initial commit

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'