def saveImage(menuitem, image, filename, format, mode):
immidge = oofimage.getImage(image)
if immidge and (mode == "w" or not os.path.exists(filename)):
if config.dimension() == 3:
# A separate file will be stored for each slice. The
# filename must contain '%i', which will be replaced by an
# integer to differentiate the slices. If the given name
# doesn't contain '%i', '_%i' will be appended to it. If
# the given name looks like "name.suffix", the new name
# will be "name_%i.suffix".
path, fname = os.path.split(filename)
if "%i" not in fname:
if not os.path.exists(path):
os.makedirs(path)
fn = fname.rsplit(".", 1)
if len(fn) > 1:
fname = fn[0] + "_%i." + fn[1]
# filename = path + "/" + fn[0] + "_%i." + fn[1]
else:
fname = fn[0] + "_i"
# filename = path + "/" + filename + "_%i"
filename = os.path.join(path, fname)
immidge.save(filename, format.string())
else:
reporter.warn("Image was not saved!")
def getBase(self, registration):
# Get the original value of the parameter, in base form,
# and store it so you can pass it to widgets for other representations.
try:
self.base_value = registration.getParamValuesAsBase()
except ValueError, exc:
reporter.warn(exc)
def delete(self, name):
reg = self.data[name].object
if hasattr(reg, "parent"):
self.materialmanager.delete_prop(name)
reg.unregister()
self.data.delete(name)
else:
reporter.warn("Predefined properties cannot be deleted!")
def delete(self, name):
reg = self.data[name].object
if hasattr(reg, "parent"):
self.materialmanager.delete_prop(name)
reg.unregister()
self.data.delete(name)
else:
reporter.warn("Predefined properties cannot be deleted!")
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
def profile_start(menuitem, filename, fudge):
global prof
## import hotshot
## prof = hotshot.Profile(filename)
## prof.start()
if thread_enable.enabled():
reporter.warn("Multithreaded profiling is unreliable!\nUse the --unthreaded startup option.")
from ooflib.common.EXTRA import profiler
prof = profiler.Profiler(filename, fudge=fudge)
def _modify(menuitem, skeleton, modifier):
context = skeletoncontext.skeletonContexts[skeleton]
context.reserve()
start_nnodes = context.getObject().nnodes()
start_nelems = context.getObject().nelements()
try:
context.begin_writing()
cdebug.ProfilerStart("mod.prof")
try:
skel = modifier.apply(context.getObject())
## skel is None whenever the modifier fails
## or is interrupted from finishing its task
if skel is None:
reporter.warn("Modify Process Interrupted")
return
context.pushModification(skel)
skel.needsHash()
finally:
context.end_writing()
## If the skeleton is modified in postProcess, use
## begin/end_writing inside the function call to guarantee
## that no dead-locking occurs because of possible switchboard
## calls that may make use of begin/end_reading(). See
## cfiddlenodes.spy for an example.
modifier.postProcess(context)
modifier.cleanUp()
cdebug.ProfilerStop()
skel.incrementTimestamp()
end_nnodes = context.getObject().nnodes()
end_nelems = context.getObject().nelements()
if end_nnodes > start_nnodes:
reporter.report(end_nnodes - start_nnodes, "more nodes.")
elif end_nnodes < start_nnodes:
reporter.report(start_nnodes - end_nnodes, "fewer nodes.")
if end_nelems > start_nelems:
reporter.report(end_nelems - start_nelems, "more elements.")
elif end_nelems < start_nelems:
reporter.report(start_nelems - end_nelems, "fewer elements.")
