1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
|
# -----------------------------------------------------------------------
# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
# 2013-2016, CWI, Amsterdam
#
# Contact: astra@astra-toolbox.com
# Website: http://www.astra-toolbox.com/
#
# This file is part of the ASTRA Toolbox.
#
#
# The ASTRA Toolbox is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# The ASTRA Toolbox is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
#
# -----------------------------------------------------------------------
"""Additional functions for PyAstraToolbox.
.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl>
"""
from . import creators as ac
import numpy as np
try:
from six.moves import range
except ImportError:
# six 1.3.0
from six.moves import xrange as range
from . import data2d
from . import data3d
from . import projector
from . import algorithm
from . import pythonutils
def clear():
"""Clears all used memory of the ASTRA Toolbox.
.. note::
This is irreversible.
"""
data2d.clear()
data3d.clear()
projector.clear()
algorithm.clear()
def data_op(op, data, scalar, gpu_core, mask=None):
"""Perform data operation on data.
:param op: Operation to perform.
:param data: Data to perform operation on.
:param scalar: Scalar argument to data operation.
:param gpu_core: GPU core to perform operation on.
:param mask: Optional mask.
"""
cfg = ac.astra_dict('DataOperation_CUDA')
cfg['Operation'] = op
cfg['Scalar'] = scalar
cfg['DataId'] = data
if not mask == None:
cfg['MaskId'] = mask
cfg['option']['GPUindex'] = gpu_core
alg_id = algorithm.create(cfg)
algorithm.run(alg_id)
algorithm.delete(alg_id)
def add_noise_to_sino(sinogram_in, I0, seed=None):
"""Adds Poisson noise to a sinogram.
:param sinogram_in: Sinogram to add noise to.
:type sinogram_in: :class:`numpy.ndarray`
:param I0: Background intensity. Lower values lead to higher noise.
:type I0: :class:`float`
:returns: :class:`numpy.ndarray` -- the sinogram with added noise.
"""
if not seed==None:
curstate = np.random.get_state()
np.random.seed(seed)
if isinstance(sinogram_in, np.ndarray):
sinogramRaw = sinogram_in
else:
sinogramRaw = data2d.get(sinogram_in)
max_sinogramRaw = sinogramRaw.max()
sinogramRawScaled = sinogramRaw / max_sinogramRaw
# to detector count
sinogramCT = I0 * np.exp(-sinogramRawScaled)
# add poison noise
sinogramCT_C = np.zeros_like(sinogramCT)
for i in range(sinogramCT_C.shape[0]):
for j in range(sinogramCT_C.shape[1]):
sinogramCT_C[i, j] = np.random.poisson(sinogramCT[i, j])
# to density
sinogramCT_D = sinogramCT_C / I0
sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D)
if not isinstance(sinogram_in, np.ndarray):
data2d.store(sinogram_in, sinogram_out)
if not seed==None:
np.random.set_state(curstate)
return sinogram_out
def move_vol_geom(geom, pos, is_relative=False):
"""Moves center of volume geometry to new position.
:param geom: Input volume geometry
:type geom: :class:`dict`
:param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])
:type pos: :class:`tuple`
:param is_relative: Whether new position is relative to the old position
:type is_relative: :class:`bool`
:returns: :class:`dict` -- Volume geometry with the new center
"""
ret_geom = geom.copy()
ret_geom['option'] = geom['option'].copy()
if not is_relative:
ret_geom['option']['WindowMinX'] = -geom['GridColCount']/2.
ret_geom['option']['WindowMaxX'] = geom['GridColCount']/2.
ret_geom['option']['WindowMinY'] = -geom['GridRowCount']/2.
ret_geom['option']['WindowMaxY'] = geom['GridRowCount']/2.
if len(pos)>2:
ret_geom['option']['WindowMinZ'] = -geom['GridSliceCount']/2.
ret_geom['option']['WindowMaxZ'] = geom['GridSliceCount']/2.
ret_geom['option']['WindowMinX'] += pos[0]
ret_geom['option']['WindowMaxX'] += pos[0]
ret_geom['option']['WindowMinY'] += pos[1]
ret_geom['option']['WindowMaxY'] += pos[1]
if len(pos)>2:
ret_geom['option']['WindowMinZ'] += pos[2]
ret_geom['option']['WindowMaxZ'] += pos[2]
return ret_geom
def geom_size(geom, dim=None):
"""Returns the size of a volume or sinogram, based on the projection or volume geometry.
