def Client(host, port):
sok = initiate_handshake(host, port)
start_time = current_time()
monitor = {}
file_thread = Thread(target=write_file, args=(sok, monitor))
file_thread.start()
data, addr = sok.recvfrom(buffer_size)
timeout_interval = 0.5
while (True):
try:
process_data(sok, data, monitor)
sok.settimeout(timeout_interval)
data, addr = sok.recvfrom(buffer_size)
except socket.timeout:
print('will try after {} seconds'.format(timeout_interval))
timeout_interval *= 2
except ConnectionRefusedError:
print('It seems the server is not online, sleeping for {} seconds'.
format(timeout_interval))
time.sleep(timeout_interval)
timeout_interval *= 2
finally:
if timeout_interval > 10:
print('no response since 10 seconds. exiting')
monitor['disconnected'] = True
break
if monitor.get('finished', False):
print("transfer Complete in", current_time() - start_time)
break
def update(self):
for axis in self.position:
# Calculate time since update was last run
elapsed_time = current_time() - self.time_of_last_update[axis]
# Determine if position change needed
try:
inverse_velocity = 1 / abs( self.velocity[axis] + self.acceleration[axis] * elapsed_time )
except ZeroDivisionError:
inverse_velocity = 0
if (elapsed_time >= inverse_velocity):
# Calculate acceleration toward center
self.acceleration[axis] = -(self.position[axis] - 500)
# Calculate velocity
self.velocity[axis] = self.velocity[axis] + self.acceleration[axis] * elapsed_time
# Edge bouncing
if not (0 <= self.position[axis] <= 1000):
self.velocity[axis] = -self.velocity[axis]/1.1
# Teleport back inside displayed range
if (self.position[axis] > 500):
self.position[axis] = 1000
else:
self.position[axis] = 0
# Move to new position
self.position[axis] = self.position[axis] + int(elapsed_time * self.velocity[axis])
# Calculate position accuracy lost due to rounding
lost_position = ((elapsed_time * self.velocity[axis]) - int(elapsed_time * self.velocity[axis]))
# Reset the timer and adjust time for loss of position
self.time_of_last_update[axis] = current_time() - lost_position * 1/self.velocity[axis]
def solve(self):
t0 = current_time()
self.actual.solve()
t1 = current_time()
self.normal_equations_solving_time += t1 - t0
self.journal.step_norm_history.append(self.actual.step().norm())
if self.journal.step_history is not None:
self.journal.step_history.append(self.actual.step().deep_copy())
def solve(self):
t0 = current_time()
self.actual.solve()
t1 = current_time()
self.normal_equations_solving_time += t1 - t0
self.journal.step_norm_history.append(self.actual.step().norm())
if self.journal.step_history is not None:
self.journal.step_history.append(self.actual.step().deep_copy())
def run(self):
previous_update = current_time()
while True:
os.system('clear')
# Go through each particle
for particle in self.plane:
print(particle.position)
# Sleep to maintain update rate
update_delay = previous_update + self.update_interval - current_time()
previous_update = current_time()
sleep(max(0, update_delay))
def build_up(self, objective_only=False):
t0 = current_time()
self.actual.build_up(objective_only)
t1 = current_time()
self.normal_equations_building_time += t1 - t0
if objective_only: return
self.journal.parameter_vector_norm_history.append(
self.actual.parameter_vector_norm())
self.journal.objective_history.append(self.actual.objective())
self.journal.gradient_norm_history.append(
self.actual.opposite_of_gradient().norm_inf())
if self.journal.gradient_history is not None:
self.journal.gradient_history.append(-self.actual.opposite_of_gradient())
if self.journal.scale_factor_history is not None:
self.journal.scale_factor_history.append(self.actual.scale_factor())
def run(self):
logger.info('Running')
previous_update = current_time()
while not self.exit.is_set():
# Update each particle
for particle in self.plane:
particle.update()
# stuff and things
self.send.send(self.plane)
# Sleep to maintain update rate
update_delay = self.update_interval - (current_time() - previous_update)
previous_update = current_time()
sleep(max(0, update_delay))
def build_up(self, objective_only=False):
t0 = current_time()
self.actual.build_up(objective_only)
t1 = current_time()
self.normal_equations_building_time += t1 - t0
if objective_only: return
self.journal.parameter_vector_norm_history.append(
self.actual.parameter_vector_norm())
self.journal.objective_history.append(self.actual.objective())
self.journal.gradient_norm_history.append(
self.actual.opposite_of_gradient().norm_inf())
if self.journal.gradient_history is not None:
self.journal.gradient_history.append(-self.actual.opposite_of_gradient())
if self.journal.scale_factor_history is not None:
self.journal.scale_factor_history.append(self.actual.scale_factor())
