def plot(iter_info):
nI = iter_info.agent_output.grid_nI
nJ = iter_info.agent_output.grid_nJ
res = iter_info.agent_output.grid_res
# Reduce the height
nI /= 3
width = toolbox_plotting.mm2inch(nJ*res)
height = toolbox_plotting.mm2inch(nI*res)
figure = toolbox_plotting.SlideFigure(width=width, height=height)
axis = figure.add_subplot('', 111, frameon=False)
num_capsules = 0
num_transconjugants = 0
num_recipients = 0
num_donors = 0
for cell in iter_info.agent_output.get_all_cells():
if cell.species == 'EPS':
#continue
cell.color = '0.5'
num_capsules += 1
elif cell.species == 'Donor':
cell.color = 'r'
num_donors += 1
elif cell.species == 'Recipient':
if int(cell.vars['copyNumber']) > 0:
cell.color = 'g'
num_transconjugants += 1
else:
cell.color = 'b'
num_recipients += 1
toolbox_idynomics.draw_cell_2d(axis, cell, total_radius=True)
print('%d capsules'%(num_capsules))
print('%d donors'%(num_donors))
print('%d transconjugants'%(num_transconjugants))
print('%d recipients'%(num_recipients))
#toolbox_idynomics.plot_cells_2d(axis, iter_info.agent_output)
#axis.set_title(r'Biofilm (%s g.L$^{-1}$)'%(solute_name))
width = nJ * res
height = nI * res
base_thickness = 0.25*res
axis.fill_between([0, width], [0]*2, y2=[-base_thickness]*2,
facecolor='k', zorder=-1)
axis.set_xlim(-base_thickness, width+base_thickness)
axis.set_ylim(-base_thickness, height+base_thickness)
lb, rt = 0.01, 0.99
figure.subplots_adjust(left=lb, bottom=lb, right=rt, top=rt)
figure.save(os.path.join(sim.figures_dir,
'biofilm_%s(%d).png'%(options.solute_name, iter_info.number)))
else:
species_color_dict = toolbox_idynomics.get_default_species_colors(sim)
toolbox_idynomics.save_color_dict(species_color_dict, color_dict_path)
nI, nJ, nK, res = sim.find_domain_dimensions()
if options.i_max > 0:
nI = options.i_max
counter = 0
if options.figure_type == None:
if options.height > 0: height = options.height
else: height = toolbox_plotting.mm2inch(nI * res)
if options.width > 0: width = options.width
else: width = toolbox_plotting.mm2inch(nJ * res)
figure = toolbox_plotting.SlideFigure(width=width, height=height)
else:
script = "figure = toolbox_plotting." + options.figure_type + "Figure("
if nI > 2 * nJ:
script += "height='double'"
elif nJ > 2 * nI:
script += "double_column=True, height='single'"
else:
script += "double_column=True, height='double'"
script += ")"
try:
exec(script)
except:
print 'Could not make figure!'
print script
#!/usr/bin/python
from __future__ import division
from __future__ import with_statement
import numpy
import toolbox_plotting
import toolbox_schematic_new as toolbox_schematic
fig = toolbox_plotting.SlideFigure()
axis = fig.add_subplot('', 111, frameon=True, projection='3d')
#X, Y = numpy.meshgrid([0, 1], [0, 1])
#axis.plot_surface(X, Y, 0.3, color='k', zorder=1)
Y, Z = numpy.meshgrid([0, 1], [0, 0.5])
axis.plot_surface(1.0, Y, Z, color='k', zorder=1)
sphere = toolbox_schematic.Sphere()
sphere.set_defaults(edgecolor='none', facecolor='r', zorder=0)
sphere.set_points((0.5, 0.5, 0.5), 0.5)
sphere.draw(axis)
axis.set_xlabel('x')
axis.set_ylabel('y')
axis.set_zlabel('z')