Merge pull request #15 from jtschwar/multi_modal

Fused Multi Modal Tomography
jtschwar · Jan 18, 2024 · ade270c · ade270c
2 parents 3858abc + 8a2c158
commit ade270c
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diff --git a/fused_multi_modal/.vscode/settings.json b/fused_multi_modal/.vscode/settings.json
@@ -0,0 +1,10 @@
+{
+    "files.associations": {
+        "variant": "cpp",
+        "chrono": "cpp",
+        "__tuple": "cpp",
+        "tuple": "cpp",
+        "array": "cpp",
+        "vector": "cpp"
+    }
+}
diff --git a/fused_multi_modal/Utils/Makefile b/fused_multi_modal/Utils/Makefile
@@ -0,0 +1,23 @@
+#Makefile
+#!/bin/sh
+include ./make.inc
+
+GPUCONFIG = astra_ctvlib`python3-config --extension-suffix`
+MMGPUCONFIG = mm_astra`python3-config --extension-suffix`
+MPIGPUCONFIG = mpi_astra_ctvlib`python3-config --extension-suffix`
+MMTVCONFIG = MM_tv`python3-config --extension-suffix`
+
+all: shared_library mm_astra 
+
+shared_library:
+	cd container; make; cd ..
+	cd regularizers; make; cd ..
+	nvcc -shared container/*.o regularizers/*.o -o aux_func.so
+
+mm_astra: mm_astra.cpp mm_astra.hpp
+	$(CXX) $(CXXFLAGS) $(EIGEN) $(ASTRA) $(CUDA) $(NonPAR_HDF5_INC) mm_astra.cpp -o $(MMGPUCONFIG) $(ASTRA_LIB) aux_func.so 
+
+clean:
+	rm -rf *.so *.o
+
+
diff --git a/fused_multi_modal/Utils/container/Makefile b/fused_multi_modal/Utils/container/Makefile
@@ -0,0 +1,15 @@
+#Makefile
+#!/bin/sh
+
+include ./make.inc
+
+all: matrix_op matrix3d matrix4d
+
+matrix_op: matrix_ops.cu matrix_ops.h
+	$(CUDAXX) matrix_ops.cu 
+
+matrix4d: Matrix4D.o Matrix4D.h
+	$(CXX) $(CXXFLAGS) Matrix4D.cpp matrix_ops.o
+
+clean:
+	rm -rf *.so *.o
diff --git a/fused_multi_modal/Utils/container/Matrix4D.cpp b/fused_multi_modal/Utils/container/Matrix4D.cpp
@@ -0,0 +1,96 @@
+#include "Matrix4D.h"
+#include "matrix_ops.h"
+#include <Eigen/Core>
+
+using namespace Eigen;
+
+typedef Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> Mat;
+
+Matrix4D::Matrix4D()
+{
+}
+
+Matrix4D::Matrix4D(int Nel, int Nx, int Ny, int Nz) {
+	nx = Nx;
+	ny = Ny;
+	nz = Nz;
+    nel = Nel;
+	data = new float [nx*ny*nz*Nel];
+	volSize = nx * ny * nz;
+}
+
+// for (int e=0; e<nel; e++) {
+    // for (int i=0; i<nx; i++) {
+        // for (int j=0; j<ny; j++) {
+            // for (int k=0; k<nz; k++)
+        // }
+    // }
+// }
+
+float Matrix4D::get_val(int e, int i, int j, int k) {
+	return data[e*(nx*ny*nz) + (ny*nz)*i + nz*j + k];
+}
+
+int Matrix4D::index(int e, int i, int j, int k){
+    return e*(nx*ny*nz) + (ny*nz)*i + nz*j + k;
+}
+
+void Matrix4D::positivity() {
+    cuda_positivity_4D(data,nx,ny,nz,nel);
+}
+
+void Matrix4D::setData2D(Mat inBuffer, int element, int slice) {
+    for (int yInd = 0; yInd < ny; yInd++) {
+      for (int zInd = 0; zInd < nz; zInd++) {
+          data[index(element,slice,yInd,zInd)] = inBuffer(yInd,zInd);
+      }
+    }
+}
+
+void Matrix4D::setData1D(Vec inBuffer, int element, int slice) {
+    int ind = 0;
+    for (int yInd = 0; yInd < ny; yInd++) {
+      for (int zInd = 0; zInd < nz; zInd++) {
+          ind = zInd + yInd * nz;
+          data[index(element,slice,yInd,zInd)] = inBuffer(ind);
+      }
+    }
+}
+
+// Return Reconstruction to Python.
+Mat Matrix4D::getData2D(int element, int slice) {
+    Mat outBuffer(ny,nz);
+    for (int yInd = 0; yInd < ny; yInd++) {
+        for (int zInd = 0; zInd < nz; zInd++) {
+            outBuffer(yInd,zInd) = data[index(element,slice,yInd,zInd)];
+        }
+    }
+    return outBuffer;
+}
+
+// Vec Matrix4D::getData1D(int element, int slice)
+// {
+//     int ind = 0;
+//     Vec outBuffer(ny*nz);
+//     for (int yInd = 0; yInd < ny; yInd++) {
+//         for (int zInd = 0; zInd < nz; zInd++) {
+//             ind = zInd + yInd * nz;
+//             outBuffer[ind] = data[index(element,slice,yInd,zInd)];
+//         }
+//     }
+//     return outBuffer;
+// }
+
+
+float *Matrix4D::getData1D(int element, int slice) {
+    int ind = 0;
+    // Vec outBuffer(ny*nz);
+    float *outBuffer[ny*nz];
+    for (int yInd = 0; yInd < ny; yInd++) {
+        for (int zInd = 0; zInd < nz; zInd++) {
+            ind = zInd + yInd * nz;
+            outBuffer[ind] = &data[index(element,slice,yInd,zInd)];
+        }
+    }
+    return *outBuffer;
+}
diff --git a/fused_multi_modal/Utils/container/Matrix4D.h b/fused_multi_modal/Utils/container/Matrix4D.h
@@ -0,0 +1,40 @@
+#ifndef matrix_4d_hpp
+#define matrix_4d_hpp
+
+#include <Eigen/Core>
+
+class Matrix4D
+{
+
+typedef Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> Mat;
+typedef Eigen::VectorXf Vec;    
+
+public:
+
+    int nx, ny, nz, nel, volSize;
+    int gpuIndex = -1;
+
+    float *data;
+
+    // Constructors
+    Matrix4D();
+    Matrix4D(int nel, int Nx, int Ny, int Nz);
+
+    // Setter Functions
+    void setData1D(Vec inBuffer, int element, int slice);
+    void setData2D(Mat inBuffer, int element, int slice);
+
+    // Getter Functions
+    float *getData1D(int element, int slice);
+    Mat getData2D(int element, int slice);
+
+    // Access Data
+    float get_val(int e, int i,int j,int k);
+
+    // Calculate Index
+    int index(int e, int i, int j, int k);
+
+    void positivity();
+};
+
+#endif
diff --git a/fused_multi_modal/Utils/container/make.inc b/fused_multi_modal/Utils/container/make.inc
@@ -0,0 +1,5 @@
+CXX = g++ -fPIC -shared 
+MPXX = mpicxx -fPIC -fopenmp
+CUDAXX = nvcc -shared -Xcompiler -fPIC -c
+CXXFLAGS = -O3 -Wno-div-by-zero -std=c++17 -I ../../thirdparty/eigen
+