Source code for qpimage.series

import h5py

from .core import QPImage
from .meta import MetaDict

[docs]class QPSeries(object): _instances = 0 def __init__(self, qpimage_list=[], meta_data={}, h5file=None, h5mode="a", identifier=None): """Quantitative phase image series Parameters ---------- qpimage_list: list A list of instances of :class:`qpimage.QPImage`. meta_data: dict Meta data associated with the input data (see :const:`qpimage.META_KEYS`). This overrides the meta data of the QPImages in `qpimage_list` and, if `h5file` is given and `h5mode` is not "r", overrides the meta data in `h5file`. h5file: str, h5py.Group, h5py.File, or None A path to an hdf5 data file where all data is cached. If set to `None` (default), all data will be handled in memory using the "core" driver of the :mod:`h5py`'s :class:`h5py:File` class. If the file does not exist, it is created. If the file already exists, it is opened with the file mode defined by `hdf5_mode`. If this is an instance of h5py.Group or h5py.File, then this will be used to internally store all data. If `h5file` is given and `qpimage_list` is not empty, all QPImages in `qpimage_list` are appended to `h5file` in the given order. h5mode: str Valid file modes are (only applies if `h5file` is a path): - "r": Readonly, file must exist - "r+": Read/write, file must exist - "w": Create file, truncate if exists - "w-" or "x": Create file, fail if exists - "a": Read/write if exists, create otherwise (default) """ if qpimage_list and not isinstance(qpimage_list, list): msg = "`qpimage_list` must be a list!" if isinstance(qpimage_list, str): msg += " Did you mean `h5file={}`?".format(qpimage_list) raise ValueError(msg) if isinstance(h5file, h5py.Group): self.h5 = h5file self._do_h5_cleanup = False else: if h5file is None: h5kwargs = {"name": "qpseries{}.h5".format( QPSeries._instances), "driver": "core", "backing_store": False, "mode": "a"} else: h5kwargs = {"name": h5file, "mode": h5mode} self.h5 = h5py.File(**h5kwargs) self._do_h5_cleanup = True QPSeries._instances += 1 if meta_data and h5mode == "r": msg = "`h5mode` must not be 'r' if `meta_data` is given!" raise ValueError(msg) # make sure self.h5 is not itself a QPImage file if "phase" in self.h5 and "amplitude" in self.h5: raise ValueError( "`h5file` is a QPImage file, not a QPSeries file!") # Write QPimage data to h5 file for qpi in qpimage_list: self.add_qpimage(qpi) # Update meta data if meta_data: meta = MetaDict(meta_data) for ii in range(len(self)): qpii = self.get_qpimage(index=ii) for mk in meta: qpii.h5.attrs[mk] = meta[mk] # Set identifier if identifier: self.h5.attrs["identifier"] = identifier def __contains__(self, qpid): """test whether a QPImage with the given identifier exists""" for ii in range(len(self)): qpi = self[ii] if "identifier" in qpi and qpi["identifier"] == qpid: exists = True break else: exists = False return exists def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): if self._do_h5_cleanup: self.h5.flush() self.h5.close() def __getitem__(self, index): return self.get_qpimage(index) def __iter__(self): for ii in range(len(self)): yield self[ii] def __len__(self): keys = list(self.h5.keys()) keys = [kk for kk in keys if kk.startswith("qpi_")] return len(keys) @property def identifier(self): """unique identifier of the series""" if "identifier" in self.h5.attrs: return self.h5.attrs["identifier"] else: return None
[docs] def add_qpimage(self, qpi, identifier=None, bg_from_idx=None): """Add a QPImage instance to the QPSeries Parameters ---------- qpi: qpimage.QPImage The QPImage that is added to the series identifier: str Identifier key for `qpi` bg_from_idx: int or None Use the background data from the data stored in this index, creating hard links within the hdf5 file. (Saves memory if e.g. all qpimages is corrected with the same data) """ if not isinstance(qpi, QPImage): raise ValueError("`fli` must be instance of QPImage!") if "identifier" in qpi and identifier is None: identifier = qpi["identifier"] if identifier and identifier in self: msg = "The identifier '{}' already ".format(identifier) \ + "exists! You can either change the identifier of " \ + " '{}' or remove it.".format(qpi) raise ValueError(msg) # determine number of qpimages num = len(self) # indices start at zero; do not add 1 name = "qpi_{}".format(num) group = self.h5.create_group(name) thisqpi = qpi.copy(h5file=group) if bg_from_idx is not None: # Create hard links refqpi = self[bg_from_idx] thisqpi._amp.set_bg(bg=refqpi._amp.h5["bg_data"]["data"]) thisqpi._pha.set_bg(bg=refqpi._pha.h5["bg_data"]["data"]) if identifier: # set identifier group.attrs["identifier"] = identifier
[docs] def get_qpimage(self, index): """Return a single QPImage of the series Parameters ---------- index: int or str Index or identifier of the QPImage Notes ----- Instead of ``qps.get_qpimage(index)``, it is possible to use the short-hand ``qps[index]``. """ if isinstance(index, str): # search for the identifier for ii in range(len(self)): qpi = self[ii] if "identifier" in qpi and qpi["identifier"] == index: group = self.h5["qpi_{}".format(ii)] break else: msg = "QPImage identifier '{}' not found!".format(index) raise KeyError(msg) else: # integer index if index < -len(self): msg = "Index {} out of bounds for QPSeries of size {}!".format( index, len(self)) raise ValueError(msg) elif index < 0: index += len(self) name = "qpi_{}".format(index) if name in self.h5: group = self.h5[name] else: msg = "Index {} not found for QPSeries of length {}".format( index, len(self)) raise KeyError(msg) return QPImage(h5file=group)