def glass_renv(**kwargs):
"""
Call to set up a standard glass 'read' environment
Args:
None
Kwargs:
threads <int> - run with given number of threads
no_window <bool> - suppress any graphics
Return:
glass <module> - the glass environment as a module
"""
try:
_, arglist = getopt.getopt(sys.argv[1:], 't:h:f', ['nw'])
except getopt.GetoptError:
arglist = []
Environment.global_opts['ncpus_detected'] = _detect_cpus()
Environment.global_opts['ncpus'] = 1
Environment.global_opts['omp_opts'] = _detect_omp()
Environment.global_opts['withgfx'] = True
Environment.global_opts['argv'] = arglist
Commands.set_env(Environment())
if 'threads' in kwargs and kwargs['threads'] >= 1:
Environment.global_opts['ncpus'] = kwargs['threads']
if 'no_window' in kwargs:
Environment.global_opts['withgfx'] = kwargs['no_window']
import glass.glcmds
import glass.scales
if Environment.global_opts['withgfx']:
import glass.plots
glass_basis('glass.basis.pixels', solver=None)
glass.basis.pixels.priors.exclude_all_priors()
return glass
def run(*args, **kwargs):
"""
Call to run a GLASS config file within a standard glass 'write' environment
Args:
args <str/tuple(str)> - input files for GLASS, e.g. '../src/glass/Examples/B1115.gls'
Kwargs:
threads <int> - run with given number of threads
no_window <bool> - suppress any graphics
Return:
None
"""
Environment.global_opts['ncpus_detected'] = _detect_cpus()
Environment.global_opts['ncpus'] = 1
Environment.global_opts['omp_opts'] = _detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
if 'thread' in kwargs and kwargs['threads'] > 1:
Environment.global_opts['ncpus'] = kwargs['threads']
if 'no_window' in kwargs:
Environment.global_opts['withgfx'] = kwargs['no_window']
import glass.glcmds
import glass.scales
if Environment.global_opts['withgfx']:
import glass.plots
with open(args[0], 'r') as f:
Commands.get_env().input_file = f.read()
Environment.global_opts['argv'] = args
try:
execfile(args[0])
except GLInputError as e:
raise e(
"An error occurred! Figure out whats wrong and give it another go..."
)
def new_env(env):
Commands.set_env(Environment())
def help():
print >> sys.stderr, "Usage: glass.py <input>"
sys.exit(2)
if __name__ == "__main__":
if len(sys.argv) < 2: help()
Environment.global_opts['ncpus_detected'] = _detect_cpus()
Environment.global_opts['ncpus'] = 1
Environment.global_opts['omp_opts'] = _detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
optlist, arglist = getopt.getopt(sys.argv[1:], 't:h', ['nw'])
for opt in optlist:
if opt[0] == '-h':
help()
elif opt[0] == '-t':
ncpus = int(opt[1])
assert ncpus > 0
#Commands.get_env().ncpus = ncpus
Environment.global_opts['ncpus'] = ncpus
elif opt[0] == '--nw':
#Commands.get_env().withgfx = False
Environment.global_opts['withgfx'] = False
f = __import__(name, globals(), locals())
for name, [f, g, help_text] in Commands.glass_command_list.iteritems():
if name in __builtins__.__dict__:
message = 'WARNING: Glass command {:s} ({:s}) overrides previous function {:s}'
print(message.format(name, f, __builtins__.__dict__[name]))
__builtins__.__dict__[name] = g
if __name__ == "__main__":
app = 'app.py'
Environment.global_opts['ncpus_detected'] = _detect_cpus()
Environment.global_opts['ncpus'] = 1
Environment.global_opts['omp_opts'] = _detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
import glass.glcmds
import glass.scales
if Environment.global_opts['withgfx']:
import glass.plots
glass_basis('glass.basis.pixels', solver=None)
exclude_all_priors()
Environment.global_opts['argv'] = [app] + sys.argv[1:]
opts = Environment.global_opts['argv']
states = [loadstate(f) for f in opts[1:]]
root, zapper = Zapp.init(gls_states=states, verbose=1)
os.system(
def runGLASS(self, GLASSconfig, config):
import matplotlib as mpl
mpl.use('Agg') # make sure this is above the other mpl imports
from matplotlib import pyplot as plt
import pylab as pl
this = self
hist = []
