Add python algebra test

src/Registration/cReg/NiftiImageData.cpp

@@ -293,11 +293,24 @@ NiftiImageData<dataType>& NiftiImageData<dataType>::operator*=(const float val)
     maths(val, mul);
     return *this;
 }
+template<class dataType>
+NiftiImageData<dataType>& NiftiImageData<dataType>::operator*=(const NiftiImageData<dataType>& rhs)
+{
+    maths(rhs, mul);
+    return *this;
+}
 
 template<class dataType>
 NiftiImageData<dataType>& NiftiImageData<dataType>::operator/=(const float val)
 {
-    maths(1.f/val, mul);
+    maths(val, div);
+    return *this;
+}
+
+template<class dataType>
+NiftiImageData<dataType>& NiftiImageData<dataType>::operator/=(const NiftiImageData<dataType>& rhs)
+{
+    maths(rhs, div);
     return *this;
 }
 
@@ -593,12 +606,18 @@ void NiftiImageData<dataType>::maths(const NiftiImageData<dataType>& c, const Ma
         throw std::runtime_error("NiftiImageData<dataType>::maths_image: at least one image is not initialised.");
     if (!NiftiImageData<dataType>::do_nifti_image_metadata_match(*this, c, true))
         throw std::runtime_error("NiftiImageData<dataType>::maths_image: metadata do not match.");
-    if (type != add && type != sub)
-        throw std::runtime_error("NiftiImageData<dataType>::maths_image: only implemented for add and subtract.");
+    if (type != add && type != sub && type != mul && type != div)
+        throw std::runtime_error("NiftiImageData<dataType>::maths_image: only implemented for add, subtract, multiply and divide.");
 
     for (int i=0; i<int(this->_nifti_image->nvox); ++i) {
         if (type == add) (*this)(i) += c(i);
-        else             (*this)(i) -= c(i);
+        else if (type == sub) (*this)(i) -= c(i);
+        else if (type == mul) (*this)(i) *= c(i);
+        else if (type == div) {
+            if (c(i) != 0) (*this)(i) /= c(i);
+            else throw std::runtime_error("NiftiImageData<dataType>::maths_image: division by zero.");
+        }
+
     }
 }
 
@@ -607,13 +626,17 @@ void NiftiImageData<dataType>::maths(const float val, const MathsType type)
 {
     if (!this->is_initialised())
         throw std::runtime_error("NiftiImageData<dataType>::maths_image_val: image is not initialised.");
-    if (type != add && type != sub && type != mul)
-        throw std::runtime_error("NiftiImageData<dataType>::maths_image_val: only implemented for add, subtract and multiply.");
+    if (type != add && type != sub && type != mul && type != div)
+        throw std::runtime_error("NiftiImageData<dataType>::maths_image_val: only implemented for add, subtract, multiply and divide.");
 
     for (int i=0; i<int(this->_nifti_image->nvox); ++i) {
         if      (type == add) (*this)(i) += val;
         else if (type == sub) (*this)(i) -= val;
-        else                  (*this)(i) *= val;
+        else if (type == mul) (*this)(i) *= val;
+        else if (type == div) {
+           if (val != 0) (*this)(i) /= val; 
+           else throw std::runtime_error("NiftiImageData<dataType>::maths_image_val: division by zero.");
+        }
     }
 }
 

src/Registration/cReg/cReg.cpp

@@ -328,8 +328,10 @@ void* cReg_NiftiImageData_maths_im(const void *res_ptr, const void* im1_ptr, con
 
         if      (maths_type == 0) res = im1 + im2;
         else if (maths_type == 1) res = im1 - im2;
+        else if (maths_type == 2) res = im1 * im2;
+        else if (maths_type == 3) res = im1 / im2; 
         else
-            throw std::runtime_error("cReg_NiftiImageData_maths_im: Bad maths type (0=add, 1=subtract).");
+            throw std::runtime_error("cReg_NiftiImageData_maths_im: Bad maths type (0=add, 1=subtract, 2=multiply, 3=divide).");
         return new DataHandle;
     }
     CATCH;
@@ -344,8 +346,9 @@ void* cReg_NiftiImageData_maths_num(const void *res_ptr, const void* im1_ptr, co
         if      (maths_type == 0) res = im1 + val;
         else if (maths_type == 1) res = im1 - val;
         else if (maths_type == 2) res = im1 * val;
+        else if (maths_type == 3) res = im1 / val; 
         else
-            throw std::runtime_error("cReg_NiftiImageData_maths_val: Bad maths type (0=add, 1=subtract, 2=multiply.");
+            throw std::runtime_error("cReg_NiftiImageData_maths_num: Bad maths type (0=add, 1=subtract, 2=multiply, 3=divide");
         return new DataHandle;
     }
     CATCH;

src/Registration/cReg/include/sirf/Reg/NiftiImageData.h

@@ -267,6 +267,8 @@ class NiftiImageData : public ImageData
 
     /// Multiplication operator
     NiftiImageData& operator*=(const float);
+    /// Multiplication operator
+    NiftiImageData& operator*=(const NiftiImageData &rhs);
 
