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master_openworm.py
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master_openworm.py
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import errno
import matplotlib
matplotlib.use('Agg')
import shutil
from subprocess import Popen, PIPE, check_output, STDOUT
import os
import pwd
import shlex
import sys
import time
import glob
import math
print("*****************************")
print("OpenWorm Master Script v0.9.3")
print("*****************************")
print("")
print("This script attempts to run a full pass through the OpenWorm scientific libraries.")
print("This depends on several other repositories being loaded to work and presumes it is running in a preloaded Docker instance.")
print("It will report out where steps are missing.")
print("Eventually all the steps will be filled in.")
print("")
print("****************************")
print("Step 1: Rebuild c302 from the latest owmeta")
print("****************************")
print("Not yet implemented. See https://github.com/openworm/c302/issues/10")
print("****************************")
print("Step 2: Execute unit tests via the c302 simulation framework")
print("****************************")
"""
from runAndPlot import run_c302
orig_display_var = None
if os.environ.has_key('DISPLAY'):
orig_display_var = os.environ['DISPLAY']
del os.environ['DISPLAY'] # https://www.neuron.yale.edu/phpBB/viewtopic.php?f=6&t=1603
run_c302(DEFAULTS['reference'],
DEFAULTS['c302params'],
'',
DEFAULTS['duration'],
DEFAULTS['dt'],
'jNeuroML_NEURON',
data_reader=DEFAULTS['datareader'],
save=True,
show_plot_already=False,
target_directory=os.path.join(os.environ['C302_HOME'], 'examples'),
save_fig_to='tmp_images')
prev_dir = os.getcwd()
os.chdir(DEFAULTS['outDir'])
try:
os.mkdir('c302_out')
except OSError as e:
if e.errno != errno.EEXIST:
raise
src_files = os.listdir(os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images'))
for file_name in src_files:
full_file_name = os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images', file_name)
print("COPY %s" % full_file_name)
if (os.path.isfile(full_file_name)):
shutil.copy2(full_file_name, 'c302_out')
shutil.rmtree(os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images'))
os.chdir(prev_dir)
if orig_display_var:
os.environ['DISPLAY'] = orig_display_var
"""
print("****************************")
print("Step 3: Run c302 + Sibernetic in the same loop.")
print("****************************")
OW_OUT_DIR = os.environ['OW_OUT_DIR']
def execute_with_realtime_output(command, directory, env=None):
p = None
try:
print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
print('>> Executing command: %s'%command)
print('>> --------------------------------------------------------------')
p = Popen(shlex.split(command),
stdout=PIPE,
stderr=STDOUT,
cwd=directory,
env=env)
with p.stdout:
for line in iter(p.stdout.readline, b''):
print('>> %s'%line.decode('utf-8'), end='')
p.wait() # wait for the subprocess to exit
except KeyboardInterrupt as e:
print("Caught CTRL+C")
if p:
p.kill()
raise e
print('>> --------------------------------------------------------------')
print('>> Command exited with %i: %s'%(p.returncode,command))
print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n')
if p.returncode!=0:
print('Exiting as the last command failed')
exit(p.returncode)
sys.path.append(os.environ['C302_HOME'])
try:
os.system('echo Granting permissions for xhost && xhost +')
except:
print("Unexpected error: %s" % sys.exc_info()[0])
OW_OUT_DIR = os.environ['OW_OUT_DIR']
try:
if os.access(OW_OUT_DIR, os.W_OK) is not True:
os.system('sudo chown -R %s:%s %s' % (os.environ['USER'], os.environ['USER'], OW_OUT_DIR))
except:
print("Unexpected error: %s" % sys.exc_info()[0])
raise
#Default is 15 ms of simulation time.