def listener(sok, monitor, rate_queue, timeout_params, progress,
last_packet_num):
timeout_interval = 0.5
while (len(monitor)):
progress = 100 - ((len(monitor) - 1) * 100 / last_packet_num + 1) + 1
print("progress = {:.2f}%".format(progress))
try:
sok.settimeout(timeout_interval)
message, clientAddress = sok.recvfrom(2048)
# sequence_num = int.from_bytes(message[0:4], byteorder='big')
first_byte = message[0]
# discard packet if message type is 0(handshake)
if first_byte >> 7 & 1 == 0:
continue
# if hash is not correct, discard ack
if message[4:8] != xxhash.xxh32(message[0:4]).digest():
continue
else:
sequence_num = (first_byte & int('7f', 16)).to_bytes(
1, byteorder='big') + message[1:4]
sequence_num = int.from_bytes(sequence_num[0:4],
byteorder='big')
if sequence_num in monitor:
# finding RTT
sampleRTT = current_time() - monitor[sequence_num]
if timeout_params.get('estRTT', -1) == -1:
timeout_params['devRTT'] = 0
timeout_params['estRTT'] = sampleRTT
else:
timeout_params['estRTT'] = 0.125 * \
(sampleRTT) + 0.875*timeout_params['estRTT']
timeout_params['devRTT'] = 0.75 * \
timeout_params['devRTT'] + \
abs(timeout_params['estRTT']-sampleRTT)
timeout_params['interval'] = timeout_params['estRTT'] + \
4*timeout_params['devRTT']
monitor.pop(sequence_num, -1)
# rate_queue.pop(sequence_num, -1)
# if rate_queue.get(sequence_num, -1) != -1:
# print("got ack for", sequence_num, "qlen", len(rate_queue),
# "RTT", current_time() - rate_queue[sequence_num])
# else:
# print("got ack for", sequence_num)
except socket.timeout:
print('will try after {} seconds'.format(timeout_interval))
timeout_interval *= 1.5
except ConnectionRefusedError:
print('It seems the server is not online, sleeping for {} seconds'.
format(timeout_interval))
time.sleep(timeout_interval)
timeout_interval *= 1.5
finally:
if timeout_interval > 10:
print('no response since 10 seconds. exiting')
monitor['disconnected'] = True
exit()
sok.close()
def run(self):
previous_update = current_time()
while True:
for event in pygame.event.get():
if event.type == pygame.QUIT:
running = False
for particle in self.plane:
surface.set_at((particle['x'], particle['y']), color)
# Put the surface we draw on, onto the screen
screen.blit(surface, (0, 0))
# Show it.
pygame.display.flip()
# Sleep to maintain update rate
update_delay = previous_update + self.update_interval - current_time()
previous_update = current_time()
sleep(max(0, update_delay))
def Server(host, port, filename, progress):
sok = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
clientAddress = (host, port)
sok.bind(clientAddress)
while (True):
message, clientAddress = sok.recvfrom(2048)
if message.decode() == 'start':
break
print('start received')
b = os.path.getsize(filename)
last_packet_num = int(b / file_buffer_size)
if b % file_buffer_size == 0:
last_packet_num -= 1
print(last_packet_num)
monitor = {}
rate_queue = {}
timeout_params = {'estRTT': 0, 'interval': 0, 'devRTT': 0}
for i in range(0, last_packet_num + 1):
monitor[i] = -1
listener_thread = Thread(target=listener,
args=(sok, monitor, rate_queue, timeout_params,
progress, last_packet_num))
listener_thread.start()
f = open(filename, "rb")
sequence_number = 0
file_data = f.read()
# send fragments
flag = 1
while (len(monitor) and flag):
send_list = monitor.copy()
for sequence_number in send_list:
# temp = current_time()
if monitor.get('disconnected', False):
flag = 0
break
if monitor.get(sequence_number, -2) == -2:
continue
time.sleep(0.02)
while (current_time() - monitor.get(sequence_number, 0) <
timeout_params['interval']):
time.sleep(0.001)
# print("sending packet", sequence_number, "qlen", len(monitor))
data = file_data[sequence_number *
file_buffer_size:file_buffer_size *
(sequence_number + 1)]
send_packet(sok, sequence_number, data, clientAddress, monitor,
last_packet_num, rate_queue)
# print('time taken', current_time()-temp)
f.close()
def send_packet(sok, sequence_number, data, clientAddress, monitor,
last_packet_num, rate_queue):
if monitor.get('disconnected', False):
return
elif sequence_number in monitor:
# timer = Timer(0.1, send_packet, args=(sok, sequence_number,
# data, clientAddress, monitor, last_packet_num, rate_queue))
# timer.start() # after 30 seconds, "hello, world" will be printed
monitor[sequence_number] = current_time()
packet_string = makepkg(sequence_number, data, last_packet_num)
sok.sendto(packet_string, clientAddress)
# rate_queue[sequence_number] = True
# print('\t\t\t\tsent packet number', sequence_number)
else:
return
Supported formats for the INPUT and OUTPUT files are CIF and ShelX
whereas REFLECTIONS file format may be any of those supported
by iotbx.reflection_file_reader.