     /// Multiplication operator
     friend NiftiImageData operator*(NiftiImageData lhs, const float val)
@@ -275,16 +277,32 @@ class NiftiImageData : public ImageData
         return lhs;
     }
 
-    /// Division operator
-    NiftiImageData& operator/=(const float);
+    /// Multiplication operator
+    friend NiftiImageData operator*(NiftiImageData lhs, const NiftiImageData& rhs)
+    {
+        lhs *= rhs;
+        return lhs;
+    }
 
     /// Division operator
+    NiftiImageData& operator/=(const float);
+    // /// Division operator
+    NiftiImageData& operator/=(const NiftiImageData &rhs);
+
+    // /// Division operator
     friend NiftiImageData operator/(NiftiImageData lhs, const float val)
     {
         lhs /= val;
         return lhs;
     }
 
+    /// Division operator
+    friend NiftiImageData operator/(NiftiImageData lhs, const NiftiImageData& rhs)
+    {
+        lhs /= rhs;
+        return lhs;
+    }
+
     /// Access data element via 1D index (const)
     float operator()(const int index) const;
 
@@ -431,7 +449,7 @@ class NiftiImageData : public ImageData
 
     enum NiftiImageDataType { _general, _3D, _3DTensor, _3DDisp, _3DDef};
 
-    enum MathsType { add, sub, mul };
+    enum MathsType { add, sub, mul, div};
 
     /// Image data as a nifti object
     std::shared_ptr<nifti_image>  _nifti_image;

src/Registration/pReg/Reg.py

@@ -1,7 +1,8 @@
 """Object-Oriented wrap for the cReg-to-Python interface pyreg.py."""
 
 # SyneRBI Synergistic Image Reconstruction Framework (SIRF)
-# Copyright 2018 - 2020 University College London
+# Copyright 2018 - 2021 University College London
+# Copyright 2018 - 2021 Science Technology Facilities Council
 #
 # This is software developed for the Collaborative Computational
 # Project in Synergistic Reconstruction for Biomedical Imaging
@@ -146,7 +147,10 @@ def get_as_deformation_field(self, ref):
 
 class NiftiImageData(SIRF.ImageData):
     """General class for nifti image data."""
-
+    _ADD      = 0
+    _SUBTRACT = 1
+    _MULTIPLY = 2
+    _DIVIDE   = 3
     def __init__(self, src=None):
         """init."""
         self.handle = None
@@ -174,11 +178,11 @@ def __add__(self, other):
         if isinstance(other, NiftiImageData):
             try_calling(
                 pyreg.cReg_NiftiImageData_maths_im(
-                    z.handle, self.handle, other.handle, 0))
+                    z.handle, self.handle, other.handle, NiftiImageData._ADD))
         else:
             try_calling(
                 pyreg.cReg_NiftiImageData_maths_num(
-                    z.handle, self.handle, float(other), 0))
+                    z.handle, self.handle, float(other), NiftiImageData._ADD))
         check_status(z.handle)
         return z
 
@@ -187,21 +191,35 @@ def __sub__(self, other):
         z = self.clone()
         if isinstance(other, NiftiImageData):
             try_calling(pyreg.cReg_NiftiImageData_maths_im(z.handle,
-                        self.handle, other.handle, 1))
+                        self.handle, other.handle, NiftiImageData._SUBTRACT))
         else:
             try_calling(pyreg.cReg_NiftiImageData_maths_num(z.handle,
-                        self.handle, float(other), 1))
+                        self.handle, float(other), NiftiImageData._SUBTRACT))
         check_status(z.handle)
         return z
 