# def status(*args):
# if len(args)<3:
# while len(args)<3:
# args.append(0)
# hist.append(args)
# update_status(hist)
#
# def status2(lst):
# # this is hack to fix the complicated stuff in glass.
# # I don't know why I put it there.. possibly its better to have the history here
# print "\n", "--"*40
# print lst
# print "--"*40
# status(lst[-1])
def update_status(hist):
currStatus = hist[-1]
if not this.request.called_directly:
this.update_state(state='PROGRESS', meta={
'text': currStatus[0],
'i' : currStatus[1],
'of' : currStatus[2],
'hist': json.dumps(hist)
})
#print ">> UPDATE_STAT: %-20s: %04i of %04i" % tuple(currStatus)
if DEBUG:
print '='*80
print "got GLASSconfig:\n"
for k, v in GLASSconfig.items():
print '%-16s : %s' % (k,v)
print '='*80
print "got config:\n"
for k, v in config.items():
print '%-16s : %s' % (k,v)
print '='*80
figpath = '/tmp/spaghettilens/'
name = str(config['model_id']) # we don't like unicode here for some reason...
path = os.path.join(figpath, name)
try: # this prevents a race condition
os.makedirs(path)
except OSError:
if not os.path.isdir(path):
raise
# don't take this outside, because only the worker has glass installed,
# the webserver doesn't
# so there will be import errors
from glass.environment import env, Environment
from glass.command import command, Commands
from glass.exmass import PointMass
from glass.exceptions import GLInputError
from glass.log import Status, setup_status_reporter
@command('Load a glass basis set')
def glass_basis(env, name, **kwargs):
#print __builtins__
env.basis_options = kwargs
f = __import__(name, globals(), locals())
for name,[f,g,help_text] in Commands.glass_command_list.iteritems():
if __builtins__.has_key(name):
print 'WARNING: Glass command %s (%s) overrides previous function %s' % (name, f, __builtins__[name])
__builtins__[name] = g
#update_status({'text':'', 'progress':(0,0)})
setup_status_reporter([update_status])
Status('init')
Environment.global_opts['ncpus_detected'] = 2
Environment.global_opts['ncpus'] = 2
Environment.global_opts['omp_opts'] = {} #_detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
if Environment.global_opts['withgfx']:
import glass.plots
import glass.glcmds
import glass.scales
GC = GLASSconfig
C = config
logfile = os.path.join(path, "glass.log")
glass_basis('glass.basis.pixels', solver='rwalk')
meta(author=GC['author'], notes=GC['notes'])
setup_log(logfile, stdout=True)
samplex_random_seed(GC['random_seed'])
# samplex_acceptance(rate=0.25, tol=0.15)
samplex_acceptance(**GC['samplex_acceptance'])
if GC['exclude_all_priors']:
exclude_all_priors()
# include_prior(
# 'lens_eq',
# 'time_delay',
# 'profile_steepness',
# 'J3gradient',
# 'magnification',
# 'hubble_constant',
# 'PLsmoothness3',
# 'shared_h',
# 'external_shear'
# )
include_prior(*GC['include_priors'])
# hubble_time(13.7)
# globject('B1115+080')
hubble_time(GC['hubbletime'])
globject(C['model_id'])
# zlens(0.31)
# pixrad(6)
# steepness(0,None)
# smooth(2,include_central_pixel=False)
# local_gradient(45)
# shear(0.01)
zlens(GC['z_lens'])
pixrad(GC['pixrad'])
steepness(*GC['steepness'])
smooth(GC['smooth_val'],include_central_pixel=GC['smooth_ic'])
local_gradient(GC['loc_grad'])
shear(GC['shear'])
hires(GC['hires'])
if GC['isSym']:
symm()
#
# A = 0.3550, 1.3220
# B = -0.9090, -0.7140
# C = -1.0930, -0.2600
# D = 0.7170, -0.6270
#
# source(1.722, A,'min',
# B,'min', 13.3,
# C,'sad', None,
# D,'sad', 11.7)
#print GC['source']
source(*GC['source'])
for i, exm in enumerate(GC['ext_masses']):
external_mass(PointMass(exm['x'],exm['y'],name='PM%02i'%i), (0, exm['m']))
# update_status({'text':'started modelling', 'progress':(0,0)})
Status('started modelling')
model(GC['n_models']) #, update_hook=status2)
# update_status({'text':'create files', 'progress':(0,5)})
Status('create files', 0,5)
savestate(os.path.join(path, 'state.glass'))
# update_status({'text':'create files', 'progress':(1,5)})
Status('create files', 1,5)
env().make_ensemble_average()
env().arrival_plot(env().ensemble_average, only_contours=True, colors='magenta', clevels=40)
env().overlay_input_points(env().ensemble_average)
pl.gca().axes.get_xaxis().set_visible(False)
pl.gca().axes.get_yaxis().set_visible(False)
pl.savefig(os.path.join(path, 'img1.png'))
pl.close()
