import os
import GMR.InputOutput as io
main_dir = io.config_dir_path()
exp_settings = io.exp_in(main_dir)
print(f'Experiment Settings:\n {exp_settings}\n')
for hs_img in exp_settings['hs_imgs']:
img_dir = os.path.join(main_dir, hs_img)
if not os.path.isdir(img_dir):
continue
corrected_img_dir = os.path.join(img_dir, 'corrected_imgs')
data_files = io.extract_files(dir_name=corrected_img_dir,
file_string='corrected_img_')
print(len(data_files))
data_cube = []
print('\nBuilding data cube...')
for index, file in enumerate(data_files):
file_path = os.path.join(corrected_img_dir, file)
corrected_img, file_name = io.array_in(file_path, mode='r')
data_cube.append(corrected_img)
io.update_progress(index / len(data_files))
print('\nSaving data cube...approximately 1min per 100 imgs')
io.array_out(array_name=data_cube,
file_name=f'{hs_img}_datacube',
import os
import numpy as np
import matplotlib.pyplot as plt
import csv
import shutil
import GMR.InputOutput as io
import GMR.DataPreparation as dprep
import GMR.DataProcessing as dproc
sensor = 'Nanohole_Array' ## Set this to the photonic crystal used ##
root = io.config_dir_path()
for date_dir in os.listdir(root):
selected_date = os.path.join(root, date_dir)
print(f'Looking at: {date_dir}')
print('Background Calibration')
bg_dir = os.path.join(selected_date, 'Background')
bg_datafiles = io.extract_files(dir_name=bg_dir,
file_string='_Background.csv')
for index, selected_file in enumerate(bg_datafiles):
file = os.path.join(bg_dir, selected_file)
zero_file = os.path.join(bg_dir, f'{sensor}_Background.csv')
wavelength, intensity, file_name = io.csv_in(file)
wav_naught, int_naught, zero_name = io.csv_in(zero_file)
fig, ax = plt.subplots(1, 1, figsize=[10, 7])