import h5py
import numpy as np
import pandas as pd
from ..core.experiment import MappingExperiment
from ..core.map import MapsStack
from ..composite.channels import CompositeChannels
from ..composite.composite import CompositeMap
from ..point_analysis.points import EDSPoints
"""This module provides functions to save trated dataset from EDXIA.
For example, it can be used to save the denoised maps,
or the representative points"""
DS_STACK_NAME = "stack"
DS_COMPOSITE_NAME = "composite"
DS_POINTS_NAME = "points"
DS_EXTRA_NAME = "extras"
DS_EXP_NAME = "experiment"
[docs]def save_dataset(filepath, exp, stack=None, composite=None, points=None, extras=None, override=True):
"""This function save a set of treated data into a hdf5 file."""
if override:
mode = "w"
else:
mode = "x"
h5f = h5py.File(filepath, mode)
save_experiment(h5f, exp)
if stack is not None:
save_stack(h5f, stack)
if composite is not None:
save_composite(h5f, composite)
if points is not None:
save_points(h5f, points)
if extras is not None:
save_extras(h5f, extras)
h5f.close()
def save_experiment(h5file, exp):
h5file.attrs["components"] = np.array(exp.list_components, dtype="S")
h5file.attrs[DS_EXP_NAME] = np.array([exp.pattern,exp.label], dtype="S")
def save_stack(h5file, stack):
dset = h5file.create_dataset(DS_STACK_NAME, data=stack.maps)
dset.attrs["components"] = np.array(stack.components, dtype="S")
def save_composite(h5file, composite):
channels = composite.channels
dset = h5file.create_dataset(DS_COMPOSITE_NAME, data=composite.map)
dset.attrs["components"] = np.array(channels.components, dtype="S")
dset.attrs["factors"] = np.array(channels.factors)
def save_points(h5file, points):
dset = h5file.create_dataset(DS_POINTS_NAME, data=points.df.values)
dset.attrs["columns"] = np.array(points.df.columns, dtype="S")
def save_extras(h5file, extras):
grp = h5file.create_group(DS_EXTRA_NAME)
for name, dmap in extras.items():
grp.create_dataset(name, data=dmap)
[docs]def read_dataset(filepath):
"""Read a set of edxia data from a hdf5 file"""
h5f = h5py.File(filepath, "r")
exp = read_experiment(h5f)
if DS_STACK_NAME in h5f.keys():
stack = read_stack(h5f, exp)
else:
stack = None
if DS_COMPOSITE_NAME in h5f.keys():
composite = read_composite(h5f, exp)
else:
composite = None
if DS_POINTS_NAME in h5f.keys():
points = read_points(h5f, exp)
else:
points = None
if DS_EXTRA_NAME in h5f.keys():
extras = read_extras(h5f)
else:
extras = None
h5f.close()
return stack, composite, points, extras
# -----------------------------------------------------------------------------
[docs]def read_experiment(h5file):
"""Read an experiment from an open hdf5 file"""
data = h5file.attrs[DS_EXP_NAME]
pattern = bytes(data[0]).decode()
label = bytes(data[1]).decode()
comp = h5file.attrs["components"].tolist()
components = [bytes(c).decode() for c in comp]
exp = MappingExperiment(pattern, label, components=components)
return exp
[docs]def read_stack(hf5file, exp):
"""Read a stack object from an open hdf5 file"""
dset = hf5file[DS_STACK_NAME]
comp = dset.attrs["components"].tolist()
components = [bytes(c).decode() for c in comp]
stack = MapsStack(components, dset.shape, exp)
stack.maps = dset[:]
return stack
[docs]def read_composite(hf5file, exp):
"""Read a composite object from an open hdf5 file"""
dset = hf5file[DS_COMPOSITE_NAME]
comp= dset.attrs["components"].tolist()
components = [bytes(c).decode() for c in comp]
factors = dset.attrs["factors"].tolist()
channels = CompositeChannels(components, factors)
composite = CompositeMap(dset[:], channels, exp)
return composite
[docs]def read_points(hf5file, exp):
"""Read a points object from an open hdf5 file"""
dset = hf5file["points"]
col = dset.attrs["columns"]
columns = [bytes(c).decode() for c in col]
points = pd.DataFrame(data=dset[:], columns=columns)
pts = EDSPoints(points, exp)
return pts
def read_extras(h5file):
extras = {}
grp = h5file[DS_EXTRA_NAME]
for name in grp.keys():
dset = grp[name]
extras[name] = dset[:]
return extras
