Start adding MPI library.

.gitignore

@@ -2,4 +2,5 @@
 **/__pycache__
 **/Results
 *.pyc
-3D/Tilt_Series/*
+3D/Tilt_Series/*
+*.so

3D/ART.py

@@ -41,7 +41,7 @@
 tiltSeries = None
 
 # Generate Tilt Angles.
-tiltAngles = np.load('Tilt_Series/'+file_name+'_tiltAngles.npy')
+tiltAngles = np.load('../Tilt_Series/'+file_name+'_tiltAngles.npy')
 
 # Generate measurement matrix
 A = parallelRay(Nray, tiltAngles)

3D/Utils/Makefile

@@ -1,10 +1,13 @@
-CXX = g++-8
+CXX = g++-8
+MPXX = mpic++
 CXXFLAGS = -O3 -Wno-div-by-zero -fopenmp -shared -std=c++11 -undefined dynamic_lookup -ffast-math -march=native
 EIGEN = -I /opt/local/include/eigen3 
 PYBIND11 = `python3 -m pybind11 --includes` 
-ctvlib_config = ctvlib`python3-config --extension-suffix`
+PYCONFIG = ctvlib`python3-config --extension-suffix`
+MPICONFIG = mpi_ctvlib`python3-config --extension-suffix`
 
-all: ctvlib
-
 ctvlib: ctvlib.cpp  ctvlib.hpp
-	$(CXX) $(CXXFLAGS) $(EIGEN) $(PYBIND11) ctvlib.cpp -o $(ctvlib_config) 
+	$(CXX) $(CXXFLAGS) $(EIGEN) $(PYBIND) $(PYBIND11) ctvlib.cpp -o $(PYCONFIG) 
+
+mpiCtvlib: mpi_ctvlib.cpp mpi_ctvlib.hpp
+	$(MPXX) $(CXXFLAGS) $(EIGEN) $(PYBIND) $(PYBIND11) mpi_ctvlib.cpp -o $(MPICONFIG) 

3D/Utils/ctvlib.cpp

@@ -46,9 +46,9 @@ ctvlib::ctvlib(int Ns, int Nray, int Nproj)
     // Initialize the 3D Matrices as zeros. 
     for (int i=0; i < Nslice; i++)
     {
-        recon[i] = Mat::Zero(Ny, Ny);
-        temp_recon[i] = Mat::Zero(Ny, Ny);
-        tv_recon[i] = Mat::Zero(Ny,Ny);
+        recon[i] = Mat::Zero(Ny, Nz);
+        temp_recon[i] = Mat::Zero(Ny, Nz);
+        tv_recon[i] = Mat::Zero(Ny,Nz);
     }
 }
 
@@ -77,7 +77,7 @@ void ctvlib::create_projections()
         {
             b(s,i) = A.row(i).dot(vec_recon);
         }
-        mat_slice.resize(Ny,Ny);
+        mat_slice.resize(Ny,Nz);
     }
 }
 
@@ -121,7 +121,7 @@ void ctvlib::ART(double beta, int dyn_ind)
             vec_recon += A.row(j).transpose() * a * beta;
         }
         mat_slice = vec_recon;
-        mat_slice.resize(Ny, Ny);
+        mat_slice.resize(Ny, Nz);
     }
 }
 
@@ -150,7 +150,7 @@ void ctvlib::sART(double beta, int dyn_ind)
             vec_recon += A.row(j).transpose() * a * beta;
         }
         mat_slice = vec_recon;
-        mat_slice.resize(Ny, Ny);
+        mat_slice.resize(Ny, Nz);
     }
 }
 
@@ -183,7 +183,7 @@ void ctvlib::SIRT(double beta, int dyn_ind)
         VectorXf vec_recon = mat_slice;
         vec_recon += A.transpose() * ( b.row(s).transpose() - A * vec_recon ) * beta;
         mat_slice = vec_recon;
-        mat_slice.resize(Ny, Ny);
+        mat_slice.resize(Ny, Nz);
     }
 }
 
@@ -256,7 +256,7 @@ void ctvlib::forwardProjection(int dyn_ind)
         {
             g(s,i) = A.row(i).dot(vec_recon);
         }
-        mat_slice.resize(Ny,Ny);
+        mat_slice.resize(Ny,Nz);
     }
 }
 
@@ -427,7 +427,7 @@ void ctvlib::restart_recon()
 {
     for (int s = 0; s < Nslice; s++)
     {
-        recon[s] = Mat::Zero(Ny,Ny);
+        recon[s] = Mat::Zero(Ny,Nz);
     }
 }