finally:
context.cancel_reservation()
# "Skeleton modified" indicates that a specific modifier has been
# applied. "Skeleton changed" indicates that something has
# changed, which might or might not have involved a
# SkeletonModifier. "Skeleton changed" is not redundant with "who
# changed", because "who changed" is issued by pushModification
# before postProcess is called, and postProcess might do most of
# the work in a SkeletonModifier.
## TODO OPT: Some modifiers send these notifications in
## postProcess. Don't send them again here.
switchboard.notify('Skeleton modified', skeleton, modifier)
switchboard.notify('Skeleton changed', skeleton)
switchboard.notify('redraw')
def optionCB(self, widget, regname):
if self.currentOption is not None:
if self.paramWidget is not None:
# If there is a current option and a current widget,
# copy the values into the parameters.
self.paramWidget.get_values()
self.paramWidget.destroy()
# Retrieve the current value of the outgoing option.
try:
old = self.getParamValues()
got_old = True
except ValueError, exc:
reporter.warn(exc)
got_old = False
def _ops_callback(menuitem, mesh, time, data, domain, sampling, destination,
**kwargs):
if parallel_enable.enabled():
menuitem.ipcmenu(mesh=mesh,
data=data,
domain=domain,
sampling=sampling,
destination=destination)
return
operation = menuitem.data() # data is a DataOperation Registration
direct = getattr(menuitem.data, 'direct', False)
if not (direct or data.allowsArithmetic()):
raise ooferror2.ErrUserError("Output '" + data.name +
"' can only be used with Direct output")
# Set the mesh in the domain, then run the operation.
domain.set_mesh(mesh)
domain.read_lock() # acquires Mesh's read lock.
try:
# The domain has all the mesh data, so we don't have to pass that data.
meshctxt = ooflib.engine.mesh.meshes[mesh]
meshctxt.precompute_all_subproblems()
t = meshctxt.getTime(time) # converts '<latest>' to time, if needed
meshctxt.restoreCachedData(t)
destination.open()
try:
if sampling.make_samples(domain):
printHeaders(destination, operation, data, domain, sampling)
# Do the calculation
operation(t, data, domain, sampling, destination)
else:
reporter.warn("Analysis domain is empty! No output produced.")
finally:
meshctxt.releaseCachedData()
destination.close()
finally:
domain.read_release()
# domain holds a reference to the mesh, and since it's a
# Parameter value, the command history holds a reference to
# domain. We need to clear the mesh reference so that the
# mesh can be destroyed when everybody else is done with it.
domain.set_mesh(None)
sampling.clearSamples()
def _modify(menuitem, skeleton, modifier):
# context is actually the Who of the skeleton
context = skeletoncontext.skeletonContexts[skeleton]
context.reserve()
start_nnodes = context.getObject().nnodes()
start_nelems = context.getObject().nelements()
try:
context.begin_writing()
try:
skel = modifier.apply(context.getObject(), context)
# skel is None whenever the modifier fails
# or is interrupted from finishing its task
if skel is None:
reporter.warn("Modify Process Interrupted")
return
context.pushModification(skel) # parallelized
skel.needsHash()
finally:
context.end_writing()
# If the skeleton is modified in postProcess, use
# begin/end_writing inside the function call to guarantee
# that no dead-locking occurs because of possible switchboard
# calls to READ or REDRAW that may make use of
# begin/end_reading(). See anneal.py for an example.
modifier.postProcess(context) # parallelize for each modifier
skel.updateGeometry() # force recalculation of homogeneity, etc
end_nnodes = context.getObject().nnodes()
end_nelems = context.getObject().nelements()
if end_nnodes > start_nnodes:
reporter.report(end_nnodes - start_nnodes, "more nodes.")
elif end_nnodes < start_nnodes:
reporter.report(start_nnodes - end_nnodes, "fewer nodes.")
if end_nelems > start_nelems:
reporter.report(end_nelems - start_nelems, "more elements.")
elif end_nelems < start_nelems:
reporter.report(start_nelems - end_nelems, "fewer elements.")
