def get_points(self):
"""
All points in the block.
"""
for axis, num in ordered_iteritems(self.n_slice):
am = self._axis_map[axis]
shape = np.array((self.resolution[0], self.resolution[1], num))
pb = np.zeros((3,), dtype=np.object)
for ii in range(3):
pb[am[ii]] = np.linspace(0, self.dims[ii], shape[ii])
if num > 1:
delta = pb[am[2]][1] - pb[am[2]][0]
else:
delta = 0.0
x1, x2 = np.meshgrid(pb[am[0]], pb[am[1]])
x1 = x1.ravel()
x2 = x2.ravel()
points = np.empty((x1.shape[0], 3), dtype=np.float64)
points[:,am[0]] = x1
points[:,am[1]] = x2
yield pb, points, delta, num, axis, am
def format_dict(d, raw=None, indent=2):
"""Format a dictionary for printing.
Parameters:
d : dict
The dictionary.
raw : dict
The raw (unadjusted) dictionary to compare with.
indent : int
The indentation level.
Return:
msg : string
The string with dictionary's key : val formatted in two columns.
"""
if raw is None:
raw = d
msg = ''
for key, val in ordered_iteritems(d):
if val == raw[key]:
msg += (' ' * indent) + ('%s : %s\n' % (key, val))
else:
msg += (' ' * indent) + ('%s : %s (%s)\n' % (key, val, raw[key]))
msg = msg[:-1]
return msg
def format_dict(d, raw=None, indent=2):
"""Format a dictionary for printing.
Parameters:
d : dict
The dictionary.
raw : dict
The raw (unadjusted) dictionary to compare with.
indent : int
The indentation level.
Return:
msg : string
The string with dictionary's key : val formatted in two columns.
"""
if raw is None:
raw = d
msg = ''
for key, val in ordered_iteritems(d):
if val == raw[key]:
msg += (' ' * indent) + ('%s : %s\n' % (key, val))
else:
msg += (' ' * indent) + ('%s : %s (%s)\n' % (key, val, raw[key]))
msg = msg[:-1]
return msg
def report(self, filename):
fd = self.fd_open(filename)
if self.is_placed:
Object.report(self, fd, header=False)
fd.write('intersections per axis:\n')
for axis, ints in ordered_iteritems(self.intersection_counters):
fd.write(' %s (%d): %s\n' % (axis, len(ints), ints))
else:
fd.write(format_dict(self.conf.get_dict(),
raw=self.requested_conf.get_dict()) + '\n')
self.fd_close()
def format_intersection_statistics(self, is_output=False):
if is_output:
space = ''
else:
space = ' '
msg = []
for axis, num in ordered_iteritems(self.box.n_slice):
msg.append(space + 'axis %s (%d sections):' % (axis, num))
ok = True
for key, obj in ordered_iteritems(self):
if not obj.has_intersection(axis):
msg.append(space + ' warning: object %s is not intersected'
% key)
ok = False
if ok:
msg.append(space
+ ' all objects intersected by at least one section')
if is_output:
output('\n'.join(msg))
return msg
def report(self, filename):
fd = self.fd_open(filename)
if self.is_placed:
Object.report(self, fd, header=False)
fd.write('intersections per axis:\n')
for axis, ints in ordered_iteritems(self.intersection_counters):
fd.write(' %s (%d): %s\n' % (axis, len(ints), ints))
else:
fd.write(
format_dict(self.conf.get_dict(),
raw=self.requested_conf.get_dict()) + '\n')
self.fd_close()
def format_statistics(self):
units = self.box.units
msg = [_dashes, 'statistics', _dashes]
msg.append(' number of objects per class:')
msg.append(format_dict(self.n_object, self.n_object_requested, 4))
msg.append(_dashes)
msg.append(' total object volume fraction: %f' \
% self.total_object_volume_fraction)
msg.append(' total object volume [(%s)^3]: %f' \
% (units, self.total_object_volume))
msg.append(' total object surface fraction [1/(%s)]: %f' \
% (units, self.total_object_surface_fraction))
msg.append(' total object surface [(%s)^2]: %f' \
% (units, self.total_object_surface))
msg.append(' total object length density [1/(%s)^2]: %f' \
% (units, self.total_object_length_density))
msg.append(' total object length [(%s)]: %f' \
