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