Merge branch 'cmaking' of https://github.com/dkazanc/Tomophantom into…

… cmaking

Conflicts:
	Wrappers/Python/setup.py.in

Core/TomoP3DModel_core.c

@@ -99,10 +99,10 @@ float TomoP3DObject_core(float *A, long N1, long N2, long N3, long Z1, long Z2,
 	psi2 = psi_gr2*((float)M_PI / 180.0f);
 	psi3 = psi_gr3*((float)M_PI / 180.0f);
 
-	float bs[3][3] = {
-		{ 0.0f,0.0f,0.0f },
-		{ 0.0f,0.0f,0.0f },
-		{ 0.0f,0.0f,0.0f } };
+    float bs[3][3] = {
+        {0.0f,0.0f,0.0f},
+        {0.0f,0.0f,0.0f},
+        {0.0f,0.0f,0.0f} };
 
 	float xh[3] = { 0.0f, 0.0f, 0.0f };
 	float xh3[3] = { 0.0f, 0.0f, 0.0f };

Core/TomoP3DModel_core.h

@@ -21,8 +21,6 @@ limitations under the License.
 #include "CCPiDefines.h"
 #include "utils.h"
 
-
-//CCPI_EXPORT float TomoP3DModel_core(float *A, int ModelSelected, int N, char *ModelParametersFilename);
 CCPI_EXPORT float TomoP3DModel_core(float *A, int ModelSelected, long N1, long N2, long N3, long Z1, long Z2, char *ModelParametersFilename);
 CCPI_EXPORT float TomoP3DObject_core(float *A, long N1, long N2, long N3, long Z1, long Z2, char *Object,
 	float C0, /* intensity */

Core/utils.c

@@ -502,82 +502,44 @@ float checkParams3D(int *params_switch, int ModelSelected, char *ModelParameters
 }
 
 /***********************************************************************************************/
-/* rotation matrix routine */
-float matrot3(float *Ad, float psi1, float psi2, float psi3)
+/* rotation matrix */
+float matrot3(float Ad[3][3], float psi1, float psi2, float psi3)
 {
-    Ad[0] = cosf(psi1)*cosf(psi2)*cosf(psi3)-sinf(psi1)*sinf(psi3);
-    Ad[1] = sinf(psi1)*cosf(psi2)*cosf(psi3)+cosf(psi1)*sinf(psi3);
-    Ad[2] = -sinf(psi2)*cosf(psi3);
-    Ad[3] = -cosf(psi1)*cosf(psi2)*sinf(psi3)-sinf(psi1)*cosf(psi3);
-    Ad[4] = -sinf(psi1)*cosf(psi2)*sinf(psi3)+cosf(psi1)*cosf(psi3);
-    Ad[5] = sinf(psi2)*sinf(psi3);
-    Ad[6] = cosf(psi1)*sinf(psi2);
-    Ad[7] = sinf(psi1)*sinf(psi2);
-    Ad[8] = cosf(psi2);
-    return *Ad;
+    Ad[0][0]=cosf(psi1)*cosf(psi2)*cosf(psi3)-sinf(psi1)*sinf(psi3);
+    Ad[0][1]=sinf(psi1)*cosf(psi2)*cosf(psi3)+cosf(psi1)*sinf(psi3);
+    Ad[0][2]=-sinf(psi2)*cosf(psi3);
+    Ad[1][0]=-cosf(psi1)*cosf(psi2)*sinf(psi3)-sinf(psi1)*cosf(psi3);
+    Ad[1][1]=-sinf(psi1)*cosf(psi2)*sinf(psi3)+cosf(psi1)*cosf(psi3);
+    Ad[1][2]=sinf(psi2)*sinf(psi3);
+    Ad[2][0]=cosf(psi1)*sinf(psi2);
+    Ad[2][1]=sinf(psi1)*sinf(psi2);
+    Ad[2][2]=cosf(psi2);
+    return 1;
 }
 
 /*matrix-vector multiplication*/
-float matvet3(float *Ad, float *V1, float *V2)
+float matvet3(float Ad[3][3], float V1[3], float V2[3])
 {
-    int l, m, counterT;
-
-    counterT = 0;
+    int l, m;        
     for(l=0; l<3; l++) {
         V2[l] = 0.0f;
         for(m=0; m<3; m++) {
-            V2[l] += Ad[counterT]*V1[m];
-            counterT++;
+            V2[l] += Ad[l][m]*V1[m];
         }}
-    return *V2;
+    return 1;
 }
 
