sme.SimulationResult.species_concentration

property SimulationResult.species_concentration

the species concentrations at this timepoint

for each species, the concentrations are provided as a 3d array, where species_concentration['A'][z][y][x] is the concentration of species “A” at the point (x,y,z)

Examples

do a short simulation and get the species concentrations from the last timepoint:

>>> import sme
>>> model = sme.open_example_model()
>>> results = model.simulate(10, 1)
>>> species_concentration = results[-1].species_concentration

this is a dict with an entry for each species:

>>> type(species_concentration)
<class 'dict'>
>>> species_concentration.keys()
dict_keys(['B_out', 'A_cell', 'B_cell', 'A_nucl', 'B_nucl'])

the concentrations are a 3d ndarray of doubles, one for each pixel in the geometry image:

>>> b_cell = species_concentration['B_cell']
>>> type(b_cell)
<class 'numpy.ndarray'>
>>> b_cell.dtype
dtype('float64')
>>> b_cell.shape
(1, 100, 100)

the concentrations can be displayed using matplotlib:

>>> import matplotlib.pyplot as plt
>>> imgplot = plt.imshow(b_cell[0])

Type:

Dict[str, numpy.ndarray]