:param geom: Geometry to calculate size from
:type geometry: :class:`dict`
:param dim: Optional axis index to return
:type dim: :class:`int`
"""
return pythonutils.geom_size(geom,dim)
def geom_2vec(proj_geom):
"""Returns a vector-based projection geometry from a basic projection geometry.
:param proj_geom: Projection geometry to convert
:type proj_geom: :class:`dict`
"""
if proj_geom['type'] == 'parallel':
angles = proj_geom['ProjectionAngles']
vectors = np.zeros((len(angles), 6))
for i in range(len(angles)):
# source
vectors[i, 0] = np.sin(angles[i])
vectors[i, 1] = -np.cos(angles[i])
# center of detector
vectors[i, 2] = 0
vectors[i, 3] = 0
# vector from detector pixel 0 to 1
vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth']
vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth']
proj_geom_out = ac.create_proj_geom(
'parallel_vec', proj_geom['DetectorCount'], vectors)
elif proj_geom['type'] == 'fanflat':
angles = proj_geom['ProjectionAngles']
vectors = np.zeros((len(angles), 6))
for i in range(len(angles)):
# source
vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
# center of detector
vectors[i, 2] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
vectors[i, 3] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
# vector from detector pixel 0 to 1
vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth']
vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth']
proj_geom_out = ac.create_proj_geom(
'fanflat_vec', proj_geom['DetectorCount'], vectors)
elif proj_geom['type'] == 'cone':
angles = proj_geom['ProjectionAngles']
vectors = np.zeros((len(angles), 12))
for i in range(len(angles)):
# source
vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
vectors[i, 2] = 0
# center of detector
vectors[i, 3] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
vectors[i, 4] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
vectors[i, 5] = 0
# vector from detector pixel (0,0) to (0,1)
vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
vectors[i, 8] = 0
# vector from detector pixel (0,0) to (1,0)
vectors[i, 9] = 0
vectors[i, 10] = 0
vectors[i, 11] = proj_geom['DetectorSpacingY']
proj_geom_out = ac.create_proj_geom(
'cone_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
# PARALLEL
elif proj_geom['type'] == 'parallel3d':
angles = proj_geom['ProjectionAngles']
vectors = np.zeros((len(angles), 12))
for i in range(len(angles)):
# ray direction
vectors[i, 0] = np.sin(angles[i])
vectors[i, 1] = -np.cos(angles[i])
vectors[i, 2] = 0
# center of detector
vectors[i, 3] = 0
vectors[i, 4] = 0
vectors[i, 5] = 0
# vector from detector pixel (0,0) to (0,1)
vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
vectors[i, 8] = 0
# vector from detector pixel (0,0) to (1,0)
vectors[i, 9] = 0
vectors[i, 10] = 0
vectors[i, 11] = proj_geom['DetectorSpacingY']
proj_geom_out = ac.create_proj_geom(
'parallel3d_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
else:
raise ValueError(
'No suitable vector geometry found for type: ' + proj_geom['type'])
return proj_geom_out
def geom_postalignment(proj_geom, factor):
"""Apply a postalignment to a vector-based projection geometry.
Can be used to model the rotation axis offset.
For 2D geometries, the argument factor is a single float specifying the
distance to shift the detector (measured in detector pixels).
For 3D geometries, factor can be a pair of floats specifying the horizontal
resp. vertical distances to shift the detector. If only a single float
is specified, this is treated as a horizontal shift.
:param proj_geom: input projection geometry
:type proj_geom: :class:`dict`
:param factor: number of pixels to shift the detector
:type factor: :class:`float`
"""
proj_geom = geom_2vec(proj_geom)
if proj_geom['type'] == 'parallel_vec' or proj_geom['type'] == 'fanflat_vec':
V = proj_geom['Vectors']
V[:,2:4] = V[:,2:4] + factor * V[:,4:6]
elif proj_geom['type'] == 'parallel3d_vec' or proj_geom['type'] == 'cone_vec':
V = proj_geom['Vectors']
V[:,3:6] = V[:,3:6] + factor[0] * V[:,6:9]
if len(factor) > 1:
V[:,3:6] = V[:,3:6] + factor[1] * V[:,9:12]
else:
raise RuntimeError('No suitable geometry for postalignment: ' + proj_geom['type'])
return proj_geom
|