A certain amount of guessing is done by the program:
- if INPUT lacks any extension, a .ins extension is appended;
- if OUTPUT is not specified,
o if INPUT is a .ins file, then OUTPUT is a .res file with the same root;
o otherwise OUTPUT has the same extension as INPUT but with "-out"
appended to INPUT root.
- if REFLECTIONS is not specified, it is INPUT root with a .hkl extension
"""
if __name__ == '__main__':
from timeit import default_timer as current_time
t0 = current_time()
import sys, optparse
parser = optparse.OptionParser(usage=here_usage,
description=here_description)
parser.add_option('--overwrite',
action='store_true',
help='allows OUTPUT to be overwritten')
parser.add_option(
'--stop-if-max-derivative-below',
type='float',
default=1e-7,
help=
'Stop refinement as soon as the largest absolute value of objective '
'derivatives is below the given threshold.')
parser.add_option(
'--stop-if-shift-norm-below',
def __init__(self, X_position, Y_position, X_velocity=0 ,Y_velocity=0, mass=600):
self.mass = mass
self.velocity = {'x':X_velocity,'y':Y_velocity}
self.position = {'x':X_position,'y':Y_position}
self.time_of_last_update = {'x':current_time(),'y':current_time()}
self.acceleration = {'x':0,'y':90.81}
import ctypes
import numpy as np
pixel_array_base = Array(ctypes.c_int, width*height)
pixel_array = np.ctypeslib.as_array(pixel_array_base.get_obj())
pixel_array = pixel_array.reshape(width, height)
from pygametranslator import Translator
Jacks_sweet_threads = Translator(recv, pixel_array)
# Start things
Jacks_sweet_thread.start()
Jacks_sweet_threads.start()
update_interval = 1/60
running = True
previous_update = current_time()
while running:
for event in pygame.event.get():
if event.type == pygame.QUIT:
running = False
pygame.surfarray.blit_array(screen, pixel_array)
pygame.display.flip()
clock.tick()
pygame.display.set_caption('FPS: ' + str(int(clock.get_fps())))
# Sleep to maintain update rate
update_delay = update_interval - (current_time() - previous_update)
previous_update = current_time()
sleep(max(0, update_delay))
def run(filenames, options):
#interpret file names
if not 1 <= len(filenames) <= 3:
raise number_of_arguments_error()
input_filename = filenames[0]
output_filename = None
reflections_filename = None
if len(filenames) == 3:
reflections_filename, output_filename = filenames[1:]
elif len(filenames) == 2:
_, ext = os.path.splitext(filenames[1])
if ext in allowed_input_file_extensions:
output_filename = filenames[1]
else:
reflections_filename = filenames[1]
# adjust file names
in_root, in_ext = os.path.splitext(input_filename)
if not in_ext: in_ext = '.ins'
if reflections_filename is None:
reflections_filename = in_root + '.hkl'
if output_filename is None:
if in_ext == '.ins':
out_root, out_ext = in_root, '.res'
else:
out_root, out_ext = in_root + '-out', in_ext
output_filename = out_root + out_ext
else:
out_root, out_ext = os.path.splitext(output_filename)
# check extensions are supported
for ext in (in_ext, out_ext):
if ext not in allowed_input_file_extensions:
raise command_line_error("unsupported extension: %s" % ext)
# Investigate whether input and ouput files do exist, are the same, etc
for filename in (input_filename, reflections_filename):
if not os.path.isfile(filename):
raise command_line_error("No such file %s" % filename)
if os.path.isfile(output_filename):
if not options.overwrite:
raise command_line_error(
"refuse to overwrite file %s (use option 'overwrite' to force it)"
% output_filename)
# Load input model and reflections
if in_ext == '.cif':
xm = refinement.model.from_cif(model=input_filename,
reflections=reflections_filename)
else:
xm = refinement.model.from_shelx(ins_or_res=input_filename,
hkl=reflections_filename,
strictly_shelxl=False)
sgi = xm.xray_structure.space_group_info()
sg = sgi.group()
print("Space group: %s" % sgi.type().hall_symbol())
print("\t* %scentric" % ('non-', '')[sg.is_centric()])
print("\t* %schiral" % ('a', '')[sg.is_chiral()])
print("%i reflections" % len(xm.fo_sq.indices))
