Source code for qpimage.integrity_check

import h5py
import numpy as np

from .core import QPImage
from .meta import DATA_KEYS

[docs]class IntegrityCheckError(BaseException): """Raised when a QPImage data set is incomplete or corrupt""" pass
[docs]def check(qpi_or_h5file, checks=["attributes", "background"]): """Checks various properties of a :class:`qpimage.core.QPImage` instance Parameters ---------- qpi_or_h5file: qpimage.core.QPImage or str A QPImage object or a path to an hdf5 file checks: list of str Which checks to perform ("attributes" and/or "background") Raises ------ IntegrityCheckError if the checks fail """ if isinstance(checks, str): checks = [checks] for ch in checks: if ch not in ["attributes", "background"]: raise ValueError("Unknown check: {}".format(check)) if isinstance(qpi_or_h5file, QPImage): qpi = qpi_or_h5file else: qpi = QPImage(h5file=qpi_or_h5file, h5mode="r") # check attributes if "attributes" in checks: check_attributes(qpi) # check background estimation if "background" in checks: check_background(qpi)
[docs]def check_attributes(qpi): """Check QPimage attributes Parameters ---------- qpi: qpimage.core.QPImage Raises ------ IntegrityCheckError if the check fails """ missing_attrs = [] for key in DATA_KEYS: if key not in qpi.meta: missing_attrs.append(key) if missing_attrs: msg = "Attributes are missing: {} ".format(missing_attrs) \ + "in {}!".format(qpi) raise IntegrityCheckError(msg)
[docs]def check_background(qpi): """Check QPimage background data Parameters ---------- qpi: qpimage.core.QPImage Raises ------ IntegrityCheckError if the check fails """ for imdat in [qpi._amp, qpi._pha]: try: fit, attrs = imdat.get_bg(key="fit", ret_attrs=True) except KeyError: # No bg correction performed pass else: kwargs = dict(attrs) # check if we have a user-defined mask image binkey = "estimate_bg_from_mask" if binkey in imdat.h5: kwargs["from_mask"] = imdat.h5[binkey].value else: kwargs["from_mask"] = None # compute background correction with h5py.File("check.h5", driver="core", backing_store=False) as h5: # imdat.__class__ is "Amplitude" or "Phase" testimdat = imdat.__class__(h5) testimdat["raw"] = imdat.raw # Set experimental bg data if given try: bg = imdat.get_bg("data") except KeyError: pass else: testimdat.set_bg(bg, key="data") # fit bg testimdat.estimate_bg(**kwargs) # compare if not np.allclose(testimdat.get_bg(key="fit"), fit): msg = "Wrong estimated (fitted) background!" raise IntegrityCheckError(msg)