# Copyright 2021 United Kingdom Research and Innovation
# Copyright 2021 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
from cil.framework import DataProcessor, AcquisitionData, ImageData, ImageGeometry, DataContainer, AcquisitionGeometry
import numpy as np
import weakref
[docs]
class Padder(DataProcessor):
"""
Processor to pad an array with a border, wrapping numpy.pad. See https://numpy.org/doc/stable/reference/generated/numpy.pad.html
It is recommended to use the static methods to configure your Padder object rather than initialising this class directly. See examples for details.
Parameters
----------
mode: str
The method used to populate the border data. Accepts: 'constant', 'edge', 'linear_ramp', 'reflect', 'symmetric', 'wrap'
pad_width: int, tuple, dict
The size of the border along each axis, see usage notes
pad_values: float, tuple, dict, default=0.0
The additional values needed by some of the modes
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
`pad_values` behaviour:
- float: Each border will use this value
- tuple(float, float): Each value will be used asymmetrically for each axis i.e. (before, after)
- dict: Specified axes and values: e.g. {'horizontal':(8, 23), 'channel':5}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.edge(pad_width=1)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[0. 0. 1. 2. 2.]
[0. 0. 1. 2. 2.]
[3. 3. 4. 5. 5.]
[6. 6. 7. 8. 8.]
[6. 6. 7. 8. 8.]]
Example
-------
>>> processor = Padder.constant(pad_width={'horizontal_y':(1,1),'horizontal_x':(1,2)}, constant_values=(-1.0, 1.0))
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[-1. -1. -1. -1. 1. 1.]
[-1. 0. 1. 2. 1. 1.]
[-1. 3. 4. 5. 1. 1.]
[-1. 6. 7. 8. 1. 1.]
[-1. 1. 1. 1. 1. 1.]
"""
[docs]
@staticmethod
def constant(pad_width=None, constant_values=0.0):
"""
Padder processor wrapping numpy.pad with mode `constant`.
Pads the data with a constant value border. Pads in all *spatial*
dimensions unless a dictionary is passed to either `pad_width` or `constant_values`
Parameters
----------
pad_width: int, tuple, dict
The size of the border along each axis, see usage notes
constant_values: float, tuple, dict, default=0.0
The value of the border, see usage notes
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
`constant_values` behaviour (value of pixels):
- float: Each border will be set to this value
- tuple(float, float): Each border value will be used asymmetrically for each axis i.e. (before, after)
- dict: Specified axes and values: e.g. {'horizontal':(8, 23), 'channel':5}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.constant(pad_width=1, constant_values=0.0)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[0. 0. 0. 0. 0.]
[0. 0. 1. 2. 0.]
[0. 3. 4. 5. 0.]
[0. 6. 7. 8. 0.]
[0. 0. 0. 0. 0.]]
"""
processor = Padder(pad_width=pad_width, mode='constant', pad_values=constant_values)
return processor
[docs]
@staticmethod
def edge(pad_width=None):
"""
Padder processor wrapping numpy.pad with mode `edge`.
Pads the data by extending the edge values in to the border. Pads in all *spatial*
dimensions unless a dictionary is passed to `pad_width`.
pad_width: int, tuple, dict
The size of the border along each axis, see usage notes
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.edge(pad_width=1)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[0. 0. 1. 2. 2.]
[0. 0. 1. 2. 2.]
[3. 3. 4. 5. 5.]
[6. 6. 7. 8. 8.]
[6. 6. 7. 8. 8.]]
