Here are listed examples on the use of the trajectory class.

The examples can be run using the raw data in the example folder of trajectory_alignment. The example reported here is equivalent to trajectory_class_example.py in the example folder.

from trajalign.traj import Traj
from matplotlib import pyplot as plt

# when a trajectory is defined, we can enter annotations
t = Traj(what="my first trajectory",mood="today is a beautiful day")
print( t )
t.annotations( 'mood' , 'all this seems pretty complicated, depressing!' )

print( t.annotations()[ 'what' ] )# read the annotation 'what'

# set the time  attribute of the trajectory
t.input_values('t',[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1]) 
print(t) #note that also the frames are automatically generated

t.annotations( 't_unit' , 's' )
print(t) 

t.input_values('coord',
		[[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1],
			[1,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9]],
		unit='apples')
print(t)

# load a real trajectory. We define the new trajectory first
d = Traj( 
		experiment = 'Sla1-GFP' , 
		date = '01/01/2000' , 
		temperature = 'cold!' , 
		note = 'Happy new millenium' )

d.load(file_name='raw_trajectories/02.data',
		frames = 0, coord = (1,2), f = 3, 
		comment_char='%', weather = 'clear and sunny' )
print(d) 
# note that the coord_unit is left empty as none was specified 
# in the attributes when calling load
d.annotations('coord_unit' , 'pxl')

d.time(0.1045,'s')
# print some elements of the trajectory
print( d.t( 0 , 1 , len(d) -1 ) )
print( d.start() )
print( d.end() )

print( d.coord( range( 0 , 10 )) )

# the trajectory lifetime
print( d.lifetime() )

#fill the missing frames
print( max( 
	[ d.frames( i ) - d.frames( i - 1 ) 
		for i in range(1, len( d )) ] 
	))
# there are some missing frames, let's fill them:
d.fill()
print( max( 
	[ d.frames( i ) - d.frames( i - 1 ) 
		for i in range(1, len( d )) ] 
	))

d.save('my_first_trajectory') #save our trajectory, as a .txt file:

# move the trajectory to its center of mass
d.translate( - d.center_mass() )

plt.figure()

#plot the trajectory 'd'
plt.plot( d.coord()[ 0 ] , d.coord()[ 1 ] ,\
		'b-' , label = 'Original traj.')

#rotate the trajectory 'd' by ~pi/2
d.rotate( 3.14/2 )
plt.plot( d.coord()[ 0 ] , d.coord()[ 1 ] ,\
		'r-' , label = 'Rotated traj.')

#create a new trajectory which is an extract of 'd'
d_short = d.extract( range( 0 , 79 ) )
plt.plot( d_short.coord()[ 0 ], d_short.coord()[ 1 ] ,\
		'g--' , label = 'first 80 data points\nof the Rotated traj.')

#start 'd' from time point 12 s
d.start( 12 ) 
plt.plot( d.coord()[ 0 ] , d.coord()[ 1 ] , 'y--' ,\
		 label = 'data points of the Rotated\ntraj. after t = 12 s')

plt.legend( loc = 'lower left' )
plt.show()