# update_status({'text':'create files', 'progress':(2,5)})
Status('create files', 2,5)
env().kappa_plot(env().ensemble_average, 0, with_contours=True, clevels=20, vmax=1, with_colorbar=False)
pl.gca().axes.get_xaxis().set_visible(False)
pl.gca().axes.get_yaxis().set_visible(False)
pl.savefig(os.path.join(path, 'img2.png'))
pl.close()
# update_status({'text':'create files', 'progress':(3,5)})
Status('create files', 3,5)
env().srcdiff_plot(env().ensemble_average)
env().overlay_input_points(env().ensemble_average)
pl.gca().axes.get_xaxis().set_visible(False)
pl.gca().axes.get_yaxis().set_visible(False)
pl.savefig(os.path.join(path, 'img3.png'))
pl.close()
# update_status({'text':'create files', 'progress':(4,5)})
Status('create files', 4,5)
env().srcdiff_plot_adv(env().ensemble_average, night=True, upsample=8)
env().overlay_input_points(env().ensemble_average)
pl.savefig(os.path.join(path, 'img3_ipol.png'), facecolor='black', edgecolor='none')
pl.close()
# update_status({'text':'create files', 'progress':(5,5)})
Status('create files', 5,5)
# upload
files = [
'state.glass',
'img1.png',
'img2.png',
'img3.png',
'img3_ipol.png',
]
host = config['upload_host']
user = config['upload_user']
destpath = config['upload_dest']
# TODO: if this woker runs on the web server, ssh connection failes
# solutions:
# have a dedicated user for uploading the files, OR
# code in a check, and on server use simple file transfer method
ssh = SSHClient()
ssh.load_system_host_keys()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh.connect(host, username=user)
scp = SCPClient(ssh.get_transport())
# update_status({'text':'upload files', 'progress':(0,5)})
Status('upload files', 0, 6)
for i, f in enumerate(files):
scp.put(os.path.join(path, f), os.path.join(destpath, f))
#update_status({'text':'upload files', 'progress':(i+1,5)})
Status('upload files', i+1, 6)
# upload log file
scp.put(logfile, os.path.join(destpath, 'glass.log'))
os.remove(logfile) # delete logfile
Status('upload files', i+1, 6)
# ...
#
# model(1000, update_hook=update_status)
#
# for i in range(40):
# print i
# time.sleep(0.5)
# if not self.request.called_directly:
# self.update_state(state='PROGRESS', meta={'solutions': ( i, 40)})
Status('finished')
return {}
######
# DEMO
##@shared_task
#@app.task(bind=True)
#def add(self, x, y):
#
# print 0
#
# time.sleep(1)
# print 1
#
# if not self.request.called_directly:
# self.update_state(state='PROGRESS', meta={'current': 0, 'total': 2})
#
#
# time.sleep(1)
# print 2
#
# if not self.request.called_directly:
# self.update_state(state='PROGRESS', meta={'current': 1, 'total': 2})
#
# time.sleep(1)
# print 3
#
#
# if not self.request.called_directly:
# self.update_state(state='PROGRESS', meta={'current': 2, 'total': 2})
#
# return x + y
def help():
print >>sys.stderr, "Usage: glass.py <input>"
sys.exit(2)
if __name__ == "__main__":
if len(sys.argv) < 2: help()
Environment.global_opts['ncpus_detected'] = _detect_cpus()
Environment.global_opts['ncpus'] = 1
Environment.global_opts['omp_opts'] = _detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
optlist, arglist = getopt.getopt(sys.argv[1:], 't:h', ['nw'])
for opt in optlist:
if opt[0] == '-h':
help()
elif opt[0] == '-t':
ncpus = int(opt[1])
assert ncpus > 0
#Commands.get_env().ncpus = ncpus
Environment.global_opts['ncpus'] = ncpus
elif opt[0] == '--nw':
#Commands.get_env().withgfx = False
Environment.global_opts['withgfx'] = False
for name,[f,g,help_text] in Commands.glass_command_list.iteritems():
if __builtins__.has_key(name):
print 'WARNING: Glass command %s (%s) overrides previous function %s' % (name, f, __builtins__.__dict__[name])
__builtins__[name] = g
#if len(sys.argv) < 2: help()
Environment.global_opts['ncpus_detected'] = 2
Environment.global_opts['ncpus'] = 2
Environment.global_opts['omp_opts'] = {} #_detect_omp()
Environment.global_opts['withgfx'] = True
Commands.set_env(Environment())
if Environment.global_opts['withgfx']:
import glass.plots
import glass.glcmds
import glass.scales
#import pytipsy
#with open(arglist[0], 'r') as f:
#Commands.get_env().input_file = f.read()
#Environment.global_opts['argv'] = arglist
##Commands.get_env().argv = arglist
def new_env(env):
Commands.set_env(Environment())
def env():
#return _env
return Commands.get_env()