"""
processor = Padder(pad_width=pad_width, mode='edge')
return processor
[docs]
@staticmethod
def linear_ramp(pad_width=None, end_values=0.0):
"""Padder processor wrapping numpy.pad with mode `linear_ramp`
Pads the data with values calculated from a linear ramp between the array edge
value and the set end_value. Pads in all *spatial* dimensions unless a dictionary
is passed to either `pad_width` or `constant_values`
pad_width: int, tuple, dict
The size of the border along each axis, see usage notes
end_values: float, tuple, dict, default=0.0
The target value of the linear_ramp, see usage notes
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
`end_values` behaviour:
- float: Each border will use this end value
- tuple(float, float): Each border end value will be used asymmetrically for each axis i.e. (before, after)
- dict: Specified axes and end values: e.g. {'horizontal':(8, 23), 'channel':5}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.linear_ramp(pad_width=2, end_values=0.0)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[0. 0. 0. 0. 0. 0. 0. ]
[0. 0. 0. 0.5 1. 0.5 0. ]
[0. 0. 0. 1. 2. 1. 0. ]
[0. 1.5 3. 4. 5. 2.5 0. ]
[0. 3. 6. 7. 8. 4. 0. ]
[0. 1.5 3. 3.5 4. 2. 0. ]
[0. 0. 0. 0. 0. 0. 0. ]]
"""
processor = Padder(pad_width=pad_width, mode='linear_ramp', pad_values=end_values)
return processor
[docs]
@staticmethod
def reflect(pad_width=None):
"""
Padder processor wrapping numpy.pad with mode `reflect`.
Pads with the reflection of the data mirrored along first and last values each axis.
Pads in all *spatial* dimensions unless a dictionary is passed to `pad_width`.
pad_width: int, tuple, dict
The size of the border along each axis, see usage notes
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.reflect(pad_width=1)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[4. 3. 4. 5. 4.]
[1. 0. 1. 2. 1.]
[4. 3. 4. 5. 4.]
[7. 6. 7. 8. 7.]
[4. 3. 4. 5. 4.]]
"""
processor = Padder(pad_width=pad_width, mode='reflect')
return processor
[docs]
@staticmethod
def symmetric(pad_width=None):
"""
Padder processor wrapping numpy.pad with mode `symmetric`.
Pads with the reflection of the data mirrored along the edge of the array.
Pads in all *spatial* dimensions unless a dictionary is passed to `pad_width`.
Parameters
----------
pad_width: int, tuple, dict
The size of the border along each axis
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.symmetric(pad_width=1)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[0. 0. 1. 2. 2.]
[0. 0. 1. 2. 2.]
[3. 3. 4. 5. 5.]
[6. 6. 7. 8. 8.]
[6. 6. 7. 8. 8.]]
"""
processor = Padder(pad_width=pad_width, mode='symmetric')
return processor
[docs]
@staticmethod
def wrap(pad_width=None):
"""
Padder processor wrapping numpy.pad with mode `wrap`.
Pads with the wrap of the vector along the axis. The first values are used to pad the
end and the end values are used to pad the beginning. Pads in all *spatial* dimensions
unless a dictionary is passed to `pad_width`.
Parameters
----------
pad_width: int, tuple, dict
The size of the border along each axis
Notes
-----
`pad_width` behaviour (number of pixels):
- int: Each axis will be padded with a border of this size
- tuple(int, int): Each axis will be padded with an asymmetric border i.e. (before, after)
- dict: Specified axes will be padded: e.g. {'horizontal':(8, 23), 'vertical': 10}
If padding angles the angular values assigned to the padded axis will be extrapolated from the first two,
and the last two angles in geometry.angles. The user should ensure the output is as expected.
Example
-------
>>> processor = Padder.wrap(pad_width=1)
>>> processor.set_input(data)
>>> data_padded = processor.get_output()
>>> print(data.array)
[[0. 1. 2.]
[3. 4. 5.]
[6. 7. 8.]]
>>> print(data_padded.array)
[[8. 6. 7. 8. 6.]
[2. 0. 1. 2. 0.]
[5. 3. 4. 5. 3.]
[8. 6. 7. 8. 6.]
[2. 0. 1. 2. 0.]]
