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#-----------------------------------------------------------------------
#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 numpy as np
import six
from libcpp.string cimport string
from libcpp.list cimport list
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 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
dc = convert_item(_dc)
for item in dc:
val = dc[item]
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = root.addChildNode(item)
listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
index = 0
if val.ndim == 2:
for i in range(val.shape[0]):
for j in range(val.shape[1]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
index += 1
del itm
elif val.ndim == 1:
for i in range(val.shape[0]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute(< string > six.b('value'), < float32 > val[i])
index += 1
del itm
else:
raise Exception("Only 1 or 2 dimensions are allowed")
del listbase
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)
del itm
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))
del itm
cdef void readOptions(XMLNode * node, dc):
cdef XMLNode * listbase
cdef XMLNode * itm
cdef int i
cdef int j
for item in dc:
val = dc[item]
if node.hasOption(item):
raise Exception('Duplicate Option: %s' % item)
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = node.addChildNode(six.b('Option'))
listbase.addAttribute(< string > six.b('key'), < string > item)
listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
index = 0
if val.ndim == 2:
for i in range(val.shape[0]):
for j in range(val.shape[1]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
index += 1
del itm
elif val.ndim == 1:
for i in range(val.shape[0]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute(< string > six.b('value'), < float32 > val[i])
index += 1
del itm
else:
raise Exception("Only 1 or 2 dimensions are allowed")
del listbase
else:
node.addOption(item, wrap_to_bytes(val))
cdef configToDict(Config *cfg):
return XMLNode2dict(cfg.self)
def castString3(input):
return input.decode('utf-8')
def castString2(input):
return input
if six.PY3:
castString = castString3
else:
castString = castString2
def stringToPythonValue(inputIn):
input = castString(inputIn)
# matrix
if ';' in input:
row_strings = input.split(';')
col_strings = row_strings[0].split(',')
nRows = len(row_strings)
nCols = len(col_strings)
out = np.empty((nRows,nCols))
for ridx, row in enumerate(row_strings):
col_strings = row.split(',')
for cidx, col in enumerate(col_strings):
out[ridx,cidx] = float(col)
return out
# vector
if ',' in input:
items = input.split(',')
out = np.empty(len(items))
for idx,item in enumerate(items):
out[idx] = float(item)
return out
try:
# integer
return int(input)
except ValueError:
try:
#float
return float(input)
except ValueError:
# string
return str(input)
cdef XMLNode2dict(XMLNode * node):
cdef XMLNode * subnode
cdef list[XMLNode * ] nodes
cdef list[XMLNode * ].iterator it
dct = {}
opts = {}
if node.hasAttribute(six.b('type')):
dct['type'] = castString(node.getAttribute(six.b('type')))
nodes = node.getNodes()
it = nodes.begin()
while it != nodes.end():
subnode = deref(it)
if castString(subnode.getName())=="Option":
opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value'))
else:
dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent())
del subnode
inc(it)
if len(opts)>0: dct['options'] = opts
return dct
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