 /*matrix-matrix multiplication*/
-// float matmat3(float *A, float *B, float *C)
-// {
-//     float Am[3][3];
-//     float Bm[3][3];
-//     float Cm[3][3];
-//     
-//     Am[0][0]=A[0];
-//     Am[0][1]=A[1];
-//     Am[0][2]=A[2];
-//     Am[1][0]=A[3];
-//     Am[1][1]=A[4];
-//     Am[1][2]=A[5];
-//     Am[2][0]=A[6];
-//     Am[2][1]=A[7];
-//     Am[2][2]=A[8];
-//     
-//     Bm[0][0]=B[0];
-//     Bm[0][1]=B[1];
-//     Bm[0][2]=B[2];
-//     Bm[1][0]=B[3];
-//     Bm[1][1]=B[4];
-//     Bm[1][2]=B[5];
-//     Bm[2][0]=B[6];
-//     Bm[2][1]=B[7];
-//     Bm[2][2]=B[8];
-//     
-//     int i, j, k;
-//     for(i=0; i<3; i++) {
-//         for(j=0; j<3; j++) {
-//             Cm[i][j]=0.0f;
-//             for(k=0; k<3; k++) {
-//                 Cm[i][j] += Am[i][k]*Bm[k][j];
-//             }
-//         }}
-//     
-//     C[0] = Cm[0][0];
-//     C[1] = Cm[0][1];
-//     C[2] = Cm[0][2];
-//     C[3] = Cm[1][0];
-//     C[4] = Cm[1][1];
-//     C[5] = Cm[1][2];
-//     C[6] = Cm[2][0];
-//     C[7] = Cm[2][1];
-//     C[8] = Cm[2][2];
-//     
-//     
-//     return *C;
-// }
+/*float matmat3(float Am[3][3], float Bm[3][3], float Cm[3][3])
+{
+    int i, j, k;
+    for(i=0; i<3; i++) {
+        for(j=0; j<3; j++) {
+             Cm[i][j]=0.0f;
+             for(k=0; k<3; k++) {
+                 Cm[i][j] += Am[i][k]*Bm[k][j];
+             }
+        }}
+    return 1;  
+}
+*/

Core/utils.h

@@ -23,9 +23,9 @@ extern "C" {
 #endif
 CCPI_EXPORT float checkParams2D(int *params_switch, int ModelSelected, char *ModelParametersFilename);
 CCPI_EXPORT float checkParams3D(int *params_switch, int ModelSelected, char *ModelParametersFilename);
-CCPI_EXPORT float matrot3(float *Ad, float psi1, float psi2, float psi3);
-CCPI_EXPORT float matvet3(float *Ad, float *V1, float *V2);
-// float matmat3(float *A, float *B, float *C);
+CCPI_EXPORT float matrot3(float Ad[3][3], float psi1, float psi2, float psi3);
+CCPI_EXPORT float matvet3(float Ad[3][3], float V1[3], float V2[3]);
+// CCPI_EXPORT float matmat3(float Am[3][3], float Bm[3][3], float Cm[3][3]);
 #ifdef __cplusplus
 }
 #endif

Wrappers/MATLAB/Model2DGeneratorDemo.m

@@ -10,8 +10,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat
@@ -21,7 +19,7 @@
 % Generate 2D phantom:
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP); 
 figure; imagesc(G, [0 1]); daspect([1 1 1]); colormap hot;

Wrappers/MATLAB/Model2D_tGeneratorDemo.m

@@ -10,8 +10,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 ModelNo = 100; % Select a model from Phantom2DLibrary.dat
@@ -21,10 +19,10 @@
 % Generate 2D+t phantom:
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP);
-figure(1); imagesc(G, [0 1]); daspect([1 1 1]); title('2D+t model, t=3 here'); colormap hot;
+figure(1); imagesc(G(:,:,3), [0 1]); daspect([1 1 1]); title('2D+t model, t=3 here'); colormap hot;
 %%
 % Lets look at more finely discretized temporal model and related sinograms
 ModelNo = 101; % Select a model from Phantom2DLibrary.dat
@@ -34,7 +32,7 @@
 % Generate 2D phantom:
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP);
 
@@ -58,7 +56,7 @@
 timeFrames = 25; %must be the same as in model
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP);
 

Wrappers/MATLAB/Model3DGeneratorDemo.m

@@ -8,8 +8,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 ModelNo = 10; % Select a model
@@ -19,7 +17,7 @@
 % generate 3D phantom (modify your PATH bellow):
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 tic; [G] = TomoP3DModel(ModelNo,N,pathTP); toc;
 

Wrappers/MATLAB/Model3D_tGeneratorDemo.m

@@ -8,8 +8,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 ModelNo = 100; % Select a model
@@ -19,7 +17,7 @@
 % generate 4D phantom (modify your PATH bellow):
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP3DModel(ModelNo,N,pathTP);
 
@@ -38,11 +36,10 @@
 % generate 4D phantom (modify your PATH bellow):
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom3DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP3DModel(ModelNo,N,pathTP);
 
-%%
 sliceM = round(0.5*N);
 figure(2);
 ll = 10;

Wrappers/MATLAB/Reconstruction_Demo.m

@@ -10,8 +10,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat
@@ -21,7 +19,7 @@
 % Generate 2D phantom:
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP); 
 figure; imagesc(G, [0 1]); daspect([1 1 1]); colormap hot;