sim_duration = 15.0
if 'DURATION' in os.environ:
sim_duration = float(os.environ['DURATION'])
noc302 = False
if 'NOC302' in os.environ:
noc302 = bool(os.environ['NOC302'])
DEFAULTS = {'duration': sim_duration,
'dt': 0.005,
'dtNrn': 0.05,
'logstep': 100,
'reference': 'FW',
'c302params': 'C2',
'verbose': False,
'device': 'CPU',
'configuration': 'worm_crawl_half_resolution',
'noc302': noc302,
'datareader': 'UpdatedSpreadsheetDataReader2',
'outDir': OW_OUT_DIR}
my_env = os.environ.copy()
DISPLAY = ':44'
my_env["DISPLAY"] = DISPLAY
# Xvfb or X virtual framebuffer is a display server implementing the X11 display server protocol.
# In contrast to other display servers, Xvfb performs all graphical operations in virtual memory without showing any screen output.
os.system('echo Starting xvfb && Xvfb %s -listen tcp -ac -screen 0 1920x1080x24+32 &'%DISPLAY) # TODO: terminate xvfb after recording
try:
command = """python sibernetic_c302.py
-duration %s
-dt %s
-dtNrn %s
-logstep %s
-device=%s
-configuration %s
-reference %s
-c302params %s
-datareader %s
-outDir %s""" % \
(DEFAULTS['duration'],
DEFAULTS['dt'],
DEFAULTS['dtNrn'],
DEFAULTS['logstep'],
DEFAULTS['device'],
DEFAULTS['configuration'],
DEFAULTS['reference'],
DEFAULTS['c302params'],
DEFAULTS['datareader'],
'simulations')
#DEFAULTS['outDir'])
if noc302: command += ' -noc302'
execute_with_realtime_output(command, os.environ['SIBERNETIC_HOME'], env=my_env)
except KeyboardInterrupt as e:
pass
sibernetic_sim_dir = '%s/simulations' % os.environ['SIBERNETIC_HOME']
all_subdirs = []
for dirpath, dirnames, filenames in os.walk(sibernetic_sim_dir):
for directory in dirnames:
if directory.startswith('%s_%s' % (DEFAULTS['c302params'], DEFAULTS['reference'])):
all_subdirs.append(os.path.join(dirpath, directory))
if directory.startswith('Sibernetic'):
all_subdirs.append(os.path.join(dirpath, directory))
latest_subdir = max(all_subdirs, key=os.path.getmtime)
print('\n========================================================================\n')
print('Finished main simulation, data saved in: %s'%latest_subdir)
execute_with_realtime_output('ls -alt %s'%latest_subdir, os.environ['SIBERNETIC_HOME'], env=my_env)
try:
os.mkdir('%s/output' % OW_OUT_DIR)
except OSError as e:
if e.errno != errno.EEXIST:
raise
new_sim_out = '%s/output/%s' % (OW_OUT_DIR, os.path.split(latest_subdir)[-1])
try:
os.mkdir(new_sim_out)
except OSError as e:
if e.errno != errno.EEXIST:
raise
# Copy PNGs, created during the Sibernetic simulation, in a separate child-directory to find them more easily
figures = glob.glob('%s/*.png' % latest_subdir)
for figure in figures:
print("Moving %s to %s"%(figure, new_sim_out))
shutil.move(figure, new_sim_out)
