summaryrefslogtreecommitdiffstats
path: root/python
diff options
context:
space:
mode:
Diffstat (limited to 'python')
-rw-r--r--python/astra/PyIncludes.pxd2
-rw-r--r--python/astra/__init__.py1
-rw-r--r--python/astra/data2d_c.pyx27
-rw-r--r--python/astra/plugin.py121
-rw-r--r--python/astra/plugin_c.pyx67
-rw-r--r--python/astra/utils.pyx78
-rw-r--r--python/docSRC/index.rst1
-rw-r--r--python/docSRC/plugins.rst8
8 files changed, 233 insertions, 72 deletions
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 35dea5f..77346b0 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -62,6 +62,7 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
float32 getWindowMaxX()
float32 getWindowMaxY()
Config* getConfiguration()
+ bool isEqual(CVolumeGeometry2D*)
cdef extern from "astra/Float32Data2D.h" namespace "astra":
cdef cppclass CFloat32CustomMemory:
@@ -89,6 +90,7 @@ cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra":
float32 getProjectionAngle(int)
float32 getDetectorWidth()
Config* getConfiguration()
+ bool isEqual(CProjectionGeometry2D*)
cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D":
cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType":
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/data2d_c.pyx b/python/astra/data2d_c.pyx
index 4919bf2..801fd8e 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -34,6 +34,9 @@ from cython cimport view
cimport PyData2DManager
from .PyData2DManager cimport CData2DManager
+cimport PyProjector2DManager
+from .PyProjector2DManager cimport CProjector2DManager
+
cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument
@@ -54,6 +57,8 @@ import operator
from six.moves import reduce
cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
+cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr()
+
cdef extern from "CFloat32CustomPython.h":
cdef cppclass CFloat32CustomPython:
@@ -164,7 +169,6 @@ def store(i, data):
cdef CFloat32Data2D * pDataObject = getObject(i)
fillDataObject(pDataObject, data)
-
def get_geometry(i):
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef CFloat32ProjectionData2D * pDataObject2
@@ -179,6 +183,27 @@ def get_geometry(i):
raise Exception("Not a known data object")
return geom
+cdef CProjector2D * getProjector(i) except NULL:
+ cdef CProjector2D * proj = manProj.get(i)
+ if proj == NULL:
+ raise Exception("Projector not initialized.")
+ if not proj.isInitialized():
+ raise Exception("Projector not initialized.")
+ return proj
+
+def check_compatible(i, proj_id):
+ cdef CProjector2D * proj = getProjector(proj_id)
+ cdef CFloat32Data2D * pDataObject = getObject(i)
+ cdef CFloat32ProjectionData2D * pDataObject2
+ cdef CFloat32VolumeData2D * pDataObject3
+ if pDataObject.getType() == TWOPROJECTION:
+ pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
+ return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry())
+ elif pDataObject.getType() == TWOVOLUME:
+ pDataObject3 = <CFloat32VolumeData2D * >pDataObject
+ return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry())
+ else:
+ raise Exception("Not a known data object")
def change_geometry(i, geom):
cdef Config *cfg
diff --git a/python/astra/plugin.py b/python/astra/plugin.py
new file mode 100644
index 0000000..3e3528d
--- /dev/null
+++ b/python/astra/plugin.py
@@ -0,0 +1,121 @@
+#-----------------------------------------------------------------------
+#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
+from . import data2d
+from . import data2d_c
+from . import data3d
+from . import projector
+import inspect
+import traceback
+
+class base(object):
+
+ def astra_init(self, cfg):
+ args, varargs, varkw, defaults = inspect.getargspec(self.initialize)
+ if not defaults is None:
+ nopt = len(defaults)
+ else:
+ nopt = 0
+ if nopt>0:
+ req = args[2:-nopt]
+ opt = args[-nopt:]
+ else:
+ req = args[2:]
+ 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))))
+
+ args = [optDict[k] for k in req]
+ kwargs = dict((k,optDict[k]) for k in opt if k in optDict)
+ self.initialize(cfg, *args, **kwargs)
+
+class ReconstructionAlgorithm2D(base):
+
+ def astra_init(self, cfg):
+ self.pid = cfg['ProjectorId']
+ self.s = data2d.get_shared(cfg['ProjectionDataId'])
+ self.v = data2d.get_shared(cfg['ReconstructionDataId'])
+ self.vg = projector.volume_geometry(self.pid)
+ self.pg = projector.projection_geometry(self.pid)
+ if not data2d_c.check_compatible(cfg['ProjectionDataId'], self.pid):
+ raise ValueError("Projection data and projector not compatible")
+ if not data2d_c.check_compatible(cfg['ReconstructionDataId'], self.pid):
+ raise ValueError("Reconstruction data and projector not compatible")
+ super(ReconstructionAlgorithm2D,self).astra_init(cfg)
+
+class ReconstructionAlgorithm3D(base):
+
+ def astra_init(self, cfg):
+ self.pid = cfg['ProjectorId']
+ self.s = data3d.get_shared(cfg['ProjectionDataId'])
+ self.v = data3d.get_shared(cfg['ReconstructionDataId'])
+ self.vg = data3d.get_geometry(cfg['ReconstructionDataId'])
+ self.pg = data3d.get_geometry(cfg['ProjectionDataId'])
+ super(ReconstructionAlgorithm3D,self).astra_init(cfg)
+
+def register(className):
+ """Register plugin with ASTRA.
+
+ :param className: Class name or class object to register
+ :type className: :class:`str` or :class:`class`
+
+ """
+ p.register(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..8d6816b
--- /dev/null
+++ b/python/astra/plugin_c.pyx
@@ -0,0 +1,67 @@
+#-----------------------------------------------------------------------
+#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 className)
+ bool registerPlugin(string name, string className)
+ bool registerPluginClass(object 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(className, name=None):
+ if inspect.isclass(className):
+ if name==None:
+ fact.registerPluginClass(className)
+ else:
+ fact.registerPluginClass(six.b(name), className)
+ else:
+ if name==None:
+ fact.registerPlugin(six.b(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 260c308..9871ac6 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) or isinstance(val, tuple):
+ val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
break
@@ -125,6 +129,8 @@ cdef void readOptions(XMLNode node, 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
@@ -143,73 +149,3 @@ 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":
- if subnode.hasAttribute('value'):
- opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value'))
- else:
- opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent())
- else:
- dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent())
- inc(it)
- if len(opts)>0: dct['options'] = opts
- return dct
diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst
index b7cc6d6..dcc6590 100644
--- a/python/docSRC/index.rst
+++ b/python/docSRC/index.rst
@@ -19,6 +19,7 @@ Contents:
creators
functions
operator
+ plugins
matlab
astra
.. astra
diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst
new file mode 100644
index 0000000..dc7c607
--- /dev/null
+++ b/python/docSRC/plugins.rst
@@ -0,0 +1,8 @@
+Plugins: the :mod:`plugin` module
+=========================================
+
+.. automodule:: astra.plugin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-21 10:38:09 +0000