pure pyFAI integration

pyFAI_integrate.py

"""example to do pure pyFAI integration"""

import os
import tifffile as tif
from pyFAI.azimuthalIntegrator import AzimuthalIntegrator

def pyFAI_integrate(data_dir, poni_fp, npt=1450, mask=None):
    """helper function to integrate a series of images inside data_dir with geometry and mask provided
    
    Parameters
    ----------
    data_dir : str
       path to directory filled with images you want to integrate
    poni_fp : str
       filepath to poni file contains calibration parameters
    npt : int, optional
       number of integration grid. default to 1450.
    mask : ndarray, optional
       mask object that follows pyFAI logic. Default is None (no mask)
       
    Example
    -------
    data_dir = '~/xpdUser/tiff_base/<my_sample_dir>/'
    poni_fp = '~/xpdUser/config_base/<latest_poni_file>.poni'
    mask = np.load('~/xpdUser/config_base/xpdacq_mask.npy')
    pyFAI_integrate(data_dir, ponit_fp, mask=mask)
    """"
    fn_list = os.listdir(data_dir)
    az = AzimuthalIntegrator()
    az.load(poni_fp)
    print(az)  # display calibration information displayed
    total_num = len(fn_list)
    for ind, fn in enumerate(fn_list):
        stem, tail = os.path.splitext(fn)
        print("INFO: integrate {}/{}".format(ind+1, total_num))
        img = tif.imread(os.path.join(data_dir, fn))
        az.integrate1d(img, npt, filename=stem, mask=mask)