File size: 2,153 Bytes
5ad11ec |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 |
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"
|