summaryrefslogtreecommitdiffstats
path: root/python/astra/data3d_c.pyx
blob: 84472c12b84ce7434b7d868925c6e41539ef004e (plain)
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
#-----------------------------------------------------------------------
#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
#
#Author: Daniel M. Pelt
#Contact: D.M.Pelt@cwi.nl
#Website: http://dmpelt.github.io/pyastratoolbox/
#
#
#This file is part of the Python interface to the
#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
#
#The Python interface to 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 Python interface to 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 Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
#
#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra

import six

cimport cython

cimport PyData3DManager
from .PyData3DManager cimport CData3DManager

from .PyIncludes cimport *
import numpy as np

cimport numpy as np
np.import_array()

cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument

cimport utils
from .utils import wrap_from_bytes

cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()

cdef extern from *:
    CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL

cdef extern from "CFloat32CustomPython.h":
    cdef cppclass CFloat32CustomPython:
        CFloat32CustomPython(arrIn)

def create(datatype,geometry,data=None, link=False):
    cdef Config *cfg
    cdef CVolumeGeometry3D * pGeometry
    cdef CProjectionGeometry3D * ppGeometry
    cdef CFloat32Data3DMemory * pDataObject3D
    cdef CConeProjectionGeometry3D* pppGeometry
    cdef CFloat32CustomMemory * pCustom
    if datatype == '-vol':
        cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
        pGeometry = new CVolumeGeometry3D()
        if not pGeometry.initialize(cfg[0]):
            del cfg
            del pGeometry
            raise Exception('Geometry class not initialized.')
        if link:
            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
        else:
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
        del cfg
        del pGeometry
    elif datatype == '-sino' or datatype == '-proj3d':
        cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry)
        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
        if (tpe == "parallel3d"):
            ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D();
        elif (tpe == "parallel3d_vec"):
            ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D();
        elif (tpe == "cone"):
            ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D();
        elif (tpe == "cone_vec"):
            ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
        else:
            raise Exception("Invalid geometry type.")

        if not ppGeometry.initialize(cfg[0]):
            del cfg
            del ppGeometry
            raise Exception('Geometry class not initialized.')
        if link:
            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
        else:
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
        del ppGeometry
        del cfg
    elif datatype == "-sinocone":
        cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry)
        pppGeometry = new CConeProjectionGeometry3D()
        if not pppGeometry.initialize(cfg[0]):
            del cfg
            del pppGeometry
            raise Exception('Geometry class not initialized.')
        if link:
            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry, pCustom)
        else:
            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
    else:
        raise Exception("Invalid datatype.  Please specify '-vol' or '-proj3d'.")

    if not pDataObject3D.isInitialized():
        del pDataObject3D
        raise Exception("Couldn't initialize data object.")

    if not link: fillDataObject(pDataObject3D, data)

    pDataObject3D.updateStatistics()

    return man3d.store(<CFloat32Data3D*>pDataObject3D)

def get_geometry(i):
    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
    cdef CFloat32ProjectionData3DMemory * pDataObject2
    cdef CFloat32VolumeData3DMemory * pDataObject3
    if pDataObject.getType() == THREEPROJECTION:
        pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject
        geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration())
    elif pDataObject.getType() == THREEVOLUME:
        pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject
        geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration())
    else:
        raise Exception("Not a known data object")
    return geom

def change_geometry(i, geom):
    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
    cdef CFloat32ProjectionData3DMemory * pDataObject2
    cdef CFloat32VolumeData3DMemory * pDataObject3
    if pDataObject.getType() == THREEPROJECTION:
        pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject
        # TODO: Reduce code duplication here
        cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom)
        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
        if (tpe == "parallel3d"):
            ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D();
        elif (tpe == "parallel3d_vec"):
            ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D();
        elif (tpe == "cone"):
            ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D();
        elif (tpe == "cone_vec"):
            ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
        else:
            raise Exception("Invalid geometry type.")
        if not ppGeometry.initialize(cfg[0]):
            del cfg
            del ppGeometry
            raise Exception('Geometry class not initialized.')
        del cfg
        if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \
            ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \
            ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()):
            del ppGeometry
            raise Exception(
                "The dimensions of the data do not match those specified in the geometry.")
        pDataObject2.changeGeometry(ppGeometry)
        del ppGeometry

    elif pDataObject.getType() == THREEVOLUME:
        pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject
        cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom)
        pGeometry = new CVolumeGeometry3D()
        if not pGeometry.initialize(cfg[0]):
            del cfg
            del pGeometry
            raise Exception('Geometry class not initialized.')
        del cfg
        if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \
            pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \
            pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()):
            del pGeometry
            raise Exception(
                "The dimensions of the data do not match those specified in the geometry.")
        pDataObject3.changeGeometry(pGeometry)
        del pGeometry

    else:
        raise Exception("Not a known data object")


cdef fillDataObject(CFloat32Data3DMemory * obj, data):
    if data is None:
        fillDataObjectScalar(obj, 0)
    else:
        if isinstance(data, np.ndarray):
            fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32))
        else:
            fillDataObjectScalar(obj, np.float32(data))

cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s):
    cdef int i
    for i in range(obj.getSize()):
        obj.getData()[i] = s

@cython.boundscheck(False)
@cython.wraparound(False)
cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data):
    if (not data.shape[0] == obj.getDepth()) or (not data.shape[1] == obj.getHeight()) or (not data.shape[2] == obj.getWidth()):
        raise Exception(
            "The dimensions of the data do not match those specified in the geometry.")
    cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData3D()[0][0]
    cView[:] = data

cdef CFloat32Data3D * getObject(i) except NULL:
    cdef CFloat32Data3D * pDataObject = man3d.get(i)
    if pDataObject == NULL:
        raise Exception("Data object not found")
    if not pDataObject.isInitialized():
        raise Exception("Data object not initialized properly.")
    return pDataObject

@cython.boundscheck(False)
@cython.wraparound(False)
def get(i):
    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
    outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C')
    cdef float [:,:,::1] mView = outArr
    cdef float [:,:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1],:outArr.shape[2]]> pDataObject.getData3D()[0][0]
    mView[:] = cView
    return outArr

def get_shared(i):
    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
    outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C')
    cdef np.npy_intp shape[3]
    shape[0] = <np.npy_intp> pDataObject.getDepth()
    shape[1] = <np.npy_intp> pDataObject.getHeight()
    shape[2] = <np.npy_intp> pDataObject.getWidth()
    return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0])

def get_single(i):
    raise Exception("Not yet implemented")

def store(i,data):
    cdef CFloat32Data3D * pDataObject = getObject(i)
    fillDataObject(dynamic_cast_mem(pDataObject), data)

def dimensions(i):
    cdef CFloat32Data3D * pDataObject = getObject(i)
    return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth())

def delete(ids):
    try:
        for i in ids:
            man3d.remove(i)
    except TypeError:
        man3d.remove(ids)

def clear():
    man3d.clear()

def info():
    six.print_(wrap_from_bytes(man3d.info()))