"""
processor = Padder(pad_width=pad_width, mode='wrap')
return processor
def __init__(self,
mode='constant',
pad_width=None,
pad_values=0):
kwargs = {'mode': mode,
'pad_width': pad_width,
'pad_values': pad_values,
'_data_array': False,
'_geometry': None,
'_shape_in':None,
'_shape_out':None,
'_shape_out_full':None,
'_labels_in':None,
'_processed_dims':None,
'_pad_width_param':None,
'_pad_values_param':None,
}
super(Padder, self).__init__(**kwargs)
def check_input(self, data):
if isinstance(data, (ImageData,AcquisitionData)):
self._data_array = True
self._geometry = data.geometry
elif isinstance(data, DataContainer):
self._data_array = True
self._geometry = None
elif isinstance(data, (ImageGeometry, AcquisitionGeometry)):
self._data_array = False
self._geometry = data
else:
raise TypeError('Processor supports following data types:\n' +
' - ImageData\n - AcquisitionData\n - DataContainer\n - ImageGeometry\n - AcquisitionGeometry')
if self._data_array:
if data.dtype != np.float32:
raise TypeError("Expected float32")
if self.mode not in ['constant', 'edge', 'linear_ramp', 'reflect', 'symmetric', 'wrap']:
raise Exception("Wrong mode. One of the following is expected:\n" +
"constant, edge, linear_ramp, reflect, symmetric, wrap")
if self.pad_width is None:
raise ValueError('Please, specify pad_width')
return True
def _create_tuple(self, value, dtype):
try:
out = (dtype(value),dtype(value))
except TypeError:
try:
out = (dtype(value[0]),dtype(value[1]))
except:
raise TypeError()
return out
def _get_dimensions_from_dict(self, dict):
dimensions = []
for k in dict.keys():
if k not in self._labels_in:
raise ValueError('Dimension label not found in data. Expected labels from {0}. Got {1}'.format(self._geometry.dimension_labels, k))
dimensions.append(k)
return dimensions
def _set_up(self):
data = self.get_input()
offset = 4-data.ndim
#set defaults
self._labels_in = [None]*4
self._labels_in[offset::] = data.dimension_labels
self._shape_in = [1]*4
self._shape_in[offset::] = data.shape
self._shape_out_full = self._shape_in.copy()
self._processed_dims = [0,0,0,0]
self._pad_width_param = [(0,0)]*4
self._pad_values_param = [(0,0)]*4
# if pad_width or set_values is passed a dictionary these keys specify the axes to run over
if isinstance(self.pad_width, dict) and isinstance(self.pad_values, dict):
if self.pad_width.keys() != self.pad_values.keys():
raise ValueError('Dictionaries must contain the same axes')
dimensions = self._get_dimensions_from_dict(self.pad_width)
elif isinstance(self.pad_width, dict):
dimensions = self._get_dimensions_from_dict(self.pad_width)
elif isinstance(self.pad_values, dict):
dimensions = self._get_dimensions_from_dict(self.pad_values)
else:
spatial_dimensions =[
'vertical',
'horizontal',
'horizontal_y',
'horizontal_x'
]
dimensions = list(set(spatial_dimensions) & set(self._labels_in))
# get pad_widths for these dimensions
for dim in dimensions:
try:
values = self.pad_width[dim]
except TypeError:
values = self.pad_width
try:
i = self._labels_in.index(dim)
self._pad_width_param[i] = self._create_tuple(values, int)
except TypeError:
raise TypeError("`pad_width` should be a integer or a tuple of integers. Got {0} for axis {1}".format(values, dim))
# get pad_values for these dimensions
for dim in dimensions:
try:
values = self.pad_values[dim]
except TypeError:
values = self.pad_values
try:
i = self._labels_in.index(dim)
self._pad_values_param[i] = self._create_tuple(values, float)
except TypeError:
raise TypeError("`pad_values` should be a float or a tuple of floats. Got {0} for axis {1}".format(values, dim))
#create list of processed axes and new_shape
for i in range(4):
if self._pad_width_param[i] != (0,0):
self._processed_dims[i] = 1
self._shape_out_full[i] += self._pad_width_param[i][0] + self._pad_width_param[i][1]
self._shape_out = tuple([i for i in self._shape_out_full if i > 1])
def _process_acquisition_geometry(self):
"""
Creates the new acquisition geometry