finally:
context.cancel_reservation()
switchboard.notify('redraw')
switchboard.notify('Skeleton modified', skeleton, modifier)
def _modify(menuitem, skeleton, modifier):
# context is actually the Who of the skeleton
context = skeletoncontext.skeletonContexts[skeleton]
context.reserve()
start_nnodes = context.getObject().nnodes()
start_nelems = context.getObject().nelements()
try:
context.begin_writing()
try:
skel = modifier.apply(context.getObject(), context)
# skel is None whenever the modifier fails
# or is interrupted from finishing its task
if skel is None:
reporter.warn("Modify Process Interrupted")
return
context.pushModification(skel) # parallelized
skel.needsHash()
finally:
context.end_writing()
# If the skeleton is modified in postProcess, use
# begin/end_writing inside the function call to guarantee
# that no dead-locking occurs because of possible switchboard
# calls to READ or REDRAW that may make use of
# begin/end_reading(). See anneal.py for an example.
modifier.postProcess(context) # parallelize for each modifier
end_nnodes = context.getObject().nnodes()
end_nelems = context.getObject().nelements()
if end_nnodes > start_nnodes:
reporter.report(end_nnodes - start_nnodes, "more nodes.")
elif end_nnodes < start_nnodes:
reporter.report(start_nnodes - end_nnodes, "fewer nodes.")
if end_nelems > start_nelems:
reporter.report(end_nelems - start_nelems, "more elements.")
elif end_nelems < start_nelems:
reporter.report(start_nelems - end_nelems, "fewer elements.")
finally:
context.cancel_reservation()
switchboard.notify("redraw")
switchboard.notify("Skeleton modified", skeleton, modifier)
def apply(self, oldskeleton, context):
#skel = oldskeleton.properCopy(skeletonpath=context.path())
# vigilante doesn't really need a properCopy!
skel = oldskeleton.deputyCopy()
skel.activate()
suckers = skel.illegalElements()
# illegalset holds the elements to be checked. It is
# initially set to the illegal elements in the unmodified
# skeleton, but new element can be added to it if moving one
# node fixes two elements and breaks one.
illegalset = set()
for el in suckers:
illegalset.add(el)
random.shuffle(suckers)
nguilty = len(suckers)
# arbitrary number just to keep us out of an infinite loop
max = 222
count = 0
while illegalset and count < max:
count += 1
self.smoothIllegalElements(skel, illegalset, suckers)
ndone = nguilty - len(illegalset)
if illegalset:
reporter.warn("Could not remove all illegal elements!")
reporter.report("%d illegal element%s removed." % (ndone, "s" *
(ndone != 1)))
## TODO: There are cases in which this doesn't work, that
## could be solved by moving a node *towards* the average
## position of its neighbors, but not all the way. Try moving
## problem nodes until their elements become barely legal.
skel.cleanUp()
skel.checkIllegality()
return skel
def apply(self, oldskeleton, context):
# skel = oldskeleton.properCopy(skeletonpath=context.path())
# vigilante doesn't really need a properCopy!
skel = oldskeleton.deputyCopy()
skel.activate()
suckers = skel.illegalElements()
# illegalset holds the elements to be checked. It is
# initially set to the illegal elements in the unmodified
# skeleton, but new element can be added to it if moving one
# node fixes two elements and breaks one.
illegalset = set()
for el in suckers:
illegalset.add(el)
random.shuffle(suckers)
nguilty = len(suckers)
# arbitrary number just to keep us out of an infinite loop
max = 222
count = 0
while illegalset and count < max:
count += 1
self.smoothIllegalElements(skel, illegalset, suckers)
ndone = nguilty - len(illegalset)
if illegalset:
reporter.warn("Could not remove all illegal elements!")
reporter.report("%d illegal element%s removed." % (ndone, "s" * (ndone != 1)))
## TODO: There are cases in which this doesn't work, that
## could be solved by moving a node *towards* the average
## position of its neighbors, but not all the way. Try moving
## problem nodes until their elements become barely legal.
skel.cleanUp()
skel.checkIllegality()
return skel
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 _warning(menuitem):
reporter.warn("You'd better be home by 11, young lady!")
def saveImage(menuitem, image, filename, overwrite):
immidge = oofimage.getImage(image)
if immidge and (overwrite or not os.path.exists(filename)):
immidge.save(filename)
else:
reporter.warn("Image was not saved!")
