Scripted modeling - no GUI

Process some data with a kinetic model and then plot it all without using the GUI

from tmaven.app import setup_maven

#### Analyze some data
## Make a new MAVEN instance
maven  = setup_maven(['--log_stdout'])

## Load data
maven.io.load_smdtmaven_hdf5('./notes/example_smd.hdf5','L1-tRNA')

## Turn on only the first 10 trajectorys
maven.data.flag_ons*=False
maven.data.flag_ons[:10]+=True

## Run vbFRET model selection with 1 through 6 states
maven.modeler.run_fret_vbhmm_modelselection(1,6)



#### Make some plots
import matplotlib.pyplot as plt
fig,ax =plt.subplots(2)

## Plot a 1D histogram in the first plots using the raw data instead of the Viterbi data
maven.plots.data_hist1d.prefs['idealized'] = False
maven.plots.data_hist1d.plot(fig,ax[0])

## Plot a trajectory in the second plot
ax[1].plot(maven.data.corrected[0,:,0],'g')
ax[1].plot(maven.data.corrected[0,:,1],'r')

plt.show()