######################################
#   list of experimental conditions  #
######################################

# list of experimental conditions

[conditions]

# list each different experimental condition as 'conditions' followed by a period, 
# followed by a unique condition name
# indentation makes this easier to read but is optional

    # basefname input gives the prefix of all file names for that condition
    # file numbers may be specified in one of two ways:
        # 1) by explicitly listing all file numbers in the array "fnum" (e.g., pTG824 below)
        # 2) by providing a range (e.g., pTG800 below) with the first and last file numbers
        # to include, and any files to leave out listed in the array "exclude"
        # Provide only #1 or #2, but not both. If both are provided, the "fnum" input will 
        # be given precedence.
    
    [conditions.pTG824]
    basefname = 'test_data/2comp_'     # base file name of all movies in this condition
    fnum = [0,3]     # list of file numbers to include
    title = 'SNAPf-3xNLS + H2B-Halo-SNAPf (pTG824)' # title to use for plotting

    [conditions.pTG800]
    basefname = 'test_data/pTG800_'    # base file name of all movies
    first = 78                  # first movie file to analyze
    last = 80
    exclude = [80] # files to exclude 
    title = 'Halo-SNAPf-3xNLS + H2B-SNAPf (pTG800)' # title to use for plotting



# file name format
[file_format]

# number of digits in each file name
# For instance, choose ndigits = 3 if file numbers are numbered 
# 000, 001, 002, etc.
ndigits = 3

# file name extension
extension = 'nd2'


######################################
#  parameters for particle tracking  #
######################################

# Image reading and filtering settings
[filter]
    start = 0 
    method = "identity"
    chunk_size = 100

# Spot detection settings
[detect]
    method = "llr"  # llr = log likelihood ratio
    k = 1.0  # width of Gaussian
    w = 9    # window size
    t = 18.0 # threshold (actual threshold, not rescaled arbitrarily)

# Subpixel localization settings
[localize]
    method = 'ls_int_gaussian' # least-squares sub-pixel localization using integrated Gaussian model w/ Gaussian-distributed noise
    window_size = 9
    sigma = 1.0
    ridge = 0.001
    max_iter = 10
    damp = 0.3

# Tracking settings
[track]
    method = 'euclidean'
    pixel_size_um = 0.160 # for most cameras
    frame_interval = 0.00748 # change appropriately
    search_radius = 1 # in microns--maximum permitted between frames
    max_blinks = 0
    min_I0 = 0.0 # minimum PSF intensity for spot detection to start a trajectory
    scale = 7.0  


#######################################
#  parameters for trajectory sorting  #
#######################################

# illumination sequence parameters
[illumination_sequence]
ncycles = 10    # number of cycles of the sequence r-v-r-r-g-r
r = 250         # number of red frames
v = 1           # number of violet frames
g = 1           # number of green frames
framewindow = 30    # number of frames after green/violet pulse to include in PAPA/DR trajectories


#############################################
#  parameters for state array SPT analysis  #
#############################################

[saspt]
focal_depth = 0.7