diff --git a/Tutorial_BioEM/Euler_Angle_List_Prior b/Tutorial_BioEM/Euler_Angle_List_Prior
index 9e684c122b71a607786ea978dcafa1676c1fe7fb..da43a30feb3d9d35ed8201882cf33f2a97b2d292 100644
--- a/Tutorial_BioEM/Euler_Angle_List_Prior
+++ b/Tutorial_BioEM/Euler_Angle_List_Prior
@@ -6,4 +6,3 @@
0.836000 1.369000 2.640000 0.640000
-1.375000 0.400000 3.018000 0.360000
-1.375000 0.400000 3.018000 0.360000
- 0.836000 1.369000 2.640000 0.640000
diff --git a/Tutorial_BioEM/Param_Input_Priors b/Tutorial_BioEM/Param_Input_Priors
index 152236188344a8536b206851932e7e7782f14b00..9167f6817f0e48c6441df2c634c72acb111816f2 100644
--- a/Tutorial_BioEM/Param_Input_Priors
+++ b/Tutorial_BioEM/Param_Input_Priors
@@ -16,4 +16,4 @@ DISPLACE_CENTER 10 2
####### Priors ###############
PRIOR_MODEL 0.005
-PRIOR_ANGLES
+#PRIOR_ANGLES
diff --git a/Tutorial_BioEM/Param_Input_Quat b/Tutorial_BioEM/Param_Input_Quat
index 4a25c1b2187974a386e5afeb616e006eafdd295a..92f5f095f16127a8e4f93e8b71bab4179067110d 100644
--- a/Tutorial_BioEM/Param_Input_Quat
+++ b/Tutorial_BioEM/Param_Input_Quat
@@ -4,7 +4,7 @@ PIXEL_SIZE 1.77
##### Quaterion grid points: #######
USE_QUATERNIONS
-GRIDPOINTS_QUATERNION 5
+#GRIDPOINTS_QUATERNION 5
##### Constrast transfer integration: #######
CTF_B_FACTOR 100.0 300.5 8
diff --git a/Tutorial_BioEM/Param_Input_Short b/Tutorial_BioEM/Param_Input_Short
index 946da802c7a4eb42e7b5a876ae72a38181ffd4e8..586ffab17ed2b3538994ba26e23cbed080c27d87 100644
--- a/Tutorial_BioEM/Param_Input_Short
+++ b/Tutorial_BioEM/Param_Input_Short
@@ -3,11 +3,11 @@ PIXEL_SIZE 1.77
GRIDPOINTS_ALPHA 10
GRIDPOINTS_BETA 5
GRIDPOINTS_ENVELOPE 4
-START_ENVELOPE 0.0002
-END_ENVELOPE 0.0012
+START_ENVELOPE 0.002
+END_ENVELOPE 0.012
GRIDPOINTS_PSF_PHASE 4
START_PSF_PHASE 0.004
-END_PSF_PHASE 0.016
+END_PSF_PHASE 0.06
GRIDPOINTS_PSF_AMP 1
START_PSF_AMP 1.
END_PSF_AMP 1.
diff --git a/bioem.cpp b/bioem.cpp
index 85c5cc46cd34541abe65f4471ffbf30e23e191a0..9b3d9dcc7a93ac16d786751750bfa3d4bc51bf7c 100644
--- a/bioem.cpp
+++ b/bioem.cpp
@@ -266,7 +266,7 @@ int bioem::configure(int ac, char* av[])
// ********************* Reading Parameter Input ***************************
if(!param.printModel){
// Standard definition for BioEM
- param.readParameters(infile.c_str(),Inputanglefile.c_str());
+ param.readParameters(infile.c_str());
// ********************* Reading Particle Maps Input **********************
RefMap.readRefMaps(param, mapfile.c_str());
@@ -290,7 +290,7 @@ int bioem::configure(int ac, char* av[])
exit(1);
}
- if(!param.printModel)param.CalculateGridsParam();
+ if(!param.printModel)param.CalculateGridsParam(Inputanglefile.c_str());
}
#ifdef WITH_MPI
if (mpi_size > 1)
@@ -298,8 +298,7 @@ int bioem::configure(int ac, char* av[])
if (DebugOutput >= 2 && mpi_rank == 0) timer.ResetStart();
MPI_Bcast(¶m, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
- cout << "HERE MPI" << param.nTotGridAngles << " "<< param.nTotGridAngles * sizeof(myfloat3_t*) << "\n";
-//if (mpi_rank != 0)param.angles = (myfloat3_t*) mallocchk( 4 * param.nTotGridAngles * sizeof(myfloat_t*));
+// cout << "HERE MPI " << param.nTotGridAngles << " " << param.nTotGridAngles * sizeof(myfloat3_t*) << "\n";
if (mpi_rank != 0)param.angles = (myfloat3_t*) mallocchk(3 * param.nTotGridAngles * sizeof (myfloat3_t*));
MPI_Bcast(param.angles, 3 * param.nTotGridAngles * sizeof (myfloat3_t*),MPI_BYTE, 0, MPI_COMM_WORLD);
