From 18b6d25f7e4f0943b3592f3bb4f6ca5ed9c285d3 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Fri, 19 Jun 2015 22:28:06 +0200
Subject: Add support for Python algorithm plugins
---
python/astra/__init__.py | 1 +
python/astra/plugin.py | 95 +++++++++++++++++++++++++++++++++++++++++++++++
python/astra/plugin_c.pyx | 59 +++++++++++++++++++++++++++++
python/astra/utils.pyx | 72 +++--------------------------------
4 files changed, 160 insertions(+), 67 deletions(-)
create mode 100644 python/astra/plugin.py
create mode 100644 python/astra/plugin_c.pyx
(limited to 'python/astra')
diff --git a/python/astra/__init__.py b/python/astra/__init__.py
index 6c15d30..10ed74d 100644
--- a/python/astra/__init__.py
+++ b/python/astra/__init__.py
@@ -34,6 +34,7 @@ from . import algorithm
from . import projector
from . import projector3d
from . import matrix
+from . import plugin
from . import log
from .optomo import OpTomo
diff --git a/python/astra/plugin.py b/python/astra/plugin.py
new file mode 100644
index 0000000..ccdb2cb
--- /dev/null
+++ b/python/astra/plugin.py
@@ -0,0 +1,95 @@
+#-----------------------------------------------------------------------
+#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/>.
+#
+#-----------------------------------------------------------------------
+
+from . import plugin_c as p
+from . import log
+
+class base(object):
+
+ def astra_init(self, cfg):
+ try:
+ try:
+ req = self.required_options
+ except AttributeError:
+ log.warn("Plugin '" + self.__class__.__name__ + "' does not specify required options")
+ req = {}
+
+ try:
+ opt = self.optional_options
+ except AttributeError:
+ log.warn("Plugin '" + self.__class__.__name__ + "' does not specify optional options")
+ opt = {}
+
+ try:
+ optDict = cfg['options']
+ except KeyError:
+ optDict = {}
+
+ cfgKeys = set(optDict.keys())
+ reqKeys = set(req)
+ optKeys = set(opt)
+
+ if not reqKeys.issubset(cfgKeys):
+ for key in reqKeys.difference(cfgKeys):
+ log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified")
+ raise ValueError("Missing required options")
+
+ if not cfgKeys.issubset(reqKeys | optKeys):
+ log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys))))
+
+ self.initialize(cfg)
+ except Exception as e:
+ log.error(str(e))
+ raise
+
+def register(name, className):
+ """Register plugin with ASTRA.
+
+ :param name: Plugin name to register
+ :type name: :class:`str`
+ :param className: Class name or class object to register
+ :type className: :class:`str` or :class:`class`
+
+ """
+ p.register(name,className)
+
+def get_registered():
+ """Get dictionary of registered plugins.
+
+ :returns: :class:`dict` -- Registered plugins.
+
+ """
+ return p.get_registered()
+
+def get_help(name):
+ """Get help for registered plugin.
+
+ :param name: Plugin name to get help for
+ :type name: :class:`str`
+ :returns: :class:`str` -- Help string (docstring).
+
+ """
+ return p.get_help(name)
\ No newline at end of file
diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx
new file mode 100644
index 0000000..91b3cd5
--- /dev/null
+++ b/python/astra/plugin_c.pyx
@@ -0,0 +1,59 @@
+#-----------------------------------------------------------------------
+#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
+import inspect
+
+from libcpp.string cimport string
+from libcpp cimport bool
+
+cdef CPluginAlgorithmFactory *fact = getSingletonPtr()
+
+from . import utils
+
+cdef extern from "astra/PluginAlgorithm.h" namespace "astra":
+ cdef cppclass CPluginAlgorithmFactory:
+ bool registerPlugin(string name, string className)
+ bool registerPluginClass(string name, object className)
+ object getRegistered()
+ string getHelp(string name)
+
+cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory":
+ cdef CPluginAlgorithmFactory* getSingletonPtr()
+
+def register(name, className):
+ if inspect.isclass(className):
+ fact.registerPluginClass(six.b(name), className)
+ else:
+ fact.registerPlugin(six.b(name), six.b(className))
+
+def get_registered():
+ return fact.getRegistered()
+
+def get_help(name):
+ return utils.wrap_from_bytes(fact.getHelp(six.b(name)))
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index ddb37aa..3746b8e 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -30,7 +30,6 @@ cimport numpy as np
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
@@ -40,6 +39,9 @@ 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()
@@ -91,6 +93,8 @@ cdef void readDict(XMLNode root, _dc):
dc = convert_item(_dc)
for item in dc:
val = dc[item]
+ if isinstance(val, list):
+ val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
break
@@ -142,69 +146,3 @@ cdef void readOptions(XMLNode node, dc):
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())
- inc(it)
- if len(opts)>0: dct['options'] = opts
- return dct
--
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