# At last...
for sc in xm.xray_structure.scatterers():
sc.flags.set_grad_site(True)
if sc.flags.use_u_iso(): sc.flags.set_grad_u_iso(True)
if sc.flags.use_u_aniso(): sc.flags.set_grad_u_aniso(True)
ls = xm.least_squares()
print("%i atoms" % len(ls.reparametrisation.structure.scatterers()))
print("%i refined parameters" % ls.reparametrisation.n_independents)
steps = lstbx.normal_eqns_solving.naive_iterations(
non_linear_ls=ls,
n_max_iterations=options.max_cycles,
gradient_threshold=options.stop_if_max_derivative_below,
step_threshold=options.stop_if_shift_norm_below)
print("Normal equations building time: %.3f s" % \
steps.non_linear_ls.normal_equations_building_time)
print("Normal equations solving time: %.3f s" % \
steps.non_linear_ls.normal_equations_solving_time)
t0 = current_time()
cov = ls.covariance_matrix_and_annotations()
print("Covariance matrix building: %.3f" % (current_time() - t0))
# Write result to disk
if out_ext != '.cif':
raise NotImplementedError("Write refined structure to %s file" %
out_ext)
with open(output_filename, 'w') as out:
xm.xray_structure.as_cif_simple(out)
def run(self):
print(self.name + ' ready')
# Less spag bowl (and great variable naming)
i = self.indexs
particles_to_update = self.frame.get()
while particles_to_update is not None:
for particle_index in particles_to_update:
# Check to see if the position would have changed, and the particle should be updated
axis_to_update = []
for particle_axis in self.particle_list[particle_index]:
# Calculate time since particle was last updated
elapsed_time = current_time() - particle_axis[
i['time of update']]
# Determine if a position change is needed
try:
inverse_velocity = 1 / (
particle_axis[i['velocity']] +
particle_axis[i['acceleration']] * elapsed_time)
except ZeroDivisionError:
inverse_velocity = 0
# Determine which axis needs to be updated
axis_to_update.append(
elapsed_time >= abs(inverse_velocity))
if any(axis_to_update):
move_distance = axis_to_update
# Calculate potential new distance
for axis_index, update_required in enumerate(
axis_to_update):
particle_axis = self.particle_list[particle_index][
axis_index] # Less spaghetti
if update_required:
# Calculate acceleration toward center sometimes
particle_axis[i['acceleration']] = 2 * (
(self.size[axis_index] + 1) / 2 -
particle_axis[i['position']])
# Get elapsed_time
elapsed_time = current_time() - particle_axis[
i['time of update']]
# Calculate velocity
particle_axis[i['velocity']] = particle_axis[
i['velocity']] + particle_axis[
i['acceleration']] * elapsed_time
# Calculate new position
move_distance[
axis_index] = elapsed_time * particle_axis[
i['velocity']]
# Calculate position accuracy lost due to rounding
lost_position = int(move_distance[axis_index]
) - move_distance[axis_index]
# Reset the timer and adjust time for loss of position
try:
particle_axis[
i['time of update']] = current_time(
) + lost_position / particle_axis[
i['velocity']]
except ZeroDivisionError:
particle_axis[
i['time of update']] = current_time()
# Determine positions crossed to reach new position
final = [
int(move_distance[i['x']]),
int(move_distance[i['y']])
]
coord = [0, 0]
if 0 in final:
slope = [0, 0]
else:
slope = [final[1] / final[0], final[0] / final[1]]
lmao = 0 if abs(final[1]) < abs(final[0]) else 1
move_distance = [0, 0]
# Check each coordinate for an obstruction
while coord[lmao] != final[lmao]:
coord[lmao] += sign(final[lmao])
previous_point = move_distance
move_distance = [
coord[lmao],
int(slope[lmao] * coord[lmao])
] if lmao is 0 else [
int(slope[lmao] * coord[lmao]), coord[lmao]
]
# Check for inteferance with walls
for axis_index in range(len(move_distance)):
if not (0 <= self.particle_list[particle_index]
[axis_index][i['position']] +
move_distance[axis_index] <=
self.size[axis_index]):
# Reverse direction
self.particle_list[particle_index][axis_index][
i['velocity']] = -self.particle_list[
particle_index][axis_index][
i['velocity']]
# Move back inside wall range
move_distance[axis_index] = previous_point[
