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-rw-r--r--Wrappers/Python/ccpi/common.py143
-rw-r--r--Wrappers/Python/setup.py76
-rw-r--r--recipes/python/bld.bat13
-rw-r--r--recipes/python/build.sh9
-rw-r--r--recipes/python/meta.yaml36
5 files changed, 277 insertions, 0 deletions
diff --git a/Wrappers/Python/ccpi/common.py b/Wrappers/Python/ccpi/common.py
new file mode 100644
index 0000000..6450951
--- /dev/null
+++ b/Wrappers/Python/ccpi/common.py
@@ -0,0 +1,143 @@
+# -*- coding: utf-8 -*-
+# This work is part of the Core Imaging Library developed by
+# Visual Analytics and Imaging System Group of the Science Technology
+# Facilities Council, STFC
+
+# Copyright 2018 Edoardo Pasca
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+# http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import abc
+import numpy
+import os
+import sys
+import time
+
+if sys.version_info[0] >= 3 and sys.version_info[1] >= 4:
+ ABC = abc.ABC
+else:
+ ABC = abc.ABCMeta('ABC', (), {})
+
+def find_key(dic, val):
+ """return the key of dictionary dic given the value"""
+ return [k for k, v in dic.items() if v == val][0]
+
+class CCPiBaseClass(object):
+ def __init__(self, **kwargs):
+ self.acceptedInputKeywords = []
+ self.pars = {}
+ self.debug = True
+
+ def setParameter(self, **kwargs):
+ '''set named parameter for the reconstructor engine
+
+ raises Exception if the named parameter is not recognized
+
+ '''
+ for key , value in kwargs.items():
+ if key in self.acceptedInputKeywords:
+ self.pars[key] = value
+ else:
+ raise KeyError('Wrong parameter "{0}" for {1}'.format(key,
+ self.__class__.__name__ ))
+ # setParameter
+
+ def getParameter(self, key):
+ if type(key) is str:
+ if key in self.acceptedInputKeywords:
+ return self.pars[key]
+ else:
+ raise KeyError('Unrecongnised parameter: {0} '.format(key) )
+ elif type(key) is list:
+ outpars = []
+ for k in key:
+ outpars.append(self.getParameter(k))
+ return outpars
+ else:
+ raise Exception('Unhandled input {0}' .format(str(type(key))))
+ #getParameter
+
+ def log(self, msg):
+ if self.debug:
+ print ("{0}: {1}".format(self.__class__.__name__, msg))
+
+class DataSet(ABC):
+ '''Abstract class to hold data'''
+
+ def __init__ (self, array, deep_copy=True, dimension_labels=None,
+ **kwargs):
+ '''Holds the data'''
+
+ self.shape = numpy.shape(array)
+ self.number_of_dimensions = len (self.shape)
+ self.dimension_labels = {}
+
+ if dimension_labels is not None and \
+ len (dimension_labels) == self.number_of_dimensions:
+ for i in range(self.number_of_dimensions):
+ self.dimension_labels[i] = dimension_labels[i]
+ else:
+ for i in range(self.number_of_dimensions):
+ self.dimension_labels[i] = 'dimension_{0:02}'.format(i)
+
+ if deep_copy:
+ self.array = array[:]
+ else:
+ self.array = array
+
+ def as_array(self, dimensions=None):
+ if dimensions is None:
+ return self.array
+ else:
+ # check that all the requested dimensions are in the array
+ # this is done by checking the dimension_labels
+ proceed = True
+ axis_order = []
+ if type(dimensions) == list:
+ for dl in dimensions:
+ if dl not in self.dimension_labels.values():
+ proceed = False
+ break
+ else:
+ axis_order.append(find_key(self.dimension_labels, dl))
+ print (axis_order)
+ # transpose the array and slice away the unwanted data
+ unwanted_dimensions = self.dimension_labels.copy()
+ for ax in axis_order:
+ unwanted_dimensions.pop(ax)
+ new_shape = []
+ #for i in range(axis_order):
+ # new_shape.append(self.shape(axis_order[i]))
+ new_shape = [self.shape[ax] for ax in axis_order]
+ return numpy.reshape(
+ numpy.delete( self.array , unwanted_dimensions.keys() ) ,
+ new_shape
+ )
+ #return numpy.transpose(self.array, new_shape)
+
+
+
+
+
+if __name__ == '__main__':
+ shape = (2,3,4,5)
+ size = shape[0]
+ for i in range(1, len(shape)):
+ size = size * shape[i]
+ a = numpy.asarray([i for i in range( size )])
+ a = numpy.reshape(a, shape)
+ ds = DataSet(a, False, ['X', 'Y','Z' ,'W'])
+ b = ds.as_array(['Z' ,'W'])
+
+
+
+ \ No newline at end of file
diff --git a/Wrappers/Python/setup.py b/Wrappers/Python/setup.py
new file mode 100644
index 0000000..31fe195
--- /dev/null
+++ b/Wrappers/Python/setup.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+import setuptools
+from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Distutils import build_ext
+
+import os
+import numpy
+import platform
+import sys
+
+cil_version=os.environ['CIL_VERSION']
+if cil_version == '':
+ print("Please set the environmental variable CIL_VERSION")
+ sys.exit(1)
+
+library_include_path = []
+library_lib_path = []
+try:
+ library_include_path = [ os.environ['LIBRARY_INC'] ]
+ library_lib_path = [ os.environ['LIBRARY_LIB'] ]
+except:
+ if platform.system() == 'Windows':
+ pass
+ else:
+ try:
+ library_include_path = [ os.environ['PREFIX']+'/include' ]
+ library_lib_path = [ os.environ['PREFiX']+'/lib' ]
+ except:
+ pass
+ pass
+extra_include_dirs = [numpy.get_include()]
+extra_library_dirs = []
+extra_compile_args = []
+extra_link_args = []
+extra_libraries = []
+
+if platform.system() == 'Windows':
+ extra_compile_args += ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB',
+ '/openmp','/DHAS_TIFF','/DCCPiReconstructionIterative_EXPORTS']
+ extra_include_dirs += ["..\\..\\Core\\src\\","..\\..\\Core\\src\\Algorithms","..\\..\\Core\\src\\Readers", "."]