"""
geometry = self._geometry.copy()
for i, dim in enumerate(self._labels_in):
if not self._processed_dims[i]:
continue
offset = (self._pad_width_param[i][0] -self._pad_width_param[i][1])*0.5
if dim == 'channel':
geometry.set_channels(num_channels= geometry.config.channels.num_channels + \
self._pad_width_param[i][0] + self._pad_width_param[i][1])
elif dim == 'angle':
# extrapolate pre-values from a[1]-a[0]
# extrapolate post-values from a[-1]-a[-2]
a = self._geometry.angles
end_values = (
a[0]-(a[1]-a[0] )* self._pad_width_param[i][0],
a[-1]+(a[-1]-a[-2] )* self._pad_width_param[i][1]
)
geometry.config.angles.angle_data = np.pad(a, (self._pad_width_param[i][0],self._pad_width_param[i][1]), mode='linear_ramp',end_values=end_values)
elif dim == 'vertical':
geometry.config.panel.num_pixels[1] += self._pad_width_param[i][0]
geometry.config.panel.num_pixels[1] += self._pad_width_param[i][1]
geometry.config.shift_detector_in_plane(offset, dim)
elif dim == 'horizontal':
geometry.config.panel.num_pixels[0] += self._pad_width_param[i][0]
geometry.config.panel.num_pixels[0] += self._pad_width_param[i][1]
geometry.config.shift_detector_in_plane(offset, dim)
return geometry
def _process_image_geometry(self):
"""
Creates the new image geometry
"""
geometry = self._geometry.copy()
for i, dim in enumerate(self._labels_in):
if not self._processed_dims[i]:
continue
offset = (self._pad_width_param[i][0] -self._pad_width_param[i][1])*0.5
if dim == 'channel':
geometry.channels += self._pad_width_param[i][0]
geometry.channels += self._pad_width_param[i][1]
elif dim == 'vertical':
geometry.voxel_num_z += self._pad_width_param[i][0]
geometry.voxel_num_z += self._pad_width_param[i][1]
geometry.center_z -= offset * geometry.voxel_size_z
elif dim == 'horizontal_x':
geometry.voxel_num_x += self._pad_width_param[i][0]
geometry.voxel_num_x += self._pad_width_param[i][1]
geometry.center_x -= offset * geometry.voxel_size_x
elif dim == 'horizontal_y':
geometry.voxel_num_y += self._pad_width_param[i][0]
geometry.voxel_num_y += self._pad_width_param[i][1]
geometry.center_y -= offset * geometry.voxel_size_y
return geometry
def _process_data(self, dc_in):
arr_in = dc_in.array.reshape(self._shape_in)
if self.mode in ['reflect', 'symmetric', 'wrap', 'edge']:
arr_out = np.pad(arr_in, self._pad_width_param, mode=self.mode,).squeeze()
elif self.mode == 'constant':
arr_out = np.pad(arr_in, self._pad_width_param, mode=self.mode, \
constant_values=self._pad_values_param).squeeze()
elif self.mode == 'linear_ramp':
arr_out = np.pad(arr_in, self._pad_width_param, mode=self.mode, \
end_values=self._pad_values_param).squeeze()
return arr_out
def process(self, out=None):
data = self.get_input()
# pad geometry
if isinstance(self._geometry, ImageGeometry):
new_geometry = self._process_image_geometry()
elif isinstance(self._geometry, AcquisitionGeometry):
new_geometry = self._process_acquisition_geometry()
else:
new_geometry = None
# return if just acting on geometry
if not self._data_array:
return new_geometry
# pad data
if out is None:
arr_out = self._process_data(data)
if isinstance(new_geometry, ImageGeometry):
return ImageData(arr_out,deep_copy=False, geometry=new_geometry)
elif isinstance(new_geometry, AcquisitionGeometry):
return AcquisitionData(arr_out,deep_copy=False, geometry=new_geometry)
else:
return DataContainer(arr_out,deep_copy=False, dimension_labels=data.dimension_labels)
else:
# check size and shape if passed out
try:
out.array = out.array.reshape(self._shape_out_full)
except:
raise ValueError("Array of `out` not compatible. Expected shape: {0}, data type: {1} Got shape: {2}, data type: {3}".format(self._shape_out_full, np.float32, out.array.shape, out.array.dtype))
if new_geometry is not None:
if out.geometry != new_geometry:
raise ValueError("Geometry of `out` not as expected. Got {0}, expected {1}".format(out.geometry, new_geometry))
out.array = self._process_data(data)
return out
