inputs.yaml

---
general_inputs:
    #save settings (file name, path, calibration path for magnification calibration)
    file_name                       : 'test_run_01'
    folder_name                     : 'C:\Users\Rates001\Downloads'

    #model for feedback experiment
    # choose between 'AutomaticPath' for migration experiment | 'PID_LEXY_SAM' for concentration experiments
    model                           : 'AutomaticPath'

    #Microscope in use
    # choose from the following options | 'micromanager' | 'demo'
    microscope                      : 'demo'

    #number of measurement points and their time interval in seconds
    n_time_points                   : 240
    time_interval_s                 : 15

    #acquisition settings: list of tuples with name of channel and exposure time, fluorescence setting, and attenuation for optogenetic signal
    coolLED                         : 15
    attenuation                     : 1.4
    channels                        : 
    - ['4-mCherry',100]

    #size of the cell in pixel [width, height] for segmentation
    cell_size                       : [200,200]

functionalities_PID_LEXY_SAM: 
    #size of the nucleus in pixel [width, height] for box ONLY for LEXY
    nucleus_size                    : [300,300]

    #setpoint_array is for concentration experiments. It is a list of tuples, each tuple has the format (time,setpoint), to assign a new controller setpoint at a certain time (in seconds).
    setpoint_array                  : 
    - [0,0.5]
    - [900,0.3]
    - [1800,0.4]
    - [2700,0.2]

    # LEXY controlled parameter (One of: ["nucleus_intensity", "cytosol_intensity", "ratio"], corresponding to nucleus, cytosol and nucleus-cytosol ratio control )
    LEXY_control_parameter          : 'normalized_cytosol_intensity'

    # Minimum and maximum intensity of controlled variable (nucleus, cytosol, ration), used for normalization
    LEXY_normalization_parameters   : 
    - 43
    - 110

    # Use gain scheduling or anti-windup in LEXY PID controller
    use_gainscheduling              : False
    use_antiwindup                  : False

    #PID_coef is a list with 3 floats, representing the P,I, and D coefficients for the LEXY controller
    PID_coef                        : [9.0,0.005,0.3]

    #set illuminate_nucleus as True for LEXY to only illuminate nucleus, set it as False to illuminate the full cell
    illuminate_nucleus              : False

functionalities_AutomaticPath: 
    #power_array is for migration experiments. It is a list of lists, each inner list has the format (loop,step,power), to assign a new led power at a certain loop and step on that loop.
    power_array                     : 
    - [0,0,1]
    - [1,0,2]

    #type of path to draw. Choose between circle | square | triangle | vline | hline
    path_type                       : 
    - 'circle'

    #path_pos has the structure [(x,y), r, n] with x,y center of path, r size of path (for circle and square), and n number of points
    path_pos                        : 
    - [[800, 800], 350, 40]

advanced_inputs:
    #max_height and offset: (int) set image display size
    max_height                      : 700
    offset                          : 0

    #waiting time if you have a multichannel measurement - in seconds
    waiting_multichannel            : 1

    #extra_zoom: (int, 0 or 1) 1.5x manual magnification. 
    extra_zoom                      : 0

    #cali_coordinates: (list of tuples with pair of ints) coordinates of the 3 spots used for calibration. If you want to use coordinate from file, set this as None.
    cali_coordinates                : 
    - [250,300]
    - [350,200]
    - [360,300]

    #calibration file name
    cal_file_path                   : 'cal_file_60.txt'

    #demo path. Leave emty if you want to use demo images from repository
    demo_path                       : ''

    #segmentation algorithm. Choose between SAM | Threshold
    segmentation                       : 'Threshold'
...