%run -i load_bromo.py

# Simulation time step
t_step = 0.5e-6   # seconds

# Time duration of the simulation
t_max = .3 # seconds

# Particles definition
P = gen_particles(15, box)

# Particle simulation definition
S = ParticlesSimulation(D=D, t_step=t_step, t_max=t_max, particles=P, box=box, psf=psf)

S.open_store(chunksize=2**20)

# Simulate 3D diffusion and emission
S.sim_motion_em_chunk(total_emission=False, delete_pos=True)

# Generate timestamps
S.sim_timestamps_em_store(max_rate=3e5, bg_rate=2e3, seed=1)

S.compact_name_core()

S.compact_name_core(t_max=True)

S.compact_name()









print 'Main groups:\n'
for node in S.store.data_file.root:
    print node
    for n in node:
        print '\t%s' % n.name
        print '\t    %s' % n.title

group = '/parameters'

print 'Numeric attributes (nodes) in %s:\n' % group

print S.store.data_file.get_node(group)
for node in S.store.data_file.get_node(group)._f_list_nodes():
    print '\t%s' % node.name
    print '\t    %s' % node.title

group = '/parameters'

print 'Attributes in %s:\n' % group

print S.store.data_file.get_node(group)
for attr in S.store.data_file.get_node(group)._v_attrs._f_list():
    print '\t%s' % attr
    print '\t    %s' % type(S.store.data_file.get_node(group)._v_attrs[attr])

group = '/psf'

print 'Nodes in in %s:\n' % group

print S.store.data_file.get_node(group)
for node in S.store.data_file.get_node(group)._f_list_nodes():
    print '\t%s %s' % (node.name, node.shape)
    print '\t    %s' % node.title

node_name = '/psf/default_psf'
node = S.store.data_file.get_node(node_name)

print "\n%s %s: '%s'" % (node.name, node.shape, node.title)
print '\n    List of attributes:'
for attr in node.attrs._f_list():
    print '\t%s' % attr
    print "\t    %s" % repr(node._v_attrs[attr])

group = '/trajectories'

print 'Nodes in in %s:\n' % group

print S.store.data_file.get_node(group)
for node in S.store.data_file.get_node(group)._f_list_nodes():
    print '\t%s %s' % (node.name, node.shape)
    print '\t    %s' % node.title

node_name = '/trajectories/emission'
node = S.store.data_file.get_node(node_name)

print "\n%s %s: '%s'" % (node.name, node.shape, node.title)
print '\n    List of attributes:'
for attr in node.attrs._f_list():
    print '\t%s' % attr
    print "\t    %s" % repr(node._v_attrs[attr])

group = '/timestamps'

print 'Nodes in in %s:\n' % group

print S.store.data_file.get_node(group)
for node in S.store.data_file.get_node(group)._f_list_nodes():
    print '\t%s' % node.name
    print '\t    %s' % node.title

























from IPython.core.display import HTML
HTML(open("./styles/custom2.css", "r").read())