Wrappers/MATLAB/SpectralPhantomDemo.m

@@ -10,8 +10,6 @@
 close all;clc;clear;
 % adding paths
 fsep = '/';
-pathtoModels = sprintf(['..' fsep 'functions' fsep 'models' fsep], 1i);
-addpath(pathtoModels);
 addpath('compiled'); addpath('supplem'); 
 
 
@@ -22,7 +20,7 @@
 % generate the 2D phantom:
 curDir   = pwd;
 mainDir  = fileparts(curDir);
-pathtoLibrary = sprintf([fsep 'functions' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+pathtoLibrary = sprintf([fsep '..' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
 pathTP = strcat(mainDir, pathtoLibrary); % path to TomoPhantom parameters file
 [G] = TomoP2DModel(ModelNo,N,pathTP);
 

Wrappers/MATLAB/install/compile_mex_linux.m

@@ -6,10 +6,13 @@
 
 mkdir compiled
 
-PathFunc = sprintf(['..' fsep 'functions' fsep], 1i);
-cd(PathFunc);
+PathFunc = sprintf(['..' fsep '..' fsep 'Core' fsep], 1i);
 
-Pathmove = sprintf(['..' fsep 'matlab' fsep 'compiled' fsep], 1i);
+copyfile(PathFunc, 'mex_wrappers');
+
+cd('mex_wrappers');
+
+Pathmove = sprintf(['..' fsep 'compiled' fsep], 1i);
 
 fprintf('%s \n', 'Building functions...');
 mex TomoP2DModel.c TomoP2DModel_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
@@ -24,7 +27,11 @@
 movefile('TomoP3DModel.mex*',Pathmove);
 mex TomoP3DObject.c TomoP3DModel_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
 movefile('TomoP3DObject.mex*',Pathmove);
+mex TomoP2DSinoNum.c TomoP2DSinoNum_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+movefile('TomoP2DSinoNum.mex*',Pathmove);
+
+delete TomoP2DModel_core* TomoP2DModelSino_core* TomoP3DModel_core* TomoP2DSinoNum_core* CCPiDefines.h utils* CMakeLists.txt;
+
 fprintf('%s \n', 'All compiled!');
 
 cd(UpPath);
-cd matlab

Wrappers/MATLAB/install/compile_mex_windows.m

@@ -14,10 +14,13 @@
 
 mkdir compiled
 
-PathFunc = sprintf(['..' fsep 'functions' fsep], 1i);
-cd(PathFunc);
-Pathmove = sprintf(['..' fsep 'matlab' fsep 'compiled' fsep], 1i);
+PathFunc = sprintf(['..' fsep '..' fsep 'Core' fsep], 1i);
 
+copyfile(PathFunc, 'mex_wrappers');
+
+cd('mex_wrappers');
+
+Pathmove = sprintf(['..' fsep 'compiled' fsep], 1i);
 % One way to compile using Matlab-installed MinGW: 
 fprintf('%s \n', 'Building functions...');
 mex TomoP2DModel.c TomoP2DModel_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
@@ -32,6 +35,11 @@
 movefile('TomoP3DModel.mex*',Pathmove);
 mex TomoP3DObject.c TomoP3DModel_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
 movefile('TomoP3DObject.mex*',Pathmove);
+mex TomoP2DSinoNum.c TomoP2DSinoNum_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
+movefile('TomoP2DSinoNum.mex*',Pathmove);
+
+
+delete TomoP2DModel_core* TomoP2DModelSino_core* TomoP3DModel_core* TomoP2DSinoNum_core* CCPiDefines.h utils* CMakeLists.txt;
 
 %%% The second approach to compile using TDM-GCC which follows this
 %%% discussion:
@@ -55,7 +63,9 @@
 % movefile('TomoP3DModel.mex*',Pathmove);
 % mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" TomoP3DObject.c TomoP3DModel_core.c utils.c
 % movefile('TomoP3DObject.mex*',Pathmove);
-% fprintf('%s \n', 'All compiled!');
+% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" TomoP2DSinoNum.c TomoP2DSinoNum_core.c utils.c
+% movefile('TomoP2DSinoNum.mex*',Pathmove);
+% delete TomoP2DModel_core* TomoP2DModelSino_core* TomoP3DModel_core* TomoP2DSinoNum_core* CCPiDefines.h utils* CMakeLists.txt;
 
-cd(UpPath);
-cd matlab
+fprintf('%s \n', 'All compiled!');
+cd(UpPath);

Wrappers/Python/Demos/DemoModel.py

@@ -22,7 +22,7 @@
 model = 1 # selecting a model
 N_size = 512
 #specify a full path to the parameters file
-pathTP = '../../functions/models/Phantom2DLibrary.dat'
+pathTP = '../../../PhantomLibrary/models/Phantom2DLibrary.dat'
 #objlist = modelfile2Dtolist(pathTP, model) # one can extract parameters
 #This will generate a N_size x N_size phantom (2D)
 phantom_2D = TomoP2D.Model(model, N_size, pathTP)