def __init__(self, config):
self._fm = FunctionManagerINI(config)
self._setup_mesh(self._fm.getpath('fem', 'mesh')[:-5])
self._load_config(self._fm.getpath('fem', 'config'))
self.global_preprocessing_time = fc.Stopwatch()
self.local_preprocessing_time = fc.Stopwatch()
self.solving_time = fc.Stopwatch()
self._set_degree(self.degree)
def sample(self, r, potential, fem=None):
if fem is None:
fem = self._fem
self._anything_new = True
try:
idx_r = np.where(np.isclose(self.R, r))[0][0]
except IndexError:
print(self.R)
print(r)
print(self.R - r)
raise
sampling_time = np.nan
if potential is not None:
logging.info('Sampling 3D')
hits = 0
exceptions = 0
misses = 0
r2 = self.scalp_radius**2
XZ = np.array(list(self._xz))
sample_stopwatch = fc.Stopwatch()
with sample_stopwatch:
for idx_xz, (x, z) in enumerate(XZ):
r_xz_2 = x**2 + z**2
if r_xz_2 > r2:
misses += len(self.Y_SAMPLE)
continue
for idx_y, y in enumerate(self.Y_SAMPLE):
if r_xz_2 + y**2 > r2:
misses += 1
continue
try:
v = potential(x, y, z)
except Exception as e:
if x < 0 or z < 0 or abs(
y
) > self.scalp_radius or x > self.scalp_radius or z > self.scalp_radius:
logger.warning('coords out of bounding box')
exceptions += 1
else:
hits += 1
self.POTENTIAL[idx_r, idx_xz, idx_y] = v
sampling_time = float(sample_stopwatch)
logger.info('H={} ({:.2f}),\tM={} ({:.2f}),\tE={} ({:.2f})'.format(
hits, hits / float(hits + misses + exceptions), misses,
misses / float(hits + misses + exceptions), exceptions,
exceptions / float(hits + exceptions)))
self.STATS.append(
(r, sampling_time, fem.iterations, float(fem.solving_time),
float(fem.local_preprocessing_time),
float(fem.global_preprocessing_time)))
self.COMPLETED[idx_r] = True
return 0 if np.isnan(sampling_time) else sampling_time
def sample(self, r, potential, fem=None):
if fem is None:
fem = self._fem
self._anything_new = True
try:
idx_r = np.where(np.isclose(self.R, r))[0][0]
except IndexError:
print(self.R)
print(r)
print(self.R - r)
raise
sampling_time = np.nan
if potential is not None:
logging.info('Sampling 2D')
angle = fem.FRACTION_OF_SPACE * np.pi
SIN_COS = np.array([np.sin(angle), np.cos(angle)])
r2 = self.scalp_radius**2
sample_stopwatch = fc.Stopwatch()
with sample_stopwatch:
for idx_xz, xz in enumerate(self.X_SAMPLE):
x, z = SIN_COS * xz
xz2 = xz**2
for idx_y, y in enumerate(self.Y_SAMPLE):
if xz2 + y**2 > r2:
continue
try:
v = potential(x, y, z)
except Exception as e:
pass
else:
self.POTENTIAL[idx_r, idx_xz, idx_y] = v
sampling_time = float(sample_stopwatch)
self.STATS.append(
(r, sampling_time, fem.iterations, float(fem.solving_time),
float(fem.local_preprocessing_time),
float(fem.global_preprocessing_time)))
self.COMPLETED[idx_r] = True
return 0 if np.isnan(sampling_time) else sampling_time
'k': k,
'slice_thickness': controller.slice_thickness,
'slice_radius': controller.slice_radius,
'slice_conductivity': controller.slice_conductivity,
'saline_conductivity': controller.saline_conductivity,
'degree': degree,
'STATS': stats,
'sampling_frequency': controller.sampling_frequency,
}
POTENTIAL = controller.POTENTIAL
results['POTENTIAL'] = POTENTIAL
AS = controller.A
results['A'] = AS
save_stopwatch = fc.Stopwatch()
anything_new = False
with fc.Stopwatch() as unsaved_time:
for idx_y, src_y in enumerate(X):
for idx_x, src_x in enumerate(X):
for idx_z, src_z in enumerate(X[:idx_x + 1]):
logger.info(
'Gaussian SD={}, x={}, y={}, z={} ({}, deg={})'
.format(sd, src_x, src_y, src_z,
mesh_name, degree))
idx_xz = idx_x * (idx_x + 1) // 2 + idx_z
if not np.isnan(AS[idx_y, idx_xz]):
logger.info('Already found, skipping')
continue