrees method that converts the
# angle args from radians to degrees.
angleargs = self.angle_type.radians2Degrees(
*datum.angletuple)
# Create an instance of the Orientation subclass.
orient = self.angle_type(*angleargs)
if self.angle_offset != 0:
orient = orient.rotateXY(self.angle_offset)
# Insert this point into the OrientMap object.
self.set_angle(od, ij, orient.corient)
prog.setMessage("%d/%d orientations" % (count, npts))
prog.setFraction(float(count) / npts)
count += 1
if prog.stopped():
return None
return od
def _read(self, tslfile, prog):
data, hexgrid = self.readData(tslfile, prog)
npts = len(data)
rows = list(getrows(data)) # sorts data
if hexgrid is None:
# readData didn't set hexgrid. The grid is hexagonal if
# the first two rows don't start at the same x.
hexgrid = rows[0][0].position[0] != rows[1][0].position[0]
if hexgrid:
# Throw out every other row.
reporter.warn("Converting hexagonal lattice to rectangular"
" by discarding alternate rows.")
rows = rows[::2] # discard odd numbered rows
nx = len(rows[0])
ny = len(rows)
count = 0
for row in rows:
count += 1
if len(row) != nx:
raise ooferror.ErrUserError(
"Orientation map data appears to be incomplete.\n"
"len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))
# TSL puts the origin at the top left, so it's using a left
# handed coordinate system! If flip_y==True, fix that. Also,
# make sure there are no negative x or y values.
ymax = rows[-1][0].position[1]
ymin = rows[0][0].position[1]
xmax = rows[0][-1].position[0]
xmin = rows[0][0].position[0]
for row in rows:
for point in row:
if self.flip_x:
point.position[0] = xmax - point.position[0]
else:
point.position[0] = point.position[0] - xmin
if self.flip_y:
point.position[1] = ymax - point.position[1]
else:
point.position[1] = point.position[1] - ymin
# If flipped, the rows are still ordered top to bottom, but
# the coordinates increase bottom to top.
# pixel size
dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
pxlsize = primitives.Point(dx, dy)
width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
# If we assume that the points are in the centers of the
# pixels, then the actual physical size is one pixel bigger
# than the range of the xy values.
size = primitives.Point(width, height) + pxlsize
od = orientmapdata.OrientMap(primitives.iPoint(nx, ny), size)
prog.setMessage("%d/%d orientations" % (0, npts))
count = 0
for row in rows:
for datum in row:
ij = primitives.iPoint(
int(round(datum.position[0] / pxlsize[0])),
int(round(datum.position[1] / pxlsize[1])))
try:
self.phaselists[datum.phasename].append(ij)
except KeyError:
self.phaselists[datum.phasename] = [ij]
self.set_angle(od, ij, datum.euler())
prog.setMessage("%d/%d orientations" % (count, npts))
prog.setFraction(float(count) / npts)
count += 1
if prog.stopped():
return None
prog.finish()
return od