% (units, self.total_object_length))
msg.append(_dashes)
msg.append(' missed objects per axis:')
missed = {}.fromkeys(self.box.n_slice.keys(), 0)
for obj in self.itervalues():
for axis, ints in obj.intersection_counters.iteritems():
missed[axis] += len(ints) == 0
for axis, val in ordered_iteritems(missed):
msg.append(' %s: %d' % (axis, val))
msg.extend(self.format_intersection_statistics())
msg.append(_dashes)
ipac = {}.fromkeys(self.box.n_slice.keys())
for axis in ipac.iterkeys():
volumes = self.section_volumes[axis]
ipac[axis] = {}.fromkeys(volumes.keys(), 0)
for key, obj in self.iteritems():
for axis, ints in obj.intersection_counters.iteritems():
val = len(ints)
ipac[axis][obj.obj_class] += val
msg.append(' intersections per class:')
for axis, iac in ordered_iteritems(ipac):
msg.append(' axis: %s' % axis)
for key, ints in ordered_iteritems(iac):
msg.append(' %s: % 3d average: %5.2f for %d objects' \
% (key, ints,
float(ints) / self.n_object[key],
self.n_object[key]))
msg.append(_dashes)
msg.append(' volumes per class:')
for axis, volumes in ordered_iteritems(self.section_volumes):
msg.append(' axis: %s' % axis)
for key, val in ordered_iteritems(volumes):
stats = self.stats_per_class[key]
msg.append(' class: %s' % key)
msg.append(' true volume V1 [(%s)^3]: %f' \
% (units, stats.volume))
msg.append(' section-based volume V2 [(%s)^3]: %f' \
% (units, val))
msg.append(' true volume fraction: %f' \
% (stats.volume / self.box.volume))
msg.append(' section-based volume fraction: %f' \
% (val / self.box.volume))
msg.append(' ratio V2/V1 (accuracy estimate): %f' \
% (val / stats.volume))
msg.append(_dashes)
msg.append(' surfaces per class:')
for axis, surfaces in ordered_iteritems(self.section_surfaces):
msg.append(' axis: %s' % axis)
for key, val in ordered_iteritems(surfaces):
stats = self.stats_per_class[key]
msg.append(' class: %s' % key)
msg.append(' true (approximate) surface S1 [(%s)^2]: %f' \
% (units, stats.surface))
msg.append(' section-based surface S2 [(%s)^2]: %f' \
% (units, val))
msg.append(' true (approximate) surface fraction: %f' \
% (stats.surface / self.box.volume))
msg.append(' section surface fraction [1/(%s)]: %f' \
% (units, val / self.box.volume))
msg.append(' ratio S2/S1 (accuracy estimate): %f' \
% (val / stats.surface))
msg.append(_dashes)
msg.append(' lengths per class:')
for axis, iac in ordered_iteritems(ipac):
msg.append(' axis: %s' % axis)
for key, n_i in ordered_iteritems(iac):
val = 2.0 * n_i / self.box.get_area(axis) * self.box.volume
val /= self.box.n_slice[axis]
stats = self.stats_per_class[key]
msg.append(' class: %s' % key)
msg.append(' true length L1 [(%s)]: %f' \
% (units, stats.length))
msg.append(' section-based length L2 [(%s)]: %f' \
% (units, val))
msg.append(' true length density [1/(%s)^2]: %f' \
% (units, stats.length / self.box.volume))
msg.append(' section length density [1/(%s)^2]: %f' \
% (units, val / self.box.volume))
msg.append(' ratio L2/L1 (accuracy estimate): %f' \
% (val / stats.length))
msg.append(_dashes)
msg.append(' circumferences per object:')
msg.append(_dashes)
keys = [point[:2] for point in self.points]
header = '|'.join([' %s:% 4d' % key for key in keys])
msg.append(' ' + '|' + header + '|')
coor = '|'.join(['%7.2f' % point[2] for point in self.points])
msg.append('coordinate ' + '|' + coor + '|')
msg.append('-' * 12 + '--------' * len(keys))
for name, circs in ordered_iteritems(self.section_circumferences):
line = [' '] * len(keys)
for circ in circs:
ic = keys.index(circ[:2])
line[ic] = '%7.2f' % circ[-1]
msg.append(name.ljust(12) + '|' + '|'.join(line) + '|')
# import pdb; pdb.set_trace()
msg.append(_dashes)
return msg