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
|
#-----------------------------------------------------------------------
#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
cimport numpy as np
import numpy as np
import six
from libcpp.string cimport string
from libcpp.vector cimport vector
from cython.operator cimport dereference as deref, preincrement as inc
from cpython.version cimport PY_MAJOR_VERSION
cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument
from .PyXMLDocument cimport XMLNode
from .PyIncludes cimport *
cdef extern from "astra/PluginAlgorithm.h" namespace "astra":
object XMLNode2dict(XMLNode)
cdef Config * dictToConfig(string rootname, dc):
cdef Config * cfg = new Config()
cfg.initialize(rootname)
try:
readDict(cfg.self, dc)
except Exception as e:
del cfg
six.print_(e.strerror)
return NULL
return cfg
def convert_item(item):
if isinstance(item, six.string_types):
return item.encode('ascii')
if type(item) is not dict:
return item
out_dict = {}
for k in item:
out_dict[convert_item(k)] = convert_item(item[k])
return out_dict
def wrap_to_bytes(value):
if isinstance(value, six.binary_type):
return value
s = str(value)
if PY_MAJOR_VERSION == 3:
s = s.encode('ascii')
return s
def wrap_from_bytes(value):
s = value
if PY_MAJOR_VERSION == 3:
s = s.decode('ascii')
return s
cdef void readDict(XMLNode root, _dc):
cdef XMLNode listbase
cdef XMLNode itm
cdef int i
cdef int j
cdef double* data
dc = convert_item(_dc)
for item in dc:
val = dc[item]
if isinstance(val, list) or isinstance(val, tuple):
val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = root.addChildNode(item)
data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64))
if val.ndim == 2:
listbase.setContent(data, val.shape[1], val.shape[0], False)
elif val.ndim == 1:
listbase.setContent(data, val.shape[0])
else:
raise Exception("Only 1 or 2 dimensions are allowed")
elif isinstance(val, dict):
if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'):
readOptions(root, val)
else:
itm = root.addChildNode(item)
readDict(itm, val)
else:
if item == six.b('type'):
root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val))
else:
itm = root.addChildNode(item, wrap_to_bytes(val))
cdef void readOptions(XMLNode node, dc):
cdef XMLNode listbase
cdef XMLNode itm
cdef int i
cdef int j
cdef double* data
for item in dc:
val = dc[item]
if node.hasOption(item):
raise Exception('Duplicate Option: %s' % item)
if isinstance(val, list) or isinstance(val, tuple):
val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = node.addChildNode(six.b('Option'))
listbase.addAttribute(< string > six.b('key'), < string > item)
data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64))
if val.ndim == 2:
listbase.setContent(data, val.shape[1], val.shape[0], False)
elif val.ndim == 1:
listbase.setContent(data, val.shape[0])
else:
raise Exception("Only 1 or 2 dimensions are allowed")
else:
node.addOption(item, wrap_to_bytes(val))
cdef configToDict(Config *cfg):
return XMLNode2dict(cfg.self)
|
