%load_ext autoreload
%autoreload 2


%run nb_init.py

eptm = lj.Epithelium(graphXMLfile='../saved_graphs/01000_2014-02-19T14_07_40.552058/xml/after_apopto.xml',
                     identifier='01000_2014-02-19T14_07_40.552058')

eptm_before = lj.Epithelium(graphXMLfile="../saved_graphs/xml/before_apoptosis.xml", identifier='0',
                            paramfile='../default/params.xml')

anisotropies, alignments = eptm.cells.get_anisotropies()
#

eptm.graph.set_vertex_filter(eptm.is_cell_vert)
fig, axes = plt.subplots(2, 1, sharex=True)
axes[0].plot(eptm.zeds.fa, anisotropies.fa.clip(0, 4), 'ro', alpha=0.5)
axes[1].plot(eptm.zeds.fa, alignments.fa, 'ro', alpha=0.5)
eptm.graph.set_vertex_filter(None)
axes[1]




fig, axes = plt.subplots(2, 1, sharex=True)

eptm_before.graph.set_vertex_filter(eptm_before.is_cell_vert)
axes[0].plot(eptm_before.zeds.fa, anisotropies_before.fa, 'bo', alpha=0.5)
axes[1].plot(eptm_before.zeds.fa, alignments_before.fa, 'bo', alpha=0.5)
eptm_before.graph.set_vertex_filter(None)


anisotropies_before, alignments_before = eptm_before.cells.get_anisotropies()

eptm_before.graph.set_vertex_filter(eptm_before.is_cell_vert)
print(anisotropies_before.fa.mean())
print(alignments_before.fa.mean())
eptm_before.graph.set_vertex_filter(None)


lj.local_slice(eptm_before, zed_amp=1., theta_amp=np.pi/2, theta_c=0)

eptm_before.sigmas.a = eptm_before.thetas.a * eptm_before.rhos.a.mean()
ax = lj.draw_polygons(eptm_before, eptm_before.zeds, eptm_before.sigmas, 
                      colors=anisotropies_before,
                      efilt=eptm_before.is_local_edge,
                      vfilt=eptm_before.is_local_vert)

lj.local_slice(eptm, zed_amp=15., theta_amp=np.pi/2, theta_c=0)
#eptm.update_rhotheta()
ax = lj.draw_polygons(eptm, eptm.zeds, eptm.sigmas, 
                      colors=alignments,
                      efilt=eptm.is_local_edge,
                      vfilt=eptm.is_local_vert)

fig, ax = plt.subplots()
ax.plot(eptm.zeds.a, eptm.contractile_grad.a, 'o')

lj.draw_polygons(eptm, eptm.zeds, eptm.thetas, colors=eptm.contractile_grad.a)

eptm.graph.set_vertex_filter(None)

eptm.graph.set_vertex_filter(eptm.is_cell_vert)
fig, ax = plt.subplots()
ax.plot(eptm.zeds.fa, eptm.cells.areas.fa, 'o', alpha=0.4)
eptm.graph.set_vertex_filter(None)

eptm.set_local_mask(None)
lj.running_local_optimum(eptm, 1e-4)

lj.draw(eptm, output3d='tissue_2d.png')