import h5py
import qpimage
from .dataset import SeriesData
[docs]class SeriesHdf5Qpimage(SeriesData):
"""Qpimage series (HDF5 format)"""
storage_type = "phase,amplitude"
def __init__(self, *args, **kwargs):
super(SeriesHdf5Qpimage, self).__init__(*args, **kwargs)
self._dataset = None
def __len__(self):
with self._qpseries() as qps:
return len(qps)
def _qpseries(self):
return qpimage.QPSeries(h5file=self.path, h5mode="r")
@property
def identifier(self):
# Qpformat generates a new identifier that also depends on the given
# keyword arguments. Thus, the identifiers of source and modified
# dataset must not be identical.
with self._qpseries() as qps:
identifier = qps.identifier
if identifier is None:
identifier = ""
else:
identifier += "_"
identifier += super(SeriesHdf5Qpimage, self).identifier
return identifier
def get_identifier(self, idx):
"""Return an identifier for the data at index `idx`"""
with self._qpseries() as qps:
if "identifier" in qps[idx]:
identifier = qps[idx]["identifier"]
else:
identifier = super(SeriesHdf5Qpimage, self).get_identifier(idx)
return identifier
def get_qpimage(self, idx):
"""Return background-corrected QPImage of data at index `idx`"""
if self._bgdata:
# The user has explicitly chosen different background data
# using `get_qpimage_raw`.
qpi = super(SeriesHdf5Qpimage, self).get_qpimage(idx)
else:
# We can use the background data stored in the qpimage hdf5 file
with self._qpseries() as qps:
qpi = qps.get_qpimage(index=idx).copy()
# Force meta data
for key in self.meta_data:
qpi[key] = self.meta_data[key]
return qpi
def get_qpimage_raw(self, idx):
"""Return QPImage without background correction"""
with self._qpseries() as qps:
qpi = qps.get_qpimage(index=idx).copy()
# Remove previously performed background correction
qpi.set_bg_data(None)
# Force meta data
for key in self.meta_data:
qpi[key] = self.meta_data[key]
return qpi
@staticmethod
def verify(path):
"""Verify that `path` has the qpimage series file format"""
valid = False
try:
h5 = h5py.File(path, mode="r")
qpi0 = h5["qpi_0"]
except (OSError, KeyError):
pass
else:
if ("qpimage version" in qpi0.attrs and
"phase" in qpi0 and
"amplitude" in qpi0 and
"bg_data" in qpi0["phase"] and
"bg_data" in qpi0["amplitude"]):
valid = True
return valid