# -*- coding: utf-8 -*-
##########################################################################
# pySAP - Copyright (C) CEA, 2017 - 2018
# Distributed under the terms of the CeCILL-B license, as published by
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
import numpy
from warnings import warn
# Package import
from .observable import Observable
from pysap.base.exceptions import Exception
from pysap.plotting import plot_data
[docs]class Image(Observable):
""" Class that defines an image.
An image contains:
* data: an array of data stored in a numpy.ndarray
* data_type: whether the data is scalar, vector or matrix.
* a dictionary of metadata
If data_type is 'vector' or 'matrix', an array of dimension N will have a
spacing of size N-1, respectivelly N-2.
The following event is allowed:
* modified
"""
def __init__(self, shape=None, spacing=None, data_type="scalar",
metadata=None, **kwargs):
""" Create an image that can be modified as a numpy arrray.
Parameters
----------
shape: uplet (optional, default None)
set this parameter to created an empty image.
spacing: uplet (optional, default None)
the image spacing, if not set consider a default isotropic spacing.
data_type: str (optional, default 'scalar')
the image data type: 'scalar', 'vector' or 'matrix'.
metadata: dict (optional, default None)
some metadata attached to this image.
kwargs: dict (optional)
extra arguments may contain the image data as 'data', the empty
image data filled value as 'value' or any argument of numpy.ndarray
constructor.
"""
# Check input parameters
if data_type not in ["scalar", "vector", "matrix"]:
raise Exception("Unknown data type '{0}'.".format(data_type))
# Define class attributes
self._scroll_axis = 0
self.data = None
self.data_type = data_type
self.metadata = metadata or {}
self._spacing = None
# Initialize the Image class
Observable.__init__(self, ["modified"])
# Image data initialization
if "data" in kwargs:
self.data = numpy.asarray(kwargs["data"])
del kwargs["data"]
else:
if shape is None:
raise Exception("Wrong shape '{0}'.".format(shape))
if "value" in kwargs:
value = kwargs["value"]
del kwargs["value"]
else:
value = None
self.data = numpy.ndarray(shape, **kwargs)
if value is not None:
self.data.fill(value)
# Image spacing initialization
if spacing is None:
self._set_spacing(self._default_spacing())
else:
self._set_spacing(spacing)
[docs] def show(self):
""" Display the image data.
"""
warn(
'The show method has been deprecated and will be removed in a '
+ 'future release. In the future Please use the Image.data '
+ 'attribute and your plotting package of choice.',
FutureWarning
)
plot_data(self.data, scroll_axis=self._scroll_axis)
[docs] def modified(self):
""" Send a modified signal to the observers.
"""
self.notify_observers("modified")
def __getitem__(self, where):
""" Get an items of the image data.
"""
return self.data[where]
def __setitem__(self, where, value):
""" Set an item to the image data.
"""
self.data[where] = value
def __array__(self):
""" Return image data as a numpy array.
"""
return numpy.asarray(self.data)
######################################################################
# Properties
######################################################################
[docs] def _get_spacing(self):
""" Get the image spacing.
"""
return self._spacing
[docs] def _set_spacing(self, spacing):
""" Set the image spacing.
Parameters
----------
spacing: uplet
the image spacing.
"""
self._spacing = numpy.asarray(spacing, dtype=numpy.single)
[docs] def _get_shape(self):
""" Get the shape of the image.
This function accounts for non-scalar data, i.e. 'vector' or 'matrix'
vs 'scalar' data types.
"""
if self.data_type == "scalar":
return self.data.shape
elif self.data_type == "vector":
return self.data.shape[:-1]
elif self.data_type == "matrix":
return self.data.shape[:-2]
[docs] def _get_dtype(self):
""" Get the image data type.
"""
return self.data.dtype
[docs] def _get_ndim(self):
""" Get the image dimension.
This function accounts for non-scalar data, i.e. 'vector' or 'matrix'
vs 'scalar' data types.
"""
if self.data_type == "scalar":
return self.data.ndim
elif self.data_type == "vector":
return self.data.ndim - 1
elif self.data_type == "matrix":
return self.data.ndim - 2
scroll_axis = property(_get_scroll_axis, _set_scroll_axis)
spacing = property(_get_spacing, _set_spacing)
shape = property(_get_shape)
dtype = property(_get_dtype)
ndim = property(_get_ndim)
######################################################################
# Private interface
######################################################################
[docs] def _default_spacing(self):
""" Return the default image spacing.
"""
dim = self._get_ndim()
return numpy.ones(dim, dtype=numpy.single)
