! Tracking Challenge: Mine Zantow 20110612_10_KL_Aq_1_GE_1_O_2p0 (1)_Case
! Camera setup parameters! 
1, 2,            ! starting_frame_for_analysis, number of frames to analyze
20               ! Camera frame rate
667, 91          ! number of pixels horizontal, vertical
0.0667, 0.0091 ! width of field-of-view in meters, height of field-of-view in meters:  0.00512m/512pixels = 10 microns/pixel
0.0050           ! particle diameter
 
! 
500000			  ! TOTAL_NUMBER_OF_CENTROIDS
50000             ! TOTAL_NUMBER_OF_REAL_TRAJECTORIES
10                ! MAXIMUM_TRAJECTORY_LENGTH
500000            ! MAXIMUM_CANDIDATE_TRAJECTORIES
 
! Search parameters
0.01, 1.0       ! v_min, max_velocity_in_flow_field_in_m_per_sec:  // if dt=0.001 s; dx = 50 pixels * 0.0667m/667pixels = 0.0001 m; V=dx/dt=0.0001m/0.001s= 1 m/s
3, 1              ! total number of loops for search velocity, exponent in search velocity equation (exponent_search_velocity)
0.35,  0.25       ! search_angle_start, search_angle_end  (radians)
0.8, 0.6          ! Acc_min_start, Acc_min_end 
0.8, 0.6          ! Acc_max_start, Acc_max_end
2                 ! The base for equation to exponentially decrease search parameters with search velocity
6, 6              ! starting and ending minimum length of a real trajectory (dev rules for setting...)
50, 50          ! starting and ending maximum length of a real trajectory
15                ! distance_to_detect_very_slow_particles.  Set this to detect particles 
0                 ! Set to 1 if want to decrease_DSA_with_particle_concentration
0                 ! reduction in search parameters at maximum particle concentration (fraction of original) 
5000              ! max number of candidate trajectories allowed -- stops program from blowing up

! Post analysis of trajectories: Curve fitting trajectories
Yes              ! use_additional_exogenous_criteria_for_real_trajs: Yes or No
50               ! max_distance_between_cent_of_a_traj, if distance exceeded, candidate traj is thrown out
1                ! apply_criteria_always?
0                ! criterion_2: max value allowed for delt_y
2                ! order of polynomial with which to curve fit trajectories using Cholesky least-squares fit method (2 is straight line fit)
  
! MTrackJ data file parameters
1                ! Flag to use or not use manually selection of velocity range for pseudocoloring
0.01, 0.3       ! vmin_manually, vmax_manually, pseudocoloring factor, 
Yes              ! Write additional MTrackJ files separated by velocity and length of traj?
  
! Debug?  Remember this creates very large output files, so run for minimum necessary frames!
1                ! Debugging switch: 1 if I want to write debugging info, 0 if not
5                ! no_columns_in_Centroid_input_for_Traj_Ident_file.  Some Centroid_input_for_Traj_Ident.txt files have 6 columns instead of 5 because they have an extra column before the last column.  Adjust read statements.