@@ -309,11 +308,11 @@ int bioem::configure(int ac, char* av[])
// param.angprior = new myfloat_t[param.NotUn_angles] ;
//
-//#ifdef PILAR_DEBUG
+#ifdef PILAR_DEBUG
for(int n=0;n<param.nTotGridAngles;n++){
cout << "CHECK: Angle orient " << mpi_rank << " "<< n << " " << param.angles[n].pos[0] << " " << param.angles[n].pos[1] << " " << param.angles[n].pos[2] << " " << param.angles[n].quat4 << " " << "\n";}
-//
-//#endif
+
+#endif
//refCtf, CtfParam, angles automatically filled by precalculare function below
MPI_Bcast(&Model, sizeof(Model), MPI_BYTE, 0, MPI_COMM_WORLD);
@@ -499,6 +498,9 @@ int bioem::run()
if (DebugOutput >= 1 && mpi_rank == 0) printf("\tMain Loop GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)², Pixels %d², OMP Threads %d, MPI Ranks %d\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, omp_get_max_threads(), mpi_size);
+ if(mpi_size > param.nTotGridAngles){
+ cout << "EXIT: Wrong MPI setup More MPI processes than orientations\n"; exit(1);
+ }
const int iOrientStart = (int) ((long long int) mpi_rank * param.nTotGridAngles / mpi_size);
int iOrientEnd = (int) ((long long int) (mpi_rank + 1) * param.nTotGridAngles / mpi_size);
if (iOrientEnd > param.nTotGridAngles) iOrientEnd = param.nTotGridAngles;
diff --git a/include/param.h b/include/param.h
index 3a72c9bd9a29d7aed3f033c7d97bb7cfb146cf82..f0711cb349edb305ccb3bd30411e3b56ae17f34c 100644
--- a/include/param.h
+++ b/include/param.h
@@ -39,8 +39,8 @@ public:
~bioem_param();
- int readParameters(const char* fileinput,const char* fileangles);
- int CalculateGridsParam();
+ int readParameters(const char* fileinput);
+ int CalculateGridsParam(const char* fileangles);
int CalculateRefCTF();
int forprintBest(const char* fileinput);
void PrepareFFTs();
@@ -85,8 +85,8 @@ public:
bool withnoise;
myfloat_t stnoise;
- std::string inanglef;
- std::string quatfile;
+// std::string inanglef;
+// std::string quatfile;
int numberGridPointsDisplaceCenter;
// Grid sampling for the convolution kernel
diff --git a/map.cpp b/map.cpp
index c902616d84a4d7926a957a4027c67d70db6c21d4..6d0caf5e0242f3e64e7aefcefe91de6e30dd263e 100644
--- a/map.cpp
+++ b/map.cpp
@@ -139,7 +139,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
char tmpLine[512] = {0};
bool first=true;
- int countpix;
+ int countpix=0;
while (!input.eof())
{
@@ -221,7 +221,6 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
ntotRefMap = nummap + 1;
maps = (myfloat_t*) reallocchk(maps, refMapSize * sizeof(myfloat_t) * ntotRefMap);
cout << "Particle Maps read from Standard File: " << ntotRefMap << "\n";
-
}
//Dumping Maps
diff --git a/param.cpp b/param.cpp
index 86a8805f0a377551c3fe4599158ba8f90ec99122..ea246d837491c5016a38a8934cb1ba66ebc6a318 100644
--- a/param.cpp
+++ b/param.cpp
@@ -52,7 +52,7 @@ bioem_param::bioem_param()
printModel = false;
}
-int bioem_param::readParameters(const char* fileinput,const char* fileangles)
+int bioem_param::readParameters(const char* fileinput)
{ // **************************************************************************************
// ***************************** Reading Input Parameters ******************************
// **************************************************************************************
@@ -89,7 +89,7 @@ int bioem_param::readParameters(const char* fileinput,const char* fileangles)
yespriorAngles=false;
//Storing angle file name if existing.
