"""proc.py
"""


from pyms.GCMS.IO.ANDI import ANDI_reader
from pyms.IntensityMatrix import build_intensity_matrix_i
from pyms.Noise.Window import window_smooth

# read the raw data as a GCMS_data object
andi_file = "data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)

# build the intensity matrix
im = build_intensity_matrix_i(data)

# get the size of the intensity matrix
n_scan, n_mz = im.size
print("Size of the intensity matrix is (n_scans, n_mz):", n_scan, n_mz)

# loop over all m/z values, fetch the corresponding IC, and perform
# noise smoothing
for ii in im.iter_ic_indices():
    print(ii+1,)
    ic = im.get_ic_at_index(ii)
    ic_smooth = window_smooth(ic, window=7)