import argparse
import os
from pathlib import Path
import numpy as np
import pandas as pd

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-i', type = str, help ="Input directory")
    parser.add_argument('-o', type = str, help="Output directory")
    parser.add_argument('-file_format', default = "*.npy", type = str, help = "File to open")

    args = parser.parse_args()

    if not args.o:
        args.o = args.i

    if not os.path.exists(args.o):
        os.makedirs(args.o)

    input_list = _get_file_paths(args.i, args.file_format)

    offset_x, offset_y = _get_x_y_offsets(input_list)

    _save_csv(args.o, offset_x, "x_offsets")

    _save_csv(args.o, offset_y, "y_offsets")

def _get_file_paths(input_dir, img_format):
    input_dir = Path(input_dir)
    path_list = [str(path) for path in list(sorted(input_dir.rglob(img_format)))]
    return path_list

def _save_csv(output_dir, df, name):
    df.to_csv(output_dir+"/"+name+".csv")


def _get_x_y_offsets(input_list):
    nFOV = len(input_list)
    num_datachannels = 16

    offset_array_x = np.zeros(shape = (nFOV, num_datachannels+1))
    offset_array_y = np.zeros(shape = (nFOV, num_datachannels+1))

    
    for fov in range(nFOV):
        tnx = np.load(input_list[fov], allow_pickle = True)
        offset_array_x[fov,0] = int(fov+1)
        offset_array_y[fov,0] = int(fov+1)
        for j in range(num_datachannels):
            offset_array_x[fov,j+1] = tnx[j].params[0][-1]
            offset_array_y[fov,j+1] = tnx[j].params[1][-1]

    pd_columns = ['FOV', 
    'Offset b/w IR1 & IR 1', 
    'Offset b/w IR1 & IR 2', 
    'Offset b/w IR1 & IR 3', 
    'Offset b/w IR1 & IR 4', 
    'Offset b/w IR1 & IR 5', 
    'Offset b/w IR1 & IR 6', 
    'Offset b/w IR1 & IR 7', 
    'Offset b/w IR1 & IR 8']

    offset_pd_x = pd.DataFrame(offset_array_x[:, ::2], columns=pd_columns)
    offset_pd_y = pd.DataFrame(offset_array_y[:, ::2], columns=pd_columns)

    return offset_pd_x, offset_pd_y


if __name__ == '__main__':
    main()
    # python get_registration_offsets.py -i "/Users/ythapliyal/Documents/Merlin_results/FiducialCorrelationWarp/XP4516"