- inanglef=std::string(fileangles);
+//f(notuniformangles)inanglef=std::string(fileangles);
NotUn_angles=0;
priorMod=1; //Default
@@ -695,7 +695,7 @@ void bioem_param::releaseFFTPlans()
fft_plans_created = 0;
}
-int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
+int bioem_param::CalculateGridsParam(const char* fileangles) //TO DO FOR QUATERNIONS
{
// **************************************************************************************
// **************** Routine that pre-calculates Euler angle grids **********************
@@ -731,7 +731,7 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
angles = (myfloat3_t*) mallocchk( 3 * angleGridPointsAlpha * angleGridPointsBeta * angleGridPointsAlpha * sizeof(myfloat3_t));
- cout << "HERE" << sizeof(myfloat3_t) << " " << sizeof(myfloat_t) << " "<< 4 * angleGridPointsAlpha * angleGridPointsBeta * angleGridPointsAlpha * sizeof(myfloat_t*) << "\n";
+
for (int ialpha = 0; ialpha < angleGridPointsAlpha; ialpha ++)
{
for (int ibeta = 0; ibeta < angleGridPointsBeta; ibeta ++)
@@ -746,23 +746,22 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
}
}
}
- cout << "HERE2 "<< n <<" " << angleGridPointsAlpha * angleGridPointsBeta * angleGridPointsAlpha << "\n";
nTotGridAngles = n;
voluang= grid_alpha * grid_alpha * cos_grid_beta / (2.f * M_PI) / (2.f * M_PI) / 2.f * priorMod;
} else{
- ifstream input(inanglef.c_str());
-
-
+ ifstream input(fileangles);
if (!input.good())
{
- cout << "Euler Angle File Failed to open file " << inanglef.c_str() << " " << endl ;
+ cout << "Euler Angle File Failed to open file " << fileangles << " " << endl ;
exit(1);
}
char line[512] = {0};
+// char saveline[512];
+
int n=0;
// First line tels the number of rows
@@ -783,8 +782,7 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
// NotUn_angles=NotUn_angles+1;
- //elete[] angles;
- // angles = new myfloat3_t[]
+
angles = (myfloat3_t*) mallocchk( NotUn_angles * 3 * sizeof(myfloat3_t));
if(yespriorAngles){
@@ -793,16 +791,48 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
}
while (!input.eof())
{
+
+ input.getline(line, 511);
+
+ if(n< NotUn_angles){
+
+/*
+ myfloat_t or1,or2,or3,or4,prior;
+
input.getline(line, 511);
- if(n< NotUn_angles){
- float a,b,g,pp;
+ strcpy(saveline, line);
+ char *token = strtok(line, " ");
+ if (token == NULL || line[0] == '#' || strlen(token) == 0)
+ {
+ // comment or blank line
+ }
+ else if (strcmp(token, "ORIENT") == 0)
+ {
+ token = strtok(NULL, " ");
+ or1 = atof(token);
+ token = strtok(NULL, " ");
+ or2 = atof(token);
+ token = strtok(NULL, " ");
+ or3 = atof(token);
+ token = strtok(NULL, " ");
+ or4 = atof(token);
+ cout << "TT " << n << " " << or1 << " " << or2 << " " << or3 << " " << or4 << "\n ";
+
+ angles[n].pos[0] = or1;
+ angles[n].pos[1] = or2;
+ angles[n].pos[2] = or3;
+ angles[n].quat4 =0.0;
+ n++;
+ }*/
+
+
+ float a=0.,b=0.,g=0.,pp=0.;
char tmpVals[60] = {0};
- strncpy (tmpVals, line, 12);
+ strncpy (tmpVals, line, 12);
sscanf (tmpVals, "%f", &a);
- cout << tmpVals <<"\n";
strncpy (tmpVals, line + 12, 12);
sscanf (tmpVals, "%f", &b);
@@ -815,11 +845,13 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
if(pp <0.0000001)cout << "Sure you're input is correct? Very small prior.\n";
angprior[n] = (myfloat_t) pp;
}
+
angles[n].pos[0] = (myfloat_t) a;
angles[n].pos[1] = (myfloat_t) b;
angles[n].pos[2] = (myfloat_t) g;
angles[n].quat4 =0.0;//just to be sure */
- if(yespriorAngles) cout << "check orient: " << n << " " << angles[n].pos[0] << " " << angles[n].pos[1] << " " << angles[n].pos[2] << " prior: " << angprior[n] << "\n";
+
+ if(yespriorAngles) cout << "check orient: " << n << " " << " " << angles[n].pos[0] << " " << angles[n].pos[1] << " " << angles[n].pos[2] << " prior: " << angprior[n]<< "\n";
}
n++;
if(NotUn_angles+1 < n) {
@@ -831,7 +863,7 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
}
nTotGridAngles = NotUn_angles;
voluang= 1./ (myfloat_t) NotUn_angles * priorMod;
- input.close();
+ input.close();
}
} else {
@@ -909,12 +941,12 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
// ifstream input(quatfile);
- ifstream input(inanglef.c_str());
+ ifstream input(fileangles);
// ifstream input("QUATERNION_LIST");
if (!input.good())
{
- cout << "Problem with Quaterion List file " << inanglef.c_str() << " " << endl ;
+ cout << "Problem with Quaterion List file " << fileangles << " " << endl ;
exit(1);
}