import io
import functools
import time
import zipfile
import numpy as np
from .dataset import SeriesData
from .single_tif_holo import SingleTifHolo
[docs]class SeriesZipTifHolo(SeriesData):
"""Off-axis hologram series (zipped TIFF files)
The data are stored as multiple TIFF files
(:class:`qpformat.file_formats.SingleTifHolo`) in a zip file.
"""
storage_type = "hologram"
def __init__(self, *args, **kwargs):
super(SeriesZipTifHolo, self).__init__(*args, **kwargs)
self._files = None
self._dataset = None
def __len__(self):
return len(self.files)
def _get_dataset(self, idx):
if self._dataset is None:
self._dataset = [None] * len(self)
if self._dataset[idx] is None:
# Use ``zipfile.ZipFile.open`` to return an open file
zf = zipfile.ZipFile(self.path)
pt = zf.open(self.files[idx])
fd = io.BytesIO(pt.read())
self._dataset[idx] = SingleTifHolo(path=fd,
meta_data=self.meta_data,
holo_kw=self.holo_kw)
return self._dataset[idx]
@staticmethod
@functools.lru_cache(maxsize=32)
def _index_files(path):
"""Search zip file for tif files"""
with zipfile.ZipFile(path) as zf:
names = sorted(zf.namelist())
names = [nn for nn in names if nn.endswith(".tif")]
phasefiles = []
for name in names:
with zf.open(name) as pt:
fd = io.BytesIO(pt.read())
if SingleTifHolo.verify(fd):
phasefiles.append(name)
return phasefiles
@property
def files(self):
"""List of hologram data file names in the input zip file"""
if self._files is None:
self._files = SeriesZipTifHolo._index_files(self.path)
return self._files
def get_time(self, idx):
"""Time for each TIFF file
If there are no metadata keyword arguments defined for the
TIFF file format, then the zip file `date_time` value is
used.
"""
# first try to get the time from the TIFF file
# (possible meta data keywords)
ds = self._get_dataset(idx)
thetime = ds.get_time()
if np.isnan(thetime):
# use zipfile date_time
zf = zipfile.ZipFile(self.path)
info = zf.getinfo(self.files[idx])
timetuple = tuple(list(info.date_time) + [0, 0, 0])
thetime = time.mktime(timetuple)
return thetime
def get_qpimage_raw(self, idx):
"""Return QPImage without background correction"""
ds = self._get_dataset(idx)
qpi = ds.get_qpimage_raw()
# set identifier
qpi["identifier"] = self.get_identifier(idx)
qpi["time"] = self.get_time(idx)
return qpi
@staticmethod
def verify(path):
"""Verify that `path` is a zip file containing TIFF files"""
valid = False
try:
zf = zipfile.ZipFile(path)
except (zipfile.BadZipfile, IsADirectoryError):
pass
else:
names = sorted(zf.namelist())
names = [nn for nn in names if nn.endswith(".tif")]
for name in names:
with zf.open(name) as pt:
fd = io.BytesIO(pt.read())
if SingleTifHolo.verify(fd):
valid = True
break
zf.close()
return valid