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Merge branch 'master' into spdhg_sampler
Signed-off-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| # 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 | ||
|
|
||
|
|
||
| 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) | ||
|
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||
|
|
||
| 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) | ||
|
|
||
| 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) |
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