def main():
"""The program."""
parser = OptionParser(usage="%prog [-n SAMPLING] ROTATIONS_FILE OUTPUT_FILE")
parser.add_option("-n", action="store", dest="n", type="int", default=None,
help="Density of sphere sampling if different from the rotation sampling.")
parser.add_option("-w", action="store_false", dest="use_weights", help="Use weights.")
options, args = parser.parse_args()
rotations_file = args[0]
output_file = args[1]
quaternions, weights = read_rotations(rotations_file)
if options.n is None:
number_of_rotations = len(quaternions)
n_sampling = rotations.rots_to_n(number_of_rotations)
else:
n_sampling = options.n
if not options.use_weights:
weights = None
table, table_weights = calculate_table(n_sampling, quaternions, weights)
save_table(output_file, table, table_weights)
def main():
"""The program."""
parser = OptionParser(
usage="%prog [-n SAMPLING] ROTATIONS_FILE OUTPUT_FILE")
parser.add_option(
"-n",
action="store",
dest="n",
type="int",
default=None,
help=
"Density of sphere sampling if different from the rotation sampling.")
parser.add_option("-w",
action="store_false",
dest="use_weights",
help="Use weights.")
options, args = parser.parse_args()
rotations_file = args[0]
output_file = args[1]
quaternions, weights = read_rotations(rotations_file)
if options.n is None:
number_of_rotations = len(quaternions)
n_sampling = rotations.rots_to_n(number_of_rotations)
else:
n_sampling = options.n
if not options.use_weights:
weights = None
table, table_weights = calculate_table(n_sampling, quaternions, weights)
save_table(output_file, table, table_weights)
def get_single_rotation_values(self, iteration, image_number):
"""Get the rotation distribution of a single image"""
self.check_ready()
try:
resp_handle = h5py.File('output/responsabilities_%.4d.h5' % iteration)
resp = resp_handle['data'][image_number, :]
resp_handle.close()
except IOError:
self.read_error.emit()
if len(resp) != self._number_of_rotations:
self._number_of_rotations = len(resp)
self._rotations_n = rotations.rots_to_n(self._number_of_rotations)
self.properties_changed.emit()
self._rotation_sphere_bins[:] = 0.
for i, resp in enumerate(resp):
self._rotation_sphere_bins[self._rotation_mapping_table[i]] += resp
self._rotation_sphere_bins[self._rotation_sphere_good_indices] /= \
self._rotation_sphere_weights[self._rotation_sphere_good_indices]
return self._rotation_sphere_bins
def get_average_rotation_values(self, iteration):
"""Get the average rotation distribution of all images"""
self.check_ready()
try:
#average_resp = loadtxt('output/average_resp_%.4d.data' % iteration)
average_resp = self._read_average_resp(iteration)
except IOError:
self.read_error.emit()
return self._rotation_sphere_bins
if len(average_resp) != self._number_of_rotations:
self._number_of_rotations = len(average_resp)
self._rotations_n = rotations.rots_to_n(self._number_of_rotations)
self.properties_changed.emit()
self._rotation_sphere_bins[:] = 0.
for i, resp in enumerate(average_resp):
self._rotation_sphere_bins[self._rotation_mapping_table[i]] += resp
self._rotation_sphere_bins[self._rotation_sphere_good_indices] /= \
self._rotation_sphere_weights[self._rotation_sphere_good_indices]
#return float32(self._rotation_sphere_weights) # debug line
return self._rotation_sphere_bins
def setup_rotations(self):
"""Read the appropriate quaternion list and calculate a table for projecting."""
self._number_of_rotations = len(self._read_average_resp(0))
self._rotations_n = rotations.rots_to_n(self._number_of_rotations)
if self._rotation_sphere_coordinates is None:
raise RuntimeError("Must call set_sampling_coordinates before setting up rotations")
filename = "{directory}/data/rotations_table_n{n}.h5".format(directory=os.path.split(__file__)[0], n=self._rotations_n)
print filename
with h5py.File(filename, "r") as file_handle:
self._rotation_sphere_weights = file_handle['weights'][...]
self._rotation_mapping_table = file_handle['table'][...]
self._rotation_sphere_good_indices = self._rotation_sphere_weights > 0.
self._number_of_bins = len(self._rotation_sphere_weights)
self._rotation_sphere_bins = numpy.zeros(self._number_of_bins)
self._setup_done = True