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)