def setup():
'''
Create McssResults
Select species
Create Surfaces with species and surface data (x, y, timepoints)
'''
import mcss_results
results = mcss_results.McssResults('tests/pulsePropagation-2_runs.h5')
# print results.timepoints
#print results.species_information(); exit()
species = 'proteinGFP', 'proteinCI', 'proteinLuxI'
results.select_species(*species)
surfaces = results.surfaces()
means = mcss_results.mean(surfaces, 0)
# zmax = np.max(mcss_results.mean(surfaces, 0))
return results, [Surface(s, means[i]) for i, s in enumerate(species)]
results.step = 1 results.start = 240 results.stop = 840 results.select_species(*species) print 'surfaces' surfaces = results.surfaces() print surfaces.shape numruns, numsurfaces, lenx, leny, numtimepoints = surfaces.shape numcompartments = lenx * leny print 'mean over runs' surfaces = mean(surfaces, 0) print surfaces.shape #print 'Y1' #surfaces = np.array((surfaces[0], )) #print 'Y2' #surfaces = np.array((surfaces[1], )) print 'subtraction' surfaces = np.array((surfaces[0] - surfaces[1], )) print surfaces.shape print 'interpolation' surfaces = np.array([interpolate(surfaces[i], xymultiplier, tmultiplier) for i in range(len(surfaces))]) print surfaces.shape
