from burstInfer.process_raw_data import process_raw_data
from burstInfer.HMM import HMM
from burstInfer.export_em_parameters import export_em_parameters
#%%
# Import ML parameters
max_likelihood_estimate = pd.read_csv('result_694826350.csv', header=0, index_col=None)
#%%
# Import and process data (synthetic fluorescent traces)
ms2_signals = genfromtxt('synthetic_fluorescent_traces_w13.csv', delimiter=',', skip_header=1) # TODO
# Strip away leading column of row indices
ms2_signals = ms2_signals[:,1:]
# Create dictionary containing list of signals (integer is which column to start
# with, 0 in our case)
processed_signals = process_raw_data(ms2_signals,0)
#%%
# Set up HMM parameters.
K = 2 # Number of allowed promoter states - always 2 ATM.
n_traces = len(processed_signals['Processed Signals'])
eps = 10**(-3) # Error tolerance
n_steps = 50 # Number of maximum EM steps
PERMITTED_MEMORY = 256 # Number of allowed compound states
# The parameters will probably need to be altered.
W = 13 # Window size
t_MS2 = 30 # Time for Pol II to traverse MS2 probe (s)
deltaT = 20 # Time resolution (s)
kappa = t_MS2 / deltaT
compound_states = K**W
#%%
# Import and process data (synthetic fluorescent traces)
ms2_signals = genfromtxt('uwt_e1_no_bd.csv', delimiter=',',
skip_header=1) # TODO
# Strip away leading column of row indices
signal_holder = ms2_signals[:, 1:]
# Sort signals by mean value (to identify very weak signals)
sorted_by_means = signal_holder[signal_holder[:, 2].argsort()]
# Filter out weak signals
weak_signals_removed = sorted_by_means[20:, :]
# Select only cluster / region of interest from whole embryo
filtered_by_cluster = weak_signals_removed[weak_signals_removed[:, 1] == 0]
# Generate dict of signals for input to model
processed_signals = process_raw_data(filtered_by_cluster, 11)
#%%
# Set up HMM parameters.
K = 2 # Number of allowed promoter states - always 2 ATM.
n_traces = len(processed_signals['Processed Signals'])
eps = 10**(-3) # Error tolerance
n_steps = 1 # Number of maximum EM steps
PERMITTED_MEMORY = 256 # Number of allowed compound states
# The parameters will probably need to be altered.
W = 19 # Window size
t_MS2 = 30 # Time for Pol II to traverse MS2 probe (s)
deltaT = 20 # Time resolution (s)
kappa = t_MS2 / deltaT
compound_states = K**W