def write_out(saving_dir: str, filename: str, pdfgetter: PDFGetter) -> dict:
"""Write out data in pdfgetter into files"""
data_dirs = {}
for out_type in pdfgetter.config.outputtypes:
data_dir = Path(saving_dir).joinpath(out_type)
if not data_dir.exists():
data_dir.mkdir()
data_dirs.update({out_type: data_dir})
dct = {}
for out_type in pdfgetter.config.outputtypes: # out_type in ('iq', 'sq', 'fq', 'gr')
data_dir = data_dirs.get(out_type)
out_file = data_dir.joinpath(
Path(filename).with_suffix(".{}".format(out_type)).name)
pdfgetter.writeOutput(str(out_file), out_type)
dct.update({out_type: str(out_file)})
return dct
def run_pipe(tiff_file: str,
saving_dir: str = ".",
poni_file: str = None,
pdfgetter: PDFGetter = None,
refine_func: Callable = None) -> dict:
"""
A pipeline process to integrate, transform and fit the data and return a dictionary of path to the resulting files.
Parameters
----------
tiff_file
Path to the tiff file.
saving_dir
Path to the directory where the output data files will be saved. Default "."
poni_file
Path to the poni file. If None, the poni file in the saving_dir will be used.
pdfgetter
A PDFgetter to transform the chi file to gr file. If None, a default one will be created, see
make_default_pdfgetter. Default None
refine_func
A function func(gr_file: str) to refine the G(r) of Ni. If None, a default refine function will be used, see
refine. Default None
Returns
-------
res_dct
a dictionary that contains keys: "poni", "chi", "gr", "Rw", "csv", "fgr".
"""
def find_poni(dir_to_search):
files_found = recfind(dir_to_search, r".*\.poni")
if len(files_found) < 1:
raise Exception(f"Not found poni file in {dir_to_search}")
elif len(files_found) > 1:
_poni_file = files_found[0]
print(f"Multiple file found in {dir_to_search}.\nUse {_poni_file}")
else:
_poni_file = files_found[0]
return _poni_file
poni_file = poni_file if poni_file else find_poni(saving_dir)
wl = load(poni_file)["Wavelength"] * 1e10 # unit A
result = dict(poni=poni_file, wl=wl)
print(f"Run pipeline with wavelength: {wl:.4f} and poni file: {poni_file}")
result["chi"], _ = xpdtools_int(poni_file,
tiff_file,
chi_dir=saving_dir,
alpha=2.0)
pdfgetter = pdfgetter if pdfgetter else make_default_pdfgetter()
chi_q, chi_i = loaddata(result["chi"]).T
pdfgetter(chi_q, chi_i)
result["gr"] = os.path.splitext(result["chi"])[0] + ".gr"
pdfgetter.writeOutput(result["gr"], "gr")
if refine_func:
pass
else:
refine_func = default_refine
result["Rw"], result["csv"], result["fgr"] = refine_func(
result["gr"], saving_dir)
return result