# Copy reports etc.
reports = glob.glob('%s/report*' % latest_subdir)
for report in reports:
print("Moving %s to %s"%(report, new_sim_out))
shutil.move(report, new_sim_out)
# Copy WCON file(s)
wcons = glob.glob('%s/*.wcon' % latest_subdir)
for wcon in wcons:
print("Moving %s to %s"%(wcon, new_sim_out))
shutil.move(wcon, new_sim_out)
time.sleep(2)
# Rerun and record simulation
execute_with_realtime_output('ls -alt /tmp/.X11-unix', os.environ['SIBERNETIC_HOME'], env=my_env)
os.system('export DISPLAY=%s'%DISPLAY)
execute_with_realtime_output('ls -alt /tmp/.X11-unix', os.environ['SIBERNETIC_HOME'], env=my_env)
sibernetic_movie_name = '%s.mp4' % os.path.split(latest_subdir)[-1]
command = 'tmux new-session -d -P -s SiberneticRecording "DISPLAY=%s ffmpeg -r 30 -f x11grab -draw_mouse 0 -s 1920x1080 -i %s -filter:v "crop=1200:800:100:100" -cpu-used 0 -b:v 384k -qmin 10 -qmax 42 -maxrate 384k -bufsize 1000k -an %s/%s"' % (DISPLAY, DISPLAY, new_sim_out, sibernetic_movie_name)
execute_with_realtime_output(command, os.environ['SIBERNETIC_HOME'], env=my_env)
time.sleep(3)
execute_with_realtime_output('tmux list-sessions', os.environ['SIBERNETIC_HOME'], env=my_env)
command = './Release/Sibernetic -f %s -l_from lpath=%s' % (DEFAULTS['configuration'], latest_subdir)
execute_with_realtime_output(command, os.environ['SIBERNETIC_HOME'], env=my_env)
execute_with_realtime_output('tmux send-keys -t SiberneticRecording q', os.environ['SIBERNETIC_HOME'], env=my_env)
execute_with_realtime_output('tmux send-keys -t SiberneticRecording "exit" C-m', os.environ['SIBERNETIC_HOME'], env=my_env)
time.sleep(3)
execute_with_realtime_output('ls -alt %s'%latest_subdir, os.environ['SIBERNETIC_HOME'], env=my_env)
# Remove black frames at the beginning of the recorded video
command = "ffmpeg -i %s/%s -vf blackdetect=d=0:pic_th=0.70:pix_th=0.10 -an -f null - 2>&1 | grep blackdetect" % (new_sim_out, sibernetic_movie_name)
outstr = str(check_output(command, shell=True).decode('utf-8'))
outstr = outstr.split('\n')
black_start = 0.0
black_dur = None
out = outstr[0]
black_start_pos = out.find('black_start:')
black_end_pos = out.find('black_end:')
black_dur_pos = out.find('black_duration:')
if black_start_pos != -1:
black_start = float(out[black_start_pos + len('black_start:') : black_end_pos])
black_dur = float(out[black_dur_pos + len('black_duration:'):])
if black_start == 0.0 and black_dur:
black_dur = int(math.ceil(black_dur))
command = 'ffmpeg -ss 00:00:0%s -i %s/%s -c copy -avoid_negative_ts 1 %s/cut_%s' % (black_dur, new_sim_out, sibernetic_movie_name, new_sim_out, sibernetic_movie_name)
if black_dur > 9:
command = 'ffmpeg -ss 00:00:%s -i %s/%s -c copy -avoid_negative_ts 1 %s/cut_%s' % (black_dur, new_sim_out, sibernetic_movie_name, new_sim_out, sibernetic_movie_name)
os.system(command)
# SPEED-UP
try:
os.mkdir('tmp')
except OSError as e:
if e.errno != errno.EEXIST:
raise
os.system('ffmpeg -ss 1 -i %s/cut_%s -vf "select=gt(scene\,0.1)" -vsync vfr -vf fps=fps=1/1 %s' % (new_sim_out, sibernetic_movie_name, 'tmp/out%06d.jpg'))
os.system('ffmpeg -r 100 -i %s -r 100 -vb 60M %s/speeded_%s' % ('tmp/out%06d.jpg', new_sim_out, sibernetic_movie_name))
os.system('rm -r tmp/*')
print("****************************")
print("Step 4: Run movement analysis")
print("****************************")
print("Not yet implemented.")
print("Note however the following WCON files have been generated into %s during the simulation: %s"%(new_sim_out, [w.split('/')[-1] for w in wcons]))
print("****************************")
print("Step 5: Report on movement analysis fit to real worm videos")
print("****************************")
print("Not yet implemented.")