axis_index]
# Stop checking coordinates
final[lmao] = coord[lmao]
if final[lmao] is not coord[lmao]:
# Check for collisions with particles
hit_particle = self.particle_map[
int(self.particle_list[particle_index][i['x']][
i['position']] + move_distance[i['x']]),
int(self.particle_list[particle_index][i['y']][
i['position']] + move_distance[i['y']])]
if hit_particle > 0 and hit_particle - 1 != particle_index:
# Swap velocities
self.particle_list[hit_particle - 1][axis_index][
i['velocity']], self.particle_list[
particle_index][axis_index][i[
'velocity']] = self.particle_list[
particle_index][axis_index][i[
'velocity']], self.particle_list[
hit_particle -
1][axis_index][
i['velocity']]
# Move back one point
move_distance = previous_point
# Stop checking coordinates
final[lmao] = coord[lmao]
# Create a debug particle to show where it's checking
self.particle_map[
int(self.particle_list[particle_index][i['x']][
i['position']] + move_distance[i['x']]),
int(self.particle_list[particle_index][i['y']][
i['position']] + move_distance[i['y']])] = -1
# Adjust for lost time
for axis_index, particle_axis in enumerate(final):
self.particle_list[particle_index][axis_index][
i['time of update']] = self.particle_list[
particle_index][axis_index][
i['time of update']] + abs(
particle_axis -
move_distance[axis_index]) / abs(
self.particle_list[particle_index]
[axis_index][i['velocity']])
# Update map
self.particle_map[int(self.particle_list[particle_index][
i['x']][i['position']])][int(
self.particle_list[particle_index][i['y']][
i['position']])] = 0
self.particle_map[int(
self.particle_list[particle_index][i['x']]
[i['position']] + int(move_distance[i['x']]))][int(
self.particle_list[particle_index][i['y']][
i['position']] +
int(move_distance[i['y']]))] = particle_index + 1
# Update list
for axis_index, update_required in enumerate(final):
self.particle_list[particle_index][axis_index][i[
'position']] = self.particle_list[particle_index][
axis_index][i['position']] + int(
move_distance[axis_index])
particles_to_update = self.frame.get()
print('Setting up main loop')
# Start physics threads
for process in phyics_process:
process.start()
# Setup main loop
from timeit import default_timer as current_time
from time import sleep
from numpy import where
running = True
input('Loaded, press enter to start main loop')
# Update the time since update to just before it starts
previous_update = current_time()
for particle in particle_list:
for axis in particle:
axis[i['time of update']] = previous_update
# Main loop
while running:
# Listen for window exit button
for event in pygame.event.get():
if event.type == pygame.QUIT:
running = False
# Erase debug particles
particle_map[particle_map < 0] = 0
# Request new frame from physics processes
for cpu_core in range(physics_cpus):
frame_queue[cpu_core].put(list(range(round(number_of_particles/physics_cpus*(cpu_core)), round(number_of_particles/physics_cpus*(cpu_core+1)))))
Supported formats for the INPUT and OUTPUT files are CIF and ShelX
whereas REFLECTIONS file format may be any of those supported
by iotbx.reflection_file_reader.
A certain amount of guessing is done by the program:
- if INPUT lacks any extension, a .ins extension is appended;
- if OUTPUT is not specified,
o if INPUT is a .ins file, then OUTPUT is a .res file with the same root;
o otherwise OUTPUT has the same extension as INPUT but with "-out"
appended to INPUT root.
- if REFLECTIONS is not specified, it is INPUT root with a .hkl extension
"""
if __name__ == '__main__':
from timeit import default_timer as current_time
t0 = current_time()
import sys, optparse
parser = optparse.OptionParser(
usage=here_usage,
description=here_description)
parser.add_option(
'--overwrite',
action='store_true',
help='allows OUTPUT to be overwritten')
parser.add_option(
'--stop-if-max-derivative-below',
type='float',
default=1e-7,
help='Stop refinement as soon as the largest absolute value of objective '
'derivatives is below the given threshold.')
parser.add_option(