# Copyright 2018 United Kingdom Research and Innovation
# Copyright 2018 The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Authors:
# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
import numpy
from .labels import AcquisitionDimension, Backend
from .data_container import DataContainer
from .partitioner import Partitioner
[docs]
class AcquisitionData(DataContainer, Partitioner):
'''DataContainer for holding 2D or 3D sinogram'''
__container_priority__ = 1
@property
def geometry(self):
return self._geometry
@geometry.setter
def geometry(self, val):
self._geometry = val
@property
def dimension_labels(self):
return self.geometry.dimension_labels
@dimension_labels.setter
def dimension_labels(self, val):
if val is not None:
raise ValueError("Unable to set the dimension_labels directly. Use geometry.set_labels() instead")
def __init__(self,
array = None,
deep_copy=True,
geometry = None,
**kwargs):
dtype = kwargs.get('dtype', numpy.float32)
if geometry is None:
raise AttributeError("AcquisitionData requires a geometry")
labels = kwargs.get('dimension_labels', None)
if labels is not None and labels != geometry.dimension_labels:
raise ValueError("Deprecated: 'dimension_labels' cannot be set with 'allocate()'. Use 'geometry.set_labels()' to modify the geometry before using allocate.")
if array is None:
array = numpy.empty(geometry.shape, dtype=dtype)
elif issubclass(type(array) , DataContainer):
array = array.as_array()
elif issubclass(type(array) , numpy.ndarray):
# remove singleton dimensions
array = numpy.squeeze(array)
else:
raise TypeError('array must be a CIL type DataContainer or numpy.ndarray got {}'.format(type(array)))
if array.shape != geometry.shape:
raise ValueError('Shape mismatch got {} expected {}'.format(array.shape, geometry.shape))
super(AcquisitionData, self).__init__(array, deep_copy, geometry=geometry,**kwargs)
[docs]
def get_slice(self,channel=None, angle=None, vertical=None, horizontal=None, force=False):
'''Returns a new dataset of a single slice in the requested direction.'''
try:
geometry_new = self.geometry.get_slice(channel=channel, angle=angle, vertical=vertical, horizontal=horizontal)
except ValueError:
if force:
geometry_new = None
else:
raise ValueError ("Unable to return slice of requested AcquisitionData. Use 'force=True' to return DataContainer instead.")
#get new data
#if vertical = 'centre' slice convert to index and subset, this will interpolate 2 rows to get the center slice value
if vertical == 'centre':
dim = self.geometry.dimension_labels.index('vertical')
centre_slice_pos = (self.geometry.shape[dim]-1) / 2.
ind0 = int(numpy.floor(centre_slice_pos))
w2 = centre_slice_pos - ind0
out = DataContainer.get_slice(self, channel=channel, angle=angle, vertical=ind0, horizontal=horizontal)
if w2 > 0:
out2 = DataContainer.get_slice(self, channel=channel, angle=angle, vertical=ind0 + 1, horizontal=horizontal)
out = out * (1 - w2) + out2 * w2
else:
out = DataContainer.get_slice(self, channel=channel, angle=angle, vertical=vertical, horizontal=horizontal)
if len(out.shape) == 1 or geometry_new is None:
return out
else:
return AcquisitionData(out.array, deep_copy=False, geometry=geometry_new, suppress_warning=True)
[docs]
def reorder(self, order):
'''
Reorders the data in memory as requested. This is an in-place operation.
Parameters
----------
order: list or str
Ordered list of labels from self.dimension_labels, or string 'astra' or 'tigre'.
'''
if order in Backend:
order = AcquisitionDimension.get_order_for_engine(order, self.geometry)
super().reorder(order)