def _modify(menuitem, skeleton, modifier):
global _rank
if _rank == 0:
ModifyProgressBar = menuitem.getProgressBar(modifier.get_progressbar_type())
context = skeletoncontext.skeletonContexts[skeleton]
context.reserve()
try:
context.begin_writing()
try:
if _rank == 0:
reporter.start_progressbar()
skel = modifier.apply_parallel(context.getObject(), context)
if _rank == 0:
reporter.progressbar_completed()
reporter.end_progressbar()
# skel is None whenever the modifier fails
# or is interrupted from finishing its task
if skel is None:
reporter.warn("Modify Process Interrupted")
# return will force all the finally's to be executed
return
mpitools.Barrier()
context.pushModification(skel)
skel.needsHash()
finally:
context.end_writing()
if _rank == 0:
reporter.start_progressbar()
mpitools.Barrier()
modifier.postProcess_parallel(context)
if _rank == 0:
reporter.progressbar_completed()
reporter.end_progressbar()
# If the skeleton is modified in postProcess, use
# begin/end_writing inside the function call to guarantee
# that no dead-locking occurs because of possible switchboard
# calls to READ or REDRAW that may make use of
# begin/end_reading(). See anneal.py for an example.
finally:
# guarantee that the reservation is cancelled even if an
# exception is raised
context.cancel_reservation()
if _rank == 0:
if ModifyProgressBar.query_stop() or ModifyProgressBar.get_success() < 0:
ModifyProgressBar.set_failure()
ModifyProgressBar.set_message("Failed")
return
else:
ModifyProgressBar.set_success()
ModifyProgressBar.set_message("Succeeded")
switchboard.notify("redraw")
switchboard.notify("Skeleton modified", skeleton, modifier)
def _assignMat(menuitem, mesh, elements, material):
reporter.warn(
"Explicit material assignments to mesh elements are no longer supported!"
)
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 _assigninterfacemat(menuitem, microstructure, material, skeleton,
interfaces):
reporter.warn(
"Interface Materials are not supported in this version of OOF2.")
def _assigninterfacemat(menuitem, microstructure, material,
skeleton,interfaces):
reporter.warn(
"Interface Materials are not supported in this version of OOF2.")
def saveImage(menuitem, image, filename, overwrite):
immidge = oofimage.getImage(image)
if immidge and (overwrite or not os.path.exists(filename)):
immidge.save(filename)
else:
reporter.warn("Image was not saved!")
def _assignMat(menuitem, mesh, elements, material):
reporter.warn(
"Explicit material assignments to mesh elements are no longer supported!"
)
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
def _modify(menuitem, skeleton, modifier):
global _rank
if _rank == 0:
ModifyProgressBar = menuitem.getProgressBar(
modifier.get_progressbar_type())
context = skeletoncontext.skeletonContexts[skeleton]
context.reserve()
try:
context.begin_writing()
try:
if _rank == 0:
reporter.start_progressbar()
skel = modifier.apply_parallel(context.getObject(), context)
if _rank == 0:
reporter.progressbar_completed()
reporter.end_progressbar()
# skel is None whenever the modifier fails
# or is interrupted from finishing its task
if skel is None:
reporter.warn("Modify Process Interrupted")
# return will force all the finally's to be executed
return
mpitools.Barrier()
context.pushModification(skel)
skel.needsHash()
finally:
context.end_writing()
if _rank == 0:
reporter.start_progressbar()
mpitools.Barrier()
modifier.postProcess_parallel(context)
if _rank == 0:
reporter.progressbar_completed()
reporter.end_progressbar()
# If the skeleton is modified in postProcess, use
# begin/end_writing inside the function call to guarantee
# that no dead-locking occurs because of possible switchboard
# calls to READ or REDRAW that may make use of
# begin/end_reading(). See anneal.py for an example.
finally:
# guarantee that the reservation is cancelled even if an
# exception is raised
context.cancel_reservation()
if _rank == 0:
if ModifyProgressBar.query_stop() or \
ModifyProgressBar.get_success()<0:
ModifyProgressBar.set_failure()
ModifyProgressBar.set_message("Failed")
return
else:
ModifyProgressBar.set_success()
ModifyProgressBar.set_message("Succeeded")
switchboard.notify('redraw')
switchboard.notify('Skeleton modified', skeleton, modifier)
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