     def __mul__(self, other):
         """Overloads * operator."""
         z = self.clone()
-        try_calling(pyreg.cReg_NiftiImageData_maths_num(z.handle, self.handle,
-                    float(other), 2))
+        if isinstance(other, NiftiImageData):
+            try_calling(pyreg.cReg_NiftiImageData_maths_im(z.handle,
+                        self.handle, other.handle, NiftiImageData._MULTIPLY))
+        else:
+            try_calling(pyreg.cReg_NiftiImageData_maths_num(z.handle,
+                        self.handle, float(other), NiftiImageData._MULTIPLY))
+        check_status(z.handle)
+        return z
+    def __div__(self, other):
+        """Overloads / operator."""
+        z = self.clone()
+        if isinstance(other, NiftiImageData):
+            try_calling(pyreg.cReg_NiftiImageData_maths_im(z.handle,
+                        self.handle, other.handle, NiftiImageData._DIVIDE))
+        else:
+            try_calling(pyreg.cReg_NiftiImageData_maths_num(z.handle,
+                        self.handle, float(other), NiftiImageData._DIVIDE))
         check_status(z.handle)
         return z
-
     def equal(self, other):
         """Overload comparison operator."""
         if not isinstance(other, NiftiImageData):

src/Registration/pReg/tests/CMakeLists.txt

@@ -15,12 +15,15 @@
 #  limitations under the License.
 #
 #=========================================================================
-
-if (NOT SPM_FOUND)
-	set(exclude_test "--exclude=test_pReg_spm.py")
+if (SPM_BOOL_STR EQUAL "0")
+  set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
+else()
+  set (exclude_tests "--ignore-files=\"test_algebra\"" "--exclude=TestDataContainerAlgebra")
 endif()
-
 # Make into test
-ADD_TEST(NAME REG_TEST_PYTHON
-  COMMAND ${PYTHON_EXECUTABLE} -m nose --with-coverage --cover-package=sirf.Reg --cover-erase -d -v ${CMAKE_SOURCE_DIR}/src/Registration/pReg ${exclude_test}
-  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+ADD_TEST(NAME REG_TESTS_PYTHON
+  COMMAND ${PYTHON_EXECUTABLE} -m nose --with-coverage --cover-package=sirf.Reg --cover-erase -d -v ${CMAKE_SOURCE_DIR}/src/Registration/pReg ${exclude_tests})
+
+add_test(NAME REG_PYTHON_ALGEBRA
+  COMMAND ${PYTHON_EXECUTABLE} -m unittest test_algebra
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

src/Registration/pReg/tests/test_algebra.py

@@ -0,0 +1,41 @@
+#========================================================================
+# Copyright 2021 Science Technology Facilities Council
+#
+# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF).
+#
+# 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.txt
+#
+# 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 os
+import unittest
+import sirf.Reg as reg
+from sirf.Utilities import  examples_data_path, TestDataContainerAlgebra
+
+
+class TestNiftiImageDataAlgebra(unittest.TestCase, TestDataContainerAlgebra):
+
+    def setUp(self):
+        image1 = reg.ImageData(os.path.join(
+            examples_data_path('Registration'),'test2.nii.gz')
+        )
+        image2 = reg.ImageData(os.path.join(
+            examples_data_path('Registration'),'test2.nii.gz')
+        )
+
+        self.image1 = image1
+        self.image2 = image2
+
+    def tearDown(self):
+        #shutil.rmtree(self.cwd)
+        pass

src/Registration/pReg/tests/test_pReg.py

@@ -29,7 +29,7 @@
     print('WARNING: nibabel is not installed, so not running corresponding tests')
 
 import sirf.Reg
-from pUtilities import *
+from sirf.Utilities import is_operator_adjoint
 
 # Paths
 SIRF_PATH = os.environ.get('SIRF_PATH')

src/Registration/pReg/tests/test_pReg_spm.py

@@ -30,7 +30,11 @@
 import time
 import numpy as np
 import sirf.Reg
-from pUtilities import *
+import unittest
+
+has_spm = hasattr(sirf.Reg, 'SPMRegistration')
+
+
 
 # Paths
 SIRF_PATH = os.environ.get('SIRF_PATH')
@@ -136,7 +140,7 @@ def try_spm():
     sys.stderr.write('# --------------------------------------------------------------------------------- #\n')
     time.sleep(0.5)
 
-
+@unittest.skipUnless(has_spm, "SPM not available")
 def test():
     try_spm()
 

src/common/CMakeLists.txt

@@ -63,7 +63,6 @@ if (BUILD_PYTHON)
   INSTALL(FILES "${CMAKE_CURRENT_BINARY_DIR}/pysirf.py" DESTINATION "${PYTHON_DEST}/sirf")
   file(GLOB PythonFiles "${CMAKE_CURRENT_LIST_DIR}/*.py")
   INSTALL(FILES ${PythonFiles} DESTINATION "${PYTHON_DEST}/sirf")
-
 endif (BUILD_PYTHON)
 
 if (BUILD_MATLAB)