+ extra_include_dirs += library_include_path
+ extra_library_dirs += library_lib_path
+ extra_libraries += ['tiff' , 'cilrec']
+ if sys.version_info.major == 3 :
+ extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64']
+ else:
+ extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64']
+else:
+ extra_include_dirs += ["../../Core/src/","../../Core/src/Algorithms","../../Core/src/Readers", "."]
+ extra_include_dirs += library_include_path
+ extra_compile_args += ['-fopenmp','-O2', '-funsigned-char', '-Wall','-Wl,--no-undefined','-DHAS_TIFF','-DCCPiReconstructionIterative_EXPORTS']
+ extra_libraries += ['tiff' , 'cilrec']
+ if sys.version_info.major == 3 :
+ extra_libraries += ['boost_python3', 'boost_numpy3','gomp']
+ else:
+ extra_libraries += ['boost_python', 'boost_numpy','gomp']
+
+
+setup(
+ name='ccpi-reconstruction',
+ description='This is a CCPi Core Imaging Library package for Iterative Reconstruction codes',
+ version=cil_version,
+ cmdclass = {'build_ext': build_ext},
+ ext_modules = [Extension("ccpi.reconstruction.parallelbeam",
+ sources=[ "src/diamond_module.cpp",
+ "src/diamond_wrapper.cpp"],
+ include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries, extra_link_args=extra_link_args ),
+ Extension("ccpi.reconstruction.conebeam",
+ sources=[ "src/conebeam_module.cpp",
+ "src/conebeam_wrapper.cpp"],
+ include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries ) ],
+ zip_safe = False,
+ packages = {'ccpi','ccpi.reconstruction'}
+)
diff --git a/recipes/python/bld.bat b/recipes/python/bld.bat
new file mode 100644
index 0000000..f4c395c
--- /dev/null
+++ b/recipes/python/bld.bat
@@ -0,0 +1,13 @@
+IF NOT DEFINED CIL_VERSION (
+ECHO CIL_VERSION Not Defined.
+exit 1
+)
+
+mkdir "%SRC_DIR%\ccpi"
+xcopy /e "%RECIPE_DIR%\..\..\.." "%SRC_DIR%\ccpi"
+cd ccpi\Wrappers\python
+
+%PYTHON% setup.py build_ext
+if errorlevel 1 exit 1
+%PYTHON% setup.py install
+if errorlevel 1 exit 1
diff --git a/recipes/python/build.sh b/recipes/python/build.sh
new file mode 100644
index 0000000..0c6ad30
--- /dev/null
+++ b/recipes/python/build.sh
@@ -0,0 +1,9 @@
+if [ -z "$CIL_VERSION" ]; then
+ echo "Need to set CIL_VERSION"
+ exit 1
+fi
+mkdir ${SRC_DIR}/ccpi
+cp -r "${RECIPE_DIR}/../../../" ${SRC_DIR}/ccpi
+
+cd ${SRC_DIR}/ccpi/Wrappers/python
+$PYTHON setup.py install
diff --git a/recipes/python/meta.yaml b/recipes/python/meta.yaml
new file mode 100644
index 0000000..63a5a3a
--- /dev/null
+++ b/recipes/python/meta.yaml
@@ -0,0 +1,36 @@
+package:
+ name: ccpi-reconstruction
+ version: {{ environ['CIL_VERSION'] }}
+
+
+build:
+ preserve_egg_dir: False
+ script_env:
+ - CIL_VERSION
+# number: 0
+
+requirements:
+ build:
+ - python
+ - numpy
+ - setuptools
+ - boost ==1.64.0
+ - boost-cpp ==1.64.0
+ - cython
+ - libtiff
+ - cil_reconstruction
+
+ run:
+ - python
+ - numpy
+ - boost ==1.64
+ - libtiff
+ - h5py
+ - scipy
+ - cil_reconstruction
+
+
+about:
+ home: http://www.ccpi.ac.uk
+ license: BSD license
+ summary: 'CCPi Toolbox